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
