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. It is highly recommended to change the login from "admin" with password "admin" to the server if it is going live.
   • tomcat/xnat-conf.properties: XNAT database configuration properties. There is a default version
   • prometheus/prometheus.yaml: Prometheus configuration

3. Start the system

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

Note that at this point, if you go to localhost/xnat you won't see a working web application. It takes upwards of a minute to initialize the database, and you can follow progress by reading the docker compose log of the server:

docker-compose logs -f --tail=20 xnat-web
Attaching to xnatdockercompose_xnat-web_1
xnat-web_1    | INFO: Starting Servlet Engine: Apache Tomcat/7.0.82
xnat-web_1    | Oct 24, 2017 3:17:02 PM org.apache.catalina.startup.HostConfig deployWAR
xnat-web_1    | INFO: Deploying web application archive /opt/tomcat/webapps/xnat.war
xnat-web_1    | Oct 24, 2017 3:17:14 PM org.apache.catalina.startup.TldConfig execute
xnat-web_1    | INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
xnat-web_1    | SOURCE: /opt/tomcat/webapps/xnat/
xnat-web_1    | ===========================
xnat-web_1    | New Database -- BEGINNING Initialization
xnat-web_1    | ===========================
xnat-web_1    | ===========================
xnat-web_1    | Database initialization complete.
xnat-web_1    | ===========================
xnat-web_1    | Oct 24, 2017 3:18:27 PM org.apache.catalina.startup.HostConfig deployWAR
xnat-web_1    | INFO: Deployment of web application archive /opt/tomcat/webapps/xnat.war has finished in 84,717 ms
xnat-web_1    | Oct 24, 2017 3:18:27 PM org.apache.coyote.AbstractProtocol start
xnat-web_1    | INFO: Starting ProtocolHandler ["http-bio-8080"]
xnat-web_1    | Oct 24, 2017 3:18:27 PM org.apache.coyote.AbstractProtocol start
xnat-web_1    | INFO: Starting ProtocolHandler ["ajp-bio-8009"]
xnat-web_1    | Oct 24, 2017 3:18:27 PM org.apache.catalina.startup.Catalina start
xnat-web_1    | INFO: Server startup in 84925 ms

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

You can also grab the name and put it into ane environment variable:

$ NAME=$(docker ps -aqf "name=xnatdockercompose_xnat-web")
$ echo $NAME
42d07bc7710b

To get into a running container

docker exec -it <container ID> bash
docker exec -it $NAME bash

Read Tomcat logs

List available logs

$ docker exec -it $NAME ls  /opt/tomcat/logs/

catalina.2017-10-24.log      localhost_access_log.2017-10-24.txt
host-manager.2017-10-24.log  manager.2017-10-24.log
localhost.2017-10-24.log

View a particular log, if you don't want to use docker-compose.

docker exec -it $NAME cat /opt/tomcat/logs/catalina.2017-10-24.log

Controlling Instances

Stop Instances

Bring all the instances down (this will bring down all container and remove all the images) by running

docker-compose down --rmi all

Bring up instances

This will bring all instances up again. The -d means "detached" so you won't see any output to the terminal.

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