Squashed 'vendor/ruvector/' content from commit b64c2172
git-subtree-dir: vendor/ruvector git-subtree-split: b64c21726f2bb37286d9ee36a7869fef60cc6900
This commit is contained in:
ruv
409
examples/dna/tests/biomarker_tests.rs
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409
examples/dna/tests/biomarker_tests.rs
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//! Integration tests for the biomarker analysis engine.
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//!
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//! Tests composite risk scoring, profile vector encoding, clinical biomarker
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//! references, synthetic population generation, and streaming biomarker
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//! processing with anomaly and trend detection.
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use rvdna::biomarker::*;
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use rvdna::biomarker_stream::*;
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use std::collections::HashMap;
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// ============================================================================
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// COMPOSITE RISK SCORING TESTS
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// ============================================================================
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#[test]
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fn test_compute_risk_scores_baseline() {
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// All homozygous reference (low risk) genotypes
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let mut gts = HashMap::new();
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gts.insert("rs429358".to_string(), "TT".to_string()); // APOE ref
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gts.insert("rs7412".to_string(), "CC".to_string()); // APOE ref
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gts.insert("rs4680".to_string(), "GG".to_string()); // COMT ref
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gts.insert("rs1799971".to_string(), "AA".to_string()); // OPRM1 ref
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gts.insert("rs762551".to_string(), "AA".to_string()); // CYP1A2 fast
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gts.insert("rs1801133".to_string(), "GG".to_string()); // MTHFR ref
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gts.insert("rs1801131".to_string(), "TT".to_string()); // MTHFR ref
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gts.insert("rs1042522".to_string(), "CC".to_string()); // TP53 ref
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gts.insert("rs80357906".to_string(), "DD".to_string()); // BRCA1 ref
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gts.insert("rs4363657".to_string(), "TT".to_string()); // SLCO1B1 ref
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let profile = compute_risk_scores(>s);
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assert!(
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profile.global_risk_score < 0.3,
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"Baseline should be low risk, got {}",
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profile.global_risk_score
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);
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assert!(!profile.category_scores.is_empty());
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}
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#[test]
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fn test_compute_risk_scores_high_risk() {
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// High-risk genotype combinations
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let mut gts = HashMap::new();
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gts.insert("rs429358".to_string(), "CC".to_string()); // APOE e4/e4
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gts.insert("rs7412".to_string(), "CC".to_string());
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gts.insert("rs4680".to_string(), "AA".to_string()); // COMT Met/Met
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gts.insert("rs1799971".to_string(), "GG".to_string()); // OPRM1 Asp/Asp
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gts.insert("rs1801133".to_string(), "AA".to_string()); // MTHFR 677TT
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gts.insert("rs1801131".to_string(), "GG".to_string()); // MTHFR 1298CC
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gts.insert("rs4363657".to_string(), "CC".to_string()); // SLCO1B1 hom variant
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let profile = compute_risk_scores(>s);
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assert!(
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profile.global_risk_score > 0.4,
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"High-risk should score >0.4, got {}",
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profile.global_risk_score
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);
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}
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// ============================================================================
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// PROFILE VECTOR TESTS
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// ============================================================================
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#[test]
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fn test_profile_vector_dimension() {
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let gts = HashMap::new(); // empty genotypes
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let profile = compute_risk_scores(>s);
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assert_eq!(
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profile.profile_vector.len(),
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64,
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"Profile vector must be exactly 64 dimensions"
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);
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}
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#[test]
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fn test_profile_vector_normalized() {
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let mut gts = HashMap::new();
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gts.insert("rs429358".to_string(), "CT".to_string());
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gts.insert("rs4680".to_string(), "AG".to_string());
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let profile = compute_risk_scores(>s);
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let mag: f32 = profile
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.profile_vector
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.iter()
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.map(|x| x * x)
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.sum::<f32>()
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.sqrt();
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assert!(
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(mag - 1.0).abs() < 0.01 || mag == 0.0,
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"Vector should be L2-normalized, got magnitude {}",
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mag
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);
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}
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// ============================================================================
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// BIOMARKER REFERENCE TESTS
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// ============================================================================
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#[test]
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fn test_biomarker_references_exist() {
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let refs = biomarker_references();
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assert!(
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refs.len() >= 13,
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"Should have at least 13 biomarker references, got {}",
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refs.len()
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);
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}
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#[test]
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fn test_z_score_computation() {
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let refs = biomarker_references();
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let cholesterol_ref = refs.iter().find(|r| r.name == "Total Cholesterol").unwrap();
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// Normal value should have |z| < 2
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let z_normal = z_score(180.0, cholesterol_ref);
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assert!(
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z_normal.abs() < 2.0,
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"Normal cholesterol z-score should be small: {}",
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z_normal
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);
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// High value should have z > 0
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let z_high = z_score(300.0, cholesterol_ref);
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assert!(
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z_high > 0.0,
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"High cholesterol should have positive z-score: {}",
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z_high
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);
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}
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#[test]
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fn test_biomarker_classification() {
