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Docs: Update README with current status and add config/quickstart guides

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Changes:
- Updated README.md with current Phase 2.3 completion status
- Added detailed development progress section
- Added backend API endpoints documentation
- Added environment configuration guide
- Added local development and Docker quick start
- Added deployment instructions

New Documentation:
- thoughts/CONFIG.md - Comprehensive configuration guide
- thoughts/QUICKSTART.md - 5-minute quick start guide

All configuration files are now documented and up-to-date.
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344
README.md
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@ -1,101 +1,73 @@
### /home/asoliver/desarrollo/normogen/README.md # Normogen
```markdown
1: # Normogen
2:
3: ## Overview
4:
5: Normogen is a privacy-focused health data tracking and management platform. The name comes from Mapudungun, relating to Balanced Life.
6:
7: ## Vision
8:
9: To record as many variables related to health as possible, store them in a secure, private manner, to be used by you, not by corporations. From medication reminders to pattern analysis, Normogen puts you in control of your health data.
10:
11: ## Technology Stack
12:
13: ### Backend
14: - **Framework**: Axum 0.7.x
15: - **Runtime**: Tokio 1.x
16: - **Middleware**: Tower, Tower-HTTP
17: - **Database**: MongoDB (with zero-knowledge encryption)
18: - **Language**: Rust
19:
20: ### Mobile (iOS + Android)
21: - **Framework**: React Native 0.73+
22: - **Language**: TypeScript
23: - **State Management**: Redux Toolkit 2.x
24: - **Data Fetching**: RTK Query 2.x
25: - **Health Sensors**: react-native-health, react-native-google-fit
26: - **Encryption**: react-native-quick-crypto
27:
28: ### Web
29: - **Framework**: React 18+
30: - **Language**: TypeScript
31: - **State Management**: Redux Toolkit 2.x
32: - **Data Fetching**: RTK Query 2.x
33: - **Charts**: Recharts
34:
35: ### Deployment
36: - Docker on Linux
37:
38: ## Platform Strategy
39:
40: **Primary: Mobile Apps** - Daily health tracking, sensor integration, QR scanning, push notifications
41:
42: **Secondary: Web Browser** - Extensive reporting, visualization, profile management
43:
44: ## Key Features
45:
46: - Zero-knowledge encryption
47: - Multi-person profiles
48: - Family structure management
49: - Secure sharing with expiring links
50: - Mobile apps with health sensor integration
51: - Web interface for complex visualizations
52:
53: ## Security Model
54:
55: - Client-side encryption: Data encrypted before leaving device
56: - Zero-knowledge: Server stores only encrypted data
57: - Proton-style encryption: AES-256-GCM with PBKDF2 key derivation
58: - Shareable links: Self-contained decryption keys in URLs
59: - Privacy-first: No data selling, subscription-based revenue
60:
61: ## Documentation
62:
63: - [Introduction](./introduction.md) - Project vision and detailed feature specification
64: - [Encryption Implementation Guide](./encryption.md) - Zero-knowledge encryption architecture
65: - [Research](./thoughts/research/) - Technical research and planning documents
66:
67: ## Development Status
68:
69: Phase: Planning/Documentation
70:
71: ### Completed
72: - Project vision and requirements
73: - Security architecture design
74: - Encryption implementation guide
75: - Git repository initialization
76: - **Rust framework selection: Axum**
77: - **Mobile/Web framework selection: React Native + React**
78: - **State management selection: Redux Toolkit 2.x**
79:
80: ### Next Steps
81: - Authentication system design (JWT with recovery phrases)
82: - Database schema design
83: - Create proof-of-concept with Axum
84: - Implement basic CRUD API
85: - Build mobile apps with health sensor integration
86: - Build web companion app
87: - Add encryption layer
88: - Implement sharing functionality
89:
90: ## Open Source
91:
92: Normogen is open-source. Both server and client code will be publicly available.
93:
94: Note: This project is currently in the planning phase. No implementation code has been written yet.
```
## Overview
Normogen is a privacy-focused health data tracking and management platform. The name comes from Mapudungun, relating to Balanced Life.
## Vision
To record as many variables related to health as possible, store them in a secure, private manner, to be used by you, not by corporations. From medication reminders to pattern analysis, Normogen puts you in control of your health data.
