agentic-flow 1.9.0 → 1.9.1

package/agentic-flow/examples/crispr-cas13-pipeline/tests/property_tests.rs

@@ -1,371 +0,0 @@
-// Property-based tests using proptest
-// These tests verify mathematical properties and invariants hold for all inputs
-
-use proptest::prelude::*;
-
-#[cfg(test)]
-mod alignment_properties {
-    use super::*;
-
-    proptest! {
-        /// Property: Alignment score is always within valid range
-        #[test]
-        fn test_alignment_score_bounds(
-            _seq1 in "[ACGT]{20,200}",
-            _seq2 in "[ACGT]{20,200}"
-        ) {
-            // TODO: Implement when alignment function exists
-            // Property: All alignment scores in defined range (e.g., 0-100)
-            // Given: Any valid DNA sequences
-            // Expected: score_min ≤ alignment_score ≤ score_max
-            prop_assert!(true);
-        }
-
-        /// Property: Perfect match always gives maximum score
-        #[test]
-        fn test_perfect_match_max_score(
-            seq in "[ACGT]{20,200}"
-        ) {
-            // TODO: Implement when alignment function exists
-            // Property: Aligning identical sequences gives maximum score
-            // Given: Any DNA sequence aligned to itself
-            // Expected: alignment_score(seq, seq) == MAX_SCORE
-            prop_assert!(true);
-        }
-
-        /// Property: Alignment is commutative (symmetric)
-        #[test]
-        fn test_alignment_commutativity(
-            _seq1 in "[ACGT]{20,100}",
-            _seq2 in "[ACGT]{20,100}"
-        ) {
-            // TODO: Implement when alignment function exists
-            // Property: align(A, B) ≈ align(B, A)
-            // Note: May differ slightly due to orientation, but score magnitude similar
-            // Expected: |score(A,B) - score(B,A)| < epsilon
-            prop_assert!(true);
-        }
-
-        /// Property: Adding mismatches decreases score monotonically
-        #[test]
-        fn test_mismatch_score_monotonicity(
-            seq in "[ACGT]{50,50}"
-        ) {
-            // TODO: Implement when alignment function exists
-            // Property: More mismatches → lower score
-            // Given: seq vs seq_with_n_mismatches(seq, n)
-            // Expected: score(n=0) > score(n=1) > score(n=2) > ...
-            prop_assert!(true);
-        }
-
-        /// Property: CIGAR string length consistency
-        #[test]
-        fn test_cigar_length_consistency(
-            _seq1 in "[ACGT]{20,100}",
-            _seq2 in "[ACGT]{20,100}"
-        ) {
-            // TODO: Implement when alignment function exists
-            // Property: Sum of CIGAR operations matches query length
-            // Given: Alignment with CIGAR string
-            // Expected: sum(M + I + S) == query_length
-            prop_assert!(true);
-        }
-    }
-}
-
-#[cfg(test)]
-mod offtarget_prediction_properties {
-    use super::*;
-
-    proptest! {
-        /// Property: Off-target scores are normalized [0.0, 1.0]
-        #[test]
-        fn test_offtarget_score_normalization(
-            _guide in "[ACGT]{20,25}",
-            _target in "[ACGT]{20,25}"
-        ) {
-            // TODO: Implement when prediction function exists
-            // Property: All off-target scores in [0.0, 1.0]
-            // Given: Any guide RNA and potential target site
-            // Expected: 0.0 ≤ prediction_score ≤ 1.0
-            prop_assert!(true);
-        }
-
-        /// Property: Perfect match always scores 1.0
-        #[test]
-        fn test_offtarget_perfect_match(
-            guide in "[ACGT]{23,23}"
-        ) {
-            // TODO: Implement when prediction function exists
-            // Property: Guide RNA vs itself gives maximum score
-            // Given: Any 23-nt guide RNA
-            // Expected: predict_offtarget(guide, guide) == 1.0
-            prop_assert!(true);
-        }
-
-        /// Property: More mismatches → lower off-target score
-        #[test]
-        fn test_offtarget_score_monotonicity(
-            guide in "[ACGT]{23,23}"
-        ) {
-            // TODO: Implement when prediction function exists
-            // Property: Adding mismatches never increases score
-            // Given: guide vs targets with n mismatches
-            // Expected: score(n=0) ≥ score(n=1) ≥ score(n=2) ≥ ...
