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From "Gianfrancesco, Milena" <Milena.Gianfrance...@ucsf.edu>
Subject Trouble loading CPE tutorial
Date Tue, 11 Oct 2016 16:23:44 GMT
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


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