agentic-flow 1.9.0 → 1.9.1

package/agentic-flow/examples/crispr-cas13-pipeline/docs/SECURITY_AUDIT.md

@@ -1,756 +0,0 @@
-# Security Audit Report: CRISPR-Cas13 Bioinformatics Pipeline
-
-**Audit Date:** 2025-10-12
-**Auditor:** Security Review Agent (Swarm Coordination)
-**Project:** CRISPR-Cas13 Bioinformatics Pipeline v0.1.0
-**Audit Type:** Static Code Analysis + Architecture Review
-
----
-
-## Executive Summary
-
-This security audit evaluates the CRISPR-Cas13 Bioinformatics Pipeline against industry security standards. The codebase demonstrates **good security fundamentals** with type-safe design and proper error handling, but requires additional security controls before production deployment, especially for handling sensitive genomic and patient data.
-
-### Security Posture: **MODERATE RISK**
-
-- **Current State:** Development/Prototype
-- **Recommended State:** Production-ready after remediation
-- **Time to Secure:** ~4-6 weeks for critical items
-
----
-
-## 1. Threat Model
-
-### Assets
-
-1. **Genomic Data** (Confidentiality: Critical)
-   - Patient DNA/RNA sequences
-   - CRISPR guide designs
-   - Off-target analysis results
-
-2. **Patient Metadata** (Confidentiality: Critical, Integrity: High)
-   - PHI (Protected Health Information)
-   - Treatment records
-   - Research identifiers
-
-3. **System Infrastructure** (Availability: High)
-   - API services
-   - Databases (PostgreSQL, MongoDB)
-   - Message queues (Kafka)
-   - Storage (S3/MinIO)
-
-### Threat Actors
-
-1. **External Attackers**
-   - Motivation: Data theft, ransomware
-   - Capability: Medium to High
-   - Vectors: API attacks, injection, DoS
-
-2. **Malicious Insiders**
-   - Motivation: Data exfiltration, sabotage
-   - Capability: High (system access)
-   - Vectors: Abuse of privileges, data export
-
-3. **Accidental Disclosure**
-   - Source: Misconfiguration, bugs
-   - Impact: HIPAA violations, reputation damage
-
-### Attack Surface
-
-```
-┌─────────────────────────────────────────┐
-│         External Attack Surface         │
-├─────────────────────────────────────────┤
-│  1. REST API Endpoints                  │
-│     - /health (public)                  │
-│     - /api/v1/targets (no auth)         │
-│     - /api/v1/predict (no auth)         │
-│                                         │
-│  2. WebSocket Connections               │
-│     - Real-time updates (planned)       │
-│                                         │
-│  3. File Upload Endpoints               │
-│     - FASTQ/BAM files (planned)         │
-└─────────────────────────────────────────┘
-
-┌─────────────────────────────────────────┐
-│         Internal Attack Surface         │
-├─────────────────────────────────────────┤
-│  1. Database Access                     │
-│     - PostgreSQL (metadata)             │
-│     - MongoDB (genomic data)            │
-│     - Redis (cache)                     │
-│                                         │
-│  2. Message Queues                      │
-│     - Kafka (job orchestration)         │
-│                                         │
-│  3. Object Storage                      │
-│     - S3/MinIO (raw data)               │
-└─────────────────────────────────────────┘
-```
-
----
-
-## 2. Vulnerability Assessment
-
-### 🔴 CRITICAL Vulnerabilities
-
-**None identified in current implementation**
-
-The prototype does not expose production-sensitive functionality. However, the following would be CRITICAL if deployed:
-
-#### CVE-POTENTIAL-001: Missing Authentication
-- **Component:** API Service (all endpoints)
-- **CWE:** CWE-306 (Missing Authentication for Critical Function)
-- **Impact:** Unauthorized access to patient data
-- **Exploitability:** Trivial
-- **Remediation:** Implement OAuth2+JWT before production
-
-#### CVE-POTENTIAL-002: Missing Authorization
-- **Component:** API Service (data access)
-- **CWE:** CWE-862 (Missing Authorization)
-- **Impact:** Privilege escalation, data access beyond permissions
-- **Exploitability:** Trivial (once authenticated)
-- **Remediation:** Implement RBAC with fine-grained permissions
-
-### 🟡 HIGH Severity Issues
-
-#### SEC-001: Insufficient Input Validation
-- **Location:** `crates/api-service/src/routes.rs`
-- **Issue:** API endpoints accept unvalidated user input
-- **Attack Vector:**
-  ```rust
-  pub async fn create_target(
-      Json(_payload): Json<CreateTargetRequest>,  // No validation!
