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common-workflow-language / schema_salad

Semantic Annotations for Linked Avro Data
https://www.commonwl.org/v1.2/SchemaSalad.html
Apache License 2.0
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new Python codegen loader behaves differently #728

Closed mr-c closed 1 year ago

mr-c commented 1 year ago

the path context for loading the run field has changed from the directory of the loaded file, to the current working directory.

This breaks a test in cwl-utils: https://github.com/common-workflow-language/cwl-utils/actions/runs/6057702539/job/16439137675?pr=240#step:7:144

testdata/md5sum.cwl is a CWL workflow with run: dockstore-tool-md5sum.cwl referring to its sibling file: testdata/dockstore-tool-md5sum.cwl

@acoleman2000 Can you look into this? I can't release your enhancements to schema-salad until this is resolved. Thanks!

mr-c commented 1 year ago

Possibly related to the changes at https://github.com/common-workflow-language/schema_salad/commit/b96f052ca4e3bf888fc8b19e5d1f50b198815608#diff-9b3bfeab727fa5c3302c6eda143a8379c03d1e89e8fa7011186c6154aa6ed3e1R743 (added call to check_exists in new code at https://github.com/common-workflow-language/schema_salad/commit/b96f052ca4e3bf888fc8b19e5d1f50b198815608#diff-9b3bfeab727fa5c3302c6eda143a8379c03d1e89e8fa7011186c6154aa6ed3e1R145)

mr-c commented 1 year ago

Ah, looks like it was an error in our cwl-utils test; we weren't setting the URI at https://github.com/common-workflow-language/cwl-utils/blob/cf9c592c5967aa303f32b50d3cc65205b5d63ff4/tests/test_parser.py#L42