-            prop_assert!(true);
-        }
-
-        /// Property: Score is symmetric (position matters but order doesn't)
-        #[test]
-        fn test_offtarget_position_independence(
-            _guide in "[ACGT]{23,23}"
-        ) {
-            // TODO: Implement when prediction function exists
-            // Property: Mismatch at position i has consistent effect
-            // Note: Position matters (PAM-proximal weighted more) but deterministic
-            // Expected: Same mismatch pattern → same score
-            prop_assert!(true);
-        }
-
-        /// Property: Batch prediction consistency
-        #[test]
-        fn test_batch_prediction_consistency(
-            _guides in prop::collection::vec("[ACGT]{23,23}", 1..10),
-            _targets in prop::collection::vec("[ACGT]{23,23}", 1..10)
-        ) {
-            // TODO: Implement when batch prediction exists
-            // Property: Batch prediction gives same scores as individual
-            // Given: List of guide-target pairs
-            // Expected: batch_predict(pairs) == [predict(p) for p in pairs]
-            prop_assert!(true);
-        }
-    }
-}
-
-#[cfg(test)]
-mod normalization_properties {
-    use super::*;
-
-    proptest! {
-        /// Property: TPM normalization sums to 1 million
-        #[test]
-        fn test_tpm_sum_invariant(
-            counts in prop::collection::vec(0u32..1000000, 100..1000)
-        ) {
-            // TODO: Implement when TPM normalization exists
-            // Property: TPM values always sum to 1,000,000
-            // Given: Any array of raw read counts
-            // Expected: sum(tpm_normalize(counts)) == 1_000_000
-            // Allow small floating-point tolerance
-            prop_assert!(true);
-        }
-
-        /// Property: Normalization preserves non-negativity
-        #[test]
-        fn test_normalization_non_negativity(
-            counts in prop::collection::vec(0u32..1000000, 10..100)
-        ) {
-            // TODO: Implement when normalization exists
-            // Property: Normalized values are always non-negative
-            // Given: Non-negative input counts
-            // Expected: All normalized values ≥ 0.0
-            prop_assert!(true);
-        }
-
-        /// Property: Normalization preserves relative ordering
-        #[test]
-        fn test_normalization_order_preservation(
-            counts in prop::collection::vec(0u32..1000000, 10..100)
-        ) {
-            // TODO: Implement when normalization exists
-            // Property: If count[i] > count[j], then normalized[i] > normalized[j]
-            // Given: Raw counts
-            // Expected: Relative ranking preserved after normalization
-            prop_assert!(true);
-        }
-
-        /// Property: Log transformation handles zeros correctly
-        #[test]
-        fn test_log_transform_zero_handling(
-            counts in prop::collection::vec(0u32..1000000, 10..100)
-        ) {
-            // TODO: Implement when log transform exists
-            // Property: log2(x + 1) never produces -inf or NaN
-            // Given: Any counts including zeros
-            // Expected: All log-transformed values are finite
-            prop_assert!(true);
-        }
-
-        /// Property: Normalization is idempotent (for some methods)
-        #[test]
-        fn test_normalization_idempotence(
-            counts in prop::collection::vec(1u32..1000000, 10..100)
-        ) {
-            // TODO: Implement when normalization exists
-            // Property: Normalizing twice gives same result as once
-            // Given: Raw counts
-            // Expected: normalize(normalize(x)) ≈ normalize(x)
-            // Note: Applies to methods like quantile normalization
-            prop_assert!(true);
-        }
-    }
-}
-
-#[cfg(test)]
-mod statistical_properties {
-    use super::*;
-
-    proptest! {
-        /// Property: P-values are always in [0, 1]
-        #[test]
-        fn test_pvalue_bounds(
-            _group1 in prop::collection::vec(0.0f64..1000.0, 3..20),
-            _group2 in prop::collection::vec(0.0f64..1000.0, 3..20)
-        ) {
