agentic-flow 1.9.0 → 1.9.1

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

@@ -1,340 +0,0 @@
-// Integration tests for end-to-end pipeline workflows
-// These tests verify the entire system working together
-
-#[cfg(test)]
-mod pipeline_integration_tests {
-    use super::*;
-
-    /// End-to-end test: FASTQ input → alignment → off-target prediction → results
-    #[tokio::test]
-    async fn test_complete_pipeline_execution() {
-        // TODO: Test full pipeline end-to-end
-        // 1. Submit FASTQ files (simulated or test data)
-        // 2. Trigger alignment engine
-        // 3. Run off-target prediction on alignments
-        // 4. Perform immune response analysis
-        // 5. Verify results available via API
-        // Expected: Complete workflow finishes successfully
-        // Target: <30 minutes for 1M reads
-        assert!(true, "Placeholder - implement when full pipeline exists");
-    }
-
-    /// Test: Pipeline handles multiple concurrent jobs
-    #[tokio::test]
-    async fn test_concurrent_job_processing() {
-        // TODO: Test concurrent job execution
-        // Given: Submit 5 analysis jobs simultaneously
-        // Expected: All jobs processed without interference
-        // Verify: Job queue and orchestration work correctly
-        // Target: Linear scaling up to available workers
-        assert!(true, "Placeholder - implement when orchestrator exists");
-    }
-
-    /// Test: Pipeline recovers from worker failure
-    #[tokio::test]
-    async fn test_pipeline_fault_tolerance() {
-        // TODO: Test fault tolerance and recovery
-        // Given: Kill worker process mid-job
-        // Expected: Job automatically reassigned to another worker
-        // Verify: No data loss, job completes successfully
-        assert!(true, "Placeholder - implement when orchestrator exists");
-    }
-
-    /// Test: Pipeline handles very large datasets
-    #[tokio::test]
-    #[ignore] // Long-running test
-    async fn test_large_scale_dataset_processing() {
-        // TODO: Test with realistic large dataset
-        // Given: 100 million RNA-seq reads
-        // Expected: Pipeline completes without memory issues
-        // Verify: Streaming processing, memory < 32 GB
-        // Target: <2 hours processing time
-        assert!(true, "Placeholder - implement when pipeline exists");
-    }
-}
-
-#[cfg(test)]
-mod database_integration_tests {
-    use super::*;
-
-    /// Test: PostgreSQL database operations
-    #[tokio::test]
-    async fn test_postgres_crud_operations() {
-        // TODO: Test PostgreSQL CRUD operations
-        // 1. Create test database schema
-        // 2. Insert job records
-        // 3. Query jobs by status
-        // 4. Update job status
-        // 5. Delete completed jobs
-        // Verify: All operations succeed
-        assert!(true, "Placeholder - implement when DB layer exists");
-    }
-
-    /// Test: MongoDB document storage
-    #[tokio::test]
-    async fn test_mongodb_document_storage() {
-        // TODO: Test MongoDB document operations
-        // 1. Store alignment results (large documents)
-        // 2. Query by job ID
-        // 3. Update results incrementally
-        // 4. Test aggregation queries
-        // Verify: Document integrity maintained
-        assert!(true, "Placeholder - implement when MongoDB integrated");
-    }
-
-    /// Test: Database transaction handling
-    #[tokio::test]
-    async fn test_database_transaction_rollback() {
-        // TODO: Test transaction rollback on failure
-        // Given: Multi-step database operation that fails midway
-        // Expected: Transaction rolled back, no partial data
-        // Verify: Database state consistent
-        assert!(true, "Placeholder - implement when transactions used");
-    }
-
-    /// Test: Database connection pool under load
-    #[tokio::test]
-    async fn test_connection_pool_under_load() {
-        // TODO: Test connection pool behavior under load
-        // Given: 100 concurrent database queries
-        // Expected: Connection pool manages connections efficiently
-        // Verify: No connection exhaustion, timeouts handled
-        // Target: <50ms per query at 100 concurrency
-        assert!(true, "Placeholder - implement when DB pool exists");
-    }