-  ) -> Json<CreateTargetResponse> {
-      // Payload is blindly trusted
-  }
-  ```
-- **Risk:**
-  - Buffer overflow attempts
-  - Malformed data causing panics
-  - Resource exhaustion (huge inputs)
-- **Remediation:**
-  ```rust
-  pub async fn create_target(
-      Json(payload): Json<CreateTargetRequest>,
-  ) -> Result<Json<CreateTargetResponse>, ApiError> {
-      // Validate guide RNA
-      validate_guide_rna(&payload.guide_rna)?;
-      validate_target_sequence(&payload.target_sequence)?;
-
-      // Length limits
-      if payload.guide_rna.len() > 100 {
-          return Err(ApiError::BadRequest("Guide RNA too long".to_string()));
-      }
-      // ... rest of logic
-  }
-
-  fn validate_guide_rna(rna: &str) -> Result<(), ApiError> {
-      if rna.len() < 22 || rna.len() > 30 {
-          return Err(ApiError::BadRequest("Invalid guide RNA length".to_string()));
-      }
-      if !rna.chars().all(|c| matches!(c, 'A'|'C'|'G'|'U'|'a'|'c'|'g'|'u')) {
-          return Err(ApiError::BadRequest("Invalid RNA sequence".to_string()));
-      }
-      Ok(())
-  }
-  ```
-
-#### SEC-002: Lack of Rate Limiting
-- **Location:** API Service (entire application)
-- **Issue:** No protection against brute force or DoS attacks
-- **Attack Vector:**
-  ```bash
-  # Attacker can overwhelm the API
-  for i in {1..1000000}; do
-      curl -X POST http://api/v1/predict -d '{"target_id":"x"}' &
-  done
-  ```
-- **Impact:**
-  - Service degradation
-  - Resource exhaustion
-  - Denial of Service
-- **Remediation:**
-  ```rust
-  use tower::ServiceBuilder;
-  use tower_http::limit::RateLimitLayer;
-
-  let app = Router::new()
-      .route("/api/v1/targets", post(routes::create_target))
-      .layer(
-          ServiceBuilder::new()
-              .layer(RateLimitLayer::new(
-                  100,  // 100 requests
-                  Duration::from_secs(60)  // per minute
-              ))
-      );
-  ```
-
-#### SEC-003: Missing Security Headers
-- **Location:** API Service
-- **Issue:** No security headers in HTTP responses
-- **Risk:** XSS, clickjacking, MIME sniffing attacks
-- **Remediation:**
-  ```rust
-  use tower_http::set_header::SetResponseHeaderLayer;
-
-  let app = Router::new()
-      .layer(SetResponseHeaderLayer::if_not_present(
-          header::X_CONTENT_TYPE_OPTIONS,
-          HeaderValue::from_static("nosniff"),
-      ))
-      .layer(SetResponseHeaderLayer::if_not_present(
-          header::X_FRAME_OPTIONS,
-          HeaderValue::from_static("DENY"),
-      ))
-      .layer(SetResponseHeaderLayer::if_not_present(
-          header::STRICT_TRANSPORT_SECURITY,
-          HeaderValue::from_static("max-age=31536000; includeSubDomains"),
-      ));
-  ```
-
-### 🟢 MEDIUM Severity Issues
-
-#### SEC-004: Secrets in Environment Variables
-- **Location:** Configuration (dotenv)
-- **Issue:** Secrets loaded from `.env` files
-- **Risk:**
-  - Accidental commit to version control
-  - Process dump exposure
-  - Container inspection
-- **Recommendation:**
-  - Use secrets management system (Vault, AWS Secrets Manager)
-  - Rotate secrets regularly
-  - Never log secrets
-  ```rust
-  // Example: Redact secrets in logs
-  #[derive(Debug)]
-  pub struct Config {
-      pub database_url: String,  // Don't log directly
-      #[debug(skip)]
-      pub api_key: String,  // Skipped in debug output
-  }
-  ```
-
-#### SEC-005: No Audit Logging
-- **Location:** Entire application
-- **Issue:** No audit trail for sensitive operations
-- **Risk:**
-  - No forensic capability after breach
-  - Compliance violations (HIPAA requires audit logs)
-  - Can't detect insider threats
-- **Recommendation:**
-  ```rust
