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From Pei Chen <chen...@apache.org>
Subject Re: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
Date Fri, 27 Mar 2015 18:12:35 GMT
Hoang,
3.0 was released a long time ago (02/2013).  (according to the tag/history,
it did't have the null fix until 6/2013 3.1?)
http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.0.0-incubating/ctakes-dependency-parser/src/main/java/org/apache/ctakes/dependency/parser/util/DependencyUtility.java


On Fri, Mar 27, 2015 at 1:46 PM, Pham, Hoang <HPham@tuftsmedicalcenter.org>
wrote:

> To Timothy,
>
> Sorry, I misspell your name before.
>
> Thank You,
>
> Hoang Pham
>
>
> -----Original Message-----
> From: Pham, Hoang [mailto:HPham@tuftsmedicalcenter.org]
> Sent: Fri 3/27/2015 1:38 PM
> To: dev@ctakes.apache.org
> Subject: RE: Ctakes Null Pointer Error for
> org.apache.ctakes.dependency.parser.util.DependencyUtility
>
> To Tomothy,
>
> I have cTakes 3.0 install. I looked at the class and there is a null check
> but for some reason, it is not catching. Also, when I use the indexes that
> came with cTakes install, the program would parse without any errors.
>
> Thank You,
>
> Hoang Pham
>
>
> -----Original Message-----
> From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
> Sent: Fri 3/27/2015 9:38 AM
> To: dev@ctakes.apache.org
> Subject: Re: Ctakes Null Pointer Error for
> org.apache.ctakes.dependency.parser.util.DependencyUtility
>
> 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.
> >
>
>
> 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.
>
> 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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