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cwltool --pack adds an 'id' to InputRecordSchemas that is invalid #1505

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mr-c opened this issue Sep 4, 2021 · 1 comment · Fixed by common-workflow-language/schema_salad#430

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mr-c commented Sep 4, 2021 •

edited

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The raw yaml is now publicly accessible at https://github.com/umccr/cwl-ica/blob/main/workflows/bcl-conversion/3.7.5/bcl-conversion__3.7.5.cwl

None of the schemas present have the id attribute in them either:

fastq-list-row: https://github.com/umccr/cwl-ica/blob/main/schemas/fastq-list-row/1.0.0/fastq-list-row__1.0.0.yaml
settings-by-samples: https://github.com/umccr/cwl-ica/blob/main/schemas/settings-by-samples/1.0.0/settings-by-samples__1.0.0.yaml

Originally posted by @alexiswl in common-workflow-language/cwl-utils#71 (comment)

The text was updated successfully, but these errors were encountered:

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mr-c commented Sep 4, 2021

Good news, --pack is not the culprit. The extra id fields were added before

cwltool/cwltool/pack.py

Line 137 in b67a5e0

loadingContext, docobj, uri = fetch_document(uri, loadingContext)

(the main loop)

In fact, it is schema_salad that injects the extra id fields: https://github.com/common-workflow-language/schema_salad/blob/b2abeb5ff6a31686b4844019671a1049933f339c/schema_salad/ref_resolver.py#L999
(dating back to 2015: common-workflow-language/schema_salad@a10d387 )

mr-c mentioned this issue

resolver: inject fewer IDs common-workflow-language/schema_salad#430

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mr-c closed this as completed in common-workflow-language/schema_salad#430

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