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From Pei Chen <chen...@apache.org>
Subject Re: Error while running DrugMentionAnnotator.xml
Date Mon, 10 Aug 2015 17:37:13 GMT
Chandra,
How are you wiring up the DrugMentionAnnotator?
The default AggregatePlaintextFastUMLSProcessor.xml should already
have the Drug NER included.
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml

In general, you'll most likely need to something like the below if you
have a custom/modified pipeline:

<typeSystemDescription>
       <imports>
         <import name="org.apache.ctakes.drugner.types.TypeSystem"/>
       </imports>
</typeSystemDescription>

Related Thread:
http://mail-archives.apache.org/mod_mbox/ctakes-user/201403.mbox/%3CCAPqz87oUZ=hPzc_Fo_ZLaEf3PVQcm9xSYuMs15iyMgapsxX9gg@mail.gmail.com%3E

If you're using uimaFIT to wire your pipeline together, I would highly
recommend using the Automatic Type System Discovery.

Hope that helps.


On Sat, Aug 8, 2015 at 12:12 PM, RANGA CHANDRA GUDIVADA
<chandhragupta_in@hotmail.com> wrote:
> Hello All,
>
> I am getting the below error while trying to run the analysis engine "DrugMentionAnnotator.xml"
from user install CVD.  Please let me know if anyone has similar issues and were able to successfully
fix it.
>
> Ctakes Version used : apache-ctakes-3.2.2
> Ctakes Resources : ctakes-resources-3.2.1.1-bin
>
>
>
> Caused by: org.apache.uima.cas.CASRuntimeException: JCas type "org.apache.ctakes.drugner.type.FrequencyAnnotation"
used in Java code,  but was not declared in the XML type descriptor.
>     at org.apache.uima.jcas.impl.JCasImpl.getType(JCasImpl.java:412)
>     at org.apache.uima.jcas.impl.JCasImpl.getCasType(JCasImpl.java:436)
>     at org.apache.uima.jcas.impl.JFSIndexRepositoryImpl.getAnnotationIndex(JFSIndexRepositoryImpl.java:80)
>     at org.apache.ctakes.drugner.ae.DrugMentionAnnotator.removeAnnotations(DrugMentionAnnotator.java:306)
>     at org.apache.ctakes.drugner.ae.DrugMentionAnnotator.removeDrugNerTypes(DrugMentionAnnotator.java:299)
>     at org.apache.ctakes.drugner.ae.DrugMentionAnnotator.process(DrugMentionAnnotator.java:260)
>     ... 45 more
>
> Thanks
> Chandra
>
>
>
>
>
>
>
>

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