XNAT Open Source Development

XNAT Custom Features

& Open Source DevelopmentJohn Paulett

[email protected]

June 30, 2010

Goal

Introduce potential contributors to the

methods and tools for contributing to XNAT

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XNAT is Open Source!

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XNAT is Open Source!

Freedom

Leverage others’ work

Contribute

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HOW CAN I CONTRIBUTE?

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Bug Reports & Feature Requests

[email protected]

For sensitive issues, [email protected]

Provide details!

• Environment

• Versions

• Steps to reproduce

• Screenshots

• Logs

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“Report a problem”

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Share Custom Schemas

(Jenny Gurney’s previous Customizations talk)

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Create Something New

Leverage the REST API

Examples: PyXNAT, xnatfs

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Develop XNAT

Fix Bugs

Add Features

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XNAT ECOSYSTEM

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XNAT Internals

xdat_core - org.nrg.xft

– translates between XML schema & other formats

– XFTItem.java

xdat_core - org.nrg.xdat

– admin, security, search infrastructure around XFT

– Web app structure

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XNAT Internals

xdat_release/plugin_resources - org.nrg.xnat

– REST API

– Uploading & Downloading

– Neuroimaging specific models

xdat_release/projects

– Site customizations

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3 TOOLS OF A XNAT DEVELOPER

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#1 – Version Control with Mercurial

hg.xnat.org

Replacement for CVS & Subversion

Distributed (everyone has full repo & can commit)

Sane branching & merging

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Why Leave CVS?

Network connectivity required

Lack of support for renaming/moving files

Lack of atomic commits

Single point of failure

Expensive branch operations

Day-long merges

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Mercurial Quick Start

hg clone http://hg.xnat.org/xdat_release

# view differences

hg diff

# commit and send changes to remote repo

hg commit

hg push

# get the latest remote changes

hg pull --update

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hg.xnat.org

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Integration Manager Workflow

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blessed repository

integration manager

developer private

developer public

developer private

developer public

Mercurial Resources

mercurial.selenic.com

hgbook.red-bean.com

hginit.com

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#2 – Maven

Build & Dependency Management

Migrating to Maven 2

– xdat_release & pipelines still use Maven 1

(hidden behind bin/setup.sh)

– New projects should use Maven 2

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Why not Ant?

Dependency management

– Reduce blobs in version control system

Standardized project layout & commands

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xdat_core & Maven

$ cd xdat_core

$ mvn clean install

[INFO] Scanning for projects...

...

[INFO] BUILD SUCCESSFUL

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#2 – Eclipse IDE

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Useful Eclipse Plugins

• Mercurial

• Maven

• XML Schema Editor

• Velocity

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HELPFUL TOOLS

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Debugging with JPDA

Connect to external Tomcat & Applet

processes with Eclipse debugger

Set breakpoints, examine state

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Connect Tomcat process with Eclipse debugger

DEMO: FIX A BUG & SUBMIT A PATCH

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1) Clone & Set up Projects

hg clone http://hg.xnat.org/xdat_core

mvn clean install

hg clone http://hg.xnat.org/xdat_release

...

bin/setup.sh -Ddeploy=true

...

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2) Register in Eclipse

cp sample.classpath .classpath

cp sample.project .project

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3) Fix Code

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4) Test it!

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5) Commit

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6) Publish the Change

Options include:

• Sending patch file

• Forking on Bitbucket

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Go Forth and Develop

http://nrg.wikispaces.com/XNAT+2010+Workshop+-

+Custom+Features+and+Open+Source+Development

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