XNAT Installation Overview

XNAT:

XNAT is a Java web application, written in Java. Apache Tomcat is an open-source server for dynamic Java web applications. XNAT relies on Java, Apache Tomcat 9, Postgresql and Nginx.

Using this xnat-setup script, XNAT is deployed as a docker stack. 3 docker containers run together in a network. The three base images are:

Tomcat/JDK - Tomcat version 9 / JDK 21 - Docker image: tomcat:9.0.115-jdk21-temurin-noble
Postgresql - Version: 16 - Docker image: postgres:16
nginx:stable-alpine

During the build process, the latest versions of these images are pulled from https://hub.docker.com/ and new Docker images are created and run as docker containers as part of a docker stack. During the build process, a file docker-compose.yml is created that contains the resources and information regarding the 3 containers that run based on the images created.

During the build process, XNAT is downloaded as a .war file, for example xnat.war. This is a compressed file containing the web application. This is placed in the folder inside of the tomcat:

/usr/local/tomcat/webapps/ROOT

This is the location inside the Tomcat Docker container filesystem, and not on the host filesystem.

Postgresql:

Postgresql is the database backend of XNAT. It stores all the data for XNAT. The database name is xnat.

Nginx:

Nginx is a server used as a front-end proxy - it manages the SSL certificates and routes traffic towards the Tomcat web server, which hosts XNAT.

UFW / iptables:

Iptables is the Linux firewall software. iptables can be tricky to configure. UFW (Uncomplicated Firewall) is a tool to ease the configuration of iptables. An example of a UFW command:

ufw allow https

This is DISABLED by default. If running inside Docker, install UFW on your host computer and configure the firewall.

File system:

As these are virtual machines, their filesystems are also virtual. Certain directories are mapped to the host server. All the mount directories are contained within /xnat-data. This is configured within the xnat.cfg file. Highly recommend to stay with the default at present.

Postgresql:
/xnat-data/postgresql/ - this is the postgresql database

Nginx:
/xnat-data/xnat
              ./certificates   - this contains the SSL certificates and is on the NGinx container (/etc/ssl)
              ./nginx_logs   - the log files pertaining to the Ngnix container (var/log/nginx/

Tomcat:
/xnat-data/xnat
              ./archive
              ./build
              ./tomcat_logs
              ./scripts
              ./inbox

/xnat-data/import_data  - place directories of sessions here and they are automatically imported into XNAT.

Log File:

The tomcat XNAT logfiles are located:

/data/xnat/home/logs/

This is the location inside the container if running within Docker. This is mapped, by default to: