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From "RYAN C. CORNIA" <ryan.cor...@utah.edu>
Subject Re: Examples Error
Date Wed, 28 Aug 2013 21:36:41 GMT
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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