Actions
Bug #10869
closed[CWL] Unsupported scheme in url
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
Updated by Peter Amstutz almost 8 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.
Updated by Peter Amstutz almost 8 years ago
- Target version set to 2017-01-18 sprint
Branch up 10869-cwl-keep-ref
Updated by Radhika Chippada almost 8 years ago
Would it be too time consuming to add / update a test to test this path? All existing tests passed.
LGTM
Actions