Valid workflow cannot have RDF generated due to lack of urlencoding #444
Comments
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Good catch. IIRC the spec doesn't put any restrictions on identifiers, although maybe it should. I think urlencoding is probably the right fix. |
jmchilton
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Jun 27, 2017
8b6ddb1 Merge pull request common-workflow-language#461 from MarkRobbo/rdfs-namespace eb64c56 Add rdfs namespaces where used e5f4086 Merge pull request common-workflow-language#416 from common-workflow-language/mr-c-patch-1 4cf45da Merge pull request common-workflow-language#459 from common-workflow-language/airflow-badge 100635d add badge and promote Airflow upwards db0c837 Merge pull request common-workflow-language#407 from common-workflow-language/fix-support-link 0d88a24 Merge pull request common-workflow-language#455 from ohsu-comp-bio/cwl-tes-implementation 8d76233 Merge pull request common-workflow-language#453 from common-workflow-language/fix-conflicting-ids 3496956 fix conflicting IDs 15a7d51 Merge pull request common-workflow-language#452 from common-workflow-language/hmenager-patch-1 78940a8 Add ELIXIR + BioExcel participating organizations 05fcef8 remove funnel from list since we are no longer maintaining it 09c2d0c Merge pull request common-workflow-language#445 from common-workflow-language/toil-backend-update 873ebfa Merge pull request common-workflow-language#448 from common-workflow-language/skanwal-patch-1 d52c2b1 Update README.md 77f38c8 Merge pull request common-workflow-language#447 from common-workflow-language/avro-spec 615646e Fix broken avro spec link a863f80 Merge pull request common-workflow-language#441 from common-workflow-language/more-contributors 9e84f13 Merge pull request common-workflow-language#444 from common-workflow-language/mr-c-patch-2 506508b Merge pull request common-workflow-language#432 from michael-kotliar/master dfbb124 update list of schedulers and platforms for Toil f7c68c4 add matching SVG c2c1f1e Added more contributors 50e9d25 Merge pull request common-workflow-language#439 from common-workflow-language/link-cwlgen 6362e57 Add link to python-cwlgen. 04c3f8e Add Airflow in Implementations Section of Readme e150035 Merge pull request common-workflow-language#426 from common-workflow-language/fix-wc-test 6acb016 Fix wc test by using wc -l to avoid padding issues on different implementions of 'wc' (!) d80919e Revert "Fix identifier conflicts (checked by cwltool for the first time) by giving ids" f2ea521 Merge pull request common-workflow-language#418 from mdmiller53/master 2ade169 Update README.md 9930c4a Merge pull request common-workflow-language#417 from common-workflow-language/fix-id-conflicts fcc593a Fix identifier conflicts (checked by cwltool for the first time) by giving ids to embedded tools and workflows. 60b4701 Move blog link out of support section d038d86 Merge pull request common-workflow-language#355 from StarvingMarvin/master f6b6f74 Merge pull request common-workflow-language#409 from common-workflow-language/LourensVeen-uml-sketch e4b4b99 Add UML sketch 81d5e1e Merge branch 'master' of https://github.com/common-workflow-language/common-workflow-language 074a420 Merge branch 'master' of github.com:StarvingMarvin/common-workflow-language 1f5ccec Use explicit anchor b0e1212 fix support link 1452e65 Merge pull request common-workflow-language#406 from sharmatime/patch-1 b60a48c Update README.md aa44386 Merge pull request common-workflow-language#400 from common-workflow-language/v1.1.0-dev1 e6dc6e4 Use ShellCommandRequirement for stderr tests. 7098e43 turn off shell quoting for stderr tests 8de0b2b sync remaining updates made to v1.0 8ab5eb9 stderr redirect tests use "echo" instead of checking for the usage message of "egrep". a90334a Merge pull request common-workflow-language#399 from common-workflow-language/Consonance 9566984 add platform support list for Consonance d0fc2df Add missing files. f0f8b67 Sync v1.1 conformance test suite to changes in v1.0 suite. 50f052e Merge pull request common-workflow-language#340 from Jeltje/master f8a2d76 Add Consonance 776eb3b Merge pull request common-workflow-language#397 from common-workflow-language/ohofmann-clarifications af0b112 participating organization clarifications c7958cf Merge pull request common-workflow-language#395 from common-workflow-language/dir5-allow-symlink 12c12ce Merge pull request common-workflow-language#366 from common-workflow-language/support-link-and-collabs 142e34e Make the "dir5.cwl" pass if the implementation uses symlinks. 