normogen/docs/AI_AGENT_GUIDE.md

AI Agent Guide - Normogen Repository

Last Updated: 2026-03-09
Project: Normogen - Open-source health data platform
Repository Type: Monorepo (Rust backend + React frontend + Mobile placeholder)

---

🤖 Quick Start for AI Agents

1-minute Overview

• Backend: Rust (Axum web framework, MongoDB database)
• Frontend: React (TypeScript, Material-UI, Zustand state)
• Mobile: Placeholder (not yet implemented)
• Documentation: Organized in docs/ directory
• Current Phase: 2.8 (Drug Interactions & Advanced Features)

Essential Commands

# Backend
cd backend && cargo build              # Build backend
cd backend && cargo test               # Run tests
cd backend && cargo clippy             # Lint
cd backend && docker compose up -d     # Run with Docker

# Frontend
cd web/normogen-web && npm install     # Install dependencies
cd web/normogen-web && npm start       # Dev server
cd web/normogen-web && npm test        # Run tests

# Testing
./docs/testing/quick-test.sh           # Quick smoke tests
./docs/testing/test-api-endpoints.sh   # API tests

---

📁 Repository Structure

normogen/
├── backend/                 # Rust backend (Axum + MongoDB)
│   ├── src/
│   │   ├── handlers/       # API route handlers (auth, users, medications, etc.)
│   │   ├── models/         # Data models & repositories
│   │   ├── auth/           # JWT authentication
│   │   ├── security/       # Rate limiting, audit logging, session management
│   │   ├── middleware/     # Custom middleware (JWT auth, rate limiting)
│   │   ├── services/       # Business logic (OpenFDA, interactions)
│   │   ├── config/         # Configuration management
│   │   ├── db/             # MongoDB implementation
│   │   └── main.rs         # Entry point, router setup
│   ├── tests/              # Integration tests
│   ├── Cargo.toml          # Rust dependencies
│   └── docker-compose.yml  # Docker deployment
│
├── web/                     # React frontend
│   └── normogen-web/
│       ├── src/
│       │   ├── pages/      # Page components (Login, Register, etc.)
│       │   ├── components/ # Reusable components
│       │   ├── services/   # API service layer (axios)
│       │   ├── store/      # Zustand state management
│       │   └── types/      # TypeScript type definitions
│       └── package.json
│
├── mobile/                  # Mobile app (placeholder)
├── shared/                  # Shared code (placeholder)
├── thoughts/                # Development notes
└── docs/                    # Organized documentation
    ├── product/            # Product definition, roadmap
    ├── implementation/     # Phase plans, specs
    ├── testing/            # Test scripts & results
    ├── deployment/         # Deployment guides
    └── development/        # Git workflow, CI/CD

---

🔑 Key Concepts

Backend Architecture

Technology Stack

• Language: Rust (edition 2021)
• Web Framework: Axum 0.7 (async, tower-based)
• Database: MongoDB 7.0
• Authentication: JWT (jsonwebtoken 9)
  • Access tokens: 15 minute expiry
  • Refresh tokens: 30 day expiry
  • PBKDF2 password hashing (100K iterations)
• Security: Rate limiting (tower-governor), audit logging

Project Structure Pattern

The backend follows a modular architecture:

// Entry point: src/main.rs
mod config;        // Configuration from environment
mod db;            // Database trait + MongoDB impl
mod models;        // Data models with repositories
mod auth;          // JWT service
mod security;      // Security features (audit, sessions, lockout)
mod handlers;      // HTTP request handlers
mod middleware;    // Middleware (JWT, rate limiting)
mod services;      // Business logic (OpenFDA, interactions)

#[tokio::main]
async fn main() -> anyhow::Result<()> {
    // Load config → Connect DB → Initialize services → Build router
}

Handler Pattern

All API handlers follow this pattern:

// In src/handlers/
pub async fn handler_name(
    State(state): State<AppState>,
    Json(req): Json<RequestType>,
) -> Result<Json<ResponseType>, ApiError> {
    // 1. Validate request
    // 2. Call service/repository
    // 3. Return response
}

Authentication Flow

1. User registers/logs in → JWT tokens generated
2. Access token in Authorization header → middleware::jwt_auth_middleware validates
3. User ID extracted and available in handlers
4. Protected routes require valid JWT

Database Pattern

• Repository pattern: Each model has a Repository trait
• MongoDB implementation: db::MongoDb wraps mongodb::Client
• Collections accessed via Database from MongoDB

Frontend Architecture

Technology Stack

• Framework: React 19.2.4 + TypeScript 4.9.5
• UI Library: Material-UI (MUI) 7.3.9
• State Management: Zustand 5.0.11
• HTTP Client: Axios 1.13.6
• Routing: React Router DOM 7.13.1

Project Structure

src/
├── pages/          # Route components (LoginPage, RegisterPage, etc.)
├── components/     # Reusable components (ProtectedRoute, etc.)
├── services/       # API service (axios instance with interceptors)
├── store/          # Zustand stores (auth, user, etc.)
├── types/          # TypeScript interfaces (API types)
└── App.tsx         # Main app with routing