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let refs = biomarker_references();
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let glucose_ref = refs.iter().find(|r| r.name == "Fasting Glucose").unwrap();
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let class_normal = classify_biomarker(85.0, glucose_ref);
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// Should be normal range
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let class_high = classify_biomarker(200.0, glucose_ref);
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// Should be high/critical
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assert_ne!(format!("{:?}", class_normal), format!("{:?}", class_high));
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}
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// ============================================================================
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// SYNTHETIC POPULATION TESTS
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// ============================================================================
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#[test]
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fn test_synthetic_population() {
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let pop = generate_synthetic_population(100, 42);
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assert_eq!(pop.len(), 100);
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// All vectors should be 64-dim
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for profile in &pop {
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assert_eq!(profile.profile_vector.len(), 64);
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}
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// Risk scores should span a range
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let scores: Vec<f64> = pop.iter().map(|p| p.global_risk_score).collect();
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let min = scores.iter().cloned().fold(f64::INFINITY, f64::min);
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let max = scores.iter().cloned().fold(f64::NEG_INFINITY, f64::max);
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assert!(
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max - min > 0.1,
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"Population should have risk score variance, range: {:.3}..{:.3}",
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min,
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max
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);
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}
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#[test]
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fn test_synthetic_population_deterministic() {
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let pop1 = generate_synthetic_population(50, 42);
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let pop2 = generate_synthetic_population(50, 42);
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assert_eq!(pop1.len(), pop2.len());
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for (a, b) in pop1.iter().zip(pop2.iter()) {
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assert!((a.global_risk_score - b.global_risk_score).abs() < 1e-10);
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}
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}
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// ============================================================================
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// STREAMING TESTS
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// ============================================================================
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#[test]
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fn test_ring_buffer_basic() {
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let mut rb: RingBuffer<f64> = RingBuffer::new(5);
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for i in 0..3 {
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rb.push(i as f64);
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}
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assert_eq!(rb.len(), 3);
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let items: Vec<f64> = rb.iter().cloned().collect();
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assert_eq!(items, vec![0.0, 1.0, 2.0]);
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}
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#[test]
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fn test_ring_buffer_overflow() {
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let mut rb: RingBuffer<f64> = RingBuffer::new(3);
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for i in 0..5 {
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rb.push(i as f64);
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}
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assert_eq!(rb.len(), 3);
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let items: Vec<f64> = rb.iter().cloned().collect();
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assert_eq!(items, vec![2.0, 3.0, 4.0]);
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}
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#[test]
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fn test_stream_generation() {
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let config = StreamConfig::default();
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let num_biomarkers = config.num_biomarkers;
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let readings = generate_readings(&config, 1000, 42);
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// generate_readings produces count * num_biomarkers total readings
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assert_eq!(readings.len(), 1000 * num_biomarkers);
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// All values should be positive
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for r in &readings {
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assert!(
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r.value > 0.0,
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"Biomarker values should be positive: {} = {}",
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r.biomarker_id,
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r.value
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);
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}
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}
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#[test]
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fn test_stream_processor() {
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let config = StreamConfig::default();
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let num_biomarkers = config.num_biomarkers;
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let readings = generate_readings(&config, 500, 42);
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let mut processor = StreamProcessor::new(config);
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for reading in &readings {
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processor.process_reading(reading);
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}
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let summary = processor.summary();
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assert_eq!(summary.total_readings, 500 * num_biomarkers as u64);
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assert!(
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summary.anomaly_rate < 0.2,
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"Anomaly rate should be reasonable: {}",
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summary.anomaly_rate
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);
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}
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#[test]
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fn test_anomaly_detection() {
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let config = StreamConfig {
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anomaly_probability: 0.0, // No random anomalies
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num_biomarkers: 1,
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..StreamConfig::default()
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};
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let readings = generate_readings(&config, 200, 42);
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let mut processor = StreamProcessor::new(config);
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for reading in &readings {
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processor.process_reading(reading);
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}
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// With no anomaly injection, anomaly rate should be very low
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let summary = processor.summary();
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assert!(
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summary.anomaly_rate < 0.1,
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"Without injection, anomaly rate should be low: {}",
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summary.anomaly_rate
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);
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}
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// ============================================================================
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// GENE-GENE INTERACTION TESTS
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// ============================================================================
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#[test]
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fn test_mthfr_comt_interaction() {
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// MTHFR A1298C hom + COMT Met/Met should amplify neurological score
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let mut gts_both = HashMap::new();
