Talk from 2010 XNAT Workshop

1. XNAT Custom Features
& Open Source Development
John Paulett
jpaulett@wustl.edu
June 30, 2010

2. Goal
Introduce potential contributors to the
methods and tools for contributing to XNAT
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3. XNAT is Open Source!
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4. XNAT is Open Source!
Freedom
Leverage others’ work
Contribute
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5. HOW CAN I CONTRIBUTE?
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6. Bug Reports & Feature Requests
xnat_discussion@googlegroups.com
For sensitive issues, bugs@xnat.org
Provide details!
• Environment
• Versions
• Steps to reproduce
• Screenshots
• Logs
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7. “Report a problem”
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8. Share Custom Schemas
(Jenny Gurney’s previous Customizations talk)
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9. Create Something New
Leverage the REST API
Examples: PyXNAT, xnatfs
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10. Develop XNAT
Fix Bugs
Add Features
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11. XNAT ECOSYSTEM
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13. 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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14. 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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15. 3 TOOLS OF A XNAT DEVELOPER
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16. #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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17. 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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18. 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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19. hg.xnat.org
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20. Integration Manager Workflow
blessed developer developer
repository public public
integration developer developer
manager private private
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21. Mercurial Resources
mercurial.selenic.com
hgbook.red-bean.com
hginit.com
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22. #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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23. Why not Ant?
Dependency management
– Reduce blobs in version control system
Standardized project layout & commands
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24. xdat_core & Maven
$ cd xdat_core
$ mvn clean install
[INFO] Scanning for projects...
...
[INFO] BUILD SUCCESSFUL
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25. #2 – Eclipse IDE
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26. Useful Eclipse Plugins
• Mercurial
• Maven
• XML Schema Editor
• Velocity
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27. HELPFUL TOOLS
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28. Debugging with JPDA
Connect to external Tomcat & Applet
processes with Eclipse debugger
Set breakpoints, examine state
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29. Connect Tomcat process with Eclipse debugger

30. DEMO: FIX A BUG & SUBMIT A PATCH
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31. 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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32. 2) Register in Eclipse
cp sample.classpath .classpath
cp sample.project .project
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33. 3) Fix Code
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36. 4) Test it!
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37. 5) Commit
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38. 6) Publish the Change
Options include:
• Sending patch file
• Forking on Bitbucket
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43. Go Forth and Develop
http://nrg.wikispaces.com/XNAT+2010+Workshop+-
+Custom+Features+and+Open+Source+Development
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