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From "Khanna, Ritu" <ri...@med.umich.edu>
Subject ctakes 3.2.2/ytex exception when processing large number of documents
Date Fri, 12 Aug 2016 15:55:07 GMT
Hello All,

We are processing a large number of medical documents in chunks. We ran the CPE with ytex
DBCollectionReader/AggregateUMLSPlainFastProcessor/DBConsumer.
Our first batch has about 145,000 documents. However, after running for more than 48 hours
and processing 78,823 documents the process was terminated with the exception pasted below:

>>>>
15 Jul 2016 17:55:53  INFO DBCollectionReader - loading document with id = {INST
ANCE_ID=720494072, INSTANCE_KEY=677503859}
Jul 15, 2016 5:55:53 PM org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEn
gine_impl callAnalysisComponentProcess(407)
SEVERE: Exception occurred
org.apache.uima.analysis_engine.AnalysisEngineProcessException: EXCEPTION MESSAG
E LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource f
or bundle java.util.PropertyResourceBundle, key text is null for docId=null
        at org.apache.ctakes.core.ae.SimpleSegmentAnnotator.process(SimpleSegmen
tAnnotator.java:59)
        at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCa
sAnnotator_ImplBase.java:48)
        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.cal
lAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.pro
cessAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterato
r.processUntilNextOutputCas(ASB_impl.java:567)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterato
r.<init>(ASB_impl.java:409)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.ja
va:342)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.pro
cessAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
        at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(A
nalysisEngineImplBase.java:267)
        at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext
(ProcessingUnit.java:897)
        at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(Process
ingUnit.java:577)

Jul 15, 2016 5:55:53 PM org.apache.uima.analysis_engine.impl.AggregateAnalysisEn
gine_impl processAndOutputNewCASes(275)
SEVERE: Exception occurred
org.apache.uima.analysis_engine.AnalysisEngineProcessException: EXCEPTION MESSAG
E LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource f
or bundle java.util.PropertyResourceBundle, key text is null for docId=null
        at org.apache.ctakes.core.ae.SimpleSegmentAnnotator.process(SimpleSegmen
tAnnotator.java:59)
        at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCa
sAnnotator_ImplBase.java:48)
        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.cal
lAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.pro
cessAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterato
r.processUntilNextOutputCas(ASB_impl.java:567)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterato
r.<init>(ASB_impl.java:409)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.ja
va:342)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.pro
cessAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
        at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(A
nalysisEngineImplBase.java:267)
        at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext
(ProcessingUnit.java:897)
        at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(Process
ingUnit.java:577)

org.apache.uima.analysis_engine.AnalysisEngineProcessException: EXCEPTION MESSAG
E LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource f
or bundle java.util.PropertyResourceBundle, key text is null for docId=null
        at org.apache.ctakes.core.ae.SimpleSegmentAnnotator.process(SimpleSegmen
tAnnotator.java:59)
        at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCa
sAnnotator_ImplBase.java:48)
        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.cal
lAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.pro
cessAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterato
r.processUntilNextOutputCas(ASB_impl.java:567)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterato
r.<init>(ASB_impl.java:409)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.ja
va:342)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.pro
cessAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
        at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(A
nalysisEngineImplBase.java:267)
        at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext
(ProcessingUnit.java:897)
        at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(Process
ingUnit.java:577)
Jul 15, 2016 5:55:53 PM org.apache.uima.collection.impl.cpm.engine.ProcessingUni
t process
SEVERE: The container AggregatePlaintextFastUMLSProcessor returned the following
 error message: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResource
Exception: Can't find resource for bundle java.util.PropertyResourceBundle, key
text is null for docId=null (Thread Name: [Procesing Pipeline#1 Thread]::)
Jul 15, 2016 5:55:53 PM org.apache.uima.collection.impl.cpm.engine.ProcessingUni
t maybeLogSevereException(2502)
SEVERE: Thread: [Procesing Pipeline#1 Thread]::, message: EXCEPTION MESSAGE LOCA
LIZATION FAILED: java.util.MissingResourceException: Can't find resource for bun
dle java.util.PropertyResourceBundle, key text is null for docId=null
org.apache.uima.analysis_engine.AnalysisEngineProcessException: EXCEPTION MESSAG
E LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource f
or bundle java.util.PropertyResourceBundle, key text is null for docId=null
        at org.apache.ctakes.core.ae.SimpleSegmentAnnotator.process(SimpleSegmen
tAnnotator.java:59)
        at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCa
sAnnotator_ImplBase.java:48)
        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.cal
lAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.pro
cessAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterato
r.processUntilNextOutputCas(ASB_impl.java:567)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterato
r.<init>(ASB_impl.java:409)
        at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.ja
va:342)
        at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.pro
cessAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
        at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(A
nalysisEngineImplBase.java:267)
        at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.processNext
(ProcessingUnit.java:897)
        at org.apache.uima.collection.impl.cpm.engine.ProcessingUnit.run(Process
ingUnit.java:577)
>>>>

Any help in resolving this will be appreciated.
Ctakes version: 3.2.2

Thanks,
Ritu

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