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gts_both.insert("rs1801131".to_string(), "GG".to_string()); // A1298C hom_alt
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gts_both.insert("rs4680".to_string(), "AA".to_string()); // COMT Met/Met
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let both = compute_risk_scores(>s_both);
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let mut gts_one = HashMap::new();
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gts_one.insert("rs4680".to_string(), "AA".to_string()); // COMT Met/Met only
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let one = compute_risk_scores(>s_one);
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let n_both = both.category_scores.get("Neurological").unwrap().score;
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let n_one = one.category_scores.get("Neurological").unwrap().score;
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assert!(
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n_both > n_one,
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"MTHFR×COMT interaction should amplify: {n_both} > {n_one}"
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);
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}
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#[test]
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fn test_drd2_comt_interaction() {
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// DRD2 Taq1A + COMT variant should amplify neurological score
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let mut gts = HashMap::new();
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gts.insert("rs1800497".to_string(), "AA".to_string()); // DRD2 hom_alt
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gts.insert("rs4680".to_string(), "AA".to_string()); // COMT Met/Met
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let with = compute_risk_scores(>s);
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let mut gts2 = HashMap::new();
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gts2.insert("rs1800497".to_string(), "AA".to_string()); // DRD2 only
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let without = compute_risk_scores(>s2);
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let n_with = with.category_scores.get("Neurological").unwrap().score;
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let n_without = without.category_scores.get("Neurological").unwrap().score;
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assert!(
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n_with > n_without,
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"DRD2×COMT interaction should amplify: {n_with} > {n_without}"
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);
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}
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// ============================================================================
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// GENE-BIOMARKER CORRELATION TESTS
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// ============================================================================
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#[test]
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fn test_apoe_lowers_hdl_in_population() {
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let pop = generate_synthetic_population(300, 88);
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let (mut apoe_hdl, mut ref_hdl) = (Vec::new(), Vec::new());
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for p in &pop {
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let hdl = p.biomarker_values.get("HDL").copied().unwrap_or(0.0);
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// APOE carriers have elevated neurological scores from rs429358
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let neuro = p
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.category_scores
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.get("Neurological")
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.map(|c| c.score)
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.unwrap_or(0.0);
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if neuro > 0.3 {
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apoe_hdl.push(hdl);
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} else {
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ref_hdl.push(hdl);
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}
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}
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if !apoe_hdl.is_empty() && !ref_hdl.is_empty() {
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let avg_apoe = apoe_hdl.iter().sum::<f64>() / apoe_hdl.len() as f64;
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let avg_ref = ref_hdl.iter().sum::<f64>() / ref_hdl.len() as f64;
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assert!(
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avg_apoe < avg_ref,
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"APOE e4 should lower HDL: {avg_apoe} < {avg_ref}"
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);
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}
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}
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#[test]
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fn test_cusum_changepoint_detection() {
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let mut p = StreamProcessor::new(StreamConfig {
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window_size: 20,
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..Default::default()
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});
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// Establish baseline
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for i in 0..30 {
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p.process_reading(&BiomarkerReading {
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timestamp_ms: i * 1000,
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biomarker_id: "glucose".into(),
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value: 85.0,
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reference_low: 70.0,
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reference_high: 100.0,
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is_anomaly: false,
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z_score: 0.0,
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});
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}
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// Inject a sustained shift (changepoint)
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for i in 30..50 {
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p.process_reading(&BiomarkerReading {
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timestamp_ms: i * 1000,
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biomarker_id: "glucose".into(),
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value: 120.0,
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reference_low: 70.0,
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reference_high: 100.0,
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is_anomaly: false,
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z_score: 0.0,
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});
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}
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let stats = p.get_stats("glucose").unwrap();
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// After sustained shift, CUSUM should have triggered at least once
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// (changepoint_detected resets after trigger, but the sustained shift
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// will keep re-triggering, so the final state may or may not be true)
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assert!(
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stats.mean > 90.0,
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"Mean should shift upward after changepoint: {}",
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stats.mean
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);
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}
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#[test]
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fn test_trend_detection() {
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let config = StreamConfig {
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drift_rate: 0.5, // Strong upward drift
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anomaly_probability: 0.0,
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num_biomarkers: 1,
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window_size: 50,
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..StreamConfig::default()
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};
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let readings = generate_readings(&config, 200, 42);
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let mut processor = StreamProcessor::new(config);
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for reading in &readings {
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processor.process_reading(reading);
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}
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// Should detect positive trend
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let summary = processor.summary();
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for (_, stats) in &summary.biomarker_stats {
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assert!(
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stats.trend_slope > 0.0,
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"Should detect upward trend, got slope: {}",
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stats.trend_slope
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);
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}
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}
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Reference in New Issue
Block a user