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NickAkhmetov/CAT-1490 Add ATAC modality support to scFind queries#3961

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nickakhmetov/cat-1490-scfind-atac
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NickAkhmetov/CAT-1490 Add ATAC modality support to scFind queries#3961
NickAkhmetov wants to merge 11 commits intomainfrom
nickakhmetov/cat-1490-scfind-atac

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@NickAkhmetov NickAkhmetov commented Mar 18, 2026

Summary

This PR adds support for querying ATAC experiments using the scfind API.

While implementing this, I also improved error handling for scFind requests throughout the site and adjusted gene pathway validation to be done server-side to cut down on back-and-forth. The old flow had the client requesting the pathway genes directly from the ubkg API, then sending them to the flask back-end for validation; the new flow sends the request for pathway genes to our back-end, which also evaluates which genes are available for the selected modality.

Design Documentation/Original Tickets

https://hms-dbmi.atlassian.net/browse/CAT-1490

Testing

Added unit/integration tests

Screenshots/Video

Note that PMAIP and BBC3 are not present in the RNAseq index; pathway gene validation handling has been updated to account for the current selected modality.

image image

Checklist

  • Code follows the project's coding standards
    • Lint checks pass locally
    • New CHANGELOG-your-feature-name-here.md is present in the root directory, describing the change(s) in full sentences.
  • Unit tests covering the new feature have been added
  • All existing tests pass
  • Any relevant documentation in JIRA/Confluence has been updated to reflect the new feature
  • Any new functionalities have appropriate analytics functionalities added

Additional Notes

Please specify any additional information or context relevant to this PR.

@NickAkhmetov NickAkhmetov marked this pull request as ready for review March 19, 2026 16:05
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