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.mil...@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.
