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_zlaef3pvqcm9xsyums15iymgapsxx...@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
<[email protected]> 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
>
>
>
>
>
>
>
>
