agentic-flow 1.9.0 → 1.9.2

package/agentic-flow/examples/crispr-cas13-pipeline/crates/offtarget-predictor/tests/prediction_test.rs

@@ -1,245 +0,0 @@
-// Unit tests for off-target prediction - ML model accuracy and edge cases
-#[cfg(test)]
-mod offtarget_predictor_tests {
-    use super::*;
-
-    // Core prediction functionality tests
-    #[test]
-    fn test_perfect_match_prediction() {
-        // TODO: Test prediction for perfect match
-        // Given: guide RNA perfectly matches target site
-        // Expected: off-target score = 1.0 (highest probability)
-        // Verify confidence interval is narrow
-        assert!(
-            true,
-            "Placeholder - implement when prediction function exists"
-        );
-    }
-
-    #[test]
-    fn test_single_mismatch_prediction() {
-        // TODO: Test prediction with single mismatch
-        // Given: guide RNA with 1 mismatch to potential off-target
-        // Expected: score between 0.6-0.9 depending on position
-        // Verify PAM-proximal mismatches penalized more
-        assert!(
-            true,
-            "Placeholder - implement when prediction function exists"
-        );
-    }
-
-    #[test]
-    fn test_multiple_mismatch_prediction() {
-        // TODO: Test prediction with multiple mismatches
-        // Given: guide RNA with 3+ mismatches
-        // Expected: off-target score < 0.3 (low probability)
-        // Verify score decreases with mismatch count
-        assert!(
-            true,
-            "Placeholder - implement when prediction function exists"
-        );
-    }
-
-    #[test]
-    fn test_pam_sequence_validation() {
-        // TODO: Test PAM (Protospacer Adjacent Motif) validation
-        // Given: potential off-target with/without valid PAM
-        // Expected: sites without PAM get score = 0.0
-        // Verify PAM sequence requirements for Cas13
-        assert!(true, "Placeholder - implement when PAM validation exists");
-    }
-
-    #[test]
-    fn test_mismatch_position_weighting() {
-        // TODO: Test position-dependent mismatch weighting
-        // Given: mismatches at different positions in guide RNA
-        // Expected: seed region mismatches penalized more than distal
-        // Verify position weight matrix is applied correctly
-        assert!(
-            true,
-            "Placeholder - implement when position weighting exists"
-        );
-    }
-
-    // Feature extraction tests
-    #[test]
-    fn test_sequence_feature_extraction() {
-        // TODO: Test feature extraction from sequences
-        // Verify k-mer features calculated correctly
-        // Test GC content calculation
-        // Validate thermodynamic features (ΔG, Tm)
-        assert!(
-            true,
-            "Placeholder - implement when feature extraction exists"
-        );
-    }
-
-    #[test]
-    fn test_structural_feature_extraction() {
-        // TODO: Test RNA secondary structure features
-        // Verify structure prediction integration
-        // Test accessibility score calculation
-        assert!(
-            true,
-            "Placeholder - implement when structure features exist"
-        );
-    }
-
-    #[test]
-    fn test_chromatin_context_features() {
-        // TODO: Test chromatin accessibility features
-        // Verify DNase-seq/ATAC-seq integration
-        // Test histone modification features
-        assert!(
-            true,
-            "Placeholder - implement when chromatin features exist"
-        );
-    }
-
-    // ML model tests
-    #[test]
-    fn test_model_loading() {
-        // TODO: Test ML model loading from file
-        // Verify model weights loaded correctly
-        // Test model version compatibility
-        // Validate model architecture matches expected
-        assert!(true, "Placeholder - implement when model loading exists");
-    }
-
-    #[test]
-    fn test_model_inference_performance() {
-        // TODO: Test model inference speed
-        // Given: batch of 1000 potential off-targets
-        // Expected: inference completes in <1 second
-        // Target: >1000 predictions/second
-        assert!(true, "Placeholder - implement when model exists");
-    }
-
-    #[test]
-    fn test_batch_prediction_consistency() {
-        // TODO: Test batch vs single prediction consistency
-        // Given: same site predicted individually vs in batch
-        // Expected: identical scores within floating-point tolerance
-        // Verify batch optimization doesn't affect accuracy
