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From Pei Chen <chen...@apache.org>
Subject Re: Examples Error
Date Wed, 28 Aug 2013 21:45:01 GMT
> Is that the correct aggregate?
<cTAKES_HOME>
  /desc
    /ctakes-clinical-pipeline
      /desc
        /collection_processing_engine
          /test1.xml
That looks like a CPE Descriptor xml (rather than a Aggregate Analysis
Engine pipeline); Did you try to open that as and AnalysisEngine instead of
a CPE?

I honestly haven't try the instructions on the CDA pipeline, so if that
doesn't work, I'll give it a whirl.
Also, did you know that there is a 3.1 RC being voted on as we speak? Also,
something to consider- I'm not sure if it may have been a known bug that
was fixed.
--Pei



On Wed, Aug 28, 2013 at 5:36 PM, RYAN C. CORNIA <ryan.cornia@utah.edu>wrote:

> I didn't make any changes, just downloaded the CTAKES binary zip file,
> unzipped it, downloaded the resource file, merged it with the CTAKES
> binary zip resources, and walked through the examples.
>
> I just re-tried the example using only 1 file in my input directory, which
> contained the example text from the user guide:
>
> Dr. Nutritious
>
> Medical Nutrition Therapy for Hyperlipidemia
> Referral from: Julie Tester, RD, LD, CNSD
> Phone contact: (555) 555-1212
> Height: 144 cm Current Weight: 45 kg Date of current weight: 02-29-2001
> Admit Weight: 53 kg BMI: 18 kg/m2
> Diet: General
> Daily Calorie needs (kcals): 1500 calories, assessed as HB + 20% for
> activity.
> Daily Protein needs: 40 grams, assessed as 1.0 g/kg.
> Pt has been on a 3-day calorie count and has had an average intake of 1100
> calories.
> She was instructed to drink 2-3 cans of liquid supplement to help promote
> weight gain.
> She agrees with the plan and has my number for further assessment. May
> want a Resting
> Metabolic Rate as well. She takes an aspirin a day for knee pain.
>
>
>
> It failed as well with the same error. The user guide says to use:
>
> <cTAKES_HOME>
>   /desc
>     /ctakes-clinical-pipeline
>       /desc
>         /collection_processing_engine
>           /test1.xml
>
>
> Is that the correct aggregate?
>
> -Ryan
>
> On 8/28/13 3:27 PM, "Pei Chen" <chenpei@apache.org> wrote:
>
> >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+Instal
> >>l+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(CdaCasInitial
> >>izer.java:220)
> >> at
> >>
> >>org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnn
> >>otator_ImplBase.java:48)
> >> at
> >>
> >>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAna
> >>lysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
> >> at
> >>
> >>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.process
> >>AndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
> >> at
> >>
> >>org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.pr
> >>ocessUntilNextOutputCas(ASB_impl.java:567)
> >> at
> >>
> >>org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<i
> >>nit>(ASB_impl.java:409)
> >> at
> >>
> >>org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:3
> >>42)
> >> at
> >>
> >>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.process
> >>AndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
> >> at
> >>
> >>org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(Analy
> >>sisEngineImplBase.java:267)
> >> at
> >>
> >>org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(Pro
> >>cessingUnit.java:897)
> >> at
> >>
> >>org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingU
> >>nit.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(ClinicalN
> >>otePreProcessor.java:174)
> >> at
> >>
> >>org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitial
> >>izer.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(CdaCasInitial
> >>izer.java:220)
> >> at
> >>
> >>org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnn
> >>otator_ImplBase.java:48)
> >> at
> >>
> >>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAna
> >>lysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
> >> at
> >>
> >>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.process
> >>AndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
> >> at
> >>
> >>org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.pr
> >>ocessUntilNextOutputCas(ASB_impl.java:567)
> >> at
> >>
> >>org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<i
> >>nit>(ASB_impl.java:409)
> >> at
> >>
> >>org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:3
> >>42)
> >> at
> >>
> >>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.process
> >>AndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
> >> at
> >>
> >>org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(Analy
> >>sisEngineImplBase.java:267)
> >> at
> >>
> >>org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(Pro
> >>cessingUnit.java:897)
> >> at
> >>
> >>org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingU
> >>nit.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(ClinicalN
> >>otePreProcessor.java:174)
> >> at
> >>
> >>org.apache.ctakes.preprocessor.ae.CdaCasInitializer.process(CdaCasInitial
> >>izer.java:158)
> >> ... 10 more
> >>
> >> Any idea what is going on?
> >>
> >> Thanks,
> >> Ryan
> >>
> >>
> >>
>
>

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