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From Aveek Mukhopadhyay <mukhopadhyay...@buckeyemail.osu.edu>
Subject RE: Resource Initialization Exception with cTakes 3.0.0
Date Wed, 12 Jun 2013 20:24:08 GMT

I am using all the 3.0 resources, the ctakes-resources-3.0.1.zip etc, and experienced this
issue first. Then I thought it probably needs 4.x .jar files and so I added lucene 4.x .jar
files and added it to the classpath, but it made no difference, it still gives the same error.

-Aveek
________________________________________
From: Chen, Pei [Pei.Chen@childrens.harvard.edu]
Sent: Wednesday, June 12, 2013 3:24 PM
To: user@ctakes.apache.org
Subject: RE: Resource Initialization Exception with cTakes 3.0.0

I just took a look at the 3.0.0 release tag again.
Note: cTAKES 3.0 still needs Lucene 3.x (it should work with the lucene 3.x jar and 3.0 of
resources:
http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.0.1.zip (not ctakes-resources-3.1.0.zip
which was rebuilt for Lucene 4).
http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.0.0-incubating/pom.xml

The indexes and resources have been upgraded to Lucene 4.x only in trunk and the future cTAKES
3.1 release.

Could you confirm your setup again?- i.e. A lucene 4.x jar shouldn't appear in cTAKES 3.0...
--Pei

