Reprotech - Veterinary Biotechnology Platform

🚀 GitHub Codespace Quick Start

This repository is fully configured for GitHub Codespaces with automated setup and development tools.

One-Click Setup

1. Open in Codespace: Click the "Code" button → "Codespaces" → "Create codespace on main"
2. Wait for Setup: The devcontainer will automatically:
   • Install Python 3.11 and Node.js 18
   • Set up virtual environments
   • Install all dependencies
   • Configure the database with sample data
   • Set up VS Code extensions and tasks

🎯 Development URLs

Once the Codespace is running:

• Frontend: http://localhost:5174 (React + Vite + TypeScript)
• Backend: http://localhost:8002 (FastAPI + SQLAlchemy)
• API Documentation: http://localhost:8002/docs (Swagger UI)

🛠️ Available VS Code Tasks

Press Ctrl+Shift+P (or Cmd+Shift+P on Mac) and type "Tasks: Run Task":

• Start Both Servers: Starts both frontend and backend simultaneously
• Start Backend Server: FastAPI server on port 8002
• Start Frontend Server: React/Vite server on port 5174
• Setup Database: Initialize SQLite database with sample data
• Test API: Validate API functionality

📁 Project Structure

reprotech/
├── .devcontainer/          # Codespace configuration
│   ├── devcontainer.json   # Container settings
│   └── setup.sh           # Automated setup script
├── .vscode/               # VS Code configuration
│   ├── tasks.json         # Development tasks
│   ├── launch.json        # Debug configurations
│   └── settings.json      # Editor settings
├── scripts/               # Helper scripts
│   ├── start-dev.sh       # Start development environment
│   ├── test-env.sh        # Run environment tests
│   └── cleanup.sh         # Clean up processes and cache
├── reprotech-backend/     # FastAPI Backend
│   ├── app/              # Application code
│   │   ├── api/          # API routes and endpoints
│   │   ├── core/         # Core functionality (database, config)
│   │   ├── models/       # SQLAlchemy models
│   │   ├── schemas/      # Pydantic schemas
│   │   └── services/     # Business logic
│   ├── .env              # Environment variables
│   ├── requirements.txt  # Python dependencies
│   └── sample_data.db    # SQLite database
└── reprotech-frontend/    # React Frontend
    ├── src/              # Source code
    │   ├── components/   # Reusable UI components
    │   ├── modules/      # Feature modules (45+ vet biotech modules)
    │   ├── hooks/        # Custom React hooks
    │   └── utils/        # Utility functions
    ├── package.json      # Node.js dependencies
    └── vite.config.ts    # Vite configuration

� 45+ Veterinary Biotechnology Modules

The platform includes comprehensive modules for:

Animal Management

• Animal registration and profiles
• Health records and monitoring
• Breeding management
• Performance tracking

Laboratory Services

• Sample collection and tracking
• Laboratory test management
• Results processing and reporting
• Quality control

Genomic Analysis

• DNA sequencing workflows
• Genetic testing and analysis
• Breeding optimization
• Disease susceptibility screening

Biobanking

• Sample storage and inventory
• Chain of custody tracking
• Storage condition monitoring
• Sample retrieval systems

Research & Development

• Experimental design tools
• Data collection and analysis
• Research project management
• Collaboration tools

And many more...

🔧 Manual Commands

If you prefer manual control:

# Start development environment
./scripts/start-dev.sh

# Test the environment
./scripts/test-env.sh

# Clean up processes
./scripts/cleanup.sh

# Start backend only
cd reprotech-backend
source .venv/bin/activate
uvicorn app.main:app --reload --host 0.0.0.0 --port 8002

# Start frontend only
cd reprotech-frontend
npm run dev

🗄️ Database Information

• Type: SQLite (development) with PostgreSQL production support
• Sample Data: 2 customers, 4 animals with full veterinary profiles
• Authentication: Removed for development (all endpoints are public)

🔑 API Endpoints (No Auth Required for Development)

GET /api/v1/dev/customers/              # List all customers
GET /api/v1/dev/customers/{id}          # Get customer by ID
GET /api/v1/dev/customers/{id}/animals  # Get customer's animals
GET /api/v1/dev/animals/                # List all animals
GET /api/v1/dev/status                  # API status check

