Yes, there is a null check near it but in a different method. I'm a little confused though because his line numbers do align with the most current version.
Anyways, Hoang, here are your options: 1) If you have the src distribution you can insert a null check yourself based on the one in trunk and rebuild ctakes 2) If you have the bin distribution a) upgrade to a newer version b) Modify the descriptor to make the attribute classifiers not run Anything I missed? What's probably happening is that your dictionary is finding an entity/event that the default dictionary doesn't, and there is a null pointer in the dependency parse for that new entity. Tim On 03/27/2015 02:12 PM, Pei Chen wrote: > 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?) > https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_repos_asf_ctakes_tags_ctakes-2D3.0.0-2Dincubating_ctakes-2Ddependency-2Dparser_src_main_java_org_apache_ctakes_dependency_parser_util_DependencyUtility.java&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=lwkep42G2WNYF08UZTv_xXc3EX-jrqv-lnvHAIOTrFQ&s=W8vWGifRf7UeJlqO4n3TpeldqHKshhov_E9VwNlqqj4&e= > > > > On Fri, Mar 27, 2015 at 1:46 PM, Pham, Hoang <[email protected]> > wrote: > >> To Timothy, >> >> Sorry, I misspell your name before. >> >> Thank You, >> >> Hoang Pham >> >> >> -----Original Message----- >> From: Pham, Hoang [mailto:[email protected]] >> Sent: Fri 3/27/2015 1:38 PM >> To: [email protected] >> 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:[email protected]] >> Sent: Fri 3/27/2015 9:38 AM >> To: [email protected] >> 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. >>
