lingering steps for water and soil example data

[turbomam]

• checkout main and run make test
  • clean up with git stash and or make schema_cleanup clean
• copy contents of console to a text editor like Sublime Text
• sort lines
• make unique
• copy any errors or warnings below

• there may also be actionable "INFOs". Would require additional investigation.

  Also look for commented lines in the example data files

Remember, ideally the invalid examples would only have one invalid aspect, so they could be fixed and then would pass.

Are we going to keep all of these? What are they good for?

• example data files in examples/
• src/data/examples... see tests/test_data.py
• src/data/invalid and src/data/valid... see examples/output/README.md target in project.Makefile

[turbomam]

This "error" is expected and desired

! poetry run check-jsonschema \
    --schemafile project/jsonschema/nmdc_submission_schema.schema.json \
    src/data/invalid/SampleData-water-data-alkalinity-list.yaml

Schema validation errors were encountered. src/data/invalid/SampleData-water-data-alkalinity-list.yaml::$.water_data[0].alkalinity: ['50 milligram per liter', '100 spoons per bucket'] is not of type 'string'

[turbomam]

WARNING:root:No namespace defined for URI: https://microbiomedata/schema/ammonium_nitrogen WARNING:root:No namespace defined for URI: https://microbiomedata/schema/ecosystem WARNING:root:No namespace defined for URI: https://microbiomedata/schema/ecosystem_category WARNING:root:No namespace defined for URI: https://microbiomedata/schema/ecosystem_subtype WARNING:root:No namespace defined for URI: https://microbiomedata/schema/ecosystem_type WARNING:root:No namespace defined for URI: https://microbiomedata/schema/lbc_thirty WARNING:root:No namespace defined for URI: https://microbiomedata/schema/lbceq WARNING:root:No namespace defined for URI: https://microbiomedata/schema/manganese WARNING:root:No namespace defined for URI: https://microbiomedata/schema/nitrate_nitrogen WARNING:root:No namespace defined for URI: https://microbiomedata/schema/nitrite_nitrogen WARNING:root:No namespace defined for URI: https://microbiomedata/schema/specific_ecosystem WARNING:root:No namespace defined for URI: https://microbiomedata/schema/zinc

---

WARNING:root:Not implemented: slot WARNING:root:There is no established path to nmdc_submission_schema - compile_python may or may not work

[turbomam]

src/data/valid/SampleData-soil-data-exhaustive.yaml:

#    horizon_meth: xxx
#    micro_biomass_C_meth: xxx
#    micro_biomass_N_meth: xxx
#    microbial_biomass_C: 111 units
#    microbial_biomass_N: 111 units

#    oxy_stat_samp: aerobe
#    rel_to_oxygen: aerobe

[turbomam]

src/data/valid/SampleData-water-data-exhaustive.yaml

#    oxy_stat_samp: anaerobe

[turbomam]

Examine local/slot_usage.tsv

[turbomam]

  RelToOxygenEnum:
    permissible_values:
      aerobe:
      anaerobe:
      facultative:
      microaerophilic:
      microanaerobe:
      obligate aerobe:
      obligate anaerobe:

---

use rel_to_oxygen_enum for both of these, globally and in all slot_usages

• oxy_stat_samp: aerobe
• rel_to_oxygen: aerobe

  rel_to_oxygen_enum:
    permissible_values:
      aerobe:
      anaerobe:
      facultative:
      microaerophilic:
      microanaerobe:
      obligate aerobe:
      obligate anaerobe:

---

  oxy_stat_samp_enum:
    permissible_values:
      aerobic:
      anaerobic:
      other:

[turbomam]

These just need to be all-lower-cased! Thanks @pkalita-lbl

#    micro_biomass_C_meth: xxx
#    micro_biomass_N_meth: xxx
#    microbial_biomass_C: 111 units
#    microbial_biomass_N: 111 units

[turbomam]

multi-valued titles:

• analysis/data type
• history/tillage

How are MIxS triad and GOLD pull-downs getting created?

Which are really MIxS, MIxS modified etc.

What help is displayed

Time and date formats

Time zone assumption/validation/labeling

[mslarae13]

@turbomam is the outstanding task here to just update example files?

Is this in the schema or submission-schema?