-
-    /// Test: Database migration compatibility
-    #[tokio::test]
-    async fn test_database_migration_forward_backward() {
-        // TODO: Test database migrations
-        // 1. Apply migrations (up)
-        // 2. Verify schema matches expected
-        // 3. Rollback migrations (down)
-        // 4. Verify original schema restored
-        // Verify: Data integrity maintained through migrations
-        assert!(true, "Placeholder - implement when sqlx migrations exist");
-    }
-}
-
-#[cfg(test)]
-mod message_queue_integration_tests {
-    use super::*;
-
-    /// Test: Kafka producer-consumer integration
-    #[tokio::test]
-    async fn test_kafka_job_queue() {
-        // TODO: Test Kafka message queue integration
-        // 1. Producer publishes job message
-        // 2. Consumer receives message
-        // 3. Verify message content matches
-        // 4. Test message ordering
-        // Expected: Messages delivered reliably
-        assert!(true, "Placeholder - implement when Kafka integrated");
-    }
-
-    /// Test: Kafka consumer group rebalancing
-    #[tokio::test]
-    async fn test_kafka_consumer_rebalancing() {
-        // TODO: Test Kafka consumer group rebalancing
-        // Given: Add/remove consumers dynamically
-        // Expected: Partitions rebalanced automatically
-        // Verify: No message loss during rebalancing
-        assert!(true, "Placeholder - implement when Kafka integrated");
-    }
-
-    /// Test: Message queue backpressure handling
-    #[tokio::test]
-    async fn test_message_queue_backpressure() {
-        // TODO: Test handling of message queue backpressure
-        // Given: Producer rate > consumer rate
-        // Expected: Queue handles backlog gracefully
-        // Verify: No message loss, appropriate throttling
-        assert!(true, "Placeholder - implement when queue exists");
-    }
-
-    /// Test: Dead letter queue for failed messages
-    #[tokio::test]
-    async fn test_dead_letter_queue() {
-        // TODO: Test dead letter queue for failed messages
-        // Given: Message processing fails repeatedly
-        // Expected: Message moved to DLQ after max retries
-        // Verify: DLQ messages can be replayed
-        assert!(true, "Placeholder - implement when DLQ configured");
-    }
-}
-
-#[cfg(test)]
-mod api_integration_tests {
-    use super::*;
-
-    /// Test: API server startup and health check
-    #[tokio::test]
-    async fn test_api_server_startup() {
-        // TODO: Test API server initialization
-        // 1. Start API server
-        // 2. Check /health endpoint responds
-        // 3. Verify database connections established
-        // 4. Check WebSocket server running
-        // Expected: All components healthy
-        assert!(true, "Placeholder - implement when API server exists");
-    }
-
-    /// Test: End-to-end API job submission flow
-    #[tokio::test]
-    async fn test_api_job_submission_flow() {
-        // TODO: Test complete API job flow
-        // 1. POST /api/v1/jobs (create job)
-        // 2. GET /api/v1/jobs/{id} (check status)
-        // 3. WebSocket connection receives updates
-        // 4. GET /api/v1/jobs/{id}/results (retrieve results)
-        // Expected: Full lifecycle works end-to-end
-        assert!(true, "Placeholder - implement when API exists");
-    }
-
-    /// Test: API authentication flow
-    #[tokio::test]
-    async fn test_api_authentication_flow() {
-        // TODO: Test authentication and authorization
-        // 1. Request without token → 401 Unauthorized
-        // 2. Login to get JWT token
-        // 3. Request with valid token → 200 OK
-        // 4. Request with expired token → 401 Unauthorized
-        // Verify: Token validation works correctly
-        assert!(true, "Placeholder - implement when auth exists");
-    }
-
-    /// Test: API rate limiting enforcement
-    #[tokio::test]
-    async fn test_api_rate_limiting() {
-        // TODO: Test API rate limiting
-        // Given: Send 100 requests in 10 seconds
-        // Expected: Rate limit triggered (429 Too Many Requests)
-        // Verify: Rate limit window resets correctly
-        assert!(true, "Placeholder - implement when rate limiting exists");
-    }
-
-    /// Test: WebSocket real-time updates
-    #[tokio::test]
