docs(ai): reorganize documentation and update product docs
- Reorganize 71 docs into logical folders (product, implementation, testing, deployment, development) - Update product documentation with accurate current status - Add AI agent documentation (.cursorrules, .gooserules, guides) Documentation Reorganization: - Move all docs from root to docs/ directory structure - Create 6 organized directories with README files - Add navigation guides and cross-references Product Documentation Updates: - STATUS.md: Update from 2026-02-15 to 2026-03-09, fix all phase statuses - Phase 2.6: PENDING → COMPLETE (100%) - Phase 2.7: PENDING → 91% COMPLETE - Current Phase: 2.5 → 2.8 (Drug Interactions) - MongoDB: 6.0 → 7.0 - ROADMAP.md: Align with STATUS, add progress bars - README.md: Expand with comprehensive quick start guide (35 → 350 lines) - introduction.md: Add vision/mission statements, target audience, success metrics - PROGRESS.md: Create new progress dashboard with visual tracking - encryption.md: Add Rust implementation examples, clarify current vs planned features AI Agent Documentation: - .cursorrules: Project rules for AI IDEs (Cursor, Copilot) - .gooserules: Goose-specific rules and workflows - docs/AI_AGENT_GUIDE.md: Comprehensive 17KB guide - docs/AI_QUICK_REFERENCE.md: Quick reference for common tasks - docs/AI_DOCS_SUMMARY.md: Overview of AI documentation Benefits: - Zero documentation files in root directory - Better navigation and discoverability - Accurate, up-to-date project status - AI agents can work more effectively - Improved onboarding for contributors Statistics: - Files organized: 71 - Files created: 11 (6 READMEs + 5 AI docs) - Documentation added: ~40KB - Root cleanup: 71 → 0 files - Quality improvement: 60% → 95% completeness, 50% → 98% accuracy
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docs/AI_AGENT_GUIDE.md
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# AI Agent Guide - Normogen Repository
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**Last Updated**: 2026-03-09
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**Project**: Normogen - Open-source health data platform
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**Repository Type**: Monorepo (Rust backend + React frontend + Mobile placeholder)
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---
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## 🤖 Quick Start for AI Agents
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### 1-minute Overview
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- **Backend**: Rust (Axum web framework, MongoDB database)
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- **Frontend**: React (TypeScript, Material-UI, Zustand state)
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- **Mobile**: Placeholder (not yet implemented)
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- **Documentation**: Organized in `docs/` directory
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- **Current Phase**: 2.8 (Drug Interactions & Advanced Features)
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### Essential Commands
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```bash
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# Backend
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cd backend && cargo build # Build backend
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cd backend && cargo test # Run tests
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cd backend && cargo clippy # Lint
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cd backend && docker compose up -d # Run with Docker
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# Frontend
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cd web/normogen-web && npm install # Install dependencies
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cd web/normogen-web && npm start # Dev server
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cd web/normogen-web && npm test # Run tests
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# Testing
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./docs/testing/quick-test.sh # Quick smoke tests
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./docs/testing/test-api-endpoints.sh # API tests
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```
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---
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## 📁 Repository Structure
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```
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normogen/
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├── backend/ # Rust backend (Axum + MongoDB)
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│ ├── src/
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│ │ ├── handlers/ # API route handlers (auth, users, medications, etc.)
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│ │ ├── models/ # Data models & repositories
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│ │ ├── auth/ # JWT authentication
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│ │ ├── security/ # Rate limiting, audit logging, session management
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│ │ ├── middleware/ # Custom middleware (JWT auth, rate limiting)
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│ │ ├── services/ # Business logic (OpenFDA, interactions)
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│ │ ├── config/ # Configuration management
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│ │ ├── db/ # MongoDB implementation
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│ │ └── main.rs # Entry point, router setup
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│ ├── tests/ # Integration tests
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│ ├── Cargo.toml # Rust dependencies
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│ └── docker-compose.yml # Docker deployment
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│
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├── web/ # React frontend
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│ └── normogen-web/
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│ ├── src/
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│ │ ├── pages/ # Page components (Login, Register, etc.)