-            // TODO: Implement when statistical tests exist
-            // Property: P-values from statistical tests in [0, 1]
-            // Given: Any two groups of measurements
-            // Expected: 0.0 ≤ p_value ≤ 1.0
-            prop_assert!(true);
-        }
-
-        /// Property: Fold-change symmetry
-        #[test]
-        fn test_fold_change_symmetry(
-            a in 1.0f64..1000.0,
-            b in 1.0f64..1000.0
-        ) {
-            // TODO: Implement when fold-change calculation exists
-            // Property: log2(A/B) = -log2(B/A)
-            // Given: Any two positive values
-            // Expected: log2_fc(A, B) == -log2_fc(B, A)
-            // Tolerance for floating-point arithmetic
-            prop_assert!(true);
-        }
-
-        /// Property: FDR correction maintains monotonicity
-        #[test]
-        fn test_fdr_monotonicity(
-            pvalues in prop::collection::vec(0.0f64..1.0, 10..100)
-        ) {
-            // TODO: Implement when FDR correction exists
-            // Property: FDR-adjusted p-values maintain ordering
-            // Given: Array of p-values
-            // Expected: If p[i] ≤ p[j], then q[i] ≤ q[j]
-            // Where q = FDR-adjusted p-values
-            prop_assert!(true);
-        }
-
-        /// Property: FDR-adjusted p-values are ≥ raw p-values
-        #[test]
-        fn test_fdr_increases_pvalues(
-            pvalues in prop::collection::vec(0.0f64..1.0, 10..100)
-        ) {
-            // TODO: Implement when FDR correction exists
-            // Property: FDR correction never decreases p-values
-            // Given: Raw p-values
-            // Expected: adjusted_p[i] ≥ raw_p[i] for all i
-            prop_assert!(true);
-        }
-
-        /// Property: T-test is symmetric for equal groups
-        #[test]
-        fn test_ttest_symmetry(
-            data in prop::collection::vec(0.0f64..100.0, 10..50)
-        ) {
-            // TODO: Implement when t-test exists
-            // Property: t_test(A, B) == t_test(B, A) (in terms of absolute t-stat)
-            // Given: Any dataset split into two groups
-            // Expected: |t_stat(g1, g2)| == |t_stat(g2, g1)|
-            prop_assert!(true);
-        }
-    }
-}
-
-#[cfg(test)]
-mod data_structure_properties {
-    use super::*;
-
-    proptest! {
-        /// Property: Sequence validation rejects invalid characters
-        #[test]
-        fn test_sequence_validation(
-            seq in "[ACGTN]{10,100}"
-        ) {
-            // TODO: Implement when sequence validation exists
-            // Property: Valid DNA sequences only contain A, C, G, T, N
-            // Given: String with only valid nucleotides
-            // Expected: validate_sequence(seq) == true
-            prop_assert!(true);
-        }
-
-        /// Property: UUID generation is unique
-        #[test]
-        fn test_uuid_uniqueness(
-            _count in 1usize..1000
-        ) {
-            // TODO: Implement when UUID generation exists
-            // Property: Generated UUIDs are unique
-            // Given: Generate N UUIDs
-            // Expected: All UUIDs are distinct
-            prop_assert!(true);
-        }
-
-        /// Property: Timestamp ordering is consistent
-        #[test]
-        fn test_timestamp_ordering(
-            _n in 1usize..100
-        ) {
-            // TODO: Implement when timestamp creation exists
-            // Property: Sequentially created timestamps are monotonic
-            // Given: Create N timestamps in sequence
-            // Expected: timestamp[i] ≤ timestamp[i+1]
-            prop_assert!(true);
-        }
-
-        /// Property: Serialization roundtrip preserves data
-        #[test]
-        fn test_serialization_roundtrip(
-            _data in prop::collection::vec("[ACGT]{20,50}", 1..10)
-        ) {
-            // TODO: Implement when serialization exists
-            // Property: deserialize(serialize(x)) == x
-            // Given: Any serializable data structure
-            // Expected: Roundtrip preserves all fields
-            prop_assert!(true);
-        }
-    }
-}
-
-#[cfg(test)]
-mod performance_properties {
-    use super::*;
-
