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From "RYAN C. CORNIA" <ryan.cor...@utah.edu>
Subject Examples Error
Date Wed, 28 Aug 2013 21:21:28 GMT
I'm new to CTAKES, and am trying to go through the user example guide ( https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+User+Install+Guide
).

My environment is OSX 10.8.4, Java 1.7.0_25.

Note: My input directory just contains example txt files. It seems to process 3 of them, then
fails. (There are 750 documents)

When I try to run the CPE, following the instructions, but pointing it to my own input/output
directories, I get the following error:

Aug 28, 2013 3:15:52 PM 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:220)
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:174)
at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:158)
... 10 more

Aug 28, 2013 3:15:52 PM 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:220)
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:174)
at org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitializer.java:158)
... 10 more

Any idea what is going on?

Thanks,
Ryan



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