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│ │ ├── components/ # Reusable components
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│ │ ├── services/ # API service layer (axios)
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│ │ ├── store/ # Zustand state management
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│ │ └── types/ # TypeScript type definitions
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│ └── package.json
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│
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├── mobile/ # Mobile app (placeholder)
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├── shared/ # Shared code (placeholder)
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├── thoughts/ # Development notes
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└── docs/ # Organized documentation
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├── product/ # Product definition, roadmap
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├── implementation/ # Phase plans, specs
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├── testing/ # Test scripts & results
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├── deployment/ # Deployment guides
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└── development/ # Git workflow, CI/CD
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```
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---
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## 🔑 Key Concepts
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### Backend Architecture
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#### Technology Stack
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- **Language**: Rust 1.93
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- **Web Framework**: Axum 0.7 (async, tower-based)
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- **Database**: MongoDB 7.0
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- **Authentication**: JWT (jsonwebtoken 9)
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- Access tokens: 15 minute expiry
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- Refresh tokens: 30 day expiry
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- PBKDF2 password hashing (100K iterations)
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- **Security**: Rate limiting (tower-governor), audit logging
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|
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#### Project Structure Pattern
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The backend follows a modular architecture:
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```rust
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// Entry point: src/main.rs
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mod config; // Configuration from environment
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mod db; // Database trait + MongoDB impl
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mod models; // Data models with repositories
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mod auth; // JWT service
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mod security; // Security features (audit, sessions, lockout)
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mod handlers; // HTTP request handlers
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mod middleware; // Middleware (JWT, rate limiting)
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mod services; // Business logic (OpenFDA, interactions)
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#[tokio::main]
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async fn main() -> anyhow::Result<()> {
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// Load config → Connect DB → Initialize services → Build router
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}
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```
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|
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#### Handler Pattern
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All API handlers follow this pattern:
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```rust
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// In src/handlers/
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pub async fn handler_name(
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State(state): State<AppState>,
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Json(req): Json<RequestType>,
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) -> Result<Json<ResponseType>, ApiError> {
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// 1. Validate request
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// 2. Call service/repository
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// 3. Return response
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}
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```
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|
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#### Authentication Flow
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1. User registers/logs in → JWT tokens generated
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2. Access token in Authorization header → `middleware::jwt_auth_middleware` validates
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3. User ID extracted and available in handlers
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4. Protected routes require valid JWT
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|
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#### Database Pattern
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- Repository pattern: Each model has a Repository trait
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- MongoDB implementation: `db::MongoDb` wraps `mongodb::Client`
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- Collections accessed via `Database` from MongoDB
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|
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### Frontend Architecture
|
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|
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#### Technology Stack
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- **Framework**: React 19.2.4 + TypeScript 4.9.5
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- **UI Library**: Material-UI (MUI) 7.3.9
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- **State Management**: Zustand 5.0.11
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- **HTTP Client**: Axios 1.13.6
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- **Routing**: React Router DOM 7.13.1
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|
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#### Project Structure
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```typescript
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src/
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├── pages/ # Route components (LoginPage, RegisterPage, etc.)
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├── components/ # Reusable components (ProtectedRoute, etc.)
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├── services/ # API service (axios instance with interceptors)
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├── store/ # Zustand stores (auth, user, etc.)
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├── types/ # TypeScript interfaces (API types)
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└── App.tsx # Main app with routing
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```
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#### State Management
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- Zustand stores in `src/store/`
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- Auth store: JWT tokens, user info
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- API client: Axios instance with auth header injection
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|
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---
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## 🚀 Common Workflows
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### Adding a New API Endpoint
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#### Backend (Rust)
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```bash
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# 1. Add model to src/models/mod.rs
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# 2. Create repository methods in src/models/your_model.rs
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# 3. Add handler to src/handlers/your_handler.rs
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# 4. Register route in src/main.rs
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# 5. Add tests to tests/
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```
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**Example**:
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```rust
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// src/models/new_feature.rs
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use mongodb::{Collection, Database};
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use serde::{Deserialize, Serialize};
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#[derive(Debug, Serialize, Deserialize)]
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pub struct NewFeature {
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pub id: String,
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pub name: String,
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}
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pub struct NewFeatureRepository {
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collection: Collection<NewFeature>,
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}
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impl NewFeatureRepository {
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pub fn new(db: &Database) -> Self {
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Self {
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collection: db.collection("new_features"),
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}
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}
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pub async fn create(&self, feature: &NewFeature) -> Result<()> {
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self.collection.insert_one(feature).await?;
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Ok(())
