Account for multiple sequencing runs in NEON surface water translator code

[sujaypatil96]

The PR updates the code in the NEON surface water translator to account for creating Manifest / manifest_set records for samples that have been sequenced multiple times. It also pulls NEON data from the latest/provisional release to update/create new DataGeneration and DataObject records for samples that were "ignored" in the first ingest.

Details

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Related issue(s)

Fixes microbiomedata/issues#1067

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")