DeepPhe-Viz-v2

A visualization platform for DeepPhe cancer phenotype data.

Project Overview

DeepPhe-Viz is a web-based application designed to visualize and interact with cancer phenotype data processed by the DeepPhe system. It provides researchers and clinicians with an intuitive interface to explore complex datasets, facilitating better understanding and analysis of cancer phenotypes.

Features

• 📊 Interactive data visualization
• 🔍 Advanced filtering and search
• 💾 Direct SQLite database access (no IndexedDB)
• 🚀 Optimized performance with caching
• 📱 Responsive design
• 🔒 Secure deployment options

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Development

Prerequisites

• Node.js (v18.x or higher)
• npm (v8.x or higher)
• Modern web browser (Chrome, Firefox, Edge recommended)

Installation

1. Clone the repository:

git clone https://github.com/DeepPhe/DeepPhe-Viz-v2.git
cd DeepPhe-Viz-v2

2. Install dependencies:

npm install

3. Start the development server:

npm start

4. Visit http://localhost:3000/ to see the visualization.

5. To stop the server, press Ctrl + C in the terminal.

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Production Deployment

🐳 Docker Deployment (Recommended)

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

# View logs
docker-compose logs -f

# Stop the application
docker-compose down

Your app will be running at: http://localhost:3000 (or your server IP:3000)

🔧 Manual Docker Commands

# Build the Docker image
docker build -t deepphe-visualizer .

# Run the container
docker run -d -p 3000:3000 --name deepphe-viz deepphe-visualizer

# View logs
docker logs -f deepphe-viz

# Stop and remove
docker stop deepphe-viz && docker rm deepphe-viz

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Build for Production

npm run build

This creates an optimized production build in the build/ directory.

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Project Structure

Viz2/
├── public/                 # Static files
│   └── demopatients.sqlite # SQLite database
├── src/
│   ├── components/         # React components
│   ├── utils/
│   │   └── db/
│   │       └── sqlite_client.js  # SQLite database client
│   └── App.js
├── build/                  # Production build (generated)
├── server.js               # Express server
├── Dockerfile              # Docker configuration
└── docker-compose.yml      # Docker Compose setup

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Database

The application uses SQLite for data storage:

• File: demopatients.sqlite
• Location: public/ directory
• Access: Direct SQL queries via sql.js

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Testing

# Run unit tests
npm test

# Run SQLite client tests
npm test -- sqlite_client.test.js

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Scripts

Command	Description
npm start	Start development server
npm run build	Build for production
npm test	Run tests

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Environment Variables

Create a .env file for custom configuration:

PORT=3000
NODE_ENV=production

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Browser Support

• Chrome (latest)
• Firefox (latest)
• Safari (latest)
• Edge (latest)

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License

See LICENSE file for details.

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Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Run tests
5. Submit a pull request