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feat: add taxonomic information about organisms#20

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emilylm merged 2 commits into
mainfrom
add-taxonomic-fields-assembly-manifest
May 4, 2026
Merged

feat: add taxonomic information about organisms#20
emilylm merged 2 commits into
mainfrom
add-taxonomic-fields-assembly-manifest

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@emilylm emilylm commented May 4, 2026

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📌 Summary

This PR introduces a taxonomy_info table for organism-level taxonomy metadata. It also updates broker claim responses to include sample.kind, and aligns related validation messages and tests.


🔄 Type of Change

  • 🐛 Bug fix (non-breaking change that fixes an issue)
  • ✨ New feature (non-breaking change that adds functionality)
  • 💥 Breaking change (fix or feature that would cause existing functionality to change)
  • 🧹 Refactor (code change that neither fixes a bug nor adds a feature)
  • 📚 Documentation update
  • ⚙️ CI / build / tooling change

🧩 Key Changes

  • Add a new taxonomy_info table, model, schemas, service layer, API endpoints, and bulk import support.
  • Migrate augustus_dataset_name out of organism into taxonomy_info, and expose taxonomy info as nested organism data.
  • Include sample.kind in broker claim responses and update related tests and assembly-helper error messaging.

✅ Checklist

  • Tests are passing locally / in CI
  • New tests have been added for new or changed functionality
  • Self-review completed
  • Documentation updated (if needed)
  • No sensitive data or secrets included

🔍 Review Notes

  • Please review the API shape change carefully: augustus_dataset_name is no longer a top-level organism field and now lives under taxonomy_info.

📎 Related Issues / Tickets

  • Closes # AP-263
  • Related to #

@emilylm
emilylm merged commit 5a80236 into main May 4, 2026
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