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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 21:18:43 GMT
I got the ResourceInitialization Exception before I included the Lucene 4 jars at 

INFO LuceneIndexReaderResourceImpl - Loading Lucene Index into
> memory:
> > /home/aveek/workspace/ctakes/ctakes-dictionary-
> > lookup/resources/org/apache/ctakes/dictionary/lookup/drug_index

The log snippet was the same as its in th first post. After I included the Lucene 4 jars,
it made no difference, I got the exact same error.

Is there any other way to fix it other than replacing the existing files with the upgraded
ones?

-Aveek
________________________________________
From: Chen, Pei [Pei.Chen@childrens.harvard.edu]
Sent: Wednesday, June 12, 2013 5:04 PM
To: user@ctakes.apache.org
Subject: RE: Resource Initialization Exception with cTakes 3.0.0

Aveek,
Are you using the trunk code base of cTAKES?  Or the released 3.0?
Just a note: If it's cTAKES 3.0, essentially what you did was upgraded to use Lucene 4.x jars
and libs and resources (which may not have been completely tested and you may have to also
to download other the other appropriate Lucene 4 indexes (umls, etc. etc.))...

I'm just curious for future reference- what was the original error in 3.0 before you included
the Lucene 4 jar?

--Pei

> -----Original Message-----
> From: Aveek Mukhopadhyay
> [mailto:mukhopadhyay.11@buckeyemail.osu.edu]
> Sent: Wednesday, June 12, 2013 4:57 PM
> To: user@ctakes.apache.org
> Subject: RE: Resource Initialization Exception with cTakes 3.0.0
>
>
> Clearing up the OrangeBook and replacing it with files from
> https://sourceforge.net/p/ctakesresources/code/HEAD/tree/trunk/ctakes-
> resources-
> dictionary/src/main/resources/org/apache/ctakes/dictionary/lookup/Orang
> eBook/ resolves the issue.
>
> Had to do the same thing for drug_index folder to make it work for
> AggregatePlaintextProcessor.xml provided by ctakes.
>
> -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.initializeExterna
> > > lR
> > > 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.initiali
> > > ze
> > > (Anal
> > > ysisEngineImplBase.java:157)
> > >       at
> > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.in
> > > it
> > > 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.in
> > > it
> > > AS
> > > B(AggregateAnalysisEngine_impl.java:431)
> > >       at
> > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in
> > > it
> > > ializ
> > > eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> > >       at
> > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in
> > > it
> > > 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.actionPe
> > > rf
> > > o
> > > rmed(AnnotatorOpenEventHandler.java:52)
> > >       at
> > >
> > javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:201
> > 8)
> > >       at
> > > javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.ja
> > > va
> > > :2
> > > 341)
> > >       at
> > >
> >
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.
> > > java:402)
> > >       at
> > >
> >
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
> > >       at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
> > >       at
> > >
> > javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:83
> > 3)
> > >       at
> > >
> >
> javax.swing.plaf.basic.BasicMenuItemUI$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(ProtectionD
> > > om
> > > ain
> > > .java:76)
> > >       at
> > > java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionD
> > > om
> > > 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(ProtectionD
> > > om
> > > 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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