State Management

• Zustand stores in src/store/
• Auth store: JWT tokens, user info
• API client: Axios instance with auth header injection

---

🚀 Common Workflows

Adding a New API Endpoint

Backend (Rust)

# 1. Add model to src/models/mod.rs
# 2. Create repository methods in src/models/your_model.rs
# 3. Add handler to src/handlers/your_handler.rs
# 4. Register route in src/main.rs
# 5. Add tests to tests/

Example:

// src/models/new_feature.rs
use mongodb::{Collection, Database};
use serde::{Deserialize, Serialize};

#[derive(Debug, Serialize, Deserialize)]
pub struct NewFeature {
    pub id: String,
    pub name: String,
}

pub struct NewFeatureRepository {
    collection: Collection<NewFeature>,
}

impl NewFeatureRepository {
    pub fn new(db: &Database) -> Self {
        Self {
            collection: db.collection("new_features"),
        }
    }
    
    pub async fn create(&self, feature: &NewFeature) -> Result<()> {
        self.collection.insert_one(feature).await?;
        Ok(())
    }
}

// src/handlers/new_feature.rs
use axum::{Json, State};
use crate::models::new_feature::{NewFeature, NewFeatureRepository};

pub async fn create_new_feature(
    State(state): State<AppState>,
    Json(req): Json<NewFeature>,
) -> Result<Json<NewFeature>, ApiError> {
    let repo = NewFeatureRepository::new(&state.db.get_database());
    repo.create(&req).await?;
    Ok(Json(req))
}

// src/main.rs
.route("/api/new-features", post(handlers::create_new_feature))

Frontend (React/TypeScript)

# 1. Add types to src/types/api.ts
# 2. Add API service to src/services/api.ts
# 3. Create Zustand store in src/store/useStore.ts
# 4. Create page/component in src/pages/ or src/components/

Example:

// src/types/api.ts
export interface NewFeature {
  id: string;
  name: string;
}

// src/services/api.ts
export const newFeatureApi = {
  create: (data: NewFeature) => 
    api.post('/api/new-features', data),
  getAll: () => 
    api.get('/api/new-features'),
};

// src/store/useStore.ts
import { create } from 'zustand';

interface NewFeatureStore {
  features: NewFeature[];
  fetchFeatures: () => Promise<void>;
}

export const useNewFeatureStore = create<NewFeatureStore>((set) => ({
  features: [],
  fetchFeatures: async () => {
    const response = await newFeatureApi.getAll();
    set({ features: response.data });
  },
}));

// src/pages/NewFeaturePage.tsx
import { useNewFeatureStore } from '../store/useStore';

export const NewFeaturePage = () => {
  const { features, fetchFeatures } = useNewFeatureStore();
  
  useEffect(() => { fetchFeatures(); }, []);
  
  return <div>{/* UI here */}</div>;
};

Running Tests

Backend Tests

# Unit tests
cd backend && cargo test

# Integration tests
cd backend && cargo test --test '*'

# Specific test
cd backend && cargo test test_name

# With output
cd backend && cargo test -- --nocapture

Frontend Tests

cd web/normogen-web && npm test

# Coverage
cd web/normogen-web && npm test -- --coverage

API Endpoint Tests

# Quick smoke test
./docs/testing/quick-test.sh

# Full API test suite
./docs/testing/test-api-endpoints.sh

# Medication-specific tests
./docs/testing/test-medication-api.sh

Deployment

Local Development

cd backend
docker compose up -d

# Check logs
docker compose logs -f backend

# Check health
curl http://localhost:6500/health

Production (Solaria)

# Use deployment script
./docs/deployment/deploy-to-solaria.sh

# Manual deployment
cd backend
docker compose -f docker-compose.prod.yml up -d

---

🔒 Security Guidelines

Authentication

• All protected routes require JWT in Authorization: Bearer <token> header
• Access tokens expire in 15 minutes
• Refresh tokens expire in 30 days
• Tokens are rotated on refresh

Rate Limiting

• General rate limiting applied to all routes
• Configured in middleware::general_rate_limit_middleware
• Account lockout after 5 failed login attempts (15min base, max 24hr)

Password Security

• PBKDF2 with 100,000 iterations
• Passwords never logged or returned in API responses
• Zero-knowledge recovery phrases

Data Validation

• Request validation using validator crate
• Input sanitization in handlers
• MongoDB uses BSON type system

---

📊 Current Implementation Status

Completed Features ✅

• JWT authentication (login, register, logout, refresh)
• User management (profile, settings, password change)
• Permission-based access control (Read, Write, Admin)
• Share management (share resources with permissions)
• Security hardening (rate limiting, audit logging, session management)
• Medication management (CRUD, dose logging, adherence tracking)
• Health statistics tracking (weight, BP, trends)
• Lab results storage
• OpenFDA integration for drug data

Implemented ✅

• Drug interaction checking (Phase 2.8) — /api/interactions/check, /check-new

In Progress / Not Started 🚧

• Automated reminder system (Phase 2.8 stretch)
• Frontend integration with backend (Phase 3)

