agentic-flow 1.9.0 → 1.9.1

package/agentic-flow/examples/crispr-cas13-pipeline/docs/monitoring/prometheus.yml

@@ -1,213 +0,0 @@
-# Prometheus Configuration for CRISPR-Cas13 Pipeline
-# Version: 1.0.0
-
-global:
-  scrape_interval: 15s
-  evaluation_interval: 15s
-  external_labels:
-    cluster: 'crispr-production'
-    environment: 'production'
-
-# Alertmanager configuration
-alerting:
-  alertmanagers:
-  - static_configs:
-    - targets:
-      - alertmanager:9093
-
-# Load rules
-rule_files:
-  - "alerts.yml"
-
-# Scrape configurations
-scrape_configs:
-  # ==================================================
-  # API Gateway
-  # ==================================================
-  - job_name: 'api-gateway'
-    kubernetes_sd_configs:
-      - role: pod
-        namespaces:
-          names:
-            - crispr-production
-    relabel_configs:
-      - source_labels: [__meta_kubernetes_pod_label_app]
-        regex: api-gateway
-        action: keep
-      - source_labels: [__meta_kubernetes_pod_name]
-        target_label: pod
-      - source_labels: [__meta_kubernetes_namespace]
-        target_label: namespace
-    metrics_path: /metrics
-    scrape_interval: 10s
-
-  # ==================================================
-  # Processing Services
-  # ==================================================
-  - job_name: 'alignment-service'
-    kubernetes_sd_configs:
-      - role: pod
-        namespaces:
-          names:
-            - crispr-production
-    relabel_configs:
-      - source_labels: [__meta_kubernetes_pod_label_app]
-        regex: alignment-service
-        action: keep
-      - source_labels: [__meta_kubernetes_pod_name]
-        target_label: pod
-    metrics_path: /metrics
-
-  - job_name: 'off-target-service'
-    kubernetes_sd_configs:
-      - role: pod
-        namespaces:
-          names:
-            - crispr-production
-    relabel_configs:
-      - source_labels: [__meta_kubernetes_pod_label_app]
-        regex: off-target-service
-        action: keep
-    metrics_path: /metrics
-
-  - job_name: 'diff-expr-service'
-    kubernetes_sd_configs:
-      - role: pod
-        namespaces:
-          names:
-            - crispr-production
-    relabel_configs:
-      - source_labels: [__meta_kubernetes_pod_label_app]
-        regex: diff-expr-service
-        action: keep
-    metrics_path: /metrics
-
-  # ==================================================
-  # Databases
-  # ==================================================
-  - job_name: 'postgresql'
-    static_configs:
-      - targets: ['postgres-exporter:9187']
-    metrics_path: /metrics
-    scrape_interval: 30s
-
-  - job_name: 'mongodb'
-    static_configs:
-      - targets: ['mongodb-exporter:9216']
-    metrics_path: /metrics
-    scrape_interval: 30s
-
-  - job_name: 'redis'
-    static_configs:
-      - targets: ['redis-exporter:9121']
-    metrics_path: /metrics
-    scrape_interval: 30s
-
-  # ==================================================
-  # Message Queue
-  # ==================================================
-  - job_name: 'kafka'
-    static_configs:
-      - targets: ['kafka-exporter:9308']
-    metrics_path: /metrics
-    scrape_interval: 15s
-
-  # ==================================================
-  # Object Storage
-  # ==================================================
-  - job_name: 'minio'
-    metrics_path: /minio/v2/metrics/cluster
-    static_configs:
-      - targets: ['minio:9000']
-    scrape_interval: 30s
-
-  # ==================================================
-  # Kubernetes Infrastructure
-  # ==================================================
-  - job_name: 'kubernetes-nodes'
-    kubernetes_sd_configs:
-      - role: node
-    relabel_configs:
-      - action: labelmap
-        regex: __meta_kubernetes_node_label_(.+)
-      - target_label: __address__
-        replacement: kubernetes.default.svc:443
-      - source_labels: [__meta_kubernetes_node_name]
-        regex: (.+)
-        target_label: __metrics_path__
-        replacement: /api/v1/nodes/${1}/proxy/metrics
-
-  - job_name: 'kubernetes-pods'
-    kubernetes_sd_configs:
-      - role: pod
-    relabel_configs:
-      - source_labels: [__meta_kubernetes_pod_annotation_prometheus_io_scrape]
-        action: keep
-        regex: true