-  pub async fn create_target(
-      Extension(user): Extension<User>,
-      Json(payload): Json<CreateTargetRequest>,
-  ) -> Result<Json<CreateTargetResponse>, ApiError> {
-      // Log before operation
-      audit_log::info(
-          user_id = user.id,
-          action = "create_target",
-          resource = "crispr_target",
-          payload = serde_json::to_string(&payload)?,
-      );
-
-      let result = service::create_target(payload).await?;
-
-      // Log after success
-      audit_log::info(
-          user_id = user.id,
-          action = "create_target",
-          status = "success",
-          resource_id = result.id,
-      );
-
-      Ok(Json(result))
-  }
-  ```
-
-#### SEC-006: Database Connection Security
-- **Location:** Database configuration
-- **Issue:** No evidence of TLS for database connections
-- **Risk:** Man-in-the-middle attacks, credential theft
-- **Recommendation:**
-  ```toml
-  # In Cargo.toml or config
-  [dependencies]
-  sqlx = { version = "0.8", features = ["runtime-tokio-native-tls", "postgres", "tls"] }
-
-  # In connection string
-  DATABASE_URL=postgresql://user:pass@host:5432/db?sslmode=require
-  ```
-
-### 🔵 LOW Severity Issues
-
-#### SEC-007: Verbose Error Messages
-- **Location:** Error handling across crates
-- **Issue:** Error messages may expose internal details
-- **Risk:** Information disclosure, aids attackers
-- **Example:**
-  ```rust
-  // Current
-  #[error("Database error: {0}")]
-  DatabaseError(String),  // May expose schema details
-
-  // Recommended
-  #[error("Database operation failed")]
-  DatabaseError,  // Generic for external users
-
-  // Log details internally
-  tracing::error!(cause = %e, "Database error: {}", e);
-  ```
-
-#### SEC-008: Dependency Vulnerabilities
-- **Location:** Cargo.toml dependencies
-- **Issue:** No automated vulnerability scanning
-- **Risk:** Known CVEs in dependencies
-- **Recommendation:**
-  ```bash
-  # Run in CI/CD
-  cargo audit
-  cargo outdated --exit-code 1
-
-  # Add to .github/workflows/security.yml
-  - name: Security audit
-    run: |
-      cargo install cargo-audit
-      cargo audit --deny warnings
-  ```
-
----
-
-## 3. Data Protection Analysis
-
-### Data Classification
-
-| Data Type | Classification | Current Protection | Required Protection |
-|-----------|---------------|-------------------|---------------------|
-| Guide RNA sequences | Confidential | None | Encryption at rest + access control |
-| Patient genomic data | Highly Sensitive (PHI) | None | HIPAA-compliant encryption |
-| Off-target predictions | Confidential | None | Encryption at rest |
-| User credentials | Sensitive | Not implemented | Hashing (Argon2), salted |
-| Audit logs | Confidential | Not implemented | Append-only, tamper-evident |
-| API keys/tokens | Sensitive | Environment vars | Secrets manager |
-
-### Encryption Analysis
-
-#### ✅ What's Protected
-- **Transport:** TLS 1.3 capability (Axum supports it)
-- **Serialization:** Type-safe with serde (prevents tampering)
-
-#### ❌ What's Missing
-1. **At-Rest Encryption**
-   - PostgreSQL: Not configured
-   - MongoDB: Not configured
-   - S3/MinIO: Not configured
-   - **Fix:** Enable transparent data encryption (TDE)
-
-2. **Field-Level Encryption**
-   - No sensitive field encryption in code
-   - **Fix:** Encrypt PHI fields before storage
-   ```rust
-   use sodiumoxide::crypto::secretbox;
-
-   pub struct EncryptedPatientData {
-       encrypted_genome: Vec<u8>,
-       nonce: secretbox::Nonce,
-   }
-   ```
-
-3. **Key Management**
-   - No key rotation strategy
-   - **Fix:** Implement KMS integration
-
-### Data Retention & Deletion
-
