Lab Management and Collaboration System

A comprehensive full-stack application for managing research laboratories, researchers, and collaborations with advanced analytics and AI-powered features.

🚀 Features

Backend

FastAPI-based REST API with automatic OpenAPI documentation
PostgreSQL database with SQLAlchemy ORM
JWT authentication for secure user management
Document processing (PDF, DOCX, TXT) with AI extraction
Email integration for lab communications
CORS support for frontend integration

Frontend

React 19 with modern hooks and functional components
Chart.js for interactive data visualizations
Tailwind CSS 4.0 for responsive, modern UI
React Router for seamless navigation
Dark mode support with theme persistence
Real-time charts for analytics dashboard

Key Modules

📊 Dashboard: Overview of labs, researchers, and projects
📈 Analytics: Advanced insights with interactive charts
🔬 Labs Management: CRUD operations with document upload
📧 Email System: Communication management
👤 User Profile: Personalized settings and preferences

📋 Prerequisites

Python 3.8+
Node.js 16+ and npm
PostgreSQL 12+
Git

🛠️ Installation & Setup

1. Clone the Repository

git clone https://github.com/ScientistSameer/History-of-Lab-Records
cd History-of-Lab-Records

2. Install Backend Dependencies

# From project root
pip install -r backend/requirements.txt

3. Install Frontend Dependencies

# From project root
npm install

4. Environment Configuration

Create a .env file in the project root:

# Database
DATABASE_URL=postgresql://username:password@localhost:5432/lab_management

# Security
SECRET_KEY=your-secret-key-here
ALGORITHM=HS256
ACCESS_TOKEN_EXPIRE_MINUTES=30

# AI/API Keys (optional)
GOOGLE_API_KEY=your-google-api-key
OPENAI_API_KEY=your-openai-key

# Email Configuration (optional)
SMTP_SERVER=smtp.gmail.com
SMTP_PORT=587
SMTP_USERNAME=your-email@gmail.com
SMTP_PASSWORD=your-app-password

# CORS
ALLOWED_ORIGINS=http://localhost:5173,http://localhost:3000

🚀 Running the Application

Quick Start (Recommended)

From the project root directory:

# Terminal 1: Start Backend from root
python -m uvicorn backend.app.main:app --reload --port 8001

# Terminal 2: Start Frontend (in a new terminal) from root
npm run dev

The application will be available at:

Frontend: http://localhost:5173
Backend API: http://localhost:8001
API Documentation: http://localhost:8001/docs

Alternative Commands

Backend:

# From project root
python -m uvicorn backend.app.main:app --reload --port 8001

# With hot reload
python -m uvicorn backend.app.main:app --reload --port 8001 --log-level debug

Frontend:

