Hello, I’m having trouble loading the CPE (on Mac using Linux, cTakes 3.2.2) following the tutorial online. It appears that a file may either be misspecified or needs to be edited, though I’m not sure where this error message is pointing to (see below message and log). As I’m not really familiar with Java, I’d appreciate any insights.
Thanks in advance, Error message: Org.apache.uima.analysis_engineAnalysisEngineProcessException CausedBy: org.xml.sax.SAXParseException; line Number: 1; columnNumber: 1; Content is not allowed in prolog. Log: Loading configuration. Loading feature templates. Loading lexica. Loading model: ........................................................................................ 11 Oct 2016 09:18:54 INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip 11 Oct 2016 09:18:55 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 11 Oct 2016 09:18:55 INFO ContextAnnotator - SCOPE ORDER: [1, 3] 11 Oct 2016 09:18:55 INFO NegationContextAnalyzer - initBoundaryData() called for ContextInitializer 11 Oct 2016 09:18:55 INFO AssertionAnalysisEngine - scope model file: /Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/resources/org/apache/ctakes/assertion/models/scope.model 11 Oct 2016 09:18:55 INFO AssertionAnalysisEngine - cue model file: /Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/resources/org/apache/ctakes/assertion/models/cue.model scope model: /Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/resources/org/apache/ctakes/assertion/models/scope.model 11 Oct 2016 09:18:57 INFO AssertionAnalysisEngine - pos model file: /Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/resources/org/apache/ctakes/assertion/models/pos.model Oct 11, 2016 9:18:57 AM org.mitre.medfacts.i2b2.cli.BatchRunner loadEnabledFeaturesFromFile INFO: opening enabled features file: /Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/resources/org/apache/ctakes/assertion/models/featureFile11b Oct 11, 2016 9:18:57 AM org.apache.uima.resource.impl.ResourceManager_impl initializeExternalResources WARNING: The external resource named assertionModelResourceImpl has been declared multiple times with different definitions. The definition of the resource in component /AggregateCdaProcessor/AssertionAnnotator/assertionAnalysisEngine/ will be used. The definition in component /AggregateCdaProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored. Oct 11, 2016 9:18:57 AM org.apache.uima.resource.impl.ResourceManager_impl initializeExternalResources WARNING: The external resource named scopeModelResourceImpl has been declared multiple times with different definitions. The definition of the resource in component /AggregateCdaProcessor/AssertionAnnotator/assertionAnalysisEngine/ will be used. The definition in component /AggregateCdaProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored. Oct 11, 2016 9:18:57 AM org.apache.uima.resource.impl.ResourceManager_impl initializeExternalResources WARNING: The external resource named cueModelResourceImpl has been declared multiple times with different definitions. The definition of the resource in component /AggregateCdaProcessor/AssertionAnnotator/assertionAnalysisEngine/ will be used. The definition in component /AggregateCdaProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored. Oct 11, 2016 9:18:57 AM org.apache.uima.resource.impl.ResourceManager_impl initializeExternalResources WARNING: The external resource named enabledFeaturesResourceImpl has been declared multiple times with different definitions. The definition of the resource in component /AggregateCdaProcessor/AssertionAnnotator/assertionAnalysisEngine/ will be used. The definition in component /AggregateCdaProcessor/AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored. 11 Oct 2016 09:18:57 INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip 11 Oct 2016 09:18:58 INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 11 Oct 2016 09:18:58 INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip 11 Oct 2016 09:18:58 INFO ContextAnnotator - SCOPE ORDER: [1, 3] 11 Oct 2016 09:18:58 INFO StatusContextAnalyzer - initBoundaryData() called for ContextInitializer 11 Oct 2016 09:18:58 INFO CdaCasInitializer - process(JCas) [Fatal Error] :1:1: Content is not allowed in prolog. Oct 11, 2016 9:18:58 AM org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl callAnalysisComponentProcess(407) SEVERE: Exception occurred org.apache.uima.analysis_engine.AnalysisEngineProcessException at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:231) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267) at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:897) at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:577) Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.ctakes.preprocessor.ClinicalNotePreProcessor.process(ClinicalNotePreProcessor.java:175) at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:169) ... 10 more Oct 11, 2016 9:18:58 AM org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl processAndOutputNewCASes(275) SEVERE: Exception occurred org.apache.uima.analysis_engine.AnalysisEngineProcessException at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:231) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267) at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:897) at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:577) Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.ctakes.preprocessor.ClinicalNotePreProcessor.process(ClinicalNotePreProcessor.java:175) at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:169) ... 10 more org.apache.uima.analysis_engine.AnalysisEngineProcessException at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:231) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267) at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:897) at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:577) Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.ctakes.preprocessor.ClinicalNotePreProcessor.process(ClinicalNotePreProcessor.java:175) at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:169) ... 10 more Oct 11, 2016 9:18:58 AM org.apache.uima.collection.impl.cpm.engine.ProcessingUnit process SEVERE: The container AggregateCdaProcessor returned the following error message: null (Thread Name: [Procesing Pipeline#1 Thread]::) Oct 11, 2016 9:18:58 AM org.apache.uima.collection.impl.cpm.engine.ProcessingUnit maybeLogSevereException(2502) SEVERE: Thread: [Procesing Pipeline#1 Thread]::, message: null org.apache.uima.analysis_engine.AnalysisEngineProcessException at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:231) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267) at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:897) at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:577) Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.ctakes.preprocessor.ClinicalNotePreProcessor.process(ClinicalNotePreProcessor.java:175) at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:169) ... 10 more org.apache.uima.analysis_engine.AnalysisEngineProcessException at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:231) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267) at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:897) at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:577) Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.ctakes.preprocessor.ClinicalNotePreProcessor.process(ClinicalNotePreProcessor.java:175) at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:169) ... 10 more
