Pei, Thanks for your response and at the moment I am not
really building any complex pipelines. I am merely running the
“DrugMentionAnnotator.xml”
from the standalone “runctakesCVD.bat”. The
original descriptor “DrugMentionAnnotator.xml” file did had the following when
I downloaded it.
<typeSystemDescription>
<imports>
<import
name="org.apache.ctakes.drugner.types.TypeSystem"/>
</imports>
</typeSystemDescription>
Here I tried to outline the entire workflow that I did
before posting my first error message in the forum,
Step1: Ran the out-of-box
“DrugMentionAnnotator.xml” and got the below error, As I mentioned before, the
downloaded descriptor did had the above xml snippet, but still threw this
error,
Caused by: org.apache.uima.cas.CASRuntimeException: JCas
type "org.apache.ctakes.typesystem.type.textspan.Segment" 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.process(DrugMentionAnnotator.java:236)
Step 2: By looking at various user posts in the forum, I found
that adding the following to the “DrugMentionAnnotator.xml” should solve the
issue
<imports>
<import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
</imports>
After adding , the <typeSystemDescription> was changed to below
<typeSystemDescription>
<imports>
<import
name="org.apache.ctakes.drugner.types.TypeSystem"/>
</imports>
<imports>
<import
name="org.apache.ctakes.typesystem.types.TypeSystem"/>
</imports>
</typeSystemDescription>
Step 3: Ran the ““DrugMentionAnnotator.xml” again with
the changes and got the below error. I can see that the earlier error was by
passed but got a new one
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)
Not sure what’s happening here. Was wondering anyone else
had similar situations to deal with.
Any help would be greatly appreciated.
ThanksChandra
> Date: Mon, 10 Aug 2015 13:37:13 -0400
> Subject: Re: Error while running DrugMentionAnnotator.xml
> From: [email protected]
> To: [email protected]
>
> 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
> >
> >
> >
> >
> >
> >
> >
> >
