XNAT Pipeline Engine

Version 1.8.3 Neuroinformatics Research Group (https://nrg.wustl.edu), Washington University in Saint Louis

Developers

• Mohana Ramaratnam, mohanakannan9@gmail.com
• Rick Herrick, rick.herrick@wustl.edu
• John Flavin, jflavin@wustl.edu

This repository was copied from a previous repository on Bitbucket, which was itself copied from a different previous repository on Bitbucket.

Installation

This version of the XNAT pipeline engine is built and installed differently from earlier versions. It uses a Gradle-based build script to manage the pipeline resources and dependencies. More importantly, instead of building directly back into the pipeline installation folder, it builds to another destination folder. You can specify the build property destination with the path to the destination folder or just use the default destination, which is the folder build/pipeline in the pipeline build folder.

You can build the pipeline engine by three different methods:

1. Call the setup.sh or setup.bat script, passing the administrator email, mail server, and XNAT server address as parameters (you can also add the optional XNAT site name parameter):

   ./setup.sh <admin email> <SMTP server> <XNAT url> [XNAT site name] [destination] [modulePath1 modulePath2 modulePath3... modulePathn]
   
   ./setup.sh you@yourlab.org mail.yourlab.org https://xnat.yourlab.org YourXNAT

2. Call the gradlew or gradlew.bat script located in the root folder of the pipeline build, along with values for all of the required and optional build parameters. Note that Gradle build parameters are passed in the form -Pparam=value.

   ./gradlew -PadminEmail=you@yourlab.org -Pdestination=/pipeline/folder \
             -PsiteName=YourXNAT -PxnatUrl=https://xnat.yourlab.org \
             -PsmtpServer=mail.yourlab.org -PmodulePaths=/path1/to/modules,/path2/to/modules \
             -PpluginsDir=/path/to/plugins -PpluginsDirProd=/path/to/plugins/on/prod

3. Lastly, you can call the gradlew or gradlew.bat script on its own, with all of the values passed on the command line in the previous method now stored in the gradle.properties file. This file just takes the standard properties file format of param=value. There's a sample version of this file already in the build folder named sample.gradle.properties. You can copy that file and fill in your own values as appropriate. This is very useful when developing pipeline modules or other code that requires frequent redeployment.

Customization

The main point of converting the pipeline build to use Gradle is to support pipeline modules. Pipeline modules are collections of code, scripts, and configuration files that can be integrated directly into the pipeline build. The purpose of this README is not to explain how to create custom pipeline modules, however a little information on how modules can be deployed is in order.

Pipeline modules can be placed in a number of locations:

• In the modules folder located inside the pipeline engine
• In any of the folders indicated by a path configured with the modulePaths build property

Pipeline modules can be structured in two ways:

• All folders and files directly under the module folder, using the same structure as the pipeline build. This is a resource-only module, i.e. it has no scripts.
• All resource folders and files in a folder named resources located under the module folder and all script folders and files in a folder named scripts located under the module folder. Scripts are treated somewhat differently from resources, in that they are renamed with the .bat extension when built on a Windows machine.

Plugins

If you have added plugins to your XNAT and these plugins add data types (have a *beans*.jar), then you need to include these in many of the pipeline executables. To do so, provide -PpluginsDir=/path/to/plugins where /path/to/plugins is the location of all your plugin jars. If you are building the pipeline engine on a machine that differs from the production environment, you can provide a mapping -PpluginsDirProd=/path/to/plugins/on/prod which will replace the /path/to/plugins in the executables.

E.g., My plugins are in /Users/me/XNATDEV/plugins on the machine on which I'm building the pipeline engine:

    $ ls /Users/me/XNATDEV/plugins
    mydata-beans-1.0-SNAPSHOT.jar
    mydata-1.0-SNAPSHOT.jar

And I plan to copy them to production to /data/xnat/home/plugins. I should run:

    ./gradlew -PadminEmail=you@yourlab.org -Pdestination=/pipeline/folder \
              -PsiteName=YourXNAT -PxnatUrl=https://xnat.yourlab.org \
              -PsmtpServer=mail.yourlab.org -PpluginsDir=/Users/me/XNATDEV/plugins
              -PpluginsDirProd=/data/xnat/home/plugins