I updated our pom to use the same hsqldb version as what I saw in the ctakes lib folder. The data coming in is from a SQL Server database.
On Tue, Oct 3, 2017 at 8:45 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > 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 > > >