-        assert!(true, "Placeholder - implement when batch prediction exists");
-    }
-
-    // Edge case tests
-    #[test]
-    fn test_genome_wide_scanning() {
-        // TODO: Test genome-wide off-target scanning
-        // Given: 23-nt guide RNA, ~3 billion bp primate genome
-        // Expected: completes scan in reasonable time (<1 hour)
-        // Verify memory usage is reasonable (<16 GB)
-        assert!(true, "Placeholder - implement when genome scan exists");
-    }
-
-    #[test]
-    fn test_high_gc_content_handling() {
-        // TODO: Test prediction for high GC content sequences
-        // Given: guide RNA with >80% GC content
-        // Expected: handles without numerical instability
-        // Verify thermodynamic calculations are accurate
-        assert!(true, "Placeholder - implement when prediction exists");
-    }
-
-    #[test]
-    fn test_low_complexity_sequence_handling() {
-        // TODO: Test prediction for low-complexity sequences
-        // Given: homopolymer or dinucleotide repeat sequences
-        // Expected: prediction flags low-complexity warning
-        // Verify doesn't report spurious off-targets
-        assert!(true, "Placeholder - implement when prediction exists");
-    }
-
-    #[test]
-    fn test_indel_tolerance_prediction() {
-        // TODO: Test prediction with small indels
-        // Given: potential off-target with 1-2 bp insertion/deletion
-        // Expected: indel-aware scoring
-        // Verify gap penalties applied correctly
-        assert!(true, "Placeholder - implement when indel handling exists");
-    }
-
-    // Validation against experimental data
-    #[test]
-    fn test_prediction_vs_experimental_data() {
-        // TODO: Test prediction accuracy vs published datasets
-        // Given: GUIDE-seq or CIRCLE-seq experimental off-targets
-        // Expected: AUC-ROC > 0.85 for top predicted sites
-        // Verify precision-recall curve matches benchmarks
-        assert!(true, "Placeholder - implement when validation data exists");
-    }
-
-    #[test]
-    fn test_false_positive_rate() {
-        // TODO: Test false positive rate control
-        // Given: set of validated non-off-targets
-        // Expected: FPR < 5% at reasonable score threshold
-        // Verify specificity matches publication standards
-        assert!(true, "Placeholder - implement when validation exists");
-    }
-
-    #[test]
-    fn test_sensitivity_analysis() {
-        // TODO: Test sensitivity to detect known off-targets
-        // Given: validated off-targets from literature
-        // Expected: sensitivity > 90% for sites with >3 reads
-        // Verify doesn't miss high-activity off-targets
-        assert!(true, "Placeholder - implement when validation exists");
-    }
-}
-
-// Property-based tests
-#[cfg(test)]
-mod offtarget_property_tests {
-    use super::*;
-
-    #[test]
-    fn proptest_score_normalization() {
-        // TODO: Property-based test for score normalization
-        // Property: All off-target scores in [0.0, 1.0]
-        // Property: Perfect match always scores 1.0
-        // Property: More mismatches → lower score
-        assert!(true, "Placeholder - implement with proptest");
-    }
-
-    #[test]
-    fn proptest_prediction_monotonicity() {
-        // TODO: Property-based test for monotonicity
-        // Property: Adding mismatches never increases score
-        // Property: Removing mismatches never decreases score
-        assert!(true, "Placeholder - implement with proptest");
-    }
-
-    #[test]
-    fn proptest_batch_invariance() {
-        // TODO: Property-based test for batch invariance
-        // Property: Prediction order doesn't affect scores
-        // Property: Batch size doesn't affect individual predictions
-        assert!(true, "Placeholder - implement with proptest");
-    }
-}
-
-// Performance benchmarking helpers
-#[cfg(test)]
-mod performance_tests {
-    use super::*;
-
-    #[test]
-    fn test_feature_extraction_performance() {
-        // TODO: Benchmark feature extraction
-        // Target: >10,000 sites/second for feature extraction
-        // Verify parallel processing scales with cores
-        assert!(true, "Placeholder - implement when features exist");
-    }
-
-    #[test]
-    fn test_memory_efficiency() {
-        // TODO: Test memory usage during prediction
-        // Given: 1 million potential off-target sites
-        // Expected: peak memory < 4 GB
-        // Verify streaming processing works correctly
-        assert!(true, "Placeholder - implement when prediction exists");
-    }
-}

