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Posted to user@ctakes.apache.org by "Gianfrancesco, Milena" <Mi...@ucsf.edu> on 2016/10/11 16:23:44 UTC
Trouble loading CPE tutorial
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