-    async fn test_websocket_realtime_updates() {
-        // TODO: Test WebSocket real-time job updates
-        // 1. Connect to WebSocket
-        // 2. Submit job via API
-        // 3. Verify status updates received via WebSocket
-        // 4. Verify completion notification received
-        // Expected: Real-time updates work correctly
-        assert!(true, "Placeholder - implement when WebSocket exists");
-    }
-}
-
-#[cfg(test)]
-mod distributed_system_tests {
-    use super::*;
-
-    /// Test: Redis distributed locking
-    #[tokio::test]
-    async fn test_redis_distributed_lock() {
-        // TODO: Test Redis distributed locking
-        // Given: Two workers try to process same job
-        // Expected: Only one worker gets lock
-        // Verify: Lock released after job completion
-        assert!(true, "Placeholder - implement when Redis locking exists");
-    }
-
-    /// Test: Distributed cache consistency
-    #[tokio::test]
-    async fn test_distributed_cache_consistency() {
-        // TODO: Test Redis cache consistency
-        // 1. Write value to cache
-        // 2. Read from multiple nodes
-        // 3. Update value
-        // 4. Verify all nodes see updated value
-        // Expected: Cache stays consistent
-        assert!(true, "Placeholder - implement when Redis cache exists");
-    }
-
-    /// Test: Service discovery and health checks
-    #[tokio::test]
-    async fn test_service_discovery() {
-        // TODO: Test Kubernetes service discovery
-        // 1. Deploy multiple service instances
-        // 2. Verify service discovery finds all instances
-        // 3. Kill one instance
-        // 4. Verify service discovery updates
-        // Expected: Automatic service discovery works
-        assert!(true, "Placeholder - implement when k8s deployed");
-    }
-}
-
-#[cfg(test)]
-mod performance_integration_tests {
-    use super::*;
-
-    /// Test: System throughput under load
-    #[tokio::test]
-    #[ignore] // Long-running performance test
-    async fn test_system_throughput() {
-        // TODO: Measure system throughput
-        // Given: 1000 jobs submitted over 10 minutes
-        // Expected: Sustained throughput >100 jobs/minute
-        // Verify: Latency stays <5 seconds at p95
-        // Target: Linear scaling with worker count
-        assert!(true, "Placeholder - implement when system complete");
-    }
-
-    /// Test: Memory usage stability over time
-    #[tokio::test]
-    #[ignore] // Long-running memory test
-    async fn test_memory_stability() {
-        // TODO: Test memory leak detection
-        // Given: Run system for 24 hours processing jobs
-        // Expected: Memory usage stays stable (no leaks)
-        // Verify: Heap growth < 5% over 24 hours
-        assert!(true, "Placeholder - implement when system stable");
-    }
-
-    /// Test: Database query performance
-    #[tokio::test]
-    async fn test_database_query_performance() {
-        // TODO: Test database query performance
-        // Given: Database with 100K job records
-        // Expected: Queries complete in <100ms at p95
-        // Verify: Indexes used correctly
-        // Target: <50ms for simple lookups
-        assert!(true, "Placeholder - implement when DB populated");
-    }
-}
-
-#[cfg(test)]
-mod data_validation_tests {
-    use super::*;
-
-    /// Test: Input data validation and sanitization
-    #[tokio::test]
-    async fn test_input_validation() {
-        // TODO: Test comprehensive input validation
-        // Given: Various invalid inputs (malformed FASTQ, etc.)
-        // Expected: Appropriate error messages returned
-        // Verify: System doesn't crash on invalid input
-        assert!(true, "Placeholder - implement when validation exists");
-    }
-
-    /// Test: Output data integrity
-    #[tokio::test]
-    async fn test_output_data_integrity() {
-        // TODO: Test output data integrity
-        // Given: Known input data
-        // Expected: Output matches expected results
-        // Verify: Checksums/hashes match reference
-        assert!(true, "Placeholder - implement when pipeline complete");
-    }
-
-    /// Test: Data format compatibility
-    #[tokio::test]
-    async fn test_data_format_compatibility() {
-        // TODO: Test handling of different data formats