package/agentic-flow/examples/crispr-cas13-pipeline/crates/processing-orchestrator/Cargo.toml

@@ -1,26 +0,0 @@
-[package]
-name = "processing-orchestrator"
-version = "0.1.0"
-edition = "2021"
-authors = ["CRISPR-Cas13 Team"]
-description = "Job orchestration for CRISPR-Cas13 pipeline"
-license = "MIT"
-
-[[bin]]
-name = "processing-orchestrator"
-path = "src/main.rs"
-
-[dependencies]
-data-models = { path = "../data-models" }
-alignment-engine = { path = "../alignment-engine" }
-offtarget-predictor = { path = "../offtarget-predictor" }
-immune-analyzer = { path = "../immune-analyzer" }
-
-tokio = { version = "1.40", features = ["full"] }
-thiserror = "1.0"
-tracing = "0.1"
-tracing-subscriber = { version = "0.3", features = ["env-filter"] }
-serde = { version = "1.0", features = ["derive"] }
-serde_json = "1.0"
-uuid = { version = "1.10", features = ["v4"] }
-rdkafka = { version = "0.36", features = ["tokio"] }

package/agentic-flow/examples/crispr-cas13-pipeline/crates/processing-orchestrator/src/jobs.rs

@@ -1,27 +0,0 @@
-//! Job management
-
-use serde::{Deserialize, Serialize};
-use uuid::Uuid;
-
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub struct Job {
-    pub id: Uuid,
-    pub job_type: JobType,
-    pub status: JobStatus,
-    pub payload: serde_json::Value,
-}
-
-#[derive(Debug, Clone, Serialize, Deserialize)]
-pub enum JobType {
-    Alignment,
-    OffTargetPrediction,
-    DifferentialExpression,
-}
-
-#[derive(Debug, Clone, Serialize, Deserialize, PartialEq, Eq)]
-pub enum JobStatus {
-    Pending,
-    Processing,
-    Completed,
-    Failed,
-}

package/agentic-flow/examples/crispr-cas13-pipeline/crates/processing-orchestrator/src/main.rs

@@ -1,35 +0,0 @@
-//! # Processing Orchestrator
-//!
-//! Job orchestration service for the CRISPR-Cas13 pipeline.
-
-use tracing_subscriber::{layer::SubscriberExt, util::SubscriberInitExt};
-
-mod jobs;
-mod scheduler;
-mod workers;
-
-#[tokio::main]
-async fn main() -> Result<(), Box<dyn std::error::Error>> {
-    // Initialize tracing
-    tracing_subscriber::registry()
-        .with(tracing_subscriber::EnvFilter::new(
-            std::env::var("RUST_LOG").unwrap_or_else(|_| "processing_orchestrator=info".into()),
-        ))
-        .with(tracing_subscriber::fmt::layer())
-        .init();
-
-    tracing::info!("Processing orchestrator starting...");
-
-    // TODO: Initialize Kafka consumers/producers
-    // TODO: Start worker pool
-    // TODO: Begin processing jobs
-
-    tracing::info!("Processing orchestrator running");
-
-    // Keep the service running
-    tokio::signal::ctrl_c().await?;
-
-    tracing::info!("Shutting down processing orchestrator");
-
-    Ok(())
-}

package/agentic-flow/examples/crispr-cas13-pipeline/crates/processing-orchestrator/src/scheduler.rs

@@ -1,24 +0,0 @@
-//! Job scheduling
-
-use crate::jobs::Job;
-
-pub struct Scheduler {
-    // TODO: Implement job scheduling logic
-}
-
-impl Scheduler {
-    pub fn new() -> Self {
-        Self {}
-    }
-
-    pub async fn schedule(&self, job: Job) -> Result<(), Box<dyn std::error::Error>> {
-        tracing::info!("Scheduling job: {:?}", job.id);
-        Ok(())
-    }
-}
-
-impl Default for Scheduler {
-    fn default() -> Self {
-        Self::new()
-    }
-}

package/agentic-flow/examples/crispr-cas13-pipeline/crates/processing-orchestrator/src/workers.rs

@@ -1,17 +0,0 @@
-//! Worker pool management
-
-pub struct WorkerPool {
-    size: usize,
-}
-
-impl WorkerPool {
-    pub fn new(size: usize) -> Self {
-        tracing::info!("Creating worker pool with {} workers", size);
-        Self { size }
-    }
-
-    pub async fn start(&self) -> Result<(), Box<dyn std::error::Error>> {
-        tracing::info!("Starting worker pool");
-        Ok(())
-    }
-}