Deployment Guide

This guide covers deploying SCIENTRY to both development and production environments, including proper configuration and setup.

Prerequisites

Docker and Docker Compose installed
Git for cloning the repository
Domain name (for production)
SSL certificate (for production)

Environment Configuration

.env File Setup

Create a .env file in the root directory with the following variables:

bash

# Database Configuration
DB_NAME=my-db
DB_USER=db-user
DB_PASS=db-password

# MongoDB Root Configuration
MONGO_INITDB_ROOT_USERNAME=root
MONGO_INITDB_ROOT_PASSWORD=root
MONGO_INITDB_DATABASE=admin

# MongoDB Data and Log Directories
MONGODB_DATA_DIR=/var/lib/mongodb-data
MONGODB_LOG_DIR=/dev/null

# Service Names (Docker Compose)
DB_HOST=LIMS_DB
DB_PORT=27017
API_HOST=lims_server
API_PORT=80

# Application Configuration
APP_NAME=LIMS
PROCESSES=4
THREADS=2

# Security
JWT_SECRET_KEY=your-secret-key-here

# Application Paths
BASE_PATH=/scientry
FILES_FOLDER=files

Environment Variables Explanation

Database Configuration

DB_NAME: Name of the database to use
DB_USER: Database user for application access. This will
DB_PASS: Database password for application access

When the app is launched the first time a user will be created using DB_USER AND DB_PASS

MongoDB Root Configuration

MONGO_INITDB_ROOT_USERNAME: Root username for MongoDB
MONGO_INITDB_ROOT_PASSWORD: Root password for MongoDB
MONGO_INITDB_DATABASE: Initial database name

Service Configuration

DB_HOST: Docker service name for the database
DB_PORT: MongoDB port (default: 27017)
API_HOST: Docker service name for the API server
API_PORT: Port for the API server

Application Settings

APP_NAME: Application name
PROCESSES: Number of worker processes
THREADS: Number of threads per process

Security

JWT_SECRET_KEY: Secret key for JWT token generation

Paths

BASE_PATH: Base URL path for the application (e.g., /scientry for https://domain.com/scientry)
FILES_FOLDER: Directory where uploaded files will be stored

Development Deployment

Using docker-compose-DEV.yml

The development configuration uses local builds and volume mounts for hot reloading.

1. Clone and Setup

bash

git clone https://github.com/your-repo/lims.git
cd lims

2. Configure .env for Development

bash

# Database Configuration
DB_NAME=lims_dev
DB_USER=dev_user
DB_PASS=dev_password

# MongoDB Root Configuration
MONGO_INITDB_ROOT_USERNAME=root
MONGO_INITDB_ROOT_PASSWORD=root
MONGO_INITDB_DATABASE=admin


DB_HOST=LIMS_DB
DB_PORT=27017
API_HOST=lims_server
API_PORT=80

# Application Configuration
APP_NAME=LIMS
PROCESSES=1
THREADS=1

# Security
JWT_SECRET_KEY=dev-secret-key

# Application Paths
BASE_PATH=
FILES_FOLDER=files

3. Start Development Environment

bash

# Start all services
docker-compose -f docker-compose-DEV.yml up -d

# View logs
docker-compose -f docker-compose-DEV.yml logs -f

# Stop services
docker-compose -f docker-compose-DEV.yml down

4. Development Features

Hot Reloading: Code changes are automatically reflected
Volume Mounts: Local files are mounted into containers
Debug Ports: Services are exposed on local ports
Development Database: Separate database for development

Development Docker Compose Configuration

The docker-compose-DEV.yml file includes:

yaml

version: '3'

services:
  lims_db:
    image: mongo
    container_name: "${DB_HOST}"
    env_file:
      - .env
    volumes:
     - ./mongo-init.sh:/docker-entrypoint-initdb.d/mongo-init.sh
     - mongodb-data:/var/lib/mongodb-data
    ports:
      - "27013:${DB_PORT}"

  lims_server:
    build: ./server
    container_name: "${API_HOST}"
    restart: always
    ports:
     - 5010:5000
    volumes:
      - ./server:/server
      - ./project-spec.json:/server/project-spec.json
      - ./files:/server/files
    env_file:
      - .env

  lims_client:
    build:
      context: ./client
      dockerfile: Dockerfile
      args:
        - BASE_PATH=$BASE_PATH
    container_name: "lims_client"
    restart: always
    volumes:
      - node_modules:/client/node_modules
    environment:
      - API_PORT=${API_PORT}
      - API_HOST=${API_HOST}
      - BASE_PATH=${BASE_PATH}
    ports:
        - "93:${API_PORT}"

volumes:
  mongodb-data:
  node_modules:

Production Deployment

Using docker-compose.yml

The production configuration uses pre-built images and optimized settings.

