Hi Jeff, I don't think that a custom dictionary should cause a null pointer exception on that line unless you have an odd null character in text or something of that ilk.
One thing that changed in ctakes 4.0 is the version of hsqldb that is being used for the dictionary database. I don’t know if that has anything to do with your problem, but it may be causing others. What is the source of your custom dictionary? There may be a better way to populate a database. Sean -----Original Message----- From: Jeff Headley [mailto:jeffun...@gmail.com] Sent: Tuesday, October 03, 2017 12:53 AM To: dev@ctakes.apache.org Subject: Re: NPE after upgrade in DefaultJCASTermAnnotator [EXTERNAL] Thank you Sean. That helped to figure out what we did. Not quite sure where we went wrong but now at least we know the cause. So a long time ago in our project using ctakes, we emptied out the tables CUI_TERMS, RXNORM, PREFTERM, and TUI and then loaded them with the values we wanted. Worked great. Now in the new version the /desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml engine seems to be using /resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab and that seems to be where things went sideways. If I don't mess with the db and keep the original, no errors. So somewhere in this if statement at line 102 in DefaultJCASTermAnnotator: if ( hitTokens[ hit ].equals( allTokens.get( i ).getText() ) || hitTokens[ hit ].equals( allTokens.get( i ).getVariant() ) ) { It's expecting to not ever have a null and I suspect we are leaving something null somewhere that really shouldn't have nulls. If it's obvioius where I've went wrong, the assistance would be appreciated. Otherwise, I'll get it figured out eventually. I suspect it's possibly because we never did anything with the SNOMEDCT_US in the prior version. On Mon, Oct 2, 2017 at 10:47 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Jeff, > > I have no problem running on your example "DIDANOSINE, 250MG (PO > Capsule Delayed Release)" or any other text. > > I don't know how you are running ctakes through com.clientproject.ctakes. > processors.CommandLineProcessor, so I don't know how closely the > standard pipeline approximates yours. > > Sean > > -----Original Message----- > From: Jeff Headley [mailto:jeffun...@gmail.com] > Sent: Sunday, October 01, 2017 11:31 PM > To: dev@ctakes.apache.org > Subject: NPE after upgrade in DefaultJCASTermAnnotator [EXTERNAL] > > After upgrading our project to version 4, we are getting a NPE from cTAKES. > The text that was being processed was DIDANOSINE, 250MG (PO Capsule > Delayed Release), though it seems to be happening to us no matter what > text we submit. The stack trace is below. Any help would be > appreciated as I'm at a loss at to what we might be doing wrong if this is > not a bug in cTAKES. > > Thank you, > Jeff > > Oct 01, 2017 11:10:16 PM > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl > processAndOutputNewCASes(273) > 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:412) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl. > processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314) > at > org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator. > processUntilNextOutputCas(ASB_impl.java:570) > at > org.apache.uima.analysis_engine.asb.impl.ASB_impl$ > AggregateCasIterator.<init>(ASB_impl.java:412) > at > org.apache.uima.analysis_engine.asb.impl.ASB_impl. > process(ASB_impl.java:344) > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. > processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265) > at > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process( > AnalysisEngineImplBase.java:269) > at > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process( > AnalysisEngineImplBase.java:284) > at > com.clientproject.ctakes.processors.CommandLineProcessor.processLine( > CommandLineProcessor.java:163) > at > java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList. > java:1374) > at > java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline. > java:580) > at > com.clientproject.ctakes.processors.CommandLineProcessor.run( > CommandLineProcessor.java:114) > at com.clientproject.ctakes.App.main(App.java:109) > Caused by: java.lang.NullPointerException at > org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator. > isTermMatch(DefaultJCasTermAnnotator.java:102) > at > org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator. > findTerms(DefaultJCasTermAnnotator.java:79) > at > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator. > findTerms(AbstractJCasTermAnnotator.java:236) > at > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator. > processWindow(AbstractJCasTermAnnotator.java:219) > at > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.proc > ess( > AbstractJCasTermAnnotator.java:156) > 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:396) > ... 12 more >