-      - source_labels: [__meta_kubernetes_pod_annotation_prometheus_io_path]
-        action: replace
-        target_label: __metrics_path__
-        regex: (.+)
-      - source_labels: [__address__, __meta_kubernetes_pod_annotation_prometheus_io_port]
-        action: replace
-        regex: ([^:]+)(?::\d+)?;(\d+)
-        replacement: $1:$2
-        target_label: __address__
-      - action: labelmap
-        regex: __meta_kubernetes_pod_label_(.+)
-      - source_labels: [__meta_kubernetes_namespace]
-        action: replace
-        target_label: kubernetes_namespace
-      - source_labels: [__meta_kubernetes_pod_name]
-        action: replace
-        target_label: kubernetes_pod_name
-
-  # ==================================================
-  # Nginx Ingress
-  # ==================================================
-  - job_name: 'nginx-ingress'
-    kubernetes_sd_configs:
-      - role: pod
-        namespaces:
-          names:
-            - ingress-nginx
-    relabel_configs:
-      - source_labels: [__meta_kubernetes_pod_label_app_kubernetes_io_name]
-        regex: ingress-nginx
-        action: keep
-    metrics_path: /metrics
-    scrape_interval: 10s
-
-  # ==================================================
-  # Blackbox Exporter (HTTP probes)
-  # ==================================================
-  - job_name: 'blackbox-http'
-    metrics_path: /probe
-    params:
-      module: [http_2xx]
-    static_configs:
-      - targets:
-        - https://api.crispr.example.com/health
-        - https://api.crispr.example.com/ready
-    relabel_configs:
-      - source_labels: [__address__]
-        target_label: __param_target
-      - source_labels: [__param_target]
-        target_label: instance
-      - target_label: __address__
-        replacement: blackbox-exporter:9115
-    scrape_interval: 30s
-
-  # ==================================================
-  # Self-monitoring
-  # ==================================================
-  - job_name: 'prometheus'
-    static_configs:
-      - targets: ['localhost:9090']
-
-# Storage configuration
-storage:
-  tsdb:
-    path: /prometheus/data
-    retention.time: 30d
-    retention.size: 500GB

package/agentic-flow/examples/crispr-cas13-pipeline/docs/security/oauth2-authentication.md

@@ -1,478 +0,0 @@
-# OAuth2 Authentication Flow - CRISPR-Cas13 Pipeline
-
-## Overview
-
-The CRISPR-Cas13 pipeline uses OAuth2 with JWT (JSON Web Tokens) for authentication and authorization. This document describes the complete authentication flow, token management, and security best practices.
-
-## Authentication Architecture
-
-```mermaid
-sequenceDiagram
-    actor User
-    participant Client as Web/CLI Client
-    participant API as API Gateway
-    participant DB as PostgreSQL
-    participant Redis as Redis Cache
-
-    User->>Client: Enter credentials
-    Client->>API: POST /api/v1/auth/login<br/>{email, password}
-
-    API->>DB: SELECT user WHERE email=?
-    DB-->>API: User record
-
-    API->>API: Verify password (bcrypt)
-
-    alt Password Valid
-        API->>API: Generate JWT access token (24h TTL)
-        API->>API: Generate refresh token (7d TTL)
-        API->>Redis: Store session<br/>SET session:{token_hash}
-        Redis-->>API: OK
-
-        API->>DB: INSERT INTO audit_log (login)
-
-        API-->>Client: 200 OK<br/>{token, refresh_token, user}
-        Client->>Client: Store tokens
-        Client-->>User: Redirect to dashboard
-    else Password Invalid
-        API-->>Client: 401 Unauthorized
-        Client-->>User: Show error
-    end
-```
-
----
-
-## Token Types
-
-### 1. Access Token (JWT)
-
-**Purpose**: Short-lived token for API authentication
-**Lifetime**: 24 hours
-**Storage**: Client-side (localStorage or secure cookie)
-
-**Token Structure**:
-```json
-{
-  "header": {
-    "alg": "RS256",
-    "typ": "JWT",
-    "kid": "key-2025-01"
-  },
-  "payload": {
-    "sub": "550e8400-e29b-41d4-a716-446655440000",
-    "email": "researcher@example.com",
-    "role": "researcher",
-    "permissions": [
-      "experiments:read",
-      "experiments:create",
-      "experiments:update:own",
-      "jobs:submit",
-      "results:read"
-    ],
-    "iat": 1705401600,
-    "exp": 1705488000,
-    "iss": "crispr-api.example.com",
-    "aud": "crispr-clients"
-  },
-  "signature": "..."
