Docker & NPM Deployment¶

This page explains how to deploy Phentrieve using Docker for the backend and NPM for frontend development.

Prerequisites¶

Docker and Docker Compose installed
Node.js and NPM installed (for frontend development)
Git for cloning the repository

Backend Deployment with Docker¶

Step 1: Clone the Repository¶

git clone https://github.com/berntpopp/phentrieve.git
cd phentrieve

Step 2: Configure Environment¶

Copy the example environment file:

cp .env.docker.example .env.docker

Edit the .env.docker file to configure:

PHENTRIEVE_HOST_DATA_DIR: Host directory for storing data
API_PORT: Port for the API (default: 8000)
Other settings as needed

Step 3: Build and Start the API Container¶

docker-compose up -d api

This will: 1. Build the API Docker image 2. Start the API container 3. Expose the API on the configured port

Step 4: Prepare Data and Build Indexes¶

# Enter the API container
docker-compose exec api bash

# Inside the container, prepare data and build indexes
phentrieve data prepare
phentrieve index build --model-name "FremyCompany/BioLORD-2023-M"

# Exit the container
exit

Frontend Development with NPM¶

For frontend development, you can use NPM directly without Docker:

Step 1: Install Frontend Dependencies¶

cd frontend
npm install

Step 2: Configure Frontend Environment¶

Create a .env file in the frontend directory:

VUE_APP_API_URL=http://localhost:8000

Step 3: Start Development Server¶

npm run serve

This will start a development server with hot-reloading at http://localhost:8080.

Building Frontend for Production¶

When you're ready to build the frontend for production:

cd frontend
npm run build

This will generate production files in the dist directory, which can be served with any web server.

Combined Docker Deployment¶

For a full deployment using Docker for both backend and frontend:

# Build and start all containers
docker-compose up -d

# Prepare data and build indexes
docker-compose exec api bash -c "phentrieve data prepare && phentrieve index build --model-name \"FremyCompany/BioLORD-2023-M\""

This will: 1. Build and start the API container 2. Build and start the frontend container with Nginx 3. Configure networking between the containers

Updating the Deployment¶

To update your deployment:

# Pull the latest code
git pull

# Rebuild and restart containers
docker-compose down
docker-compose up -d --build