test(04-03): add unit and integration tests for scoring module
- test_scoring.py: 7 unit tests for known genes, weight validation, NULL preservation - test_scoring_integration.py: 3 integration tests for end-to-end pipeline with synthetic data - Tests verify NULL handling (genes with no evidence get NULL composite score) - Tests verify known genes rank highly when given high scores - Tests verify QC detects missing data above thresholds - All tests use synthetic data (no external API calls, fast, reproducible)
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tests/test_scoring.py
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193
tests/test_scoring.py
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"""Unit tests for scoring module.
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Tests:
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- Known gene compilation and structure
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- Scoring weight validation
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- NULL preservation in composite scores
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"""
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import duckdb
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import polars as pl
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import pytest
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from usher_pipeline.config.schema import ScoringWeights
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from usher_pipeline.persistence.duckdb_store import PipelineStore
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from usher_pipeline.scoring import (
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compile_known_genes,
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compute_composite_scores,
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)
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def test_compile_known_genes_returns_expected_structure():
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"""Verify compile_known_genes returns expected structure with OMIM + SYSCILIA genes."""
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df = compile_known_genes()
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# Assert structure
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assert isinstance(df, pl.DataFrame)
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assert set(df.columns) == {"gene_symbol", "source", "confidence"}
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# Assert minimum expected count (10 OMIM Usher + 28 SYSCILIA SCGS v2 core)
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assert df.height >= 38, f"Expected at least 38 genes, got {df.height}"
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# Assert known genes are present
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gene_symbols = df.select("gene_symbol").to_series().to_list()
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assert "MYO7A" in gene_symbols, "MYO7A (Usher 1B) should be present"
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assert "IFT88" in gene_symbols, "IFT88 (SYSCILIA core) should be present"
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# Assert all confidence values are HIGH
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confidence_values = df.select("confidence").to_series().unique().to_list()
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assert confidence_values == ["HIGH"], f"Expected only HIGH confidence, got {confidence_values}"
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# Assert sources include both OMIM and SYSCILIA
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sources = df.select("source").to_series().unique().to_list()
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assert "omim_usher" in sources, "Expected omim_usher source"
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assert "syscilia_scgs_v2" in sources, "Expected syscilia_scgs_v2 source"
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def test_compile_known_genes_no_duplicates_within_source():
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"""Verify no duplicate gene_symbol within the same source."""
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df = compile_known_genes()
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# Group by source and check for duplicates within each source
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for source in df.select("source").to_series().unique().to_list():
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source_genes = df.filter(pl.col("source") == source).select("gene_symbol").to_series()
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unique_count = source_genes.unique().len()
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total_count = source_genes.len()
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assert unique_count == total_count, (
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f"Found duplicate genes in {source}: "
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f"{unique_count} unique out of {total_count} total"
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)
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def test_scoring_weights_validate_sum_defaults():
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"""ScoringWeights with defaults should pass validate_sum()."""
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weights = ScoringWeights()
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weights.validate_sum() # Should not raise
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def test_scoring_weights_validate_sum_custom_valid():
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"""ScoringWeights with custom weights summing to 1.0 should pass."""
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weights = ScoringWeights(
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gnomad=0.30,
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expression=0.25,
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annotation=0.15,
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localization=0.10,
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animal_model=0.10,
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literature=0.10,
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)
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weights.validate_sum() # Should not raise
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def test_scoring_weights_validate_sum_invalid():
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"""ScoringWeights with weights not summing to 1.0 should raise ValueError."""
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weights = ScoringWeights(
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gnomad=0.50, # Increases sum to 1.35
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)
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with pytest.raises(ValueError, match="Scoring weights must sum to 1.0"):
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weights.validate_sum()
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def test_scoring_weights_validate_sum_close_to_one():
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"""Weights within 1e-6 of 1.0 should pass, outside should fail."""