-}
-```
-
-**Signing Algorithm**: RS256 (RSA with SHA-256)
-- **Public Key**: Distributed via JWKS endpoint (`/api/v1/auth/jwks.json`)
-- **Private Key**: Stored in Kubernetes Secret, rotated quarterly
-
----
-
-### 2. Refresh Token
-
-**Purpose**: Long-lived token for obtaining new access tokens
-**Lifetime**: 7 days
-**Storage**: HttpOnly cookie (more secure than localStorage)
-
-**Token Structure** (Opaque token):
-```
-{
-  "jti": "unique-token-id",
-  "user_id": "550e8400-e29b-41d4-a716-446655440000",
-  "issued_at": 1705401600,
-  "expires_at": 1706006400
-}
-```
-
-**Storage**: Redis with TTL
-```redis
-SET refresh_token:{token_hash} "{user_id: ..., issued_at: ...}" EX 604800
-```
-
----
-
-## Authentication Flows
-
-### 1. Initial Login
-
-```http
-POST /api/v1/auth/login HTTP/1.1
-Host: api.crispr.example.com
-Content-Type: application/json
-
-{
-  "email": "researcher@example.com",
-  "password": "SecurePassword123!"
-}
-```
-
-**Success Response (200 OK)**:
-```json
-{
-  "access_token": "eyJhbGciOiJSUzI1NiIs...",
-  "refresh_token": "550e8400-e29b-41d4-a716-446655440000",
-  "token_type": "Bearer",
-  "expires_in": 86400,
-  "user": {
-    "id": "550e8400-e29b-41d4-a716-446655440000",
-    "email": "researcher@example.com",
-    "full_name": "Dr. Jane Smith",
-    "role": "researcher",
-    "institution": "Stanford University"
-  }
-}
-```
-
-**Error Response (401 Unauthorized)**:
-```json
-{
-  "error": "invalid_credentials",
-  "error_description": "Invalid email or password"
-}
-```
-
----
-
-### 2. Authenticated API Request
-
-```http
-GET /api/v1/experiments HTTP/1.1
-Host: api.crispr.example.com
-Authorization: Bearer eyJhbGciOiJSUzI1NiIs...
-```
-
-**Validation Steps** (in API Gateway middleware):
-1. Extract token from `Authorization: Bearer` header
-2. Verify JWT signature using public key
-3. Check token expiration (`exp` claim)
-4. Validate issuer (`iss`) and audience (`aud`)
-5. Extract user ID and permissions from token
-6. Check required permission for route (e.g., `experiments:read`)
-7. Inject user claims into request context
-8. Forward request to route handler
-
----
-
-### 3. Token Refresh
-
-When access token expires (24 hours), client uses refresh token to obtain new access token:
-
-```http
-POST /api/v1/auth/refresh HTTP/1.1
-Host: api.crispr.example.com
-Content-Type: application/json
-
-{
-  "refresh_token": "550e8400-e29b-41d4-a716-446655440000"
-}
-```
-
-**Success Response (200 OK)**:
-```json
-{
-  "access_token": "eyJhbGciOiJSUzI1NiIs...",
-  "refresh_token": "new-refresh-token-id",
-  "token_type": "Bearer",
-  "expires_in": 86400
-}
-```
-
-**Error Response (401 Unauthorized)**:
-```json
-{
-  "error": "invalid_token",
-  "error_description": "Refresh token has expired or been revoked"
-}
-```
-
----
-
-### 4. Logout
-
-```http
-POST /api/v1/auth/logout HTTP/1.1
-Host: api.crispr.example.com
-Authorization: Bearer eyJhbGciOiJSUzI1NiIs...
