[CTAKES-15] Runtime exception for certain documents with Assertion module

• Type: Bug
• Status: Closed
• Priority: Minor
• Resolution: Not A Problem
• Affects Version/s: 3.0-incubating
• Fix Version/s: 3.0-incubating
• Component/s: ctakes-assertion
• Assignee: Pei Chen
• Reporter: Pei Chen
• Created: 03/Aug/12 18:21
• Updated: 15/Feb/13 20:57
• Resolved: 09/Aug/12 20:06

Description

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