# From project root
npm run dev

# Build for production
npm run build

# Preview production build
npm run preview

📁 Project Structure

History-of-Lab-Records/
├── backend/                         # FastAPI server root
│   ├── app/                         # Main application logic
│   │   ├── routers/                 # API route handlers
│   │   │   ├── __init__.py          # Router package initialization
│   │   │   ├── collaboration_ai.py  # AI suggestion routes
│   │   │   ├── collaboration.py     # Lab networking routes
│   │   │   ├── doc_ingest.py        # Document processing routes
│   │   │   ├── ideal_lab.py         # Main lab management
│   │   │   ├── labs.py              # External lab directory
│   │   │   ├── researchers.py       # Staff management routes
│   │   │   └── users.py             # User profile routes
│   │   ├── services/                # Business logic layer
│   │   │   └── collaboration_ai.py  # AI processing logic
│   │   ├── __init__.py              # App package initialization
│   │   ├── auth.py                  # JWT authentication logic
│   │   ├── crud.py                  # Database create-read-update-delete
│   │   ├── database.py              # SQLAlchemy connection setup
│   │   ├── email.py                 # Mail service configuration
│   │   ├── models.py                # Database SQL tables
│   │   ├── schemas.py               # Pydantic data validation
│   │   └── main.py                  # Backend entry point
│   ├── __init__.py                  # Backend package initialization
│   ├── reset_db.py                  # Database clear script
│   ├── seed.py                      # Initial data population
│   └── requirements.txt             # Python backend dependencies
│
├── node_modules/                    # Installed frontend packages
├── other labs/                      # Raw document storage
│   ├── lab1.docx                    # Sample Word document
│   ├── lab1.pdf                     # Sample PDF document
│   ├── lab1.txt                     # Sample text file
│   ├── lab2.txt                     # Research data file
│   ├── lab3.txt                     # Lab profile data
│   ├── lab4.txt                     # Research interest data
│   └── lab5.txt                     # Collaboration history file
│
├── public/                          # Static public assets
│   ├── _redirects                   # Netlify routing rules
│
├── src/                             # React frontend source
│   ├── api/                         # Frontend API layer
│   │   ├── api/                     # Service-specific calls
│   │   │   ├── auth.js              # Login/Register API functions
│   │   │   ├── client.js            # Axios/Fetch base configuration
│   │   │   ├── collaboration_ai.js  # AI feature endpoints
│   │   │   ├── collaboration.js     # Messaging API functions
│   │   │   ├── emails.js            # Email service endpoints
│   │   │   ├── ideal_lab.js         # Core lab endpoints
│   │   │   ├── labs.js              # Directory API functions
│   │   │   ├── researchers.js       # Researcher data endpoints
│   │   │   └── users.js             # User data endpoints
│   ├── charts/                      # Chart.js components
│   ├── components/                  # Reusable UI components
│   ├── css/                         # Global Tailwind styles
│   ├── images/                      # Image asset storage
│   ├── pages/                       # Page view components
│   ├── partials/                    # Layout components
│   ├── utils/                       # Utility functions
│   ├── App.jsx                      # Main app component
│   ├── favicon.svg                  # Browser tab icon
│   └── main.jsx                     # React entry point
│
├── .env                             # Environment variables (root)
├── .env.example                     # Environment template file
├── .gitignore                       # Git excluded files
├── atlas.db                         # SQLite database file
├── index.html                       # HTML entry point
├── LICENSE                          # Project license file
├── package-lock.json                # NPM lock file
├── package.json                     # Frontend dependencies
├── pnpm-lock.yaml                   # PNPM lock file
├── postcss.config.cjs               # PostCSS configuration
├── PROJECT_STRUCTURE.md             # Detailed directory map
├── QUICK_START.md                   # Installation guide summary
├── README.md                        # General project documentation
└── vite.config.js                   # Vite configuration

🔧 Configuration Files

Root Level Configuration

package.json: Frontend dependencies and scripts vite.config.js: Vite bundler configuration postcss.config.cjs: PostCSS and Tailwind setup tailwind.config.js: Tailwind CSS customization .env: Environment variables (PROJECT ROOT)

Backend Configuration

backend/requirements.txt: Python dependencies

📚 API Documentation

Once the backend is running, visit:

Swagger UI: http://localhost:8001/docs
ReDoc: http://localhost:8001/redoc

Main Endpoints

Authentication:

POST /users/register - Register new user
POST /users/login - Login and get JWT token
GET /auth/me - Get current user info

Labs:

GET /labs/ - List all labs
POST /labs/ - Create new lab
PUT /labs/{lab_id} - Update lab details
DELETE /labs/{lab_id} - Delete lab

IDEAL Lab (Management):

GET /ideal-lab/ - Get details of the IDEAL Lab
PUT /ideal-lab/ - Update IDEAL lab details

Researchers:

GET /researchers/ - List all researchers
POST /researchers/ - Add a new researcher
GET /researchers/by-lab/{lab_id} - Get researchers assigned to a specific lab
GET /researchers/summary - Get statistical summary of researchers

Collaboration & AI:

GET /collaboration/suggestions - Get AI-driven collaboration suggestions
POST /collaboration/send-email - Send collaboration email to another lab

Document Processing:

POST /ingest/document - Extract lab info from document

General:

GET / - API health check / Root

🎨 UI Features

Dashboard

Real-time metrics cards
Interactive charts (doughnut, line, bar)
Lab distribution by domain
Researcher growth trends
AI-powered insights

Analytics

Advanced data visualizations
Workload distribution
Equipment level analysis
Resource utilization insights
Top performing labs

