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.process(
> 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
>
