Replace the use of alldocs with respective collections for record retrieval in NCBI exporter

[sujaypatil96]

Fixes microbiomedata/issues#1063

TODO:

• Make sure the export code picks up on platform and instrument_model Attributes correctly
• For data object records that are linked by a mainfest record, the SRA Action block needs to have references to all the connected files

On this branch, I...

Details

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Related issue(s)

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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...

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]

I'll review this PR this morning.

[eecavanna]

Thanks for making these changes to accommodate the new sparseness of the "all docs" (maybe one day renamed to "all refs" or something) collection, @sujaypatil96.

I made some comments related to type hints, docstrings, and 1-2 variable names.

[sujaypatil96]

Thank you for the review comments @eecavanna, they were very helpful! I was being lazy by not adding type hints and docstrings. I've done that now. I think I've addressed all your review comments, feel free to drop another review.

[eecavanna]

Thanks for making those changes, @sujaypatil96! I found the docstrings and type hints helpful in keeping track of what is happening in the code (while reading it).

I left one follow-up comment about a type hint that I thought was more broad than necessary. I'll defer to you about that. You can merge already or edit-and-merge.