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microbiomedata / submission-schema

https://microbiomedata.github.io/submission-schema/
MIT License
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Decrease reliance on yq #39

Open turbomam opened 1 year ago

turbomam commented 1 year ago

Any use of yq should be compact, general and well-documented. It should not be used to apply name-based modifications which can be handled by sheets_and_friends' modifications_and_validation script.

Currently, the validation updates specified by the --validation_config_tsv argument are only triggered when detecting

and only take these actions:

I don't think the DH datatype changes are necessary any more, as class ranges are generally replaced by the yq operations, and DH seems to understand the range specifications that consist of a linkml:type in name alone.

I would like to continue using yq for these general validation updates, or add additional trigger types to modifications_and_validation.

cc @pkalita-lbl

turbomam commented 1 year ago

see also

mslarae13 commented 6 months ago

Does this relate to https://github.com/microbiomedata/nmdc-schema/issues/1846 ?? @sierra-moxon