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Try to run "CWLFile" by default if no file provided #189

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Merged
merged 6 commits into from
Oct 14, 2016
Merged

Try to run "CWLFile" by default if no file provided #189

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9ec392a
Try to run "CWLFile" by default if no file provided, analogus behavio…
Sep 11, 2016
e7f8525
Don't use argparse default to get a better error message.
Sep 11, 2016
1a8f3fa
Merge branch 'master' into CWLFile
tetron Oct 8, 2016
9470127
Merge branch 'master' into CWLFile
tetron Oct 14, 2016
d91330a
Merge branch 'master' into CWLFile
tetron Oct 14, 2016
6ffa2f6
Fix tox
Oct 14, 2016
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6 changes: 3 additions & 3 deletions cwltool/load_tool.py
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Original file line number Diff line number Diff line change
Expand Up @@ -92,9 +92,9 @@ def validate_document(document_loader, workflowobj, uri,
"""Validate a CWL document."""
jobobj = None
if "cwl:tool" in workflowobj:
jobobj = workflowobj
uri = urlparse.urljoin(uri, jobobj["cwl:tool"])
del jobobj["cwl:tool"]
jobobj, _ = document_loader.resolve_all(workflowobj, uri)
uri = urlparse.urljoin(uri, workflowobj["https://w3id.org/cwl/cwl#tool"])
del cast(dict, jobobj)["https://w3id.org/cwl/cwl#tool"]
workflowobj = fetch_document(uri)[1]

if isinstance(workflowobj, list):
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9 changes: 6 additions & 3 deletions cwltool/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -607,9 +607,12 @@ def main(argsl=None,
_logger.info(versionfunc())

if not args.workflow:
_logger.error("")
_logger.error("CWL document required, try --help for details")
return 1
if os.path.isfile("CWLFile"):
setattr(args, "workflow", "CWLFile")
else:
_logger.error("")
_logger.error("CWL document required, try --help for details")
return 1

try:
document_loader, workflowobj, uri = fetch_document(args.workflow)
Expand Down