-    proptest! {
-        /// Property: Linear scalability with input size (for parallelizable ops)
-        #[test]
-        fn test_linear_scalability(
-            size in 100usize..10000
-        ) {
-            // TODO: Implement performance measurement
-            // Property: Processing time scales linearly with input size
-            // Given: Datasets of different sizes
-            // Expected: time(2n) ≈ 2 * time(n) for parallelizable operations
-            // Allow some variance for overhead
-            prop_assert!(true);
-        }
-
-        /// Property: Memory usage is bounded
-        #[test]
-        fn test_memory_bounds(
-            size in 100usize..10000
-        ) {
-            // TODO: Implement memory tracking
-            // Property: Memory usage grows predictably with input
-            // Given: Processing datasets of various sizes
-            // Expected: memory(n) ≤ C * n for constant C
-            // Verify streaming operations don't load everything into memory
-            prop_assert!(true);
-        }
-    }
-}

package/agentic-flow/examples/crispr-cas13-pipeline/tests/rights_preserving_test.rs

@@ -1,251 +0,0 @@
-//! Integration Tests for Rights-Preserving Countermeasure Platform
-
-use crispr_cas13_pipeline::{
-    AuditLogger, Platform, PlatformConfig, PolicyEnforcer, PrivacyConfig, PrivacyEngine,
-};
-
-#[tokio::test]
-async fn test_platform_initialization() {
-    let config = PlatformConfig::default();
-    let platform = Platform::new(config).await.unwrap();
-
-    let status = platform.status().await;
-
-    assert!(status.privacy_enabled);
-    assert!(status.policy_enforcement_enabled);
-    assert!(status.audit_enabled);
-    assert_eq!(status.api_endpoint, "0.0.0.0:8080");
-}
-
-#[tokio::test]
-async fn test_privacy_engine() {
-    let config = PrivacyConfig::default();
-    let engine = PrivacyEngine::new(config);
-
-    // Initialize budget
-    engine
-        .initialize_budget("test_user".to_string(), 10.0)
-        .await
-        .unwrap();
-
-    // Test noise application
-    let data = serde_json::json!({"value": 100.0});
-    let result = engine.apply_noise(&data, 1.0).await.unwrap();
-
-    assert_eq!(result.budget_consumed, 1.0);
-
-    // Test budget consumption
-    engine.consume_budget("test_user", 1.0).await.unwrap();
-    let remaining = engine.check_budget("test_user").await.unwrap();
-    assert_eq!(remaining, 9.0);
-}
-
-#[tokio::test]
-async fn test_privacy_anonymization() {
-    let config = PrivacyConfig::default();
-    let engine = PrivacyEngine::new(config);
-
-    let sensitive_data = serde_json::json!({
-        "patient_id": "12345",
-        "name": "John Doe",
-        "age": 35,
-        "gene_expression": 100
-    });
-
-    let anonymized = engine.anonymize_data(sensitive_data).await.unwrap();
-
-    assert!(!anonymized.as_object().unwrap().contains_key("patient_id"));
-    assert!(!anonymized.as_object().unwrap().contains_key("name"));
-    assert!(anonymized.as_object().unwrap().contains_key("age_range"));
-}
-
-#[tokio::test]
-async fn test_policy_enforcement() {
-    let enforcer = PolicyEnforcer::new(crispr_cas13_pipeline::governance::policy::PolicyConfig::default());
-    let policy = PolicyEnforcer::create_default_policy();
-
-    enforcer.add_policy(policy).await.unwrap();
-
-    // Test allow decision
-    let decision = enforcer
-        .evaluate("researcher", "read", "crispr:data:sample1")
-        .await
-        .unwrap();
-
-    assert!(decision.allowed);
-
-    // Test deny decision (no matching rule)
-    let decision = enforcer
-        .evaluate("guest", "read", "crispr:data:sample1")
-        .await
-        .unwrap();
-
-    assert!(!decision.allowed);
-}
-
-#[tokio::test]
-async fn test_audit_logging() {
-    let logger = AuditLogger::new("test-signing-key".to_string());
-
-    // Log multiple events
-    let id1 = logger
-        .log_event(
-            "data_access",
-            "user1",
-            serde_json::json!({
-                "resource": "sample1",
-                "action": "read"
-            }),
-        )
-        .await
-        .unwrap();
-
-    let id2 = logger
-        .log_event(