-```
-
-**Backend Actions**:
-1. Extract user ID from JWT
-2. Delete refresh token from Redis
-3. Add access token to blacklist (Redis) with TTL = remaining token lifetime
-4. Log logout event in audit log
-
-**Client Actions**:
-1. Delete access token from localStorage
-2. Clear refresh token cookie
-3. Redirect to login page
-
----
-
-## Role-Based Access Control (RBAC)
-
-### Roles & Permissions
-
-| Role | Permissions | Use Case |
-|------|-------------|----------|
-| **Guest** | `experiments:read:public`<br/>`results:read:public` | Public demo accounts |
-| **Researcher** | `experiments:*:own`<br/>`samples:*:own`<br/>`jobs:submit`<br/>`results:*:own` | Standard lab members |
-| **Bioinformatician** | All researcher permissions +<br/>`pipelines:configure`<br/>`data:export`<br/>`experiments:read:all` | Data analysts |
-| **Admin** | `*:*` (all permissions) | System administrators |
-
-### Permission Naming Convention
-
-```
-resource:action:scope
-```
-
-**Examples**:
-- `experiments:read:own` - Read own experiments
-- `experiments:create` - Create experiments (implicit own scope)
-- `jobs:submit` - Submit analysis jobs
-- `users:update:all` - Update all users (admin only)
-
----
-
-## Security Implementation
-
-### Password Hashing
-
-**Algorithm**: bcrypt with cost factor 12
-
-```rust
-// Hash password on registration
-use bcrypt::{hash, DEFAULT_COST};
-let password_hash = hash(password, DEFAULT_COST)?;
-
-// Verify password on login
-use bcrypt::verify;
-let valid = verify(password, &stored_hash)?;
-```
-
-**Password Requirements**:
-- Minimum 12 characters
-- At least 1 uppercase letter
-- At least 1 lowercase letter
-- At least 1 number
-- At least 1 special character
-- Not in common password list (10,000 most common)
-
----
-
-### JWT Signature Verification
-
-**Public Key Distribution** (JWKS):
-```http
-GET /api/v1/auth/jwks.json HTTP/1.1
-Host: api.crispr.example.com
-```
-
-**Response**:
-```json
-{
-  "keys": [
-    {
-      "kty": "RSA",
-      "use": "sig",
-      "kid": "key-2025-01",
-      "alg": "RS256",
-      "n": "0vx7agoebGcQSu...",
-      "e": "AQAB"
-    }
-  ]
-}
-```
-
-**Key Rotation Policy**:
-- New key generated every 90 days
-- Old key valid for additional 30 days (grace period)
-- Clients fetch JWKS on startup and cache for 24 hours
-
----
-
-### Token Blacklist (Logout & Revocation)
-
-**Redis Storage**:
-```redis
-# Add token to blacklist on logout
-SET token_blacklist:{token_hash} "revoked" EX {remaining_ttl}
-
-# Check blacklist on every request (fast O(1) lookup)
-EXISTS token_blacklist:{token_hash}
-```
-
-**Performance**: Redis GET operation <1ms, negligible impact on request latency
-
----
-
-### Rate Limiting (Brute Force Protection)
-
-**Login Endpoint** (`POST /api/v1/auth/login`):
-- **Limit**: 5 failed attempts per 15 minutes per email
-- **Lockout**: After 5 failures, block for 15 minutes
-- **Storage**: Redis with sliding window
-
-**Implementation**:
-```rust
-async fn rate_limit_login(email: &str, redis: &redis::Client) -> Result<(), ApiError> {
-    let key = format!("rate_limit:login:{}", email);
-    let mut conn = redis.get_async_connection().await?;
-
-    let count: u32 = conn.incr(&key, 1).await?;
-
-    if count == 1 {
-        conn.expire(&key, 900).await?; // 15 minutes
-    }
-
-    if count > 5 {
-        return Err(ApiError::TooManyRequests("Too many login attempts. Try again in 15 minutes."));
-    }
-
-    Ok(())
-}
-```
-
----
-
-## Security Best Practices
-
