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0200395d9e
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feat(01-02): create mapping validation gates with tests
- Add MappingValidator with configurable success rate thresholds (min_success_rate, warn_threshold)
- Add validate_gene_universe for gene count, format, and duplicate checks
- Add save_unmapped_report for manual review output
- Implement 15 comprehensive tests with mocked mygene responses (no real API calls)
- Tests cover: successful mapping, notfound handling, uniprot list parsing, batching, validation gates, universe validation
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2026-02-11 16:33:36 +08:00 |
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98a1a750dd
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feat(01-03): create provenance tracker with comprehensive tests
- ProvenanceTracker class for metadata tracking
- Records pipeline version, data source versions, config hash, timestamps
- Sidecar JSON export alongside outputs
- DuckDB _provenance table support
- 13 comprehensive tests (8 DuckDB + 5 provenance)
- All tests pass (12 passed, 1 skipped - pandas)
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2026-02-11 16:31:51 +08:00 |
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4204116772
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feat(01-01): create base API client with retry and caching
- CachedAPIClient with SQLite persistent cache
- Exponential backoff retry on 429/5xx/network errors (tenacity)
- Rate limiting with skip for cached responses
- from_config classmethod for pipeline integration
- 5 passing tests for cache creation, rate limiting, and config integration
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2026-02-11 16:25:46 +08:00 |
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4a80a0398e
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feat(01-01): create Python package scaffold with config system
- pyproject.toml: installable package with bioinformatics dependencies
- Pydantic config schema with validation (ensembl_release >= 100, directory creation)
- YAML config loader with override support
- Default config with Ensembl 113, gnomAD v4.1
- 5 passing tests for config validation and hashing
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2026-02-11 16:24:35 +08:00 |
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