Pipeline Engine Setup Missing xdat-beans jar

[Chris Fahim]

Hi Everybody,

I'm having issues setting up the pipeline.  I've hg cloned the pipeline_1_6dev and ran the setup.bat.  However I keep getting the following error:

java.lang.NoClassDefFoundError: org/nrg/xdat/bean/XnatAbstractresourceBean at
java.lang.Class.getDeclaredMethods0(Native Method) at
java.lang.Class.privateGetDeclaredMethods(Class.java:2531) at
java.lang.Class.privateGetPublicMethods(Class.java:2651) at
java.lang.Class.getMethods(Class.java:1467) at
net.sf.saxon.functions.JavaExtensionLibrary.bind(JavaExtensionLibrary.java:309) at
net.sf.saxon.functions.FunctionLibraryList.bind(FunctionLibraryList.java:83) at net.sf.saxon.expr.ExpressionParser.parseFunctionCall(ExpressionParser.java:1763) at
...


Following this post https://groups.google.com/forum/#!msg/xnat_discussion/E-_cFfh1HO8/cC5ULuFmG4wJ, about half way down it is found that the error is from xdat-beans-VERSION.jar.  The solution is to match up the jar names in the WebBasedQCImageCreator.bat, however, the xdat-beans-version.jar doesn't even exist in my PIPELINE_HOME/lib folder. 

Any ideas why the xdat-beans jar isn't even there ? 

Let me know.  Thanks.

-Chris  

[Chris Fahim]

UPDATE:

I manually copied and pasted the xdat-beans jar from my xnat/WEB-INF/lib and everything works as expected.

-Chris

[Mohana Ramaratnam]

You wont have to manually copy if the path to pipeline directory is set correctly in XNAT_HOME/build.properties file, before running XNAT setup.

Mohana

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[Herrick, Rick]

Sure. The xdat-beans jar is actually generated during the build process by parsing all of the XSDs referenced from an XML document named InstanceSettings.xml. Each data type defined in the XSDs (including any custom data types added in) generates a set of classes for working with that data type programmatically within XNAT. During the setup process, this jar is generated and copied both into the local repository for the XNAT builder and then into the deployed web application or jar AND into the pipeline engine's lib folder.

If you look in your xnat_builder folder under the subfolder plugin-resources/repository/xdat/jars, you'll find a copy of xdat-bean-XXX.jar, where XXX is your version of XNAT, e.g. 1.6.3. Copy that jar over into the lib folder for your pipeline engine, then try your setup script in the pipeline engine again.

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 827-4250

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From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] on behalf of Chris Fahim [cfa...@gmail.com]
Sent: Wednesday, May 07, 2014 4:23 PM
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Subject: [XNAT Discussion] Pipeline Engine Setup Missing xdat-beans jar

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[Chris Fahim]

Thanks Mohana and Rick.

For some reason after I ran through the setup guide my pipeline folded ended up being empty.  I have a production system of XNAT that I won't be able to redo the setup so I'm planning to build the pipeline engine manually as I described in my original post. 

So far it's working on my dev system, can you guys foresee any settings or anything being missed by building the pipeline engine manually like this ?


Thanks.


-Chris

[Herrick, Rick]

No, other than the xdat-beans jar, you should be fine (assuming you pass the proper options to the pipeline setup script of course!).

 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 827-4250