-            "data_export",
-            "user1",
-            serde_json::json!({
-                "resource": "sample2",
-                "action": "export"
-            }),
-        )
-        .await
-        .unwrap();
-
-    assert!(!id1.is_empty());
-    assert!(!id2.is_empty());
-
-    // Verify chain integrity
-    let valid = logger.verify_chain().await.unwrap();
-    assert!(valid);
-
-    // Test actor history
-    let history = logger.get_actor_history("user1").await;
-    assert_eq!(history.len(), 2);
-
-    // Test report generation
-    let report = logger.generate_report(Some("user1")).await;
-    assert_eq!(report.total_events, 2);
-    assert_eq!(report.unique_actors, 1);
-}
-
-#[tokio::test]
-async fn test_audit_chain_verification() {
-    let logger = AuditLogger::new("test-key".to_string());
-
-    // Create a chain of events
-    for i in 0..5 {
-        logger
-            .log_event(
-                &format!("event_{}", i),
-                "test_user",
-                serde_json::json!({"index": i}),
-            )
-            .await
-            .unwrap();
-    }
-
-    // Verify chain
-    let valid = logger.verify_chain().await.unwrap();
-    assert!(valid);
-
-    // Get events by time range
-    let start = chrono::Utc::now() - chrono::Duration::minutes(5);
-    let end = chrono::Utc::now() + chrono::Duration::minutes(5);
-    let events = logger.get_by_time_range(start, end).await;
-
-    assert_eq!(events.len(), 5);
-}
-
-#[tokio::test]
-async fn test_end_to_end_workflow() {
-    // Initialize platform
-    let config = PlatformConfig {
-        api_port: 8081, // Use different port for test
-        grpc_port: 50052,
-        ..Default::default()
-    };
-
-    let platform = Platform::new(config).await.unwrap();
-
-    // Get status
-    let status = platform.status().await;
-    assert!(status.privacy_enabled);
-
-    // Shutdown
-    platform.shutdown().await.unwrap();
-}
-
-#[tokio::test]
-async fn test_privacy_budget_enforcement() {
-    let config = PrivacyConfig::default();
-    let engine = PrivacyEngine::new(config);
-
-    // Initialize with limited budget
-    engine
-        .initialize_budget("limited_user".to_string(), 2.0)
-        .await
-        .unwrap();
-
-    // Consume partial budget
-    engine.consume_budget("limited_user", 1.0).await.unwrap();
-
-    // Try to exceed budget
-    let result = engine.consume_budget("limited_user", 2.0).await;
-    assert!(result.is_err());
-
-    // Verify remaining budget
-    let remaining = engine.check_budget("limited_user").await.unwrap();
-    assert_eq!(remaining, 1.0);
-}
-
-#[tokio::test]
-async fn test_comprehensive_integration() {
-    // Initialize all components
-    let privacy_config = PrivacyConfig::default();
-    let privacy_engine = PrivacyEngine::new(privacy_config.clone());
-    let policy_enforcer = PolicyEnforcer::new(crispr_cas13_pipeline::governance::policy::PolicyConfig::default());
-    let audit_logger = AuditLogger::new("integration-test-key".to_string());
-
-    // Add policy
-    let policy = PolicyEnforcer::create_default_policy();
-    policy_enforcer.add_policy(policy).await.unwrap();
-
-    // Initialize privacy budget
-    privacy_engine
-        .initialize_budget("integration_user".to_string(), 10.0)
-        .await
-        .unwrap();
-
-    // Simulate data access workflow
-    let user = "integration_user";
-    let resource = "crispr:data:sample1";
-
-    // 1. Check policy
-    let policy_decision = policy_enforcer
-        .evaluate(user, "read", resource)
-        .await
-        .unwrap();
-
-    // For this test, we expect denial since "integration_user" is not a "researcher"
-    assert!(!policy_decision.allowed); // Guest users are denied
-
-    // 2. Log audit event
-    let audit_id = audit_logger
-        .log_event(
-            "access_denied",
-            user,
-            serde_json::json!({
-                "resource": resource,
-                "reason": "not_authorized"
-            }),
-        )
-        .await
-        .unwrap();
-
-    assert!(!audit_id.is_empty());
-
-    // Verify audit chain
-    let valid = audit_logger.verify_chain().await.unwrap();
-    assert!(valid);
-}