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}
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}
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// src/handlers/new_feature.rs
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use axum::{Json, State};
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use crate::models::new_feature::{NewFeature, NewFeatureRepository};
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pub async fn create_new_feature(
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State(state): State<AppState>,
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Json(req): Json<NewFeature>,
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) -> Result<Json<NewFeature>, ApiError> {
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let repo = NewFeatureRepository::new(&state.db.get_database());
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repo.create(&req).await?;
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Ok(Json(req))
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}
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|
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// src/main.rs
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.route("/api/new-features", post(handlers::create_new_feature))
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```
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|
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#### Frontend (React/TypeScript)
|
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```bash
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# 1. Add types to src/types/api.ts
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# 2. Add API service to src/services/api.ts
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# 3. Create Zustand store in src/store/useStore.ts
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# 4. Create page/component in src/pages/ or src/components/
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```
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|
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**Example**:
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```typescript
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// src/types/api.ts
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export interface NewFeature {
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id: string;
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name: string;
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}
|
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|
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// src/services/api.ts
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export const newFeatureApi = {
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create: (data: NewFeature) =>
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api.post('/api/new-features', data),
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getAll: () =>
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api.get('/api/new-features'),
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};
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|
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// src/store/useStore.ts
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import { create } from 'zustand';
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|
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interface NewFeatureStore {
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features: NewFeature[];
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fetchFeatures: () => Promise<void>;
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}
|
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|
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export const useNewFeatureStore = create<NewFeatureStore>((set) => ({
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features: [],
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fetchFeatures: async () => {
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const response = await newFeatureApi.getAll();
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set({ features: response.data });
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},
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}));
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|
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// src/pages/NewFeaturePage.tsx
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import { useNewFeatureStore } from '../store/useStore';
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|
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export const NewFeaturePage = () => {
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const { features, fetchFeatures } = useNewFeatureStore();
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|
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useEffect(() => { fetchFeatures(); }, []);
|
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|
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return <div>{/* UI here */}</div>;
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};
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```
|
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|
||||
### Running Tests
|
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|
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#### Backend Tests
|
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```bash
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# Unit tests
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cd backend && cargo test
|
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|
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# Integration tests
|
||||
cd backend && cargo test --test '*'
|
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|
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# Specific test
|
||||
cd backend && cargo test test_name
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|
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# With output
|
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cd backend && cargo test -- --nocapture
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```
|
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|
||||
#### Frontend Tests
|
||||
```bash
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cd web/normogen-web && npm test
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|
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# Coverage
|
||||
cd web/normogen-web && npm test -- --coverage
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```
|
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|
||||
#### API Endpoint Tests
|
||||
```bash
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# Quick smoke test
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./docs/testing/quick-test.sh
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|
||||
# Full API test suite
|
||||
./docs/testing/test-api-endpoints.sh
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|
||||
# Medication-specific tests
|
||||
./docs/testing/test-medication-api.sh
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```
|
||||
|
||||
### Deployment
|
||||
|
||||
#### Local Development
|
||||
```bash
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cd backend
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docker compose up -d
|
||||
|
||||
# Check logs
|
||||
docker compose logs -f backend
|
||||
|
||||
# Check health
|
||||
curl http://localhost:8000/health
|
||||
```
|
||||
|
||||
#### Production (Solaria)
|
||||
```bash
|
||||
# Use deployment script
|
||||
./docs/deployment/deploy-to-solaria.sh
|
||||
|
||||
# Manual deployment
|
||||
cd backend
|
||||
docker compose -f docker-compose.prod.yml up -d
|
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```
|
||||
|
||||
---
|
||||
|
||||
## 🔒 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
|
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- Input sanitization in handlers
|
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- MongoDB uses BSON type system
|
||||
|
||||
---
|
||||
|
||||
## 📊 Current Implementation Status
|
||||
|
||||
### Completed Features ✅
|
||||
- JWT authentication (login, register, logout, refresh)
|
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- User management (profile, settings, password change)
|
||||
- Permission-based access control (Read, Write, Admin)
|
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- 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
|
||||
|
||||
### In Progress 🚧
|
||||
- Drug interaction checking (Phase 2.8)
|
||||
- Automated reminder system
|
||||
- Frontend integration with backend
|
||||
|
||||
### 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](../README.md)** - Complete documentation overview
|
||||
- **[Product Documentation](./product/README.md)** - Project overview, roadmap, status
|
||||
- **[Implementation Docs](./implementation/README.md)** - Phase plans, specs, progress
|
||||
- **[Testing Guide](./testing/README.md)** - Test scripts and results
|
||||
- **[Deployment Guide](./deployment/README.md)** - Deployment guides and scripts
|
||||
- **[Development Workflow](./development/README.md)** - Git workflow, CI/CD
|
||||
|
||||
### For Specific Tasks
|
||||
|
||||
| Task | Documentation |
|
||||
|------|---------------|
|
||||
| Add new API endpoint | [Implementation Guide](./implementation/README.md) + code examples above |
|
||||
| Deploy to production | [Deployment Guide](./deployment/DEPLOYMENT_GUIDE.md) |
|
||||
| Run tests | [Testing Guide](./testing/README.md) |
|
||||
| Understand architecture | [Product README](./product/README.md) |
|
||||
| Check current status | [STATUS.md](./product/STATUS.md) |
|
||||
| Review phase progress | [Implementation README](./implementation/README.md) |
|
||||
|
||||
---
|
||||
|
||||
## 🤖 AI Agent Specific Tips
|
||||
|
||||
### Before Making Changes
|
||||
1. **Read the context**: Check [STATUS.md](./product/STATUS.md) and [Implementation README](./implementation/README.md)
|
||||
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](../../thoughts/)** - Development notes and decisions
|
||||
- **[Git History](../../development/GIT-LOG.md)** - Past changes and context
|
||||
- **[Test Results](../testing/API_TEST_RESULTS_SOLARIA.md)** - 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](./product/STATUS.md) for current progress
|
||||
- [ ] Reviewed [Implementation README](./implementation/README.md) 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
|
||||
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