1d5c5b9 document Toil's slurm support 7063fc0 Merge pull request common-workflow-language#386 from common-workflow-language/cwl-ecosystem-update 85976a7 Add latest additions to the CWL ecosystem f956af5 Merge pull request common-workflow-language#385 from common-workflow-language/fix/issue/195 3a5aef3 Additional participating organizations 103c976 Merge pull request common-workflow-language#383 from andrewjesaitis/userguide_typo f95eb57 Use v1.0 style id's in inputs/outputs example 2d7707c Merge pull request common-workflow-language#376 from common-workflow-language/open-stand 6396df0 long overdue linking to open-stand.org 2d74be4 even dhough slim is larger than alpine, it reuses debian:8 that is already pulled for other tests, so overall smaller overhead a4822d8 specifying python2 as baseCommand in order for tests to work with systems where python3 is the default 360e2b9 Merge pull request common-workflow-language#371 from common-workflow-language/smoe-userguide-typo-contianer 1a571ba UserGuide.yml trivial typo 3bd20eb Merge pull request common-workflow-language#368 from bamuzesc/patch-1 bed0329 removed redundant line 4 "baseCommand: javac" 3003fc4 support instructions link, list of collabs 37c3e0a Merge pull request common-workflow-language#360 from zrilak/master 2bc1b13 Tweaks to README 87d982f Merge branch 'master' of github.com:common-workflow-language/common-workflow-language 4f80e57 some concluding remark 047c9ad UserGuide: about nested workflow d5d124c include empty.yml 3b41eda outputSource within output parameter 70f528a CWL View link dc7d391 even dhough slim is larger than alpine, it reuses debian:8 that is already pulled for other tests, so overall smaller overhead 40b65c2 Merge remote-tracking branch 'upstream/master' 25975b0 specifying python2 as baseCommand in order for tests to work with systems where python3 is the default 9ce806b empty.yml can't be quite empty..? 37ef31c How to make empty.yml 1104bf7 Fix typos in UserGuide f5c5f4d Update README.md dd083bd Clarify Xenon CWL work 97b3698 Update organizations 5473858 Merge pull request common-workflow-language#344 from common-workflow-language/import-hint-test a26c1ae add test for importing hints fd09b15 fixed typos git-subtree-dir: cwltool/schemas git-subtree-split: 8b6ddb1
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Running with latest (venv) [venv] ~/github/cwltool · (master±) $ cwltool --debug --validate https://github.com/raw/ProteinsWebTeam/ebi-metagenomics-cwl/f6b5196bd493b0872ee6e63aa3499738bb7d53d6/workflows/emg-pipeline-v3.cwl 21:31:35
/home/manu/github/cwltool/venv/bin/cwltool 1.0.20170812174804
https://github.com/raw/ProteinsWebTeam/ebi-metagenomics-cwl/f6b5196bd493b0872ee6e63aa3499738bb7d53d6/workflows/emg-pipeline-v3.cwl:1:1: unrecognized extension field `http://schema.org/license`. Did you include a $schemas section?
https://github.com/raw/ProteinsWebTeam/ebi-metagenomics-cwl/f6b5196bd493b0872ee6e63aa3499738bb7d53d6/workflows/emg-pipeline-v3.cwl:1:1: unrecognized extension field `http://schema.org/copyrightHolder`. Did you include a $schemas section?
No handlers could be found for logger "rdflib.term"
^CTraceback (most recent call last):
File "/home/manu/github/cwltool/venv/bin/cwltool", line 11, in <module>
load_entry_point('cwltool', 'console_scripts', 'cwltool')()
File "/home/manu/github/cwltool/cwltool/main.py", line 831, in main
makeTool, make_tool_kwds)
File "/home/manu/github/cwltool/cwltool/load_tool.py", line 260, in make_tool
tool = makeTool(processobj, **kwargs)
File "/home/manu/github/cwltool/cwltool/workflow.py", line 40, in defaultMakeTool
return Workflow(toolpath_object, **kwargs)
File "/home/manu/github/cwltool/cwltool/workflow.py", line 518, in __init__
self.steps.append(WorkflowStep(step, n, **kwargs))
File "/home/manu/github/cwltool/cwltool/workflow.py", line 677, in __init__
resolver=kwargs.get("resolver"))
File "/home/manu/github/cwltool/cwltool/load_tool.py", line 287, in load_tool
makeTool, kwargs if kwargs else {})
File "/home/manu/github/cwltool/cwltool/load_tool.py", line 260, in make_tool
tool = makeTool(processobj, **kwargs)
File "/home/manu/github/cwltool/cwltool/workflow.py", line 40, in defaultMakeTool
return Workflow(toolpath_object, **kwargs)
File "/home/manu/github/cwltool/cwltool/workflow.py", line 518, in __init__
self.steps.append(WorkflowStep(step, n, **kwargs))
File "/home/manu/github/cwltool/cwltool/workflow.py", line 677, in __init__
resolver=kwargs.get("resolver"))
File "/home/manu/github/cwltool/cwltool/load_tool.py", line 285, in load_tool
strict=strict, fetcher_constructor=fetcher_constructor)
File "/home/manu/github/cwltool/cwltool/load_tool.py", line 199, in validate_document
processobj, metadata = document_loader.resolve_all(workflowobj, fileuri)
File "/home/manu/github/schema_salad/schema_salad/ref_resolver.py", line 785, in resolve_all
newctx.add_schemas(document[u"$schemas"], file_base)
File "/home/manu/github/schema_salad/schema_salad/ref_resolver.py", line 369, in add_schemas
self.idx[six.text_type(s)] = None
File "/home/manu/github/schema_salad/schema_salad/ref_resolver.py", line 78, in __setitem__
return super(NormDict, self).__setitem__(self.normalize(key), value)
KeyboardInterrupt |
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Problem
When running
The workflow passes validation without issue. However when trying to generate RDF
URLs generated by cwltool are not urlencoded before generating the Turtle representation and so an error is thrown. These should be urlencoded or cwltool more restrictive on the types of symbols allowed.
Workflow Code
Overall workflow
Problem file with space in symbols
Your Environment
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