## Technology Stack
### Backend
- **Framework**: Axum 0.7.x
- **Runtime**: Tokio 1.x
- **Middleware**: Tower, Tower-HTTP
- **Database**: MongoDB (with zero-knowledge encryption)
- **Language**: Rust
- **Authentication**: JWT (PBKDF2 password hashing)
### Mobile (iOS + Android)
- **Framework**: React Native 0.73+
- **Language**: TypeScript
- **State Management**: Redux Toolkit 2.x
- **Data Fetching**: RTK Query 2.x
- **Health Sensors**: react-native-health, react-native-google-fit
- **Encryption**: react-native-quick-crypto
### Web
- **Framework**: React 18+
- **Language**: TypeScript
- **State Management**: Redux Toolkit 2.x
- **Data Fetching**: RTK Query 2.x
- **Charts**: Recharts
### Deployment
- Docker on Linux
## Platform Strategy
**Primary: Mobile Apps** - Daily health tracking, sensor integration, QR scanning, push notifications
**Secondary: Web Browser** - Extensive reporting, visualization, profile management
## Key Features
- Zero-knowledge encryption
- Multi-person profiles
- Family structure management
- Secure sharing with expiring links
- Mobile apps with health sensor integration
- Web interface for complex visualizations
- JWT-based authentication with token rotation
## Security Model
- Client-side encryption: Data encrypted before leaving device
- Zero-knowledge: Server stores only encrypted data
- Proton-style encryption: AES-256-GCM with PBKDF2 key derivation
- Shareable links: Self-contained decryption keys in URLs
- Privacy-first: No data selling, subscription-based revenue
- JWT authentication with token rotation and revocation
- PBKDF2 password hashing (100,000 iterations)
## Documentation
- [Introduction](./introduction.md) - Project vision and detailed feature specification
- [Encryption Implementation Guide](./encryption.md) - Zero-knowledge encryption architecture
- [Research](./thoughts/research/) - Technical research and planning documents
- [Project Status](./thoughts/STATUS.md) - Development progress tracking
## Monorepo Structure ## Monorepo Structure
@ -112,6 +84,163 @@ normogen/
Each platform has its own `src/` directory to keep codebases separate while sharing common code through the `shared/` directory. Each platform has its own `src/` directory to keep codebases separate while sharing common code through the `shared/` directory.
## Development Status
**Current Phase: Phase 2 - Backend Development**
### Completed
#### Phase 1 - Planning
- ✅ Project vision and requirements
- ✅ Security architecture design
- ✅ Encryption implementation guide
- ✅ Git repository initialization
#### Phase 2 - Backend (In Progress)
- ✅ **Phase 2.1** - Backend Project Initialization
- Rust project setup with Axum
- Docker configuration
- Docker Compose setup
- Kubernetes manifests
- ✅ **Phase 2.2** - MongoDB Connection & Models
- MongoDB connection pooling
- User model (email, password_hash, family_id, token_version)
- RefreshToken model (token_hash, user_id, expires_at)
- Family, Profile, HealthData models
- Medication, LabResult, Appointment models
- ✅ **Phase 2.3** - JWT Authentication
- JWT access tokens (15 min expiry)
- JWT refresh tokens (30 day expiry)
- Token rotation (old tokens revoked on refresh)
- Token revocation (logout)
- PBKDF2 password hashing (100K iterations)
- Auth endpoints: register, login, refresh, logout
- Protected routes with JWT middleware
- Health check endpoints
### In Progress
#### Phase 2 - Backend
- 🚧 **Phase 2.4** - User Management Enhancement
- Password recovery (zero-knowledge phrases)
- Email verification flow
- Enhanced profile management
- Account settings endpoints
#### Future Phases
- **Phase 2.5** - Access Control
- Permission-based middleware
- Token version enforcement
- Family access control
- **Phase 2.6** - Security Hardening
- Rate limiting
- Account lockout policies
- Security audit logging
- **Phase 3** - Core API Development
- **Phase 4** - Encryption Layer
- **Phase 5** - Mobile App Development
- **Phase 6** - Web App Development
## Backend Quick Start
### Prerequisites
- Rust 1.70+
- MongoDB 4.4+
