Problem with BioNLP'09 shared task visualization workflow

[riedelcastro]

Hi,

I'm having trouble running the BioNLP'09 Shared Task Visualization workflow. When I click the "play" button I see an "org.apache.uima.resource.ResourceInitializationException
CausedBy: org.apache.uima.resource.ResourceConfigurationException
CausedBy: java.lang.NullPointerException

I wish I could give you a console dump but after launching u-compare with javaws -viewer as described in http://u-compare.org/launch.html I can't see any console dump (neither in the console I started javaws in nor in the viewer itself). Where would the dump appear?

I'm using the newest Macbook Pro.

Cheers,
Sebastian

[kano]

Hi Sebastian,

Are you still seeing the same error with the current version of U-Compare?
In my environment the workflow is running fine.

As for the debug message dump, it should be shown in the Java Console window when you launch U-Compare from the "debug message" launch option link in http://u-compare.org/launch.html

It is very helpful for us if you could test it in MacOS, it might be related to the environment.
Thanks!

-Yoshinobu

[riedelcastro]

Hi Yoshinobu,

I still see the same error. As for the debug message dump: the problem was that on Mac OS the java console is by default inactive and has to be manually enabled through the "Java Preferences" application (this wasn't really obvious to me so a small footnote on the launch page could help other Mac OS users). With the console enabled, here is exception that is being thrown (I'm happy to send you the whole debug output if you wish)

pseudoRootController = descriptors.collectionProcessingEngine.BioNLP09Visualization org.u_compare.workflowui.workflow.CpmPanel.updatePsuedoRootAggregates(CpmPanel.java:530)
aeSpecifiers = [http://u-compare.org/lib/u-compare.jar!/descriptors/analysisEngine/advanced/primitive/BioNLP09UserDataReaderAE.xml, http://u-compare.org/lib/u-compare.jar! ... nsumer.xml] org.u_compare.workflowui.workflow.CpmPanel.removeAE(CpmPanel.java:5079)
aeListModel = [descriptors.analysisEngine.advanced.primitive.BioNLP09UserDataReaderAE, descriptors.casConsumer.UCompareXmiWriterCasConsumer] org.u_compare.workflowui.workflow.CpmPanel.removeAE(CpmPanel.java:5080)
topProcessorsList = [descriptors.analysisEngine.advanced.primitive.BioNLP09UserDataReaderAE] org.u_compare.workflowui.workflow.CpmPanel.dumpTopProcessorsList(CpmPanel.java:3942)
org.apache.uima.resource.ResourceInitializationException
at org.apache.uima.collection.impl.cpm.BaseCPMImpl.process(BaseCPMImpl.java:594)
at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.process(CollectionProcessingEngine_impl.java:111)
at org.u_compare.workflowui.workflow.CpmPanel$11$1.topLevelReached(CpmPanel.java:1464)
at org.u_compare.workflowui.workflow.CpmPanel.gotoTopLevel(CpmPanel.java:4560)
at org.u_compare.workflowui.workflow.CpmPanel$11.blockingProcessCompleted(CpmPanel.java:1397)
at kutil.gui.ProgressBarDialog$1.doInBackground(ProgressBarDialog.java:67)
at javax.swing.SwingWorker$1.call(SwingWorker.java:278)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at javax.swing.SwingWorker.run(SwingWorker.java:317)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
at java.lang.Thread.run(Thread.java:637)
Caused by: org.apache.uima.resource.ResourceConfigurationException
at org.apache.uima.collection.impl.cpm.container.CPEFactory.getCollectionReader(CPEFactory.java:462)
at org.apache.uima.collection.impl.cpm.BaseCPMImpl.process(BaseCPMImpl.java:589)
... 12 more
Caused by: java.lang.NullPointerException
at org.u_compare.collection_reader.Bionlp09SharedTaskReader.initialize(Bionlp09SharedTaskReader.java:527)
at org.apache.uima.collection.CollectionReader_ImplBase.initialize(CollectionReader_ImplBase.java:70)
at org.apache.uima.impl.CollectionReaderFactory_impl.produceResource(CollectionReaderFactory_impl.java:101)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:258)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:303)
at org.apache.uima.collection.impl.cpm.container.CPEFactory.getCollectionReader(CPEFactory.java:345)
at org.apache.uima.collection.impl.cpm.BaseCPMImpl.process(BaseCPMImpl.java:589)
at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.process(CollectionProcessingEngine_impl.java:111)
at org.u_compare.workflowui.workflow.CpmPanel$11$1.topLevelReached(CpmPanel.java:1464)
at org.u_compare.workflowui.workflow.CpmPanel.gotoTopLevel(CpmPanel.java:4560)
at org.u_compare.workflowui.workflow.CpmPanel$11.blockingProcessCompleted(CpmPanel.java:1397)
at kutil.gui.ProgressBarDialog$1.doInBackground(ProgressBarDialog.java:67)
at javax.swing.SwingWorker$1.call(SwingWorker.java:278)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at javax.swing.SwingWorker.run(SwingWorker.java:317)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
at java.lang.Thread.run(Thread.java:637)
... 13 more

[kano]

Hi Sebastian,

Thanks for your information. The console dump was enough long for debug - though I could not narrow down the specific code because I have modified the code which shifted the code line numbers.
I have applied a patch and updated U-Compare version to "1.0.4 pre".
Would you please test it again, confirming the version shown at startup is "1.0.4 pre"?

I also updated the webpage, adding MacOSX specific description as you mentioned.
Thank you very much for your helps!

-Yoshinobu

[riedelcastro]

Hmmm, when I launch U-Compare it says Version 1.0.4 2009/01/07 15:27 JST. And with this version I still get the same error message.

S

[kano]

The problem was due to a bug which was fixed in Java 1.6.0_10, Java Web Start does not check updates for nested dependencies of libraries.
Since Apple Java in Mac OSX is still 1.6.0_07 based in its latest version, we have to clear cache of Java Web Start when U-Compare adds new libraries.

Thank you very much for your cooperation!

-Yoshinobu