Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
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
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
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
RE: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
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
Re: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
Dear all, Do you know how to generate CUIs by programming, not using GUI. It will be better if you can show me the code. Thank you! Yingcheng On Fri, Mar 27, 2015 at 9:38 AM, Miller, Timothy timothy.mil...@childrens.harvard.edu wrote: 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)
Finding Cuis with API
I'm starting a new thread for this topic since it seems unrelated to the one you replied to. Check BagOfCuisGenerator, here's what it looks like in trunk: http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfCUIsGenerator.java this code will read in an input directory with text files in it and output directory, and it will write a file for every input file containing a list of the CUIs found in that file. Fair warning it is a bit out of date since it uses the pipeline with the old dictionary which is a bit slower. If that is not exactly what you need the code should still be good as an example of how to grab CUIs from a processed CAS. We are working on ways of streamlining this further. Thanks Tim On 03/27/2015 12:00 PM, Yingcheng Sun wrote: Dear all, Do you know how to generate CUIs by programming, not using GUI. It will be better if you can show me the code. Thank you! Yingcheng
Re: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
Another way that you can see it is if you look at the ClinicalPipelineFactory.java in the ctakes-clinical-pipeline/ folder. There is a method called getCUIsthat will allow you to get CUIs from the Identified Annotations. Sincerely, Michelle Chen :) Be strong and of good courage; do not be afraid, nor be dismayed, for the Lord your God is with you wherever you go. ~Joshua 1:9 On Fri, Mar 27, 2015 at 12:01 PM, Maite Meseure Hugues meseure.ma...@gmail.com wrote: Dear Yingcheng Sun, You can use BagOfCuisGenerator.java . On Fri, Mar 27, 2015 at 10:48 AM, Yingcheng Sun yxs...@case.edu wrote: Dear all, Do you know how to generate CUIs by programming, not using GUI. It will be better if you can show me the code. Thank you! Yingcheng On Fri, Mar 27, 2015 at 9:38 AM, Miller, Timothy timothy.mil...@childrens.harvard.edu wrote: 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
Re: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
Dear Yingcheng Sun, You can use BagOfCuisGenerator.java . On Fri, Mar 27, 2015 at 10:48 AM, Yingcheng Sun yxs...@case.edu wrote: Dear all, Do you know how to generate CUIs by programming, not using GUI. It will be better if you can show me the code. Thank you! Yingcheng On Fri, Mar 27, 2015 at 9:38 AM, Miller, Timothy timothy.mil...@childrens.harvard.edu wrote: 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
RE: ctakessorx for AggregatePlaintextFastUMLSProcessor.xml
Maite, You already have a thread going with me offline. If you have a question please ask it on that thread to refrain from spamming the devlist. Until I have a chance to create decent documentation you are stuck with me. Sean From: Maite Meseure Hugues [meseure.ma...@gmail.com] Sent: Friday, March 27, 2015 3:59 PM To: dev@ctakes.apache.org Subject: ctakessorx for AggregatePlaintextFastUMLSProcessor.xml Hi everyone, I am currently using AggregatePlaintextFastUMLSProcessor.xml and trying to use my own dictionary. I would like to understand ctakessnorx script file, how it's made etc, I didn't find any info. Thank you. -- -- Maïté Meseure Hugues
ctakessorx for AggregatePlaintextFastUMLSProcessor.xml
Hi everyone, I am currently using AggregatePlaintextFastUMLSProcessor.xml and trying to use my own dictionary. I would like to understand ctakessnorx script file, how it's made etc, I didn't find any info. Thank you. -- -- Maïté Meseure Hugues
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
Re: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
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.javad=BQIBaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674hm=lwkep42G2WNYF08UZTv_xXc3EX-jrqv-lnvHAIOTrFQs=W8vWGifRf7UeJlqO4n3TpeldqHKshhov_E9VwNlqqj4e= 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
RE: Ctakes Null Pointer Error for org.apache.ctakes.dependency.parser.util.DependencyUtility
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
