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Feature/baseline expression clean#133

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feature/baseline_expression_clean
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Feature/baseline expression clean#133
DSuveges wants to merge 1 commit into
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feature/baseline_expression_clean

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@DSuveges DSuveges commented May 19, 2026

Rebased collapsed version of PR #64

  • Ingestion of logics form multiple sources. - will not be part of the release pipeline, produce data to staging.
  • Merging data from staging buckets.
  • Target and biosample validation.

@DSuveges DSuveges changed the base branch from feature/baseline_expression to main May 19, 2026 13:59
@DSuveges DSuveges force-pushed the feature/baseline_expression_clean branch 3 times, most recently from b764b9e to 533a063 Compare May 19, 2026 15:28
@DSuveges DSuveges marked this pull request as ready for review May 19, 2026 15:32
Summary of the changes:
- Ingestion logic and configuration for GTEx, Pride, DICE, CellxGene
- Cell type and tissue type speicity calculation of the ingested data.
- Target and biosample validation of the ingested data.
- Logic and configuration for aggregating ingested expression data.
- Logic allows process data at different aggregation level.
@DSuveges DSuveges force-pushed the feature/baseline_expression_clean branch from 533a063 to a94113a Compare May 20, 2026 11:38
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@Tobi1kenobi , this PR runs; data is generated to gs://ot-team/dsuveges/baseline_expression_aggregated.

Configuration update:

  • Folder structure unnested: baseline_expression/aggregated -> baseline_expression_aggregated. This is required, all output datasets have a flat folder strucutre.
  • Removing old expression PTS configuration, which was left there by accident upon rebasing.

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