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INS-1715: Update dbGaP Oct 2026 - #56
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- Also reorder integer handling to prevent unintended conversion from int to float - Add tests for new function and integer handling
- Keep full phs accession to help detect when metadata needs to be reviewed again (rather than keeping previous curated values) - Add columns and assign curation groups to assist curation in the merged dbGaP output TSV - Add one-time step to backfill legacy dbGaP output with full accessions for compatibility - Update config with new field and to remove outdated merge_title_review
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Copilot review overview
🟡 Changes recommended
The merge rejects the legacy baseline before migration, and the October dbGaP version and data remain unconfigured.
Review effort: Balanced
Findings: 1
Open (4)
What changed in this PR
Updates DCEG cohort metadata and introduces version-aware dbGaP curation merging.
Changes:
- Tracks full dbGaP accessions and classifies changed studies for review.
- Adds encoding fallback, accession backfilling, integer serialization, and tests.
- Replaces the February DCEG release with September metadata.
| File | Description |
|---|---|
README.md |
Documents the revised dbGaP workflow. |
config.py |
Updates DCEG version and dbGaP mapping. |
modules/gather_dbgap_data.py |
Retains full dbGaP accessions. |
modules/merge_curated_dbgap.py |
Implements version-aware merging. |
modules/package_output_data.py |
Adds encoding and packaging improvements. |
tests/test_merge_curated_dbgap.py |
Tests merge classifications. |
tests/test_package_output_data.py |
Tests packaging helpers and integers. |
data/01_intermediate/dceg_cohorts/2026-09-28/dceg_datasets_curated.tsv |
Adds updated curated DCEG data. |
data/02_output/dceg_cohorts/2026-09-28/dceg_datasets_curated_clean.tsv |
Adds packaged DCEG output. |
data/01_intermediate/dceg_cohorts/2026-02-03/dceg_datasets_curated.tsv |
Removes superseded curated data. |
data/02_output/dceg_cohorts/2026-02-03/dceg_datasets_curated_clean.tsv |
Removes superseded packaged output. |
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Clarifies the use of deterministic UUID5 values for dbGaP studies. Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
zdorman
marked this pull request as draft
October 2, 2026 15:41
- Add main dbGaP input CSV and subsets downloaded 2026-10-02 - Update GPA and DOC lookup tables
…BIIT/INS-Data into ins-1715-update-dbgap-oct-2026
- Add new dbGaP results and result set merged with previous curation - Add bulk json results from dbGaP APIs and API error logs
zdorman
marked this pull request as ready for review
October 8, 2026 18:10
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Update dbGaP study metadata for INS with new/updated studies and updated curation (pending). This PR also includes an improved process for merging new, raw dbGaP data with previous curated data to streamline curation efforts.