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From "Chen Lin (JIRA)" <j...@apache.org>
Subject [jira] [Created] (CTAKES-246) DrugMentionAnnotator falls to infinite loop for some expression
Date Mon, 23 Sep 2013 15:16:03 GMT
Chen Lin created CTAKES-246:
-------------------------------

             Summary: DrugMentionAnnotator falls to infinite loop for some expression  
                 Key: CTAKES-246
                 URL: https://issues.apache.org/jira/browse/CTAKES-246
             Project: cTAKES
          Issue Type: Bug
          Components: ctakes-drug-ner
    Affects Versions: 3.1
            Reporter: Chen Lin
            Priority: Minor


I was using an older version of cTAKES (Revision: 1479606, the version right before type-system
changed for adding more eventMentioins from entities) to process some notes. One note seems
trigger DrugMentionAnnotator to an infinite loop. The error message was attached below.  This
error didn't occur with the newest trunk version. I am thus wondering if this was a known
bug and has been fixed in some way. My situation is that I cannot switch to the latest version
of trunk, because my down-streaming pipeline was relying on the old eventMentions. 

The actual sentences that trigger this loop is the following. 

"Blah of increased pain him long standing MS Contin was increased from 15 mg. q12 hours to
60 mg. q.12 hours."
Oddly, it worked fine if the text was "q24 hours."

Error message:
Caused by: java.lang.StackOverflowError
        at org.apache.ctakes.typesystem.type.textsem.EventMention.<init>(EventMention.java:45)
        at org.apache.ctakes.typesystem.type.textsem.MedicationEventMention.<init>(MedicationEventMention.java:58)
        at org.apache.ctakes.drugner.ae.DrugMentionAnnotator.generateAdditionalNER(DrugMentionAnnotator.java:2117)
        at org.apache.ctakes.drugner.ae.DrugMentionAnnotator.statusChangePhraseGenerator(DrugMentionAnnotator.java:2100)
        at org.apache.ctakes.drugner.ae.DrugMentionAnnotator.generateDrugMentionsAndAnnotations(DrugMentionAnnotator.java:1397)
        at org.apache.ctakes.drugner.ae.DrugMentionAnnotator.generateAdditionalNER(DrugMentionAnnotator.java:2270)
        at org.apache.ctakes.drugner.ae.DrugMentionAnnotator.statusChangePhraseGenerator(DrugMentionAnnotator.java:2100)
        at org.apache.ctakes.drugner.ae.DrugMentionAnnotator.generateDrugMentionsAndAnnotations(DrugMentionAnnotator.java:1397)
        at org.apache.ctakes.drugner.ae.DrugMentionAnnotator.generateAdditionalNER(DrugMentionAnnotator.java:2270)
        at org.apache.ctakes.drugner.ae.DrugMentionAnnotator.statusChangePhraseGenerator(DrugMentionAnnotator.java:2100)


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