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feat: Update Explorer to support index by feature_id#1222

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kaloster merged 13 commits into
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kaloster/update-gene-duplication
Jun 20, 2025
Merged

feat: Update Explorer to support index by feature_id#1222
kaloster merged 13 commits into
mainfrom
kaloster/update-gene-duplication

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@kaloster

@kaloster kaloster commented Jun 6, 2025

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This is part of GeneExpression disambiguation efforts: chanzuckerberg/single-cell-data-portal#7456

Updates:

  • This will always use schema.annotations.var.index as the column for geneIds
  • If feature_name is available - it will use it as the column for geneNames - if not it will just default to varIndex
  • Updated Gene, QuickGene and GeneSet to use a gene object { id: , name: } instead of a string to be able to utilize gene.id as the unique identifier
  • This should work with datasets that are indexed with feature_name as the var.index (pre 6.0 migration) or indexed with name_0 (feature_id) as the var.index - post 6.0 schema.

Testing

  • Tested against the example datasets (pre 6.0 migration)
  • Tested against a newly indexed dataset (post 6.0 migration)

@kaloster kaloster added the stack label Jun 6, 2025
@kaloster kaloster force-pushed the kaloster/update-gene-duplication branch 4 times, most recently from c9cd495 to 5a2a9c7 Compare June 6, 2025 20:46
@kaloster kaloster force-pushed the kaloster/update-gene-duplication branch from 83f1b8a to 5a2a9c7 Compare June 11, 2025 16:23
@kaloster kaloster force-pushed the kaloster/update-gene-duplication branch from 62ad4a6 to 8fc14f4 Compare June 11, 2025 20:49
@kaloster kaloster requested review from rainandbare and tihuan June 11, 2025 21:22
@kaloster kaloster added stack and removed stack labels Jun 11, 2025
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codecov Bot commented Jun 11, 2025

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 0.00%. Comparing base (863c8f5) to head (ebeeeb9).
Report is 1 commits behind head on main.

Additional details and impacted files
@@     Coverage Diff      @@
##   main   #1222   +/-   ##
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@kaloster kaloster added stack and removed stack labels Jun 11, 2025
@kaloster kaloster force-pushed the kaloster/update-gene-duplication branch from 1cbb9e6 to 880798e Compare June 11, 2025 21:50

@tihuan tihuan left a comment

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LGTM 🎉 Thank you so much for updating this, @kaloster 🤩 🙏

@kaloster kaloster merged commit 3daf593 into main Jun 20, 2025
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@kaloster kaloster deleted the kaloster/update-gene-duplication branch June 20, 2025 21:15
@tihuan

tihuan commented Jun 20, 2025

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@kaloster Does this mean I can merge the delimiter PR too 👀 ?

chanzuckerberg/single-cell-data-portal#7610

Thank you!

@kaloster

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@kaloster Does this mean I can merge the delimiter PR too 👀 ?

chanzuckerberg/single-cell-data-portal#7610

Thank you!

I think we'd have to wait until 6.0 schema migration is complete for this one

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