- Docker (optional, for containerized deployment)
### Local Development
```bash
# Clone repository
git clone <forgejo-url> normogen
cd normogen/backend
# Copy environment file
cp .env.example .env
# Edit .env with your configuration
# Required variables:
# MONGODB_URI=mongodb://localhost:27017
# DATABASE_NAME=normogen
# JWT_SECRET=<your-secret-key-minimum-32-characters>
# Install dependencies
cargo build
# Run the server
cargo run
# Server will start on http://127.0.0.1:8000
```
### Docker Development
```bash
# Using Docker Compose (dev mode)
cd backend
docker compose -f docker-compose.dev.yml up -d
# Check status
curl http://localhost:8000/health
# View logs
docker compose logs -f backend
```
### Testing
```bash
# Run unit tests
cargo test
# Run integration tests (requires MongoDB)
cargo test --test auth_tests
# Manual testing with provided script
./thoughts/test_auth.sh
```
## Backend API Endpoints
### Public Endpoints (No Authentication)
```
POST /api/auth/register - User registration
POST /api/auth/login - User login
POST /api/auth/refresh - Token refresh (rotates tokens)
POST /api/auth/logout - Logout (revokes token)
GET /health - Health check
GET /ready - Readiness check
```
### Protected Endpoints (JWT Required)
```
GET /api/users/me - Get user profile
```
## Environment Configuration
### Backend Environment Variables
```bash
# MongoDB Configuration
MONGODB_URI=mongodb://localhost:27017
DATABASE_NAME=normogen
# JWT Configuration
JWT_SECRET=<your-secret-key-minimum-32-characters>
JWT_ACCESS_TOKEN_EXPIRY_MINUTES=15
JWT_REFRESH_TOKEN_EXPIRY_DAYS=30
# Server Configuration
SERVER_HOST=127.0.0.1
SERVER_PORT=8000
```
See `backend/.env.example` for a complete template.
## Repository Management ## Repository Management
- **Git Hosting**: Forgejo (self-hosted) - **Git Hosting**: Forgejo (self-hosted)
@ -121,7 +250,7 @@ Each platform has its own `src/` directory to keep codebases separate while shar
## Deployment ## Deployment
### Backend Deployment ### Backend Deployment (Production)
```bash ```bash
# Clone repository # Clone repository
@ -129,11 +258,10 @@ git clone <forgejo-url> normogen
cd normogen/backend cd normogen/backend
# Setup configuration # Setup configuration
cp config/.env.example config/.env cp .env.example .env
# Edit config/.env # Edit .env with production values
# Build and run # Build and run with Docker Compose
docker compose build
docker compose up -d docker compose up -d
# Check status # Check status
@ -147,3 +275,15 @@ curl http://localhost:6000/health
**Ports**: **Ports**:
- Backend API: `6000` (host) → `8000` (container) - Backend API: `6000` (host) → `8000` (container)
- MongoDB: `27017` (standard port) - MongoDB: `27017` (standard port)
## Open Source
Normogen is open-source. Both server and client code will be publicly available.
## Contributing
See [thoughts/STATUS.md](./thoughts/STATUS.md) for current development progress and next steps.
## License
[To be determined]

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# Configuration Guide
This document explains all configuration files and environment variables for the Normogen project.
## Backend Configuration
### Environment Files
#### 1. backend/.env.example (Primary Configuration Template)
This is the main environment configuration template for the backend service.
```bash
# MongoDB Configuration
MONGODB_URI=mongodb://localhost:27017
DATABASE_NAME=normogen
# JWT Configuration
JWT_SECRET=your-secret-key-here-change-in-production
JWT_ACCESS_TOKEN_EXPIRY_MINUTES=15
JWT_REFRESH_TOKEN_EXPIRY_DAYS=30
# Server Configuration
SERVER_HOST=127.0.0.1
SERVER_PORT=8000
```
**How to use:**
```bash
cd backend
cp .env.example .env
# Edit .env with your values
```
#### 2. backend/defaults.env
This file contains default values for development. It's sourced by docker-compose files.
```bash
MONGODB_URI=mongodb://localhost:27017
DATABASE_NAME=normogen
JWT_SECRET=change-this-secret-in-production
SERVER_HOST=0.0.0.0
SERVER_PORT=8000
```
#### 3. thoughts/env.example
This is a reference copy in the thoughts directory for documentation purposes.