Labs Management

Grid and table view modes
Advanced search and filtering
Document upload for auto-extraction
Full lab profile management
Collaboration tracking

🔒 Security

JWT-based authentication
Password hashing with bcrypt
CORS configuration for frontend
SQL injection prevention via ORM
Environment-based secrets management

📦 Dependencies

Backend

FastAPI: Web framework
SQLAlchemy: ORM
Pydantic: Data validation
python-jose: JWT handling
passlib: Password hashing
python-multipart: File uploads
python-docx: DOCX processing
PyPDF2: PDF processing

Frontend

React 19: UI library
Chart.js: Data visualization
React Router: Navigation
Axios: HTTP client
Tailwind CSS: Styling
Vite: Build tool

🐛 Troubleshooting

Backend Issues

Database Connection Error:

# Check PostgreSQL is running
sudo service postgresql status

# Verify credentials in .env (root directory)
# Ensure database exists

Port Already in Use:

# Use different port
python -m uvicorn backend.app.main:app --reload --port 8002

Module Import Errors:

# Ensure you're running from project root
# Reinstall dependencies
pip install -r backend/requirements.txt

Frontend Issues

Module Not Found:

# From project root
rm -rf node_modules package-lock.json
npm install

CORS Errors:

Ensure backend CORS is configured for http://localhost:5173
Check backend/app/main.py CORS settings
Verify .env has correct ALLOWED_ORIGINS

📝 Development Workflow

Create Feature Branch

git checkout -b feature/your-feature-name

Make Changes
- Backend: Update models, add endpoints in backend/app/
- Frontend: Create components, update pages in src/
Test Locally
- Run backend: python -m uvicorn backend.app.main:app --reload --port 8001
- Run frontend: npm run dev
- Test all affected features

Commit Changes

git add .
git commit -m "feat: description of changes"

Push and Create PR

git push origin feature/your-feature-name

🚀 Deployment

Backend (Railway/Heroku/DigitalOcean)

# Set environment variables from .env
# Configure database URL
# Deploy using platform CLI or Git integration

Frontend (Vercel/Netlify)

# Build production bundle
npm run build

# Deploy dist folder
# Configure build command: npm run build
# Configure output directory: dist

🤝 Contributing

Fork the repository
Create a feature branch
Commit your changes
Push to the branch
Open a Pull Request

📄 License

This project is licensed under the MIT License.

👥 Authors

Sameer Babar

🙏 Acknowledgments

Tailwind CSS for the design system
Chart.js for visualization components
FastAPI team for excellent documentation
React community for best practices

📞 Support

For issues and questions:

Create an issue on GitHub
Email: smeer.py@gmail.com

Made with ❤️ by Sameer Babar

Name		Name	Last commit message	Last commit date
Latest commit History 11 Commits
backend		backend
other labs		other labs
public		public
src		src
.env.example		.env.example
.gitignore		.gitignore
LICENSE		LICENSE
PROJECT_STRUCTURE.md		PROJECT_STRUCTURE.md
QUICK_START.md		QUICK_START.md
README.md		README.md
index.html		index.html
package-lock.json		package-lock.json
package.json		package.json
pnpm-lock.yaml		pnpm-lock.yaml
postcss.config.cjs		postcss.config.cjs
vite.config.js		vite.config.js

Folders and files

Latest commit

History

Repository files navigation

Lab Management and Collaboration System

🚀 Features

Backend

Frontend

Key Modules

📋 Prerequisites

🛠️ Installation & Setup

1. Clone the Repository

2. Install Backend Dependencies

3. Install Frontend Dependencies

4. Environment Configuration

🚀 Running the Application

Quick Start (Recommended)

Alternative Commands

📁 Project Structure

🔧 Configuration Files

Root Level Configuration

Backend Configuration

📚 API Documentation

Main Endpoints

🎨 UI Features

Dashboard

Analytics

Labs Management

🔒 Security

📦 Dependencies

Backend

Frontend

🐛 Troubleshooting

Backend Issues

Frontend Issues

📝 Development Workflow

🚀 Deployment

Backend (Railway/Heroku/DigitalOcean)

Frontend (Vercel/Netlify)

🤝 Contributing

📄 License

👥 Authors

🙏 Acknowledgments

📞 Support

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