Ryan, >From Initial looks- That looks like an XML parse exception... Have you verified the xml contents for validity? If not, could you attach the Descriptors if possible?
On Wed, Aug 28, 2013 at 5:21 PM, RYAN C. CORNIA <[email protected]>wrote: > 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 > > >