## Environment Variables
### Required Variables
| Variable | Description | Example | Default |
|----------|-------------|---------|---------|
| `MONGODB_URI` | MongoDB connection string | `mongodb://localhost:27017` | - |
| `DATABASE_NAME` | MongoDB database name | `normogen` | - |
| `JWT_SECRET` | Secret key for JWT signing | Minimum 32 characters | - |
### Optional Variables
| Variable | Description | Example | Default |
|----------|-------------|---------|---------|
| `SERVER_HOST` | Server bind address | `0.0.0.0` | `127.0.0.1` |
| `SERVER_PORT` | Server port | `8000` | `8000` |
| `JWT_ACCESS_TOKEN_EXPIRY_MINUTES` | Access token lifetime | `15` | `15` |
| `JWT_REFRESH_TOKEN_EXPIRY_DAYS` | Refresh token lifetime | `30` | `30` |
## Docker Configuration
### docker-compose.yml (Production)
Standard production deployment with MongoDB.
```bash
cd backend
docker compose up -d
```
**Services:**
- `backend` - Axum server on port 6000 (host)
- `mongodb` - MongoDB on port 27017
**Resource Limits:**
- CPU: 1000m (1 core)
- Memory: 1000Mi (1GB)
### docker-compose.dev.yml (Development)
Development mode with hot reload and volume mounts.
```bash
cd backend
docker compose -f docker-compose.dev.yml up -d
```
**Features:**
- Hot reload on code changes
- Source code mounted as volume
- Exposes server on port 8000
## Local Development
### Quick Start
```bash
# Clone repository
git clone <forgejo-url> normogen
cd normogen/backend
# Setup environment
cp .env.example .env
# Edit .env with your configuration
# Install dependencies
cargo build
# Run server
cargo run
# Test
curl http://localhost:8000/health
```
### Testing
```bash
# Unit tests
cargo test
# Integration tests
cargo test --test auth_tests
# Manual testing script
cd ..
./thoughts/test_auth.sh
```
## Configuration Best Practices
### JWT Secret
```bash
# Generate a secure JWT secret (minimum 32 characters)
openssl rand -base64 32
# Or use a passphrase-based secret
echo "your-secure-passphrase-32-chars-minimum" | base64
```
**Security Requirements:**
- Minimum 32 characters
- Use random, high-entropy values
- Never commit to git
- Rotate periodically in production
- Use different secrets for dev/staging/production
### MongoDB Connection
```bash
# Local development
MONGODB_URI=mongodb://localhost:27017
# With authentication
MONGODB_URI=mongodb://username:password@localhost:27017
# Replica set
MONGODB_URI=mongodb://host1:27017,host2:27017,host3:27017/?replicaSet=myReplicaSet
# MongoDB Atlas (cloud)
MONGODB_URI=mongodb+srv://username:password@cluster.mongodb.net/mydb
```
### Server Configuration
```bash
# Local development (localhost only)
SERVER_HOST=127.0.0.1
SERVER_PORT=8000
# Docker/Docker Compose (all interfaces)
SERVER_HOST=0.0.0.0
SERVER_PORT=8000
# Production (behind reverse proxy)
SERVER_HOST=127.0.0.1
SERVER_PORT=8000
```
## Deployment Environments
### Development
```bash
MONGODB_URI=mongodb://localhost:27017
DATABASE_NAME=normogen_dev
JWT_SECRET=dev-secret-key-32-chars-minimum
SERVER_HOST=127.0.0.1
SERVER_PORT=8000
```
### Staging
```bash
MONGODB_URI=mongodb://staging-mongo.internal:27017
DATABASE_NAME=normogen_staging
JWT_SECRET=<use-vault-or-secret-manager>
SERVER_HOST=0.0.0.0
SERVER_PORT=8000
```
### Production
```bash
MONGODB_URI=mongodb+srv://<username>:<password>@prod-cluster.mongodb.net/normogen
DATABASE_NAME=normogen
JWT_SECRET=<use-vault-or-secret-manager>
SERVER_HOST=127.0.0.1
SERVER_PORT=8000
```
## Troubleshooting
### MongoDB Connection Issues
```bash
# Check if MongoDB is running
docker ps | grep mongo
# or
systemctl status mongod
# Test connection
mongosh "mongodb://localhost:27017"
```
### JWT Errors
```bash
# Verify JWT_SECRET is set
echo $JWT_SECRET | wc -c # Should be >= 32
# Check for special characters
# Some shells may require quotes
export JWT_SECRET="your-secret-with-special-chars-!@#$%"
```
### Port Already in Use
```bash
# Check what's using port 8000
lsof -i :8000
# or
netstat -tulpn | grep 8000
# Kill the process
kill -9 <PID>
```
## Security Checklist
Before deploying to production:
- [ ] Change `JWT_SECRET` to a strong, randomly generated value
- [ ] Enable MongoDB authentication
- [ ] Use TLS/SSL for MongoDB connections
- [ ] Set up firewall rules
- [ ] Configure reverse proxy (nginx/caddy)
- [ ] Enable HTTPS
- [ ] Set up log aggregation
- [ ] Configure monitoring and alerts
- [ ] Implement rate limiting
- [ ] Regular security updates
## Additional Resources
- [README.md](../README.md) - Project overview
- [STATUS.md](./STATUS.md) - Development progress
- [encryption.md](../encryption.md) - Encryption implementation guide
- [introduction.md](../introduction.md) - Project vision

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# Quick Start Guide
Get the Normogen backend running locally in 5 minutes.