🐛 Debugging

• VS Code Debugger: Pre-configured for FastAPI debugging
• API Testing: Built-in test scripts validate environment
• Hot Reload: Both frontend and backend support hot reloading

🚧 Development Notes

• Authentication has been temporarily removed for development
• All API endpoints are publicly accessible
• Database uses SQLite for simplicity
• Frontend proxy configured to connect to backend automatically

📋 Next Steps

1. The environment will auto-start when you open the Codespace
2. Visit http://localhost:5174 to see the frontend
3. Visit http://localhost:8002/docs to explore the API
4. Start developing your veterinary biotechnology features!

🆘 Troubleshooting

If servers don't start automatically:

1. Open terminal in VS Code
2. Run ./scripts/test-env.sh to check setup
3. Run ./scripts/start-dev.sh to start servers
4. Check the VS Code terminal outputs for any errors

For any issues, check the terminal outputs or run the test script to diagnose problems.

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Happy Coding! 🧬🐾 - Veterinary Biotechnology Platform

A comprehensive veterinary biotechnology management system for advanced reproduction, genomic intelligence, and farm operations.

🚀 Quick Start

Prerequisites

• Node.js 18+ (for frontend)
• Python 3.11+ (for backend)
• Git (for version control)

Installation & Setup

1. Clone the repository

   git clone <repository-url>
   cd reprotech

2. Start the Backend

   cd reprotech-backend
   # Activate virtual environment
   .venv\Scripts\activate  # Windows
   # Install dependencies
   pip install -r requirements.txt
   # Start the server
   python -m uvicorn app.main:app --host 0.0.0.0 --port 8000 --reload

3. Start the Frontend

   cd reprotech-frontend
   # Install dependencies
   npm install
   # Start development server
   npm run dev

4. Access the Application

   • Frontend: http://localhost:5173
   • Backend API: http://localhost:8000
   • API Documentation: http://localhost:8000/docs

Test Users

• Admin: admin@reprotech.com / admin123
• Veterinarian: dr.smith@reprotech.com / vet123
• Lab Technician: tech@reprotech.com / tech123
• Customer: user@reprotech.com / user123

🏗️ Architecture

Frontend (React + TypeScript)

• Framework: React 19.1.0 with TypeScript
• Build Tool: Vite 7.0.0
• UI Library: Tailwind CSS + Radix UI
• State Management: React Context + Custom hooks
• Routing: React Router DOM 7.6.3
• Internationalization: i18next (Arabic/English)

Backend (FastAPI + Python)

• Framework: FastAPI 0.109.0
• Server: Uvicorn 0.27.0
• Authentication: JWT-based with role-based access control
• API Documentation: OpenAPI/Swagger
• Database: PostgreSQL (ready for integration)

📊 Module Overview

🧬 Reproduction & Genetics (15 modules)

• Advanced Reproduction: Session management and embryo tracking
• Fertilization: IVF/ICSI procedures and outcomes
• Genomic Intelligence: SNP analysis and breeding optimization
• Sample Management: Biological sample tracking with QR codes
• Semen Management: Collection, analysis, and storage
• Biobank: LN₂ tank management and cryopreservation
• OPU: Ovum Pick-Up procedures
• Breeding: Natural and artificial insemination
• Embryo Transfer: Transfer procedures and pregnancy monitoring
• Phenotype: Physical characteristics tracking
• SNP Analysis: Genetic marker analysis
• BeadChip Mappings: Genomic data management

🏥 Clinical & Laboratory (8 modules)

• Clinical Hub: Centralized clinical workflow management
• Ultrasound: Reproductive ultrasound examinations
• Laboratory: Lab procedures and equipment management
• Internal Medicine: Medical treatments and diagnostics
• Vaccinations: Vaccination schedules and records
• Lab Results: Test results and reporting
• Media Preparation: Culture media management
• Realtime Monitoring: Live system monitoring

💼 Business Operations (12 modules)

