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From "Pei Chen (JIRA)" <j...@apache.org>
Subject [jira] [Created] (CTAKES-15) Runtime exception for certain documents with Assertion module
Date Fri, 03 Aug 2012 18:21:02 GMT
Pei Chen created CTAKES-15:
------------------------------

             Summary: Runtime exception for certain documents with Assertion module
                 Key: CTAKES-15
                 URL: https://issues.apache.org/jira/browse/CTAKES-15
             Project: cTAKES
          Issue Type: Bug
          Components: ctakes-assertion
    Affects Versions: 2.6-incubating
            Reporter: Pei Chen
            Priority: Minor
             Fix For: 2.6-incubating


Sample text to recreate this:

HISTORY:
blah blah
REPORT:
blah blah
IMPRESSION
blah blah
REPORT 2:
     61172
     Addendum:

Caused by: java.lang.RuntimeException: First token in sentence not found!!
        at org.mitre.medfacts.i2b2.api.ctakes.CharacterOffsetToLineTokenConverterCtakesImpl.convertCharacterOffsetToLineToken(CharacterOffsetToLineTokenConverterCtakesImpl.java:183)
~[cTAKES-2.5.0.jar:na]
        at org.mitre.medfacts.i2b2.api.ctakes.CharacterOffsetToLineTokenConverterCtakesImpl.convert(CharacterOffsetToLineTokenConverterCtakesImpl.java:107)
~[cTAKES-2.5.0.jar:na]
        at org.mitre.medfacts.zoner.ZonerCli.findHeadings(ZonerCli.java:545) ~[med-facts-zoner-1.1.jar:na]
        at org.mitre.medfacts.i2b2.cli.MedFactsRunner.findZones(MedFactsRunner.java:212) ~[med-facts-i2b2-1.2-SNAPSHOT.jar:na]
        at org.mitre.medfacts.i2b2.api.SingleDocumentProcessor.processZones(SingleDocumentProcessor.java:449)
~[med-facts-i2b2-1.2-SNAPSHOT.jar:na]
        at org.mitre.medfacts.i2b2.api.SingleDocumentProcessor.generateAnnotations(SingleDocumentProcessor.java:173)
~[med-facts-i2b2-1.2-SNAPSHOT.jar:na]
        at org.mitre.medfacts.i2b2.api.SingleDocumentProcessor.processSingleDocument(SingleDocumentProcessor.java:97)
~[med-facts-i2b2-1.2-SNAPSHOT.jar:na]
        at org.mitre.medfacts.uima.assertion.AssertionAnalysisEngine.process(AssertionAnalysisEngine.java:213)
~[cTAKES-2.5.0.jar:na]
        at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
~[uimaj-core-2.4.0.jar:2.4.0]
        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
~[uimaj-core-2.4.0.jar:2.4.0]
        ... 6 common frames omitted


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