Hi Murali, Yes, I was missing fsm lib. Thanks for that. I am encountering a different problem now. It seems it is not able to load/read the lucene indexes and throwing up the java.io.IOException: read past EOF somewhere.
Here is the error that I am getting, any thoughts on this? Exception in thread "main" org.apache.uima.resource.ResourceInitializationException at org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:79) at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603) at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(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(AnalysisEngineImplBase.java:157) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425) at org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:424) at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:165) at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:190) at com.bmi.app.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:63) Caused by: java.io.IOException: Read past EOF at org.apache.lucene.store.RAMInputStream.switchCurrentBuffer(RAMInputStream.java:92) at org.apache.lucene.store.RAMInputStream.readBytes(RAMInputStream.java:76) at org.apache.lucene.store.ChecksumIndexInput.readBytes(ChecksumIndexInput.java:45) at org.apache.lucene.store.IndexInput.readString(IndexInput.java:124) at org.apache.lucene.index.SegmentInfo.<init>(SegmentInfo.java:173) at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:258) at org.apache.lucene.index.DirectoryReader$1.doBody(DirectoryReader.java:73) at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:677) at org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:69) at org.apache.lucene.index.IndexReader.open(IndexReader.java:316) at org.apache.lucene.index.IndexReader.open(IndexReader.java:188) at org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:69) ... 30 more ________________________________ From: Murali Nagendranath [[email protected]] Sent: Monday, July 22, 2013 12:09 PM To: [email protected] Subject: Re: ctakes with uimafit Hi Aveek, Do you have the fsm lib including in your dependencies? Ex: http://svn.apache.org/repos/asf/ctakes/trunk/pom.xml <dependency> <groupId>net.sourceforge.openai</groupId> <artifactId>openaifsm</artifactId> <version>0.0.1</version> </dependency> -- Murali On Mon, Jul 22, 2013 at 12:01 PM, Mukhopadhyay, Aveek <[email protected]<mailto:[email protected]>> wrote: Hi all, I am trying to use the ctakes Aggregate Analysis Engine with uimafit, and I am stuck at a problem now. Any ideas on how to solve this? I am using maven dependencies for ctakes and have the ctakes resources project in build path. - loading feature template - loading lexica - loading model Exception in thread "main" java.lang.NoClassDefFoundError: net/openai/util/fsm/State at org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator.initialize(ContextDependentTokenizerAnnotator.java:95) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_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:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:505) at org.uimafit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:200) at com.bmi.app.App.main(App.java:54) Caused by: java.lang.ClassNotFoundException: net.openai.util.fsm.State at java.net.URLClassLoader$1.run(Unknown Source) at java.net.URLClassLoader$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) ... 22 more
