EventFlattener can't getSpecificType() since there's none

pikatech commented 6 years ago

$cat runtojson.sh 
#!/bin/bash

#SBATCH -p express
#SBATCH --mem 32000
#SBATCH --cpus-per-task 1

#cd target

export CLASSPATH=target/classes:conf:`echo lib/*.jar | tr ' ' ':'`
export JVM_OPTS="-Xms10g -Xmx25g"

if [ -z $JAVA_BIN ]; then
    JAVA_BIN=java
fi

$JAVA_BIN $JVM_OPTS -cp $CLASSPATH de.julielab.jcore.cpe.DBCPERunner -d desc/CPEMedlineToJsonES.xml $*

16:55:59.445 [[Procesing Pipeline#1 Thread]::] ERROR de.julielab.jcore.ae.eventflattener.EventFlattener - Exception occurred in document 9546437: {}
java.lang.NullPointerException: null
    at de.julielab.jcore.ae.eventflattener.EventFlattener.process(EventFlattener.java:68)
    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:401)
    at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:318)
    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:271)
    at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
    at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext(ProcessingUnit.java:895)
    at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(ProcessingUnit.java:575)
16:55:59.448 [[Procesing Pipeline#1 Thread]::] WARN de.julielab.jcore.cpe.DBStatusCallbackListener - processing of 7.document (ID: 9546437) raised exception: Error happened on: Thu Jun 21 16:55:59 CEST 2018-------------- Failed Components -------------- 
1. Process

EventMention
   sofa: _InitialView
   begin: 540
   end: 546
   confidence: <null>
   componentId: <null>
   id: "E1"
   specificType: <null>
   ref: <null>
   resourceEntryList: <null>
   textualRepresentation: <null>
   likelihood: LikelihoodIndicator
      sofa: _InitialView
      begin: 540
      end: 546
      confidence: <null>
      componentId: "de.julielab.jules.ae.LikelihoodDetection"
      id: <null>
      likelihood: "negation"
      entityAndRelationString: <null>
   tense: <null>
   modality: <null>
   arguments: FSArray
   reorderedArguments: <null>
   polarity: <null>
   relationString: <null>
   genericity: <null>
   trigger: EventTrigger
      sofa: _InitialView
      begin: 540
      end: 546
      confidence: <null>
      componentId: <null>
      id: "T17"
      specificType: "Negative_regulation"
      ref: <null>
      resourceEntryList: <null>
      textualRepresentation: <null>
      likelihood: <null>
      probability: <null>
      specifity: <null>
      importance: <null>

pikatech commented 6 years ago

jcore-event-flattener-ae has been removed from the flow for the moment.

khituras commented 3 years ago

Solved in new indexing pipeline.

JULIELab / semedico

EventFlattener can't getSpecificType() since there's none #6