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From Michelle Chen <michelle1919c...@gmail.com>
Subject Re: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
Date Fri, 27 Mar 2015 16:03:47 GMT
Another way that you can see it is if you look at the
ClinicalPipelineFactory.java in the ctakes-clinical-pipeline/ folder. There
is a method called getCUIsthat will allow you to get CUIs from the
Identified Annotations.

Sincerely,
Michelle Chen :)

"Be strong and of good courage; do not be afraid, nor be dismayed, for the
Lord your God is with you wherever you go." ~Joshua 1:9


On Fri, Mar 27, 2015 at 12:01 PM, Maite Meseure Hugues <
meseure.maite@gmail.com> wrote:

> Dear Yingcheng Sun,
>
> You can use BagOfCuisGenerator.java .
>
> On Fri, Mar 27, 2015 at 10:48 AM, Yingcheng Sun <yxs489@case.edu> wrote:
>
> > Dear all,
> >
> > Do you know how to generate CUIs by programming, not using GUI.
> > It will be better if you can show me the code.
> >
> > Thank you!
> >
> > Yingcheng
> >
> > On Fri, Mar 27, 2015 at 9:38 AM, Miller, Timothy <
> > Timothy.Miller@childrens.harvard.edu> wrote:
> >
> > > Hi Hoang,
> > > Can you let me know what version of cTAKES you're using? I looked in
> > > that location in trunk and found a null check, so it could be that it's
> > > a bug that's been fixed already. In the meantime, if you just want to
> > > see if your dictionary is working right, you could disable the
> > > SubjectAttributeClassifier which seems to be the annotator where this
> > > error is coming from. Some of the other attributes rely on dependency
> > > features as well so you might disable them temporarily as well.
> > > Tim
> > >
> > >
> > > On 03/27/2015 08:32 AM, Pham, Hoang wrote:
> > > > Hi All,
> > > >
> > > > I am trying to add my own dictionary to cTakes. I have added a lucene
> > > index for the dictionary, but when the index is added, I would receive
> a
> > > null pointer exception for the
> > > org.apache.ctakes.dependency.parser.util.DependencyUtility class.
> > > > The stack trace is:
> > > >
> > > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl
> > > callAnalysisComponentProcess(407)
> > > > SEVERE: Exception occurred
> > > > org.apache.uima.analysis_engine.AnalysisEngineProcessException:
> > > Annotator processing failed.
> > > >         at
> > >
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
> > > >         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.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.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:229)
> > > >         at
> > >
> >
> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:259)
> > > >         at Parsing.main(Parsing.java:49)
> > > > Caused by: java.lang.NullPointerException
> > > >         at
> > >
> >
> org.apache.ctakes.dependency.parser.util.DependencyUtility.getPath(DependencyUtility.java:263)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier.extract(SubjectAttributeClassifier.java:181)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:57)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:1)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.process(AssertionCleartkAnalysisEngine.java:475)
> > > >         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)
> > > >         ... 13 more
> > > >
> > > > Mar 27, 2015 8:29:54 AM
> > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl
> > > processAndOutputNewCASes(275)
> > > > SEVERE: Exception occurred
> > > > org.apache.uima.analysis_engine.AnalysisEngineProcessException:
> > > Annotator processing failed.
> > > >         at
> > >
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
> > > >         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.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.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:229)
> > > >         at
> > >
> >
> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:259)
> > > >         at Parsing.main(Parsing.java:49)
> > > > Caused by: java.lang.NullPointerException
> > > >         at
> > >
> >
> org.apache.ctakes.dependency.parser.util.DependencyUtility.getPath(DependencyUtility.java:263)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier.extract(SubjectAttributeClassifier.java:181)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:57)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:1)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.process(AssertionCleartkAnalysisEngine.java:475)
> > > >         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)
> > > >         ... 13 more
> > > >
> > > > Mar 27, 2015 8:29:54 AM
> > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl
> > > processAndOutputNewCASes(275)
> > > > SEVERE: Exception occurred
> > > > org.apache.uima.analysis_engine.AnalysisEngineProcessException:
> > > Annotator processing failed.
> > > >         at
> > >
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
> > > >         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.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.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:229)
> > > >         at
> > >
> >
> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:259)
> > > >         at Parsing.main(Parsing.java:49)
> > > > Caused by: java.lang.NullPointerException
> > > >         at
> > >
> >
> org.apache.ctakes.dependency.parser.util.DependencyUtility.getPath(DependencyUtility.java:263)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier.extract(SubjectAttributeClassifier.java:181)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:57)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:1)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.process(AssertionCleartkAnalysisEngine.java:475)
> > > >         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)
> > > >         ... 13 more
> > > >
> > > > org.apache.uima.analysis_engine.AnalysisEngineProcessException:
> > > Annotator processing failed.
> > > >         at
> > >
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
> > > >         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.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.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:229)
> > > >         at
> > >
> >
> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:259)
> > > >         at Parsing.main(Parsing.java:49)
> > > > Caused by: java.lang.NullPointerException
> > > >         at
> > >
> >
> org.apache.ctakes.dependency.parser.util.DependencyUtility.getPath(DependencyUtility.java:263)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.subject.SubjectAttributeClassifier.extract(SubjectAttributeClassifier.java:181)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:57)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.attributes.features.SubjectFeaturesExtractor.extract(SubjectFeaturesExtractor.java:1)
> > > >         at
> > >
> >
> org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.process(AssertionCleartkAnalysisEngine.java:475)
> > > >         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)
> > > >         ... 13 more
> > > >
> > > > Thank You,
> > > >
> > > > Hoang Pham
> > > > The information in this e-mail is intended only for the person to
> whom
> > > it is addressed. If you believe this e-mail was sent to you in error
> and
> > > the e-mail contains patient information, please contact the Tufts
> Medical
> > > Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you
> in
> > > error but does not contain patient information, please contact the
> sender
> > > and properly dispose of the e-mail.
> > > >
> > >
> > >
> >
>
>
>
> --
> --
>  Maïté Meseure Hugues
>

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