Dockerized XNAT

Use this repository to quickly deploy an XNAT instance on docker.

Introduction

This repository contains files to bootstrap XNAT deployment. The build creates five containers:

• Tomcat + XNAT: The XNAT web application
• Postgres: The XNAT database
• nginx: Web proxy sitting in front of XNAT
• cAdvisor: Gathers statistics about all the other containers
• Prometheus: Monitoring and alerts

Prerequisites

• docker
• docker-compose (Which is installed along with docker if you download it from their site)

Usage

1. Clone the xnat-docker-compose repository.

2. Configurations: The default configuration is sufficient to run the deployment. The following files can be modified if you want to change the default configuration

   • docker-compose.yml: How the different containers are deployed.
   • postgres/XNAT.sql: Database configuration. Mainly used to customize the database user or password. See Configuring PostgreSQL for XNAT.
   • tomcat/Dockerfile: Builds the tomcat image, into which the XNAT war will be deployed.
   • tomcat/setenv.sh: Tomcat's launch arguments, set through the JAVA_OPTS environment variable.
   • tomcat/tomcat-users.xml: Tomcat manager settings.
   • tomcat/xnat-conf.properties: XNAT database configuration properties. There is a default version
   • prometheus/prometheus.yaml: Prometheus configuration

3. Start the system

    $ cd containerized-xnat
    $ docker-compose up -d
   

4. Download latest XNAT WAR

    wget --quiet --no-cookies https://bintray.com/nrgxnat/applications/download_file?file_path=xnat-web-1.7.4.war -O webapps/xnat.war
   

Your XNAT will soon be available at http://localhost/xnat.

Troubleshooting

• Get a shell in a running container:

  To list all containers and to get container id run

  docker ps

  To get into a running container

  `docker exec -it <container ID> bash`
  

• Read Tomcat logs:

  docker exec -it <container id for xnatdocker_xnat-web_1 > tail -f /opt/tomcat/logs/catalina.2017-07-28.log

• Bring all the instances down by running

  docker-compose down --rmi all (this will bring down all container and remove all the images)

• Bring XNAT instance up again

  docker-compose up -d

Monitoring

• Browse to http://localhost:9090/graph

  To view a graph of total cpu usage for each container (nginx/tomcat/postgres.cAdvisor/Prometheus) execute the following query in the query box container_cpu_usage_seconds_total{container_label_com_docker_compose_project="xnatdocker"}

• Browse to http://localhost:8082/docker/

  Docker containers running on this host are listed under Subcontainers

  Click on any subcontainer to view its metrics