-        // Given: FASTQ, BAM, CRAM input formats
-        // Expected: All formats processed correctly
-        // Verify: Format detection and parsing work
-        assert!(true, "Placeholder - implement when I/O handlers exist");
-    }
-}

package/agentic-flow/examples/crispr-cas13-pipeline/tests/load_testing_k6.js

@@ -1,269 +0,0 @@
-// k6 load testing script for API service
-// Run with: k6 run --vus 100 --duration 5m load_testing_k6.js
-
-import http from 'k6/http';
-import { check, sleep } from 'k6';
-import { Rate, Trend, Counter } from 'k6/metrics';
-
-// Custom metrics
-const errorRate = new Rate('errors');
-const jobCreationDuration = new Trend('job_creation_duration');
-const jobStatusDuration = new Trend('job_status_duration');
-const resultRetrievalDuration = new Trend('result_retrieval_duration');
-const successfulJobs = new Counter('successful_jobs');
-
-// Configuration
-const BASE_URL = __ENV.API_URL || 'http://localhost:8080';
-const AUTH_TOKEN = __ENV.AUTH_TOKEN || 'test-token-123';
-
-// Load test scenarios
-export const options = {
-  stages: [
-    // Ramp-up: 0 to 50 users over 1 minute
-    { duration: '1m', target: 50 },
-    // Stay at 50 users for 2 minutes
-    { duration: '2m', target: 50 },
-    // Ramp-up: 50 to 100 users over 1 minute
-    { duration: '1m', target: 100 },
-    // Stay at 100 users for 3 minutes (peak load)
-    { duration: '3m', target: 100 },
-    // Spike test: 100 to 200 users over 30 seconds
-    { duration: '30s', target: 200 },
-    // Stay at 200 users for 1 minute
-    { duration: '1m', target: 200 },
-    // Ramp-down: 200 to 0 users over 1 minute
-    { duration: '1m', target: 0 },
-  ],
-  thresholds: {
-    // 99% of requests must complete within 2 seconds
-    http_req_duration: ['p(99)<2000'],
-    // Error rate must be below 1%
-    errors: ['rate<0.01'],
-    // 95% of requests must succeed
-    http_req_failed: ['rate<0.05'],
-  },
-};
-
-// Helper function to generate random job payload
-function generateJobPayload() {
-  const randomId = Math.floor(Math.random() * 1000000);
-  return JSON.stringify({
-    job_type: 'alignment',
-    input_files: [
-      { name: `sample_${randomId}_R1.fastq`, size: 1024000 + randomId },
-      { name: `sample_${randomId}_R2.fastq`, size: 1024000 + randomId },
-    ],
-    parameters: {
-      reference_genome: 'macaca_mulatta',
-      quality_threshold: 20 + (randomId % 20),
-      alignment_mode: randomId % 2 === 0 ? 'end-to-end' : 'local',
-    },
-    metadata: {
-      experiment_id: `EXP-${randomId}`,
-      sample_type: 'RNA-seq',
-      tissue: ['blood', 'liver', 'spleen'][randomId % 3],
-    },
-  });
-}
-
-// Main test scenario
-export default function () {
-  const headers = {
-    'Content-Type': 'application/json',
-    'Authorization': `Bearer ${AUTH_TOKEN}`,
-  };
-
-  // Test 1: Create analysis job
-  const jobPayload = generateJobPayload();
-  let createResponse = http.post(
-    `${BASE_URL}/api/v1/jobs`,
-    jobPayload,
-    { headers, tags: { name: 'CreateJob' } }
-  );
-
-  jobCreationDuration.add(createResponse.timings.duration);
-
-  const createSuccess = check(createResponse, {
-    'job creation status is 201': (r) => r.status === 201,
-    'job creation returns job_id': (r) => {
-      try {
-        const body = JSON.parse(r.body);
-        return body.job_id !== undefined;
-      } catch {
-        return false;
-      }
-    },
-  });
-
-  if (!createSuccess) {
-    errorRate.add(1);
-    return; // Skip subsequent tests if job creation fails
-  }
-
-  errorRate.add(0);
-  successfulJobs.add(1);
-
-  // Extract job ID for subsequent requests
-  const jobId = JSON.parse(createResponse.body).job_id;
-
-  // Wait before polling status
-  sleep(1);
-
-  // Test 2: Check job status
-  let statusResponse = http.get(
-    `${BASE_URL}/api/v1/jobs/${jobId}`,
-    { headers, tags: { name: 'GetJobStatus' } }
-  );
-
-  jobStatusDuration.add(statusResponse.timings.duration);
-
-  check(statusResponse, {
-    'job status query is 200': (r) => r.status === 200,
-    'job status has valid state': (r) => {
-      try {
-        const body = JSON.parse(r.body);
-        return ['pending', 'running', 'completed', 'failed'].includes(body.status);
-      } catch {
-        return false;
-      }
