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From "Lin, Chen" <Chen....@childrens.harvard.edu>
Subject a potential bug from drug-ner module?
Date Fri, 28 Jun 2013 17:33:58 GMT
Dear Sean and Co.,

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. Please
help shed some light. The actual sentences that trigger this loop is the following. Thank
you very much for your help!

Best,
Chen

Example Triggering sentences:
"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)

Chen Lin
Applications Development Specialist
Children's Hospital Boston
Informatics Program
300 Longwood Avenue
Enders 142
Boston, MA 02115
Phone: 617-919-3421
chen.lin@childrens.harvard.edu<mailto:chen.lin@childrens.harvard.edu>


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