Update schema references to point to nmdc_materialized_patterns variant

[eecavanna]

On this branch, I updated some references to variants of the NMDC Schema other than the nmdc_materialized_patterns variant, so that they point to the nmdc_materialized_patterns variant.

Details

None.

Related issue(s)

Partially fixes #552

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 will delegate the testing task 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)

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]

Hi @dwinston, you can add commits directly to this PR branch, in case you want to make changes related to "occurrence 1" without creating a separate PR.

[aclum]

are we not doing this using the python package or linkml. @sierra-moxon please weigh in here but we can't just have a dummy path here

[eecavanna]

we can't just have a dummy path here

Thanks—I agree. This was a mistake on my part.

---

Communicating which schema variant we expect, to the caller

The previous default value here would not work because this repository no longer contains a file at ../../../schema/nmdc.schema.json.

My intention by replacing the default value was to give a hint to the user about which variant of the schema we expect them to provide; i.e. the nmdc_materialized_patterns.schema.json variant, not the nmdc.schema.json variant. The code still won't work, though (neither file exists at the path specified).

I'll add a note to the (otherwise empty) docstring, saying that we expect the user to provide the path to the nmdc_materialized_patterns.schema.json variant of the schema when they invoke the function.

---

The default value

The Runtime repo no longer contains a schema file whose path we could use as the default value.

---

Invocations of this function

The only invocation of this function I see (in the repo) is the one right below the function's definition; i.e. this one:

if __name__ == "__main__":
    print("study test", test_gold_study_json())

That invocation relies on the function's default values.

---

The future of this script

Given that this script was already broken (due to the path being nonexistent) before this PR was created...

Do you have a sense for whether anyone uses this script anymore?

It was last updated in 2022 (before I updated the parameter's default value in this PR). I'm guessing someone wrote it to demonstrate something way back when.

Given that it lacked any documentation, maybe they did not expect it to be used by other people (or their future self) or maintained over time.

[eecavanna]

In the latest commit (i.e. 2042c09), I removed all the obsolete, hard-coded file paths and replaced them with references to CLI arguments. This way, it is the user's responsibility to tell the script where it can find these files.

[eecavanna]

I'd still like to remove this file from the repo if it's obsolete. That way, we and our successors don't spend time trying to salvage it as the rest of the code base evolves.

[aclum]

cc @turbomam what should we be using instead of the nmdc_materialized_patterns.schema.json