-#### Missing Features
-- No automatic data expiration
-- No "right to be forgotten" implementation
-- No data minimization controls
-
-#### Recommendation
-```rust
-pub struct DataRetentionPolicy {
-    pub retention_days: u32,
-    pub auto_delete: bool,
-    pub anonymize_after: u32,
-}
-
-impl DataRetentionPolicy {
-    pub async fn enforce(&self, db: &Database) -> Result<()> {
-        // Delete data older than retention period
-        db.execute(
-            "DELETE FROM genomic_data WHERE created_at < NOW() - INTERVAL '$1 days'",
-            &[&self.retention_days]
-        ).await?;
-        Ok(())
-    }
-}
-```
-
----
-
-## 4. Network Security
-
-### API Security
-
-#### Current State
-```rust
-// crates/api-service/src/main.rs
-let addr = SocketAddr::from(([127, 0, 0, 1], 3000));  // Localhost only ✅
-```
-✅ **Good:** Default binding to localhost prevents external access
-
-#### Production Requirements
-
-1. **TLS Configuration**
-   ```rust
-   use axum_server::tls_rustls::RustlsConfig;
-
-   let config = RustlsConfig::from_pem_file(
-       "cert.pem",
-       "key.pem"
-   ).await?;
-
-   axum_server::bind_rustls(addr, config)
-       .serve(app.into_make_service())
-       .await?;
-   ```
-
-2. **CORS Policy**
-   ```rust
-   use tower_http::cors::{CorsLayer, Any};
-
-   let cors = CorsLayer::new()
-       .allow_origin("https://trusted-frontend.com".parse::<HeaderValue>()?)
-       .allow_methods([Method::GET, Method::POST])
-       .allow_credentials(true);
-
-   let app = Router::new().layer(cors);
-   ```
-
-3. **Request Size Limits**
-   ```rust
-   use tower_http::limit::RequestBodyLimitLayer;
-
-   let app = Router::new()
-       .layer(RequestBodyLimitLayer::new(10 * 1024 * 1024))  // 10MB limit
-   ```
-
-### Database Security
-
-#### Issues
-- Connection strings in environment (SEC-004)
-- No connection pooling security
-- Missing least privilege access
-
-#### Recommendations
-```sql
--- Create restricted database user
-CREATE USER crispr_api WITH PASSWORD 'strong_password';
-GRANT SELECT, INSERT, UPDATE ON genomic_data TO crispr_api;
-GRANT SELECT ON reference_genomes TO crispr_api;
--- Don't grant DELETE or DROP permissions
-
--- Enable row-level security
-ALTER TABLE genomic_data ENABLE ROW LEVEL SECURITY;
-
-CREATE POLICY tenant_isolation ON genomic_data
-    FOR ALL
-    USING (tenant_id = current_setting('app.tenant_id')::uuid);
-```
-
----
-
-## 5. Compliance Assessment
-
-### HIPAA Security Rule
-
-| Requirement | Status | Evidence | Action Needed |
-|-------------|--------|----------|---------------|
-| Access Control (164.308) | ❌ | No auth implemented | Implement OAuth2+RBAC |
-| Audit Controls (164.308) | ❌ | No audit logging | Build audit system |
-| Integrity Controls (164.312) | ⚠️ | Type safety only | Add checksums, signatures |
-| Transmission Security (164.312) | ⚠️ | TLS capable | Enforce TLS 1.3+ |
-| Encryption (164.312) | ❌ | Not implemented | Enable at-rest encryption |
-
-**HIPAA Compliance Status:** **NOT COMPLIANT**
-**Estimated Time to Compliance:** 8-12 weeks
-
-### GDPR Requirements
-
-| Requirement | Status | Evidence | Action Needed |
-|-------------|--------|----------|---------------|
-| Data Minimization | ⚠️ | No policy | Define retention limits |
-| Right to Access | ❌ | No export API | Build data export |
-| Right to Erasure | ❌ | No delete cascade | Implement deletion workflow |
-| Data Portability | ❌ | No export format | Add JSON/CSV export |
-| Breach Notification | ❌ | No detection | Add intrusion detection |
-| Data Protection Officer | N/A | Organizational | Assign DPO role |
-
-**GDPR Compliance Status:** **NOT COMPLIANT**
