change nmdc-schema's MIxS import to GSC's 6.2 YAML

[turbomam]

currently slightly ahead of MIxS 6.0:
https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml

change to: https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml

see also

• consequences of changing MIxS import #299

[turbomam]

prepare for rebuild of src/schema/mixs.yaml with with make mixs-yaml-clean

then make all

[turbomam]

MAM 2024-04-15: below, I think I changed the source file or URL column values in assets/import_mixs_slots_regardless.tsv to https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/v6.2.0/src/mixs/schema/mixs.yaml

• ValueError: No such slot host_family_relation as an attribute of MimsSoil ancestors or as a slot definition in the schema
• not used in MongoDB yet
• is mentioned in sheets_and_friends/tsv_in/import_slots_regardless.tsv
• now host_fam_rel

[turbomam]

• ValueError: No such slot salinity_meth as an attribute of MimsSoil ancestors or as a slot definition in the schema
• not used in MongoDB yet
• is mentioned in sheets_and_friends/tsv_in/import_slots_regardless.tsv
• no replacement currently available

[turbomam]

• ValueError: No such slot samp_collec_device as an attribute of MimsSoil ancestors or as a slot definition in the schema
• not used in MongoDB yet
• appears in assets/misc/neon_nmdc_term_mapping.tsv
• replaced with samp_collect_device

[turbomam]

• ValueError: No such slot samp_collec_method as an attribute of MimsSoil ancestors or as a slot definition in the schema
• not used in MongoDB yet
• appears in assets/misc/neon_nmdc_term_mapping.tsv
• replaced with samp_collect_method

[turbomam]

• ValueError: No such slot soil_text_measure as an attribute of MimsSoil ancestors or as a slot definition in the schema
• not used in MongoDB yet
• replaced with [soil_texture](https://genomicsstandardsconsortium.github.io/mixs/0000335/) ???

[turbomam]

ValueError: Conflicting URIs (https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/mixs.yaml, https://w3id.org/nmdc/core) for item: sequencing

a subset in both mixs.yaml and core.yaml

not in use by nmdc-schema from core.yaml, so commented out

---

same thing for

• environment
• investigation
• nucleic acid sequence source

[turbomam]

• ValueError: File "nmdc.yaml", line 547, col 9 Class "Biosample" - unknown slot: "core field"

comment out from nmdc.yaml. ignore assets/old_python/reconsititute_mixs.py

same with

• environment field
• investigation field
• nucleic acid sequence source field
• sequencing field

[turbomam]

ValueError: File "nmdc.yaml", line 639, col 9 Class "Biosample" - unknown slot: "has numeric value" ???

• has raw value
• has unit

[turbomam]

new enum names:

      oxy_stat_samp:
        range: oxy_stat_samp_enum

ValueError: File "nmdc.yaml", line 1105, col 16 slot: Biosample_oxy_stat_samp - unrecognized range (oxy_stat_samp_enum)

  oxy_stat_samp:
    description: Oxygenation status of sample
    title: oxygenation status of sample
    examples:
      - value: aerobic
    from_schema: https://w3id.org/mixs
    keywords:
      - oxygen
      - sample
      - status
    slot_uri: MIXS:0000753
    range: OXY_STAT_SAMP_ENUM

[turbomam]

I'm sacrificing the ability to assign "new" MIxS slots to classes in nmdc.yaml without defining them. Before this branch, the build process would detect assigned and undefined MIxS slots (in Biosample and OmicsProcessing) and add them to our mixs.yaml. But it was only able to retrieve slots from a single MIxS class, like MimsSoil.

Moving forward, if an undefined slot is assigned to a class, the build will fail with an error message like ???

That could be interpreted in many cases that the slot and one of its MIxS classes should be added to assets/other_mixs_yaml_files/mixs_slots_import_sheet.tsv

This has resulted in a much shorter project.Makefile

[turbomam]

project.Makefile uses yq to convert flat MIxS slot ranges into structured nmdc-schema ranges like QuantityValue.

In this branch, I have removed all range changes for slots that haven't been used in MongoDB yet. Files in the src/data path whose name contains the sub-string iosample-exhasutive illustrate what ranges were expected in the removed yq slot range updates