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/OrangeBook/ 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.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
