erfandarzi / xnat-ubuntu

modified dockerized XNAT version for Ubuntu, out of the box.

Xnat-Ubuntu

It's a modified dockerized XNAT version from the official dockerized XNAT Git-Repo with the following changes.

• this Xnat is modified and optimized for Ubuntu
• simple installation Script (work out of the box)
• installed OHIF Viewer & LDAP Plugin
• installed Docker-Pipeline-Engine
• installed Container Plugin + Workaround
• fixed Processing URL BUG
• some specific Ubuntu changes
• APItest Script and TestPipeline

System Overview

A short environment overview with the different docker container and subsystems.

Preconditions

Ubuntu Server (>18)

Usage

• download the installScript.sh file
• copy the file to your Ubuntu Server in your root directory (Command: cd /)
• execute the file with the command: sudo bash installScript.sh
• after the installation and several minutes, look at your URL
• now make the necessary configuration (processing url & admin password change)

Necessary Configurations

• first change your admin password (default credentials -> Name: admin, PW: admin)
• change processing url to your side url under Administer -> Site Administration -> Pipeline Settings -> Processing Url
• change the side url to your side url under Administer -> Site Administration -> Site Setup -> Site Url

Folder Overview

A short overview of the XNAT folderstructure after a successful installation.

Pipeline Configurations

Add "Execute Pipeline"-Button on Options Menu in SessionData

• navigate: Administer -> Data Types ->
• choose SessionData Element witch should have Execute option
• click on the Element and on Edit-Button
• scroll down to "Available Report Actions"
• one the last entry in this table write: Name->PipelineScreen_launch_pipeline, Display Name->Build, Secure Access->edit
• scroll down again and click on the "Submit"-Button

Now should appear a "Execute Pipeline"-Button when you open a Project with the specific SessionData Element. There you can execute a Pipeline for the Project Data if you have added a Pipeline.

Add a Pipeline to your XNAT System

You can add a Sample Pipeline that is already installed with this installation.

• navigate: Administer -> Pipeline -> Add Pipeline
• choose the path: /data/xnat/pipeline/catalog/PipelineTest/SampleHelloWorldPipeline.xml
• Importend!! leave the Name Textfield empty. A Bug will accur with you choose a spezific name.
• after confirm your settings you can add this pipeline to your project and test the pipeline engine

Container Service

With this installation you can also add docker container as pipelines. Here a short example how it works with a external docker environment.

Special mention

• Sourcefiles from offical XNAT Repo: github.com/NrgXnat/xnat-docker-compose @johnflavin
• Project Supervisor: @muellerdo