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Apply projectStatus filter only if sequencingCenter is JGI in GOLD translator #881

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merged 1 commit into from
Jan 24, 2025

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@sujaypatil96 sujaypatil96 commented Jan 23, 2025

In this branch, we update the pre-processing/filtering logic that filters out the biosamples and sequencing projects in the GOLD translator.

Details

Details can be found in microbiomedata/issues#1029

Related issue(s)

Fixes microbiomedata/issues#1029

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 generation JSON files for the various translators and exporters and comparing the counts and results to what we would expect from GOLD.

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")

@sujaypatil96 sujaypatil96 marked this pull request as ready for review January 23, 2025 22:27
@sujaypatil96 sujaypatil96 requested a review from aclum January 23, 2025 22:28
@sujaypatil96 sujaypatil96 merged commit 89c7d03 into main Jan 24, 2025
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@sujaypatil96 sujaypatil96 deleted the issue-1029 branch January 24, 2025 23:56
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Apply projectStatus filter only to biosamples sequenced at JGI in GOLD translator
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