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:[email protected]] > Sent: Wednesday, June 12, 2013 4:57 PM > To: [email protected] > 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 [[email protected]] > Sent: Wednesday, June 12, 2013 3:24 PM > To: [email protected] > 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:[email protected]] > > Sent: Wednesday, June 12, 2013 3:17 PM > > To: [email protected] > > 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 [[email protected]] > > Sent: Wednesday, June 12, 2013 2:35 PM > > To: [email protected] > > 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:[email protected]] > > > Sent: Wednesday, June 12, 2013 1:37 PM > > > To: [email protected] > > > 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 >
