Bug #10869

[CWL] Unsupported scheme in url

Added by Bryan Cosca over 4 years ago. Updated over 4 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
-
Target version:
Start date:
01/12/2017
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
-

Description

https://workbench.e51c5.arvadosapi.com/pipeline_instances/e51c5-d1hrv-z2itaztpcj0kmw0

2017-01-12_15:42:32 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr Using Arvados SDK version 0.1.20161216224559
2017-01-12_15:42:32 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr arvados.cwl-runner INFO: /tmp/crunch-job/src/crunch_scripts/cwl-runner 495a7df016f63ae348000b1c046f8e1c5f1c5903 1.0.20170106184111, arvados-python-client 0.1.20161216224559, cwltool 1.0.20170105144051
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr ERROR:root:Unhandled exception
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr Traceback (most recent call last):
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr   File "/usr/lib/python2.7/dist-packages/arvados_cwl/crunch_script.py", line 90, in run
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr     t = load_tool(toolpath, runner.arv_make_tool)
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr   File "/usr/lib/python2.7/dist-packages/cwltool/load_tool.py", line 253, in load_tool
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr     strict=strict, fetcher_constructor=fetcher_constructor)
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr   File "/usr/lib/python2.7/dist-packages/cwltool/load_tool.py", line 168, in validate_document
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr     processobj, metadata = document_loader.resolve_all(workflowobj, fileuri)
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr   File "/usr/lib/python2.7/dist-packages/schema_salad/ref_resolver.py", line 788, in resolve_all
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr     self.validate_links(document, u"")
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr   File "/usr/lib/python2.7/dist-packages/schema_salad/ref_resolver.py", line 913, in validate_links
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr     self.validate_links(val, docid)
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr   File "/usr/lib/python2.7/dist-packages/schema_salad/ref_resolver.py", line 913, in validate_links
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr     self.validate_links(val, docid)
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr   File "/usr/lib/python2.7/dist-packages/schema_salad/ref_resolver.py", line 913, in validate_links
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr     self.validate_links(val, docid)
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr   File "/usr/lib/python2.7/dist-packages/schema_salad/ref_resolver.py", line 900, in validate_links
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr     document[d] = self.validate_link(d, document[d], docid)
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr   File "/usr/lib/python2.7/dist-packages/schema_salad/ref_resolver.py", line 857, in validate_link
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr     elif not self.check_exists(link):
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr   File "/usr/lib/python2.7/dist-packages/schema_salad/ref_resolver.py", line 144, in check_exists
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr     raise ValueError('Unsupported scheme in url: %s' % url)
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 stderr ValueError: Unsupported scheme in url: keep:af2f0daa63fe62b84ab3727a6fe241dc+63/filterByColumn.pl
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 child 49764 on compute196.1 exit 0 success=false
2017-01-12_15:42:40 e51c5-8i9sb-yeqysclsv1g7qxt 49511 0 failure (#1, permanent) after 9 seconds

Subtasks

Task #10872: Review 10869-cwl-keep-refResolvedRadhika Chippada

Associated revisions

Revision 7ad611f6
Added by Peter Amstutz over 4 years ago

Merge branch '10869-cwl-keep-ref' refs #10869

History

#1 Updated by Peter Amstutz over 4 years ago

It looks like crunch_script.py in arvados_cwl_runner module wasn't updated to enable support for "keep:" URLs. So this works for the containers API but not jobs. Fixing now.

#2 Updated by Peter Amstutz over 4 years ago

  • Target version set to 2017-01-18 sprint

Branch up 10869-cwl-keep-ref

#3 Updated by Peter Amstutz over 4 years ago

  • Assigned To set to Peter Amstutz

#4 Updated by Radhika Chippada over 4 years ago

Would it be too time consuming to add / update a test to test this path? All existing tests passed.

LGTM

#5 Updated by Peter Amstutz over 4 years ago

  • Status changed from New to Resolved

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