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 > > > > > > 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. > > > > > > > > > > > > > > > > -- > -- > Maïté Meseure Hugues >