## Prerequisites
- Rust 1.70 or later
- MongoDB 4.4 or later
- Git
## Step 1: Clone and Setup
```bash
# Clone repository
git clone <forgejo-url> normogen
cd normogen/backend
# Copy environment template
cp .env.example .env
```
## Step 2: Start MongoDB
### Option A: Using Docker (Recommended)
```bash
docker run -d \
--name normogen-mongo \
-p 27017:27017 \
-e MONGO_INITDB_DATABASE=normogen \
mongo:latest
```
### Option B: Using System MongoDB
```bash
# Start MongoDB service
sudo systemctl start mongod # Linux
brew services start mongodb # macOS
```
## Step 3: Configure Environment
Edit `backend/.env`:
```bash
# MongoDB Configuration
MONGODB_URI=mongodb://localhost:27017
DATABASE_NAME=normogen
# JWT Configuration (change this!)
JWT_SECRET=my-super-secret-jwt-key-32-chars
JWT_ACCESS_TOKEN_EXPIRY_MINUTES=15
JWT_REFRESH_TOKEN_EXPIRY_DAYS=30
# Server Configuration
SERVER_HOST=127.0.0.1
SERVER_PORT=8000
```
## Step 4: Build and Run
```bash
# Install dependencies and build
cargo build
# Run the server
cargo run
```
Server will start on `http://127.0.0.1:8000`
## Step 5: Test
### Health Check
```bash
curl http://localhost:8000/health
```
Expected response:
```json
{
"status": "ok",
"database": "connected"
}
```
### Register a User
```bash
curl -X POST http://localhost:8000/api/auth/register \
-H "Content-Type: application/json" \
-d '{
"email": "test@example.com",
"password": "SecurePassword123!"
}'
```
Expected response:
```json
{
"message": "User registered successfully",
"user_id": "...",
"email": "test@example.com"
}
```
### Login
```bash
curl -X POST http://localhost:8000/api/auth/login \
-H "Content-Type: application/json" \
-d '{
"email": "test@example.com",
"password": "SecurePassword123!"
}'
```
Expected response:
```json
{
"access_token": "...",
"refresh_token": "...",
"token_type": "Bearer",
"expires_in": 900
}
```
### Access Protected Endpoint
```bash
# Replace YOUR_ACCESS_TOKEN with the token from login
curl http://localhost:8000/api/users/me \
-H "Authorization: Bearer YOUR_ACCESS_TOKEN"
```
Expected response:
```json
{
"user_id": "...",
"email": "test@example.com",
"family_id": null,
"token_version": 0
}
```
## Docker Quick Start
```bash
cd backend
# Start MongoDB and backend with Docker Compose
docker compose up -d
# Check logs
docker compose logs -f backend
# Test
curl http://localhost:6000/health
```
## Next Steps
- Read [CONFIG.md](./CONFIG.md) for detailed configuration
- Read [STATUS.md](./STATUS.md) for development progress
- Run `./thoughts/test_auth.sh` for comprehensive API testing
- Check API documentation in [verification-report-phase-2.3.md](./verification-report-phase-2.3.md)
## Troubleshooting
### Port 8000 already in use
```bash
# Find and kill the process
lsof -ti:8000 | xargs kill -9
```
### MongoDB connection failed
```bash
# Check MongoDB is running
docker ps | grep mongo
# or
systemctl status mongod
# Test connection
mongosh "mongodb://localhost:27017"
```
### Compilation errors
```bash
# Clean and rebuild
cargo clean
cargo build
```
### JWT secret too short
Make sure `JWT_SECRET` in `.env` is at least 32 characters.
## Stopping the Server
```bash
# If running with cargo
Ctrl+C
# If running with Docker Compose
docker compose down
# Stop MongoDB (Docker)
docker stop normogen-mongo
docker rm normogen-mongo
```