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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
Date Fri, 27 Mar 2015 13:38:21 GMT
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
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