Use nmdc-schema-provided function to get typecode from slot pattern

[eecavanna]

On this branch, I changed how the minter gets typecodes from the schema.

Details

Previously, the minter would use a locally-defined function (named extract_typecode_from_pattern) to extract typecodes from id slot patterns. That ran the risk of falling out of sync with how the same thing is done in the nmdc-schema package. On this branch, I deleted the locally-defined function and updated the calling code to call an equivalent function (named get_typecode_for_future_ids) provided by the nmdc-schema package.

Related issue(s)

Fixes #866

Related subsystem(s)

• Runtime API (except the Minter)
• Minter
• Dagster
• Project documentation (in the docs directory)
• Translators (metadata ingest pipelines)
• MongoDB migrations
• Other

Testing

• I tested these changes (explain below)
• I did not test these changes

I tested these changes by implementing a basic doctest and running it locally via:

docker compose run --rm --no-deps fastapi sh -c 'pip install nmdc-schema==11.3.0 && python -m doctest -v nmdc_runtime/minter/config.py'

Note: I included pip install nmdc-schema==11.3.0 && in the command because I am currently unable to rebuild my fastapi container via make up-dev. This is a separate problem, predating this PR branch.

🙋 Question: Does the GHA test process run doctests?

Documentation

• I have not checked for relevant documentation yet (e.g. in the docs directory)
• I have updated all relevant documentation so it will remain accurate
• Other (explain below)

Maintainability

• Every Python function I defined includes a docstring (test functions are exempt from this)
• Every Python function parameter I introduced includes a type hint (e.g. study_id: str)
• All "to do" or "fix me" Python comments I added begin with either # TODO or # FIXME
• I used black to format all the Python files I created/modified
• The PR title is in the imperative mood (e.g. "Do X") and not the declarative mood (e.g. "Does X" or "Did X")

[eecavanna]

Note: The schema docs show this pattern:

slot_usage:
  id:
    name: id
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'

The first typecode in the (...|...) portion is, indeed, the one our team members want the minter to use when minting new IDs for instances of the MassSpectrometry class.

[dwinston]

LGTM

[dwinston]

Question: Does the GHA test process run doctests?

I don't think so.

[eecavanna]

Thanks for reviewing this, @dwinston. I will merge it in now.

I will file a ticket about updating the GHA-run test runner(s) to also find and run doctests.