ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Pei Chen <chen...@apache.org>
Subject Re: Examples Error
Date Wed, 28 Aug 2013 21:27:37 GMT
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 <ryan.cornia@utah.edu>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
>
>
>

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message