1. Server Setup

bash

git clone https://github.com/your-repo/lims.git
cd lims

2. Configure .env for Production

bash

# Database Configuration
DB_NAME=lims_prod
DB_USER=prod_user
DB_PASS=strong_production_password

# MongoDB Root Configuration
MONGO_INITDB_ROOT_USERNAME=root
MONGO_INITDB_ROOT_PASSWORD=strong_root_password
MONGO_INITDB_DATABASE=admin

# MongoDB Data and Log Directories
MONGODB_DATA_DIR=/data/lims-data
MONGODB_LOG_DIR=/var/log/mongodb

# Service Names
DB_HOST=LIMS_DB
DB_PORT=27017
API_HOST=lims_server
API_PORT=80

# Application Configuration
APP_NAME=LIMS
PROCESSES=4
THREADS=2

# Security
JWT_SECRET_KEY=very-strong-production-secret-key

# Application Paths
BASE_PATH=/lims
FILES_FOLDER=files

3. Production Docker Compose Configuration

The docker-compose.yml file includes:

yaml

version: '3'

services:
  lims_db:
    image: mongo:6.0
    container_name: "${DB_HOST}"
    env_file:
      - .env
    volumes:
     - /data/lims-data:/data/db
     - ./mongo-init.sh:/docker-entrypoint-initdb.d/mongo-init.sh
    ports:
      - "27013:${DB_PORT}"
    networks:
      - monstre

  lims_server:
    image: gitlab.linux.crg.es:5005/monstre/lims/lims_server
    container_name: ${API_HOST}
    restart: always
    volumes:
      - ./project-spec.json:/server/project-spec.json
      - /data/lims-files:/server/files
    env_file:
      - .env
    networks:
      - monstre

  lims_client:
    image: gitlab.linux.crg.es:5005/monstre/lims/lims_client
    labels:
      - "traefik.enable=true"
      - "traefik.http.routers.lims_client.rule=Host(`genome.crg.es`) && PathPrefix(`/lims`)"
      - "traefik.http.routers.lims_client.tls=true"
      - "traefik.http.routers.lims_client.entrypoints=web_https"
      - "traefik.http.services.lims_client.loadBalancer.server.port=80"
    environment:
      - API_PORT=${API_PORT}
      - API_HOST=${API_HOST}
      - BASE_PATH=${BASE_PATH}
    networks:
      - monstre

networks:
  monstre:
    external:
      name: monstre

4. Start Production Environment

bash

# Start all services
docker-compose up -d

# View logs
docker-compose logs -f

# Stop services
docker-compose down

5. Reverse Proxy Setup (Nginx)

For production without Traefik, create an Nginx configuration:

nginx

server {
    listen 80;
    server_name your-domain.com;
    return 301 https://$server_name$request_uri;
}

server {
    listen 443 ssl;
    server_name your-domain.com;

    ssl_certificate /path/to/your/certificate.crt;
    ssl_certificate_key /path/to/your/private.key;

    # Frontend
    location /lims {
        proxy_pass http://localhost:3000;
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
    }

    # API
    location /lims/api {
        proxy_pass http://localhost:5000;
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
    }
}

6. SSL Certificate

For production, use Let's Encrypt:

bash

sudo apt install certbot python3-certbot-nginx
sudo certbot --nginx -d your-domain.com

Documentation Deployment (GitHub Pages)

1. Build the Documentation

bash

cd docs
npm run docs:build

This creates a dist directory with the built documentation.

Getting Help

For deployment issues:

Check the logs: docker-compose logs or docker-compose -f docker-compose-DEV.yml logs
Review configuration: Verify .env file and Docker Compose files
Check documentation: Review the User Guide for application usage
Contact support: emilio.righi@crg.eu

Deployment Guide ​

Prerequisites ​

Environment Configuration ​

.env File Setup ​

Environment Variables Explanation ​

Database Configuration ​

When the app is launched the first time a user will be created using DB_USER AND DB_PASS ​

MongoDB Root Configuration ​

Service Configuration ​

Application Settings ​

Security ​

Paths ​

Development Deployment ​

Using docker-compose-DEV.yml ​

1. Clone and Setup ​

2. Configure .env for Development ​

3. Start Development Environment ​

4. Development Features ​

Development Docker Compose Configuration ​

Production Deployment ​

Using docker-compose.yml ​

1. Server Setup ​

2. Configure .env for Production ​

3. Production Docker Compose Configuration ​

4. Start Production Environment ​

5. Reverse Proxy Setup (Nginx) ​

6. SSL Certificate ​

Documentation Deployment (GitHub Pages) ​

1. Build the Documentation ​

Getting Help ​

Deployment Guide

Prerequisites

Environment Configuration

.env File Setup

Environment Variables Explanation

Database Configuration

When the app is launched the first time a user will be created using DB_USER AND DB_PASS

MongoDB Root Configuration

Service Configuration

Application Settings

Security

Paths

Development Deployment

Using docker-compose-DEV.yml

1. Clone and Setup

2. Configure .env for Development

3. Start Development Environment

4. Development Features

Development Docker Compose Configuration

Production Deployment

Using docker-compose.yml

1. Server Setup

2. Configure .env for Production

3. Production Docker Compose Configuration

4. Start Production Environment

5. Reverse Proxy Setup (Nginx)

6. SSL Certificate

Documentation Deployment (GitHub Pages)

1. Build the Documentation

Getting Help