> -----Original Message-----
> From: Aveek Mukhopadhyay
> [mailto:mukhopadhyay.11@buckeyemail.osu.edu]
> Sent: Wednesday, June 12, 2013 3:17 PM
> To: user@ctakes.apache.org
> Subject: RE: Resource Initialization Exception with cTakes 3.0.0
>
>
> Hi Pei,
>
> With the AggregatePlaintextProcessor.xml provided by cTakes themselves, it
> throws up the error while loading the indexes for drug_index.
>
> INFO LuceneIndexReaderResourceImpl - Loading Lucene Index into memory:
> /home/aveek/workspace/ctakes/ctakes-dictionary-
> lookup/resources/org/apache/ctakes/dictionary/lookup/drug_index
>
> With the AggregatePlaintextUMLSProcessor.xml provided by cTakes, it
> throws up the error for OrangeBook.
>
> LuceneIndexReaderResourceImpl - Loading Lucene Index into memory:
> /home/aveek/workspace/ctakes/ctakes-dictionary-
> lookup/resources/org/apache/ctakes/dictionary/lookup/OrangeBook
>
> Thanks & Regards,
> Aveek
> ________________________________________
> From: Chen, Pei [Pei.Chen@childrens.harvard.edu]
> Sent: Wednesday, June 12, 2013 2:35 PM
> To: user@ctakes.apache.org
> Subject: RE: Resource Initialization Exception with cTakes 3.0.0
>
> Hi Aveek,
> Could you also include the full path/directory to the index that causing the
> error?
>
> I vaguely recall that all of the lucene indexes have been upgraded to 4.x:
> https://issues.apache.org/jira/browse/CTAKES-12
>
> Thanks,
> Pei
>
> > -----Original Message-----
> > From: Aveek Mukhopadhyay
> > [mailto:mukhopadhyay.11@buckeyemail.osu.edu]
> > Sent: Wednesday, June 12, 2013 1:37 PM
> > To: user@ctakes.apache.org
> > Subject: Resource Initialization Exception with cTakes 3.0.0
> >
> >
> >
> > Hi,
> >
> > I am having problems loading the AE with Plain text processor. It
> > shows up the ResourceInitializationException at a point where it is
> > loading Lucene index into memory. I have Lucene.jar version of 4.2.1
> > in the classpath. Can I get any help regarding this problem, is there anything
> I am doing wrong?
> >
> >
> > Thanks & Regards,
> > Aveek
> >
> > Here is a snippet from the log file
> >
> > 6/12/13 1:31:19 PM - 13:
> > org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE:
> > Exception occurred
> > org.apache.uima.resource.ResourceInitializationException
> >       at
> >
> org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(Luc
> > eneIndexReaderResourceImpl.java:80)
> >       at
> >
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(Re
> > sourceManager_impl.java:603)
> >       at
> > org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalR
> > es
> > ources(ResourceManager_impl.java:442)
> >       at
> >
> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.
> > java:153)
> >       at
> > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize
> > (Anal
> > ysisEngineImplBase.java:157)
> >       at
> > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init
> > ialize
> > (PrimitiveAnalysisEngine_impl.java:123)
> >       at
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
> > i
> > sEngineFactory_impl.java:94)
> >       at
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> > ompositeResourceFactory_impl.java:62)
> >       at
> >
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:
> > 269)
> >       at
> >
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework
> > .java:387)
> >       at
> > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:
> > 25
> > 4)
> >       at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > AS
> > B(AggregateAnalysisEngine_impl.java:431)
> >       at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ializ
> > eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> >       at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ializ
> > e(AggregateAnalysisEngine_impl.java:185)
> >       at
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys
> > i
> > sEngineFactory_impl.java:94)
> >       at
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
> > ompositeResourceFactory_impl.java:62)
> >       at
> >
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:
> > 269)
> >       at
> >
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework
> > .java:354)
> >       at
> > org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
> >       at
> >
> org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:47
> > 7)
> >       at
> > org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerf
> > o
> > rmed(AnnotatorOpenEventHandler.java:52)
> >       at
> >
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
> >       at
> > javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java
> > :2
> > 341)
> >       at
> >
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.
> > java:402)
> >       at
> >
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
> >       at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
> >       at
> >
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
> >       at
> >
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMen
> > uItemUI.java:877)
> >       at java.awt.Component.processMouseEvent(Component.java:6505)
> >       at
> > javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
> >       at java.awt.Component.processEvent(Component.java:6270)
> >       at java.awt.Container.processEvent(Container.java:2229)
> >       at java.awt.Component.dispatchEventImpl(Component.java:4861)
> >       at java.awt.Container.dispatchEventImpl(Container.java:2287)
> >       at java.awt.Component.dispatchEvent(Component.java:4687)
> >       at
> > java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
> >       at
> > java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
> >       at
> > java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
> >       at java.awt.Container.dispatchEventImpl(Container.java:2273)
> >       at java.awt.Window.dispatchEventImpl(Window.java:2719)
> >       at java.awt.Component.dispatchEvent(Component.java:4687)
> >       at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:723)
> >       at java.awt.EventQueue.access$200(EventQueue.java:103)
> >       at java.awt.EventQueue$3.run(EventQueue.java:682)
> >       at java.awt.EventQueue$3.run(EventQueue.java:680)
> >       at java.security.AccessController.doPrivileged(Native Method)
> >       at
> > java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDom
> > ain
> > .java:76)
> >       at
> > java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDom
> > ain
> > .java:87)
> >       at java.awt.EventQueue$4.run(EventQueue.java:696)
> >       at java.awt.EventQueue$4.run(EventQueue.java:694)
> >       at java.security.AccessController.doPrivileged(Native Method)
> >       at
> > java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDom
> > ain
> > .java:76)
> >       at java.awt.EventQueue.dispatchEvent(EventQueue.java:693)
> >       at
> >
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre
> > ad.java:244)
> >       at
> >
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.j
> > a
> > va:163)
> >       at
> >
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
> > ad.java:151)
> >       at
> >
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:147)
> >       at
> >
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:139)
> >       at java.awt.EventDispatchThread.run(EventDispatchThread.java:97)
> > Caused by: org.apache.lucene.index.IndexFormatTooOldException: Format
> > version is not supported (resource:
> > ChecksumIndexInput(RAMInputStream(name=segments))): -1 (needs to
> be
> > between -9 and -11). This version of Lucene only supports indexes
> > created with release 3.0 and later.
> >       at
> >
> org.apache.lucene.codecs.lucene3x.Lucene3xSegmentInfoReader.readLegac
> > ySegmentInfo(Lucene3xSegmentInfoReader.java:128)
> >       at
> >
> org.apache.lucene.codecs.lucene3x.Lucene3xSegmentInfoReader.readLegac
> > yInfos(Lucene3xSegmentInfoReader.java:54)
> >       at
> > org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:312)
> >       at
> >
> org.apache.lucene.index.StandardDirectoryReader$1.doBody(StandardDirec
> > toryReader.java:56)
> >       at
> >
> org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfo
> > s.java:783)
> >       at
> >
> org.apache.lucene.index.StandardDirectoryReader.open(StandardDirectory
> > R
> > eader.java:52)
> >       at
> > org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:66)
> >       at
> > org.apache.lucene.index.IndexReader.open(IndexReader.java:291)
> >       at
> >
> org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(Luc
> > eneIndexReaderResourceImpl.java:70)
> >       ... 58 more



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