-**Estimated Time to Compliance:** 6-10 weeks
-
-### SOC 2 Type II
-
-| Control | Status | Gap |
-|---------|--------|-----|
-| Logical Access | ❌ | No RBAC |
-| Change Management | ⚠️ | Git only, no approval workflow |
-| Data Protection | ❌ | No encryption |
-| Monitoring | ❌ | No SIEM integration |
-| Incident Response | ❌ | No IR plan |
-
----
-
-## 6. Remediation Roadmap
-
-### Phase 1: Critical Security (Weeks 1-2)
-
-```rust
-// Week 1: Authentication
-pub async fn jwt_middleware(
-    TypedHeader(auth): TypedHeader<headers::Authorization<Bearer>>,
-    mut req: Request,
-    next: Next,
-) -> Result<Response, ApiError> {
-    let token = auth.token();
-    let claims = jwt::verify(token)?;
-
-    req.extensions_mut().insert(claims.user);
-    Ok(next.run(req).await)
-}
-
-// Week 2: Input Validation
-pub fn validate_request<T: Validate>(payload: T) -> Result<T, ApiError> {
-    payload.validate()
-        .map_err(|e| ApiError::BadRequest(e.to_string()))?;
-    Ok(payload)
-}
-```
-
-### Phase 2: Data Protection (Weeks 3-4)
-
-```rust
-// Week 3: Encryption at Rest
-pub async fn store_genomic_data(
-    data: &GenomicData,
-    encryption_key: &Key,
-) -> Result<()> {
-    let encrypted = encrypt_aes256_gcm(
-        &serde_json::to_vec(data)?,
-        encryption_key
-    )?;
-
-    database.insert(encrypted).await?;
-    Ok(())
-}
-
-// Week 4: Audit Logging
-pub struct AuditLogger {
-    db: AuditDatabase,
-}
-
-impl AuditLogger {
-    pub async fn log_event(&self, event: AuditEvent) -> Result<()> {
-        self.db.insert(event).await?;
-        Ok(())
-    }
-}
-```
-
-### Phase 3: Compliance (Weeks 5-6)
-
-```rust
-// Week 5: Data Retention
-pub async fn apply_retention_policy() -> Result<()> {
-    let policy = RetentionPolicy::load()?;
-
-    // Delete expired data
-    database.execute(
-        "DELETE FROM genomic_data WHERE created_at < $1",
-        &[Utc::now() - Duration::days(policy.retention_days)]
-    ).await?;
-
-    Ok(())
-}
-
-// Week 6: GDPR Rights
-pub async fn export_user_data(user_id: Uuid) -> Result<UserDataExport> {
-    let data = UserDataExport {
-        genomic_data: database.get_genomic_data(user_id).await?,
-        predictions: database.get_predictions(user_id).await?,
-        audit_log: database.get_audit_log(user_id).await?,
-    };
-    Ok(data)
-}
-```
-
----
-
-## 7. Security Testing Recommendations
-
-### 1. Static Analysis
-```bash
-# Add to CI/CD pipeline
-cargo clippy -- -W clippy::all -W clippy::pedantic
-cargo audit
-cargo outdated --exit-code 1
-```
-
-### 2. Dynamic Analysis
-```bash
-# Fuzzing
-cargo install cargo-fuzz
-cargo fuzz run api_parser
-
-# Runtime checks
-cargo build --features=asan  # AddressSanitizer
-RUSTFLAGS="-Z sanitizer=address" cargo test
-```
-
-### 3. Penetration Testing
-- **OWASP ZAP:** Automated vulnerability scanning
-- **Burp Suite:** Manual API testing
-- **Nmap:** Port scanning and service detection
-- **SQLMap:** SQL injection testing (if applicable)
-
-### 4. Security Code Review Checklist
-- [ ] All user inputs validated
-- [ ] SQL queries parameterized (using sqlx)
-- [ ] Secrets not in code or logs
-- [ ] Error messages don't leak info
-- [ ] Rate limiting on all endpoints
-- [ ] TLS enforced for all connections
-- [ ] Authentication on sensitive endpoints
-- [ ] Authorization checks before data access
-- [ ] Audit logging for all operations
-- [ ] Data encrypted at rest and in transit
-
----
-
-## 8. Security Metrics & KPIs
-
-### Recommended Tracking
-
-| Metric | Current | Target | Priority |
-|--------|---------|--------|----------|
-| Known vulnerabilities | Unknown | 0 | High |
-| Authentication coverage | 0% | 100% | Critical |
