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Posted to dev@ctakes.apache.org by "Pei Chen (JIRA)" <ji...@apache.org> on 2012/08/03 20:21:02 UTC
[jira] [Created] (CTAKES-15) Runtime exception for certain
documents with Assertion module
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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[jira] [Closed] (CTAKES-15) Runtime exception for certain documents
with Assertion module
Posted by "Pei Chen (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/CTAKES-15?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Pei Chen closed CTAKES-15.
--------------------------
Resolution: Not A Problem
Assignee: Pei Chen
This isn't a bug in the assertion module per se, but a limitation of UIMA's .subiterator and uimaFIT dynamic pipeline creation from the cTAKES GUI. Rejecting this jira item in favor of a more general enhancement to use uimaFIT's org.uimafit.util.JCasUtil.selectCovered(jCas,BaseToken.class, sentence); instead using .subiterator.
> 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
> Assignee: 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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