Planned 📋

• Medication refill tracking
• Advanced health analytics
• Healthcare data export (FHIR, HL7)
• Caregiver access
• Mobile app

---

🛠️ Development Guidelines

Code Style

Rust (Backend)

• Use cargo fmt for formatting
• Use cargo clippy for linting
• Follow Rust naming conventions
• Use Result<_, ApiError> for error handling
• Document public APIs with rustdoc comments

TypeScript (Frontend)

• Use functional components with hooks
• Prefer TypeScript interfaces over types
• Use Material-UI components
• Follow React best practices
• Use Zustand for state management

Commit Guidelines

• Use conventional commits: feat(scope): description
• Examples:
  • feat(backend): implement drug interaction checking
  • fix(medication): resolve adherence calculation bug
  • docs(readme): update quick start guide
  • test(auth): add refresh token rotation tests

Testing Guidelines

• Write tests for new features
• Test edge cases (empty inputs, null values, etc.)
• Use descriptive test names
• Mock external dependencies (OpenFDA API)
• Test both success and error paths

---

📚 Documentation Navigation

Quick Reference

• Main Documentation Index - Complete documentation overview
• Product Documentation - Project overview, roadmap, status
• Implementation Docs - Phase plans, specs, progress
• Testing Guide - Test scripts and results
• Deployment Guide - Deployment guides and scripts
• Development Workflow - Git workflow, CI/CD

For Specific Tasks

Task	Documentation
Add new API endpoint	Implementation Guide + code examples above
Deploy to production	Deployment Guide
Run tests	Testing Guide
Understand architecture	Product README
Check current status	STATUS.md
Review phase progress	Implementation README

---

🤖 AI Agent Specific Tips

Before Making Changes

1. Read the context: Check STATUS.md and Implementation README
2. Understand the phase: Know which phase is active (currently 2.8)
3. Check existing code: Look at similar implementations in backend/src/
4. Review tests: Check backend/tests/ for test patterns

When Implementing Features

1. Follow patterns: Use existing code as templates (see examples above)
2. Add tests: Write tests in backend/tests/ or inline with #[cfg(test)]
3. Update documentation: Add/update docs in docs/implementation/
4. Test thoroughly: Run cargo test, cargo clippy, and integration tests

When Debugging

1. Check logs: docker compose logs -f backend
2. Test API: Use scripts in docs/testing/
3. Verify MongoDB: mongosh to check data
4. Check recent changes: git log --oneline -10

Common Pitfalls to Avoid

1. Don't hardcode values - Use environment variables (see backend/src/config/mod.rs)
2. Don't skip tests - Always run tests before committing
3. Don't forget auth - Protected routes need JWT middleware
4. Don't ignore errors - Use ? operator and proper error handling
5. Don't break existing APIs - Check for existing endpoints before adding new ones

File Locations Quick Reference

• Add API handler: backend/src/handlers/
• Add model: backend/src/models/
• Add middleware: backend/src/middleware/
• Add service: backend/src/services/
• Add tests: backend/tests/
• Add config: backend/src/config/mod.rs
• Add frontend page: web/normogen-web/src/pages/
• Add frontend component: web/normogen-web/src/components/
• Add API service: web/normogen-web/src/services/api.ts
• Add types: web/normogen-web/src/types/api.ts

---

📞 Getting Help

Internal Resources

• Thoughts - Development notes and decisions
• Git History - Past changes and context
• Test Results - API test history

External Resources

• Axum Documentation: https://docs.rs/axum/
• MongoDB Rust Driver: https://docs.rs/mongodb/
• React Documentation: https://react.dev/
• Material-UI: https://mui.com/

---

🔄 Version Information

Current Versions:

• Rust: rustc 1.90.0 (1159e78c4 2025-09-14)

rustc 1.90.0 (1159e78c4 2025-09-14)

• Node: v20.20.0

v20.20.0

• Docker: Docker version 29.2.1, build a5c7197

Docker version 29.2.1, build a5c7197

Repository: origin ssh://git@gitea.soliverez.com.ar/alvaro/normogen.git (fetch)

origin ssh://git@gitea.soliverez.com.ar/alvaro/normogen.git (fetch)

Branch: git branch --show-current

---

✅ Checklist for AI Agents

Before starting work, ensure you:

• Read STATUS.md for current progress
• Reviewed Implementation README for phase context
• Understand the architecture (backend/frontend structure)
• Know which phase is active (currently 2.8)
• Have reviewed similar existing code
• Understand testing requirements

During work:

• Follow existing code patterns
• Write/update tests
• Run cargo test and cargo clippy
• Document changes in docs/implementation/
• Update relevant STATUS files

Before completing:

• All tests pass
• Code is formatted (cargo fmt)
• No clippy warnings
• Documentation updated
• Commit message follows conventions

---

This guide is maintained in: docs/AI_AGENT_GUIDE.md

Last updated: 2026-03-09
Maintained by: Project maintainers
For questions: Consult project documentation or create an issue