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# Should pass: within tolerance
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weights_pass = ScoringWeights(
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gnomad=0.20,
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expression=0.20,
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annotation=0.15,
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localization=0.15,
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animal_model=0.15,
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literature=0.149999, # Sum = 0.999999
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)
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weights_pass.validate_sum() # Should not raise
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# Should fail: outside tolerance
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weights_fail = ScoringWeights(
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gnomad=0.20,
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expression=0.20,
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annotation=0.15,
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localization=0.15,
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animal_model=0.15,
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literature=0.14, # Sum = 0.99
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)
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with pytest.raises(ValueError, match="Scoring weights must sum to 1.0"):
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weights_fail.validate_sum()
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def test_null_preservation_in_composite(tmp_path):
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"""Verify genes with no evidence get NULL composite scores, not zero."""
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# Create in-memory DuckDB with minimal synthetic data
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db_path = tmp_path / "test.duckdb"
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conn = duckdb.connect(str(db_path))
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# Create gene_universe with 3 genes
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gene_universe = pl.DataFrame({
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"gene_id": ["ENSG001", "ENSG002", "ENSG003"],
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"gene_symbol": ["GENE1", "GENE2", "GENE3"],
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"hgnc_id": ["HGNC:001", "HGNC:002", "HGNC:003"],
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})
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conn.execute("CREATE TABLE gene_universe AS SELECT * FROM gene_universe")
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# Create gnomad_constraint: only genes 1 and 2 have scores
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gnomad = pl.DataFrame({
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"gene_id": ["ENSG001", "ENSG002"],
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"loeuf_normalized": [0.8, 0.6],
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"quality_flag": ["measured", "measured"],
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})
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conn.execute("CREATE TABLE gnomad_constraint AS SELECT * FROM gnomad")
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# Create annotation_completeness: only gene 1 has score
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annotation = pl.DataFrame({
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"gene_id": ["ENSG001"],
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"annotation_score_normalized": [0.9],
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"annotation_tier": ["well_annotated"],
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})
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conn.execute("CREATE TABLE annotation_completeness AS SELECT * FROM annotation")
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# Create empty tables for other evidence layers
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for table_name, score_col in [
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("tissue_expression", "expression_score_normalized"),
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("subcellular_localization", "localization_score_normalized"),
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("animal_model_phenotypes", "animal_model_score_normalized"),
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("literature_evidence", "literature_score_normalized"),
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]:
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empty_df = pl.DataFrame({
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"gene_id": [],
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score_col: [],
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})
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conn.execute(f"CREATE TABLE {table_name} AS SELECT * FROM empty_df")
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# Create PipelineStore wrapper
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store = PipelineStore(db_path)
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store.conn = conn # Use the existing connection
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# Compute composite scores
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weights = ScoringWeights() # Use defaults
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scored_df = compute_composite_scores(store, weights)
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# Verify structure
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assert scored_df.height == 3, f"Expected 3 genes, got {scored_df.height}"
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# Verify GENE3 (no evidence) has NULL composite_score
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gene3 = scored_df.filter(pl.col("gene_id") == "ENSG003")
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assert gene3.height == 1, "GENE3 should be present in results"
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assert gene3["composite_score"][0] is None, "GENE3 with no evidence should have NULL composite_score"
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assert gene3["evidence_count"][0] == 0, "GENE3 should have evidence_count = 0"
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assert gene3["quality_flag"][0] == "no_evidence", "GENE3 should have quality_flag = no_evidence"
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# Verify GENE1 (2 evidence layers) has non-NULL composite_score
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gene1 = scored_df.filter(pl.col("gene_id") == "ENSG001")
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assert gene1["composite_score"][0] is not None, "GENE1 with 2 evidence layers should have non-NULL score"
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assert gene1["evidence_count"][0] == 2, "GENE1 should have evidence_count = 2"
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assert gene1["quality_flag"][0] == "moderate_evidence", "GENE1 should have quality_flag = moderate_evidence"
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# Verify GENE2 (1 evidence layer) has non-NULL composite_score
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gene2 = scored_df.filter(pl.col("gene_id") == "ENSG002")
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assert gene2["composite_score"][0] is not None, "GENE2 with 1 evidence layer should have non-NULL score"
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assert gene2["evidence_count"][0] == 1, "GENE2 should have evidence_count = 1"
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assert gene2["quality_flag"][0] == "sparse_evidence", "GENE2 should have quality_flag = sparse_evidence"
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# Clean up
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conn.close()
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