To Pei, Sorry, I was checking the wring folder. I'm actually using 3.2.1 dependecy-parser jar file.
Thank You, Hoang Pham -----Original Message----- From: Pei Chen [mailto:chen...@apache.org] Sent: Fri 3/27/2015 2:12 PM To: dev@ctakes.apache.org Subject: Re: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility 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 <hp...@tuftsmedicalcenter.org> wrote: > To Timothy, > > Sorry, I misspell your name before. > > Thank You, > > Hoang Pham > > > -----Original Message----- > From: Pham, Hoang [mailto:hp...@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.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. > > 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.
