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Set --tmp-outdir-prefix on MacOS to be under the shared volume by default #670

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Merged
merged 1 commit into from
Feb 23, 2018
Merged

Set --tmp-outdir-prefix on MacOS to be under the shared volume by default #670

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7 changes: 5 additions & 2 deletions cwltool/argparser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,9 @@

_logger = logging.getLogger("cwltool")

DEFAULT_TMP_PREFIX = "tmp"


def arg_parser(): # type: () -> argparse.ArgumentParser
parser = argparse.ArgumentParser(description='Reference executor for Common Workflow Language')
parser.add_argument("--basedir", type=Text)
Expand Down Expand Up @@ -71,12 +74,12 @@ def arg_parser(): # type: () -> argparse.ArgumentParser

parser.add_argument("--tmpdir-prefix", type=Text,
help="Path prefix for temporary directories",
default="tmp")
default=DEFAULT_TMP_PREFIX)

exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--tmp-outdir-prefix", type=Text,
help="Path prefix for intermediate output directories",
default="tmp")
default=DEFAULT_TMP_PREFIX)

exgroup.add_argument("--cachedir", type=Text, default="",
help="Directory to cache intermediate workflow outputs to avoid recomputing steps.")
Expand Down
13 changes: 11 additions & 2 deletions cwltool/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,12 @@
import ruamel.yaml as yaml
import schema_salad.validate as validate
import six

from schema_salad.ref_resolver import Loader, file_uri, uri_file_path
from schema_salad.sourceline import strip_dup_lineno

from . import draft2tool, workflow
from .argparser import arg_parser, generate_parser
from .argparser import arg_parser, generate_parser, DEFAULT_TMP_PREFIX
from .cwlrdf import printdot, printrdf
from .errors import UnsupportedRequirement, WorkflowException
from .executors import SingleJobExecutor, MultithreadedJobExecutor
Expand Down Expand Up @@ -529,8 +530,16 @@ def main(argsl=None, # type: List[str]
if isinstance(tool, int):
return tool

# If on MacOS platform, TMPDIR must be set to be under one of the shared volumes in Docker for Mac
# More info: https://dockstore.org/docs/faq
if sys.platform == "darwin":
tmp_prefix = "tmp_outdir_prefix"
default_mac_path = "/private/tmp/docker_tmp"
if getattr(args, tmp_prefix) and getattr(args, tmp_prefix) == DEFAULT_TMP_PREFIX:
setattr(args, tmp_prefix, default_mac_path)

for dirprefix in ("tmpdir_prefix", "tmp_outdir_prefix", "cachedir"):
if getattr(args, dirprefix) and getattr(args, dirprefix) != 'tmp':
if getattr(args, dirprefix) and getattr(args, dirprefix) != DEFAULT_TMP_PREFIX:
sl = "/" if getattr(args, dirprefix).endswith("/") or dirprefix == "cachedir" else ""
setattr(args, dirprefix,
os.path.abspath(getattr(args, dirprefix)) + sl)
Expand Down