gbanyan 56e04e68c2 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

2026-02-11 18:20:59 +08:00

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