• Customers: CRM and customer relationship management
• Finance: Financial tracking and cost analysis
• Human Resources: Employee management and payroll
• Procurement: Supply chain and purchasing
• Inventory: Stock management and tracking
• Tender Management: Bid and contract management
• Data Integration: Cross-module data synchronization
• Settings: System configuration
• Admin: User and system administration
• Analytics Dashboard: Business intelligence
• AI Analytics: Machine learning insights
• Calendar: Scheduling and event management

🐄 Farm Management (6 modules)

• Animal Management: Comprehensive animal database
• Farm Management: Farm operations and planning
• Fattening Management: Growth tracking and optimization
• Milking Management: Dairy production tracking
• Farm Analytics: Farm performance metrics
• Farm Compliance: Regulatory compliance tracking

🔬 Analytics & Intelligence (4 modules)

• Integration Hub: Cross-module data integration
• Research: Research project management
• Inventory Analytics: Supply chain optimization
• Predictive Analytics: AI-powered forecasting

🔐 Authentication & Security

Role-Based Access Control

• Admin: Full system access and administration
• Veterinarian: Clinical and animal management operations
• Lab Technician: Laboratory and technical procedures
• Customer: Limited access to assigned animals and data

Security Features

• JWT-based authentication with refresh tokens
• Password hashing with bcrypt
• CORS configuration for secure cross-origin requests
• Input validation and sanitization
• Structured error handling

🌐 API Endpoints

Core Endpoints

• GET /health - System health check
• GET /api/v1/health - API health check
• POST /api/v1/auth/login - User authentication
• GET /api/v1/auth/me - Current user information
• GET /api/v1/customers - Customer management
• GET /api/v1/animals - Animal management

Module-Specific Endpoints

• Reproduction: /api/v1/reproduction/*
• Genomics: /api/v1/genomics/*
• Finance: /api/v1/finance/*
• HR: /api/v1/hr/*
• Laboratory: /api/v1/lab-results/*

🎨 User Interface Features

Modern Design

• Responsive Design: Mobile and tablet optimized
• Dark/Light Theme: Theme switching capability
• Internationalization: Arabic and English support
• Toast Notifications: Real-time user feedback
• Loading States: Professional loading indicators
• Error Boundaries: Graceful error handling

Navigation

• Smart Navigation: Auto-prioritizes current module group
• Role-Based Menu: Dynamic menu based on user role
• Breadcrumb Navigation: Clear navigation path
• Quick Actions: Context-sensitive action buttons

🚀 Development

Frontend Development

cd reprotech-frontend
npm install
npm run dev

Backend Development

cd reprotech-backend
# Activate virtual environment
.venv\Scripts\activate
pip install -r requirements.txt
python -m uvicorn app.main:app --reload

Testing

# Frontend tests
npm run test

# Backend tests
pytest

📦 Deployment

Docker Deployment

# Build and run with Docker Compose
docker-compose up -d

Manual Deployment

1. Build frontend: npm run build
2. Start backend: python -m uvicorn app.main:app --host 0.0.0.0 --port 8000
3. Serve frontend build files

📚 Documentation

• API Documentation: http://localhost:8000/docs
• Development Guide: REPROTECH_DEVELOPMENT_GUIDE.md
• Startup Guide: REPROTECH_STARTUP_GUIDE.md
• Backend Architecture: BACKEND_STRUCTURE_PLAN.md

🤝 Contributing

1. Fork the repository
2. Create a feature branch: git checkout -b feature-name
3. Make your changes
4. Commit your changes: git commit -m 'Add feature'
5. Push to the branch: git push origin feature-name
6. Submit a pull request

📄 License

This project is proprietary software developed for veterinary biotechnology applications.

🆘 Support

For technical support or questions:

• Email: dev@reprotech.com
• Documentation: Check the documentation files in the repository
• Issues: Create an issue in the repository

🎯 Roadmap

Phase 1: Core Infrastructure ✅

• Authentication system
• Basic CRUD operations
• Role-based access control

Phase 2: Advanced Features 🚧

• Database integration
• Real-time notifications
• Advanced analytics
• Mobile app development

Phase 3: AI Integration 📋

• Machine learning models
• Predictive analytics
• Automated workflows
• Genomic intelligence

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Reprotech - Advancing veterinary biotechnology through intelligent software solutions.