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From "Chen Lin (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-246) DrugMentionAnnotator falls to infinite loop for some expression
Date Tue, 05 Nov 2013 20:48:19 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-246?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13814238#comment-13814238
] 

Chen Lin commented on CTAKES-246:
---------------------------------

Hi Pei and Co.,

Thank you for making the fix in CTAKES-251! It works for the following cases, but not all
cases.
1>
Back on prednisone 5 daily for RA since 2/09.
Peak flows decreased from 450/500 --> 350 on Flovent 1 BID, with SOB and increased albuterol
use. No nocturnal symptoms. Now back to normal on Flovent 2 BID.

HOWEVER, it seems that the fix still doesn't work for the case bellow. I will double check
my run. Thanks!
"Blah of increased pain him long standing MS Contin was increased from 15 mg. q12 hours to
60 mg. q.12 hours." 
2>
\t3/16/92 VISIT REPORTS PAIN IS SIGNIFICANTLY IMPROVED BUT STILL SIGNIFICANTLY SYMPTOMATIC.
TEGRETOL LEVEL 1/15/92 WAS 4.4 AND DOSE INCREASED FROM 200 BID TO 200 TID. WILL RECHECK LEVEL
AND CBC TODAY.

Best,
Chen

> 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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