AutoRun Error

[alvaro....@gmail.com]

Hello,

I'm getting the following error sent to me per email after each image is received by XNAT  (1.7.4.1).
Even though I have installed the Pipeline plug-in, there is no pipeline configured or active on this system...

Does anyone have an idea?


Pipeline:

/data/xnat/pipeline/catalog/xnat_tools/AutoRun.xml

Cause:

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.ArrayList.rangeCheck(ArrayList.java:668) at java.util.ArrayList.get(ArrayList.java:444) at org.nrg.pipeline.utils.ParameterUtils.resolveParameterValues(ParameterUtils.java:187) at org.nrg.pipeline.utils.ParameterUtils.setParameterValues(ParameterUtils.java:171) at org.nrg.pipeline.utils.PipelineEngineUtils.resolveXPath(PipelineEngineUtils.java:87) at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:210) at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:193) at org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:63) at org.nrg.pipeline.client.XNATPipelineLauncher.run(XNATPipelineLauncher.java:298) at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:260)

Thanks,
Alvaro

[Herrick, Rick]

I’m not sure what you mean by “I have installed the Pipeline plug-in, there is no pipeline configured or active on this system...”

 

There’s not really a pipeline plugin for the default XNAT configuration, just the pipeline engine. Is that what you mean? In this case, it looks like XNAT is trying to launch the pipeline engine to run the AutoRun pipeline, which is defined in that catalog/xnat_tools/AutoRun.xml file. The default value configured in XNAT for the pipeline engine is /data/xnat/pipeline, so that’s why it’s resolving to that full path. There are two possibilities:

 

• The pipeline engine is not installed and therefore the AutoRun.xml file doesn’t exist at that path. If this is the case, you should see a warning message like this one when you log into XNAT:

I don’t think this is the issue though. This will just fail to launch because the launcher script isn’t available.

• The AutoRun.xml configuration is missing or is messed up somehow. I’ve attached the default version of AutoRun.xml to this post. Try comparing this to what you have on your server and see if there’s anything that differs.

 

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

Phone: +1 (314) 273-1645

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[alvaro....@gmail.com]

Hello Rick,

with "plug-in" I meant the pipeline engine, which is installed in the default path (/data/xnat/pipeline) on our system.

Our AutoRun.xml file is exactly the same as yours....

[alvaro....@gmail.com]

ok, I found the problem. I was using the wrong site url in the main settings. Now it seems to be working fine.

Thanks for the help.
Alvaro

On Monday, May 7, 2018 at 4:36:59 PM UTC+2, alvaro....@gmail.com wrote: