Bump nmdc-schema from 11.0.3 to 11.1.0 and sync transitive dependencies

[eecavanna]

In this branch, I bumped the nmdc-schema package dependency from version 11.0.3 to version 11.1.0 in preparation for next week's release.

Details

I also (effectively) ran $ make update-deps to synchronize the transient dependencies with the above change.

Note: Technically, I ran the following, container-based command in an attempt to further decouple the process from my host machine:

docker compose run --rm -it --name nmdc-runtime-builder fastapi sh -c 'make update-deps'

Related issue(s)

Fixes #768

Related subsystem(s)

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

The subsystem is: Dependencies

Testing

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

I'll leave that to GitHub Actions.

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)

I am assuming there is no documentation in nmdc-runtime that will be any less accurate with respect to 11.1.0 than with respect to 11.0.3.

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]

I'll merge this in while I do the Mongo migration later today.

[eecavanna]

One of the automated tests failed. The GitHub Actions workflow log shows the following (this is an excerpt).

tests/test_ops/test_ops.py F                                             [ 92%]

================================== FAILURES ===================================
_______________ test_apply_metadata_in_functional_annotation_agg _______________

op_context = <dagster._core.execution.context.invocation.DirectOpExecutionContext object at 0x7f6be705f940>

    def test_apply_metadata_in_functional_annotation_agg(op_context):
        mongo = op_context.resources.mongo
        docs = {
            "functional_annotation_agg": [
                {
                    "metagenome_annotation_id": "nmdc:wfmtan-13-hemh0a82.1",
                    "gene_function_id": "KEGG.ORTHOLOGY:K00005",
                    "count": 10,
                    "type": "nmdc:FunctionalAnnotationAggMember",
                },
                {
                    "metagenome_annotation_id": "nmdc:wfmtan-13-hemh0a82.1",
                    "gene_function_id": "KEGG.ORTHOLOGY:K01426",
                    "count": 5,
                    "type": "nmdc:FunctionalAnnotationAggMember",
                },
            ]
        }
        # Ensure the docs are not already in the test database.
        for doc_spec in docs["functional_annotation_agg"]:
            mongo.db.functional_annotation_agg.delete_many(doc_spec)
    
        extra_run_config_data = _ensure_job__metadata_in(
            docs,
            op_context.resources.runtime_api_user_client.username,
            mongo.db,
            op_context.resources.runtime_api_site_client.client_id,
            drs_object_exists_ok=True,  # If there exists a DRS object with a matching checksum, use it.
        )
    
>       apply_metadata_in.to_job(**preset_normal).execute_in_process(
            run_config=extra_run_config_data
        )

I'll take a crack at fixing that.

[aclum]

tests aren't passing, we need to update one of the ops tests. I'll do that now.

[eecavanna]

@aclum I'm on it. I'm going to update the docs object to use the new field name. Commit incoming...

[eecavanna]

I see you took care of it. 👍 (I think we were playing "phone tag".) I expect the test to pass now. Thanks for taking care of it.

[eecavanna]

The test passed. I'll hold off on merging this in until I've done the data migration (today).