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architecture_notes.md

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XNAT deployment architecture

XNAT

XNAT is written in Java with the Velocity Template Language (VTL) framework providing front-end integration with HTML/CSS/Javascript. XNAT's interface is primarily a web server which allows direct access through a browser or programmatic access through the REST API, although other interfaces can be provided such as the DICOM SCP node which receives DICOM data.

Pipelines

XNAT provides pipeline support for local data processing. The pipelines engine is built as part of the install. Pipelines can be useful for small automated tasks to be performed when data are added. In general however it is preferred to use external processing (eg using DAX), as running local data processing will use up system resources and could make the server less responsive.

Tomcat

XNAT runs as a container within Tomcat 9.

Tomcat receives web requests from nginx internally on port 8080 and forwards them onto XNAT.

Tomcat runs under the tomcat user (it does not need to run as root as port 8080 is unprivileged).

Java

Tomcat runs under Java. Java options need to be configured in the JAVA_OPTS or CATALINA_OPTS variables when the Java process is started.

nginx

Nginx is used as a reverse proxy and handles SSL termination and static file caching.

Nginx listens on the following ports:

  • 80: unencrypted http traffic is redirected to https
  • 443: encrypted https traffic is decrypted and forwarded internally to port 8080 for tomcat to process via XNAT
  • 104: DICOM traffic is streamed to 8104 where the XNAT SCP service can receive it

Nginx has to run as root because it listens on privileged ports 80, 104 and 443.

PostgreSQL server

XNAT uses a PostgreSQL database to store metadata (project structure, custom data types, user details etc). In this setup, a PostgreSQL server is installed on a separate machine to the tomcat server.

  • The PostgreSQL database file location is mapped to local storage, or optionally a shared storage drive (external_storage_drive)
  • The database server firewall and PostgreSQL configuration only permits connections from the XNAT server
  • PostgreSQL traffic is encrypted with both client and server certificates. The certificates are generated by the Ansible scripts, which is suitable for a PostgreSQL server hosted on the same internal network as the XNAT server, which has no external access,
  • If your PostgreSQL server is on a publicly accessible network, you should obtain SSL certificates signed by a Certificate Authority.

Source image files themselves are generally kept in the archive and not stored in the PostgreSQL database.