-    },
-  });
-
-  // Test 3: List jobs with pagination
-  let listResponse = http.get(
-    `${BASE_URL}/api/v1/jobs?page=1&limit=20`,
-    { headers, tags: { name: 'ListJobs' } }
-  );
-
-  check(listResponse, {
-    'job list query is 200': (r) => r.status === 200,
-    'job list has pagination': (r) => {
-      try {
-        const body = JSON.parse(r.body);
-        return body.total !== undefined && body.jobs !== undefined;
-      } catch {
-        return false;
-      }
-    },
-  });
-
-  // Simulate varying user behavior
-  const behavior = Math.random();
-
-  if (behavior < 0.3) {
-    // 30% of users wait and check results
-    sleep(2);
-
-    // Test 4: Retrieve results (simulate completed job)
-    let resultsResponse = http.get(
-      `${BASE_URL}/api/v1/jobs/${jobId}/alignments`,
-      { headers, tags: { name: 'GetResults' } }
-    );
-
-    resultRetrievalDuration.add(resultsResponse.timings.duration);
-
-    check(resultsResponse, {
-      'results query returns 200 or 404': (r) => [200, 404].includes(r.status),
-    });
-  } else if (behavior < 0.6) {
-    // 30% of users poll status multiple times
-    for (let i = 0; i < 3; i++) {
-      sleep(0.5);
-      http.get(`${BASE_URL}/api/v1/jobs/${jobId}`, { headers });
-    }
-  } else {
-    // 40% of users just submit and leave
-    sleep(0.5);
-  }
-
-  // Random think time between requests (0.5-2 seconds)
-  sleep(Math.random() * 1.5 + 0.5);
-}
-
-// Scenario 2: Stress test with concurrent connections
-export function stressTest() {
-  const headers = {
-    'Content-Type': 'application/json',
-    'Authorization': `Bearer ${AUTH_TOKEN}`,
-  };
-
-  // Simulate burst of job submissions
-  const jobs = [];
-  for (let i = 0; i < 10; i++) {
-    const jobPayload = generateJobPayload();
-    const response = http.post(
-      `${BASE_URL}/api/v1/jobs`,
-      jobPayload,
-      { headers }
-    );
-
-    if (response.status === 201) {
-      jobs.push(JSON.parse(response.body).job_id);
-    }
-  }
-
-  // Query all submitted jobs
-  jobs.forEach((jobId) => {
-    http.get(`${BASE_URL}/api/v1/jobs/${jobId}`, { headers });
-  });
-}
-
-// Scenario 3: Spike test
-export function spikeTest() {
-  const headers = {
-    'Content-Type': 'application/json',
-    'Authorization': `Bearer ${AUTH_TOKEN}`,
-  };
-
-  // Simulate sudden spike in traffic
-  const responses = [];
-  for (let i = 0; i < 50; i++) {
-    responses.push(
-      http.post(
-        `${BASE_URL}/api/v1/jobs`,
-        generateJobPayload(),
-        { headers }
-      )
-    );
-  }
-
-  const successCount = responses.filter((r) => r.status === 201).length;
-  console.log(`Spike test: ${successCount}/50 requests succeeded`);
-}
-
-// Custom summary for detailed reporting
-export function handleSummary(data) {
-  return {
-    'load-test-summary.json': JSON.stringify(data),
-    stdout: textSummary(data, { indent: ' ', enableColors: true }),
-  };
-}
-
-function textSummary(data) {
-  const summary = [];
-
-  summary.push('='.repeat(80));
-  summary.push('LOAD TEST SUMMARY');
-  summary.push('='.repeat(80));
-
-  summary.push(`\nTest Duration: ${data.state.testRunDurationMs / 1000}s`);
-  summary.push(`Total VUs: ${data.metrics.vus?.values?.max || 0}`);
-  summary.push(`Total Iterations: ${data.metrics.iterations?.values?.count || 0}`);
-
-  summary.push('\n--- HTTP Metrics ---');
-  summary.push(`Requests: ${data.metrics.http_reqs?.values?.count || 0}`);
-  summary.push(`Failed Requests: ${data.metrics.http_req_failed?.values?.rate * 100}%`);
-  summary.push(`Request Duration (avg): ${data.metrics.http_req_duration?.values?.avg}ms`);
-  summary.push(`Request Duration (p95): ${data.metrics.http_req_duration?.values['p(95)']}ms`);
-  summary.push(`Request Duration (p99): ${data.metrics.http_req_duration?.values['p(99)']}ms`);
-
-  summary.push('\n--- Custom Metrics ---');
-  summary.push(`Error Rate: ${(data.metrics.errors?.values?.rate || 0) * 100}%`);
-  summary.push(`Successful Jobs: ${data.metrics.successful_jobs?.values?.count || 0}`);
-  summary.push(`Job Creation (avg): ${data.metrics.job_creation_duration?.values?.avg}ms`);
-  summary.push(`Job Status Query (avg): ${data.metrics.job_status_duration?.values?.avg}ms`);
-
-  summary.push('\n' + '='.repeat(80));
-
-  return summary.join('\n');
-}