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From Yingcheng Sun <yxs...@case.edu>
Subject Re: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
Date Fri, 27 Mar 2015 15:48:51 GMT
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.
> >
>
>

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