OpenClinica docker image

The OpenClinica Community edition is free and open source and is distributed under the GNU LGPL license.

This repository contains the Dockerfile, a startup script and the following instructions for running a Docker container which you can use to give OpenClinica a try. An image built with this Dockerfile is available on Docker Hub.

IMPORTANT: This image is meant for trying out OpenClinica and not meant for running a production server or for storing important study data.

Setup

0. Install Docker & docker compose

Follow the installation instructions for your host system
If you are running Docker on VirtualBox: the maximum RAM size can be adjusted through the user interface of VirtualBox (run it from the start menu, stop the virtual machine, change the configuration to e.g. 4096MB, close it and start the virtual machine using docker-machine)

1. Create a database init script

Create a file init-db.sh that adds a user and a database for OpenClinica to PostgreSQL:

#!/bin/sh
set -e
# Perform all actions as $POSTGRES_USER
export PGUSER="$POSTGRES_USER"

echo "Init openclinica db into $POSTGRES_DB"
"${psql[@]}" <<- 'EOSQL'
\dx;
  CREATE ROLE clinica LOGIN ENCRYPTED PASSWORD 'clinica' SUPERUSER NOINHERIT NOCREATEDB NOCREATEROLE;
  CREATE DATABASE openclinica WITH ENCODING='UTF8' OWNER=clinica;
EOSQL

2. Start a PostgreSQL database server

Modify where is the db-data folder to keep the postgresql data file on the OS

This expects the init-db.sh script residing in the current directory

...
  db:
    image: "postgres:9.5-alpine"
    environment:
      TZ: "UTC+7"
      POSTGRES_PASSWORD: "jollyfawn28"
      POSTGRES_INITDB_ARGS: "-E 'UTF-8' --locale=POSIX"
    ports:
      - "5432:5432"
    volumes:
      - ./db-data:/var/lib/postgresql/data
      - ./init-db.sh:/docker-entrypoint-initdb.d/init-openclinica.sh

start postgresql with docker-compose

docker-compose up -d

Please change the root database password

3. Start Tomcat serving OpenClinica and OpenClinica-ws

Adjust DB_HOST and passwords accordingly
The environment variables for log level and timezone are optional here.

  web:
    image: "dahoba/openclinica"
    environment:
      - TZ="UTC+7"
      - DB_TYPE=postgres
      - DB_HOST=db
      - DB_NAME=openclinica
      - DB_USER=clinica
      - DB_PASS=clinica
      - DB_PORT=5432
    volumes:
      - "./logs/tomcat-logs:/usr/local/tomcat/logs"
      - "./app-data/openclinica.data:/usr/local/tomcat/openclinica.data"
    ports:
      - "8080:8080"
    extra_hosts:
      - "usage.openclinica.com:127.0.0.1"
      - "designer13.openclinica.com:127.0.0.1"
    depends_on: 
      - db

4. Run OpenClinica

Open up http://<ip.of.your.host>/OpenClinica in your browser
First time login credentials: root / 12345678

Operation

To show the OpenClinica logs:

docker logs -f openclinica-docker_web_1

Build image from source

clone (Openclinica)[https://github.com/OpenClinica/OpenClinica]
clone this repo into OpenClinica folder as docker folder
cd OpenClinica/docker
modify the docker-compose.yml un-comment

     build:
       context: ../
       dockerfile: docker/Dockerfile

execute docker-compose build. This will take the source code to compile while building docker image.

dahoba/OpenClinica