agentic-flow 1.8.15 → 1.9.0

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

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+# 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*