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Dagster job to populate missing biosample records for a study from GOLD #859

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merged 7 commits into from
Jan 23, 2025

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sujaypatil96
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@sujaypatil96 sujaypatil96 commented Jan 14, 2025

This PR adds a Dagster job to create a biosample_set JSON (Biosample records) for those samples in a GOLD study that have been newly added since the previous time that we did an ingest for that study into NMDC.

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Related issue(s)

Fixes microbiomedata/issues#940

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")

@sujaypatil96 sujaypatil96 marked this pull request as ready for review January 15, 2025 23:19
@sujaypatil96 sujaypatil96 requested a review from aclum January 16, 2025 00:37
aclum
aclum previously approved these changes Jan 16, 2025
@sujaypatil96 sujaypatil96 requested a review from aclum January 22, 2025 00:59
aclum
aclum previously approved these changes Jan 23, 2025
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This PR is ready to be merged @aclum. Apologies for the request for multiple reviews.

@sujaypatil96 sujaypatil96 merged commit b3d7e0b into main Jan 23, 2025
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@sujaypatil96 sujaypatil96 deleted the issue-940-EMP500-biosample-records branch January 23, 2025 20:57
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Successfully merging this pull request may close these issues.

Ingest remaining 458 biosamples for nmdc:sty-11-547rwq94 (EMP500)
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