DO NOT MERGE minimal MIxS term subsetter

microbiomedata / sheets_and_friends

Enhance a LinkML model with imported and optionally modified slots

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Closed turbomam closed 1 year ago

turbomam commented 1 year ago

If we were going to use this:

why is do_shuttle so slow?
this branch should probably be published as a subsetting/shuttling package
document how I got the list of relevant MIxS terms (that are used for Biosample) into import_slots_regardless
document how I knew to yq -i 'del(.classes.placeholder_class)' $(word 2,$^)
document remaining differences between this output and mixs.yaml from nmdc-schema

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turbomam commented 1 year ago

issues:

[ ] in tests, need a step to add Biosample class with slots assertions to artifacts/mixs_subset.yaml, in order to get artifacts/mixs_subset_with_classes.yaml
[ ] pipe-separated examples are not split into individual examples
[ ] modifications_and_validation expects that a slot_usage is stub already available for each class x slot to be modified

classes:
  Biosample:
    slots:
      - source_mat_id
      - samp_store_temp
    slot_usage:
      samp_store_temp: { }