-### 1. Token Storage
-
-**✅ Recommended**:
-- **Access Token**: localStorage (for SPA) or memory (for native apps)
-- **Refresh Token**: HttpOnly cookie with `Secure` and `SameSite=Strict` flags
-
-**❌ Not Recommended**:
-- Storing refresh tokens in localStorage (vulnerable to XSS)
-- Storing tokens in URL parameters (visible in logs)
-
----
-
-### 2. HTTPS Only
-
-**All API endpoints require TLS 1.3**:
-- Certificate: Let's Encrypt wildcard cert for `*.crispr.example.com`
-- Renewal: Automated via cert-manager in Kubernetes
-- HSTS Header: `Strict-Transport-Security: max-age=31536000; includeSubDomains`
-
----
-
-### 3. CORS Configuration
-
-```rust
-use tower_http::cors::{CorsLayer, Any};
-
-let cors = CorsLayer::new()
-    .allow_origin(["https://app.crispr.example.com".parse().unwrap()])
-    .allow_methods([Method::GET, Method::POST, Method::PUT, Method::DELETE])
-    .allow_headers([AUTHORIZATION, CONTENT_TYPE])
-    .allow_credentials(true);
-```
-
----
-
-### 4. Token Expiration Times
-
-| Token Type | Lifetime | Rationale |
-|------------|----------|-----------|
-| Access Token | 24 hours | Balance security vs. UX |
-| Refresh Token | 7 days | Weekly re-authentication |
-| API Key (automation) | 90 days | For CI/CD pipelines |
-
----
-
-### 5. Audit Logging
-
-**All authentication events are logged**:
-```sql
-INSERT INTO audit_log (user_id, action, ip_address, user_agent, metadata)
-VALUES (
-  '550e8400-e29b-41d4-a716-446655440000',
-  'login',
-  '203.0.113.42',
-  'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36',
-  '{"success": true, "method": "password"}'
-);
-```
-
-**Monitored Events**:
-- Successful login
-- Failed login attempts
-- Token refresh
-- Logout
-- Permission denied (403)
-- Password changes
-- Account deletions
-
----
-
-## OAuth2 External Providers (Future)
-
-**Planned Integrations**:
-- **Google OAuth2**: For institutional accounts
-- **GitHub OAuth2**: For open-source collaborators
-- **ORCID**: For academic identity verification
-
-**Flow** (Authorization Code with PKCE):
-```http
-GET /api/v1/auth/oauth/google/authorize HTTP/1.1
-Host: api.crispr.example.com
-
-# Redirect to Google OAuth consent screen
-# After approval, redirect back with authorization code
-# Exchange code for tokens
-```
-
----
-
-## Compliance & Standards
-
-**Standards Followed**:
-- ✅ **RFC 6749**: OAuth 2.0 Authorization Framework
-- ✅ **RFC 7519**: JSON Web Token (JWT)
-- ✅ **RFC 7517**: JSON Web Key (JWK)
-- ✅ **OWASP Authentication Cheat Sheet**
-- ✅ **NIST SP 800-63B**: Digital Identity Guidelines
-
-**HIPAA Compliance**:
-- All PHI (Personal Health Information) encrypted at rest and in transit
-- Access logs retained for 7 years
-- User sessions automatically expire after 24 hours of inactivity
-- Multi-factor authentication (MFA) required for admin accounts
-
----
-
-## Troubleshooting
-
-### Issue: "Invalid token signature"
-**Cause**: JWT signed with old key after rotation
-**Solution**: Client should fetch new JWKS from `/api/v1/auth/jwks.json`
-
-### Issue: "Token expired"
-**Cause**: Access token TTL exceeded
-**Solution**: Use refresh token to obtain new access token
-
-### Issue: "Insufficient permissions"
-**Cause**: User lacks required permission for resource
-**Solution**: Admin must update user role or grant specific permission
-
----
-
-**Document Version**: 1.0
-**Last Updated**: 2025-10-12
-**See Also**: [API Documentation](../api/README.md), [Security Audit Report](./security-audit.md)