/xnat-docker-compose

Build an XNAT server configuration with Docker Compose

Primary LanguageShell

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

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