-| Encryption at rest | 0% | 100% | High |
-| Audit log coverage | 0% | 100% | High |
-| API input validation | 20% | 100% | High |
-| Security test coverage | 0% | 80% | Medium |
-| SAST tool integration | No | Yes | Medium |
-| Dependency freshness | Unknown | < 30 days old | Low |
-
-### Monitoring Alerts
-
-```yaml
-# Example Prometheus alerts
-- alert: UnauthorizedAPIAccess
-  expr: rate(http_requests_total{code="401"}[5m]) > 10
-  annotations:
-    summary: High rate of unauthorized access attempts
-
-- alert: SuspiciousDataAccess
-  expr: rate(genomic_data_access_total[1h]) > 1000
-  annotations:
-    summary: Unusually high data access rate
-
-- alert: VulnerableDependency
-  expr: cargo_audit_vulnerabilities > 0
-  annotations:
-    summary: Vulnerable dependency detected
-```
-
----
-
-## Conclusion
-
-### Current Security Posture
-
-**Risk Level: MODERATE (Development Phase)**
-
-The CRISPR-Cas13 Pipeline codebase demonstrates good security fundamentals:
-- ✅ Type-safe Rust implementation
-- ✅ Proper error handling
-- ✅ Well-structured architecture
-- ✅ Quality documentation
-
-However, it **lacks essential security controls** for production:
-- ❌ No authentication/authorization
-- ❌ No encryption at rest
-- ❌ No audit logging
-- ❌ Insufficient input validation
-- ❌ No compliance features
-
-### Recommendations
-
-1. **DO NOT deploy to production** without implementing Phase 1 & 2 remediations
-2. **Budget 6-12 weeks** for security hardening
-3. **Hire security consultant** for penetration testing before v1.0
-4. **Implement CI/CD security checks** immediately
-5. **Create incident response plan** before production deployment
-
-### Timeline to Production Security
-
-```
-Week 1-2:  Authentication & Authorization ─────────┐
-Week 3-4:  Data Encryption & Protection           │
-Week 5-6:  Compliance Features                    ├─► Production Ready
-Week 7-8:  Security Testing & Audit               │
-Week 9-12: Penetration Testing & Remediation ─────┘
-```
-
-### Final Assessment
-
-**Verdict:** The pipeline has a **solid security foundation** but requires significant work before handling sensitive genomic data. Prioritize authentication, encryption, and audit logging in the next sprint.
-
----
-
-## Appendix A: Security Checklist
-
-### Pre-Production Security Gate
-
-- [ ] All dependencies audited (`cargo audit` passes)
-- [ ] Authentication implemented on all endpoints
-- [ ] Authorization checks for data access
-- [ ] Input validation on all user inputs
-- [ ] Rate limiting configured
-- [ ] TLS 1.3 enforced
-- [ ] Database connections encrypted
-- [ ] Data encrypted at rest (AES-256)
-- [ ] Audit logging operational
-- [ ] Security headers configured
-- [ ] Secrets in secure vault (not env vars)
-- [ ] Data retention policy implemented
-- [ ] GDPR export/delete functions
-- [ ] Penetration test completed
-- [ ] Incident response plan documented
-
-### Ongoing Security Maintenance
-
-- [ ] Weekly dependency updates
-- [ ] Monthly vulnerability scans
-- [ ] Quarterly penetration tests
-- [ ] Annual compliance audits
-- [ ] Regular key rotation
-- [ ] Security training for developers
-
----
-
-*This security audit was conducted using static code analysis, architecture review, and threat modeling. For a complete assessment, dynamic testing and penetration testing are recommended.*
-
-**Next Steps:**
-1. Review findings with development team
-2. Prioritize remediation items
-3. Allocate resources for security sprint
-4. Schedule follow-up audit after remediation
-
----
-
-*Generated by Security Review Agent with rUv.io AI Coordination*
-*Coordination Session: swarm_1760242647952_ay8nazr90*