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From "Pei Chen (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-246) DrugMentionAnnotator falls to infinite loop for some expression
Date Mon, 04 Nov 2013 21:14:17 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-246?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13813277#comment-13813277
] 

Pei Chen commented on CTAKES-246:
---------------------------------

Chen,
Could you confirm that the fix in CTAKES-251 (available in trunk now) also fixes your use
case here?)


> 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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