Xnat 1.7.2 problem with pipelines

[Peter PW]

Hi,

I have installed XNAT 1.7.2 and pipeline version 1.7.2 on my workstation. When I try to run my custom pipelines I get the following error, it appears when the pipeline want to execute XnatRestClient :

Exception in thread "main" java.lang.NoClassDefFoundError: org.apache.commons.logging.LogFactory

        at org.apache.axis.components.logger.LogFactory.class$(LogFactory.java:45)

        at org.apache.axis.components.logger.LogFactory$1.run(LogFactory.java:45)

        at java.security.AccessController.doPrivileged(Native Method)

        at org.apache.axis.components.logger.LogFactory.getLogFactory(LogFactory.java:41)

        at org.apache.axis.components.logger.LogFactory.<clinit>(LogFactory.java:33)

        at org.apache.axis.handlers.BasicHandler.<clinit>(BasicHandler.java:43)

        at org.apache.axis.client.Service.getAxisClient(Service.java:104)

        at org.apache.axis.client.Service.<init>(Service.java:113)

        at org.nrg.xnat.client.rest.WSTool.<init>(WSTool.java:64)

        at org.nrg.xnat.client.rest.XNATRestClient.<init>(XNATRestClient.java:49)

        at org.nrg.xnat.client.rest.XNATRestClient.main(XNATRestClient.java:303)

On previous version of XNAT (1.6) the pipeline was working correctly without any problem. Could you advise me what is the cause and what can be done?

Thanks!

 

[Herrick, Rick]

The immediate issue is that the XNATRestClient script isn’t finding commons-logging-1.1.1.jar. That should be in the same folder as xnat-rest-client-1.6.4.jar. Can you verify that it’s there?

 

That said, this is working fine for me locally with the latest install of the pipeline engine. I’m able to run that script successfully from any location (i.e. it’s not dependent on any relative path to the commons-logging-1.1.1./jar). That makes me think something’s gone wrong in your pipeline installation. Can you try re-running the setup script in the pipeline installer and/or the gradlew script there (gradlew requires having the gradle.properties file populated with the installer settings: this is described in the README.md).

 

The secondary issue is that XNATRestClient is deprecated. We keep it in the pipeline engine for compatibility with existing scripts that already use it, but any new development should use XnatDataClient instead.

 

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

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[Peter PW]

Hey Rick, 

Thank you for answer. In the the lib folder both xnat-rest-client-1.6.4.jar and commons-logging-1.2.jar are present. I tried rerunning and reinstalling the pipeline engine couple of times and I get the very same error again. I also tried installing the newest Xnat using Vagrant and it appears that the same issue exist there. I know that the XnatRestClient should no longer be used but I'm not the creator of that pipelines and I can't change them for now. Do you have an idea how can I fix this?