Recover upstream acquisition provenance for legacy test fixtures
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 48/100
- Issue type
- Documentation
- Clarity
- Mostly clear
- Activity status
- Active
- Tech stack
- python
- Domain
- bioinformatics, documentation, testing-qa
Research direction
Start with the named fixture files and their introduction commits (5d0d268, 679167a, 30c9082, 863167b, 302ef49), comparing their history and header metadata with the pinned tree at 6f29cf8c5201189ae2803ad319aacca8053f7ddf. Done means documenting recovered releases, assemblies, source identifiers, and subsetting recipes, while explicitly recording what cannot be recovered and reviewing any proposed replacements as scientific test-data changes.
Written by the indexing model from the issue text.
Description
While fixing #509, the fixture audit found legacy validation/caller inputs whose repository history is available, but whose original upstream version, acquisition URL and exact subsetting recipe are not documented with the fixtures. Examples include dbnsfp_validation_set.csv, the TCGA/WUSTL MAF subsets, mouse_vcf_dbsnp_chr1_partial.vcf, and the older mutect-example*.vcf / strelka-example.vcf files.
The packaging fix preserves all existing bytes and adds a complete SHA256 inventory plus links to their introduction commits (5d0d268, 679167a, 30c9082, 863167b, 302ef49). Current payloads are reproducible from the pinned repository tree at 6f29cf8c5201189ae2803ad319aacca8053f7ddf. These repository pins establish byte identity; they do not recover the missing upstream acquisition history or independently validate the expected biology.
Follow-up:
- Recover the upstream dataset release, reference assembly, public source identifiers and subsetting recipe where the available history/header metadata permits it.
- Document any information that cannot be recovered without inventing provenance.
- If a fixture needs replacement, review it as a scientific test-data change with independent expected results, retaining necessary parser edge cases.
This is separate from #509's archive completeness fix and #464's modern shared RNA assets. The recent Osteosarc snapshot and caller/spec fixtures already carry substantially more detailed source receipts or construction notes.
- Dominant language
- Python
- Stars
- 88
- Forks
- 28
- Avg merge
- 4h 44m
- Merged PRs (30d)
- 54
Getting set up
- No Dockerfile or Docker Compose file
- No pull request template
- Read the contributing guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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