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56e04e68c2
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test(02-02): add comprehensive gnomAD integration tests
- 12 integration tests covering full pipeline: fetch->transform->load->query
- test_full_pipeline_to_duckdb: End-to-end pipeline verification with DuckDB storage
- test_checkpoint_restart_skips_processing: Checkpoint detection works correctly
- test_provenance_recorded: Provenance step records expected details
- test_provenance_sidecar_created: JSON sidecar file creation and structure
- test_query_constrained_genes_filters_correctly: Query returns only measured genes below threshold
- test_null_loeuf_not_in_constrained_results: NULL LOEUF genes excluded from queries
- test_duckdb_schema_has_quality_flag: Schema includes quality_flag with valid values
- test_normalized_scores_in_duckdb: Normalized scores in [0,1] for measured genes, NULL for others
- test_cli_evidence_gnomad_help: CLI help text displays correctly
- test_cli_evidence_gnomad_with_mock: CLI command runs end-to-end with mocked download
- test_idempotent_load_replaces_table: Loading twice replaces table (not appends)
- test_quality_flag_categorization: Quality flags correctly categorize genes
All 70 tests pass (58 existing + 12 new), no regressions
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2026-02-11 18:20:59 +08:00 |
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174c4af02d
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feat(02-01): add gnomAD transform pipeline and comprehensive tests
- Implement filter_by_coverage with quality_flag categorization (measured/incomplete_coverage/no_data)
- Add normalize_scores with LOEUF inversion (lower LOEUF = higher score)
- NULL preservation throughout pipeline (unknown != zero constraint)
- process_gnomad_constraint end-to-end pipeline function
- 15 comprehensive unit tests covering edge cases:
- NULL handling and preservation
- Coverage filtering without dropping genes
- Normalization bounds and inversion
- Mixed type handling for robust parsing
- Fix column mapping to handle gnomAD v4.x loeuf/loeuf_upper duplication
- All existing tests continue to pass
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2026-02-11 18:14:41 +08:00 |
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e4d71d0790
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test(01-04): add integration tests verifying module wiring
- test_config_to_store_roundtrip: config -> PipelineStore -> save/load
- test_config_to_provenance: config -> ProvenanceTracker -> sidecar
- test_full_setup_flow_mocked: full setup with mocked mygene (fetch, map, validate, save, provenance)
- test_checkpoint_skip_flow: verify checkpoint-restart skips re-fetch
- test_setup_cli_help: CLI help output verification
- test_info_cli: info command with config display
All tests pass with mocked API calls (no external dependencies).
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2026-02-11 16:42:13 +08:00 |
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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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