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Posted to dev@ctakes.apache.org by Christopher Baechle <cb...@my.fau.edu> on 2015/09/19 05:46:02 UTC
Creating a new annotator
I created a new annotator for finding socio-demographic information
from a clinical note. It works within eclipse, but fails when I run it
from the packaged distribution created from mvn install.
Caused by: org.apache.uima.cas.CASRuntimeException: JCas type
"org.apache.ctakes.sociodemo.Age" used in Java code, but was not
declared in the XML type descriptor.
Age is an Annotation. I didn't follow the normal convention of adding
it to org.apache.ctakes.typesystem and put it in my package
org.apache.ctakes.sociodemo.
I added my descriptor xml file to
AggregatePlaintextFastUMLSProcessor.xml. I think it might be a
classpath issue (the jvm unable to find my descriptor file). I added
the full absolute path to runctakesCVD.sh but it still persists.
Any suggestions?
Re: Creating a new annotator
Posted by Christopher Baechle <cb...@my.fau.edu>.
That was it! Thanks.
On Sat, Sep 19, 2015 at 8:00 AM, britt fitch <
britt.fitch@wiredinformatics.com> wrote:
> Did you declare the new Age type in TypeSystem.xml?
> You may want to extend one of the existing types like EntityMention or
> IdentifiedAnnotation.
>
> Cheers,
>
> Britt
>
> Britt Fitch
> Wired Informatics
> 265 Franklin St Ste 1702
> Boston, MA 02110
> http://wiredinformatics.com
> Britt.Fitch@wiredinformatics.com
>
> On Sep 18, 2015, at 11:46 PM, Christopher Baechle <cb...@my.fau.edu>
> wrote:
>
> I created a new annotator for finding socio-demographic information
> from a clinical note. It works within eclipse, but fails when I run it
> from the packaged distribution created from mvn install.
>
> Caused by: org.apache.uima.cas.CASRuntimeException: JCas type
> "org.apache.ctakes.sociodemo.Age" used in Java code, but was not
> declared in the XML type descriptor.
>
> Age is an Annotation. I didn't follow the normal convention of adding
> it to org.apache.ctakes.typesystem and put it in my package
> org.apache.ctakes.sociodemo.
>
> I added my descriptor xml file to
> AggregatePlaintextFastUMLSProcessor.xml. I think it might be a
> classpath issue (the jvm unable to find my descriptor file). I added
> the full absolute path to runctakesCVD.sh but it still persists.
>
> Any suggestions?
>
>
>
Re: Creating a new annotator
Posted by britt fitch <br...@wiredinformatics.com>.
Did you declare the new Age type in TypeSystem.xml?
You may want to extend one of the existing types like EntityMention or IdentifiedAnnotation.
Cheers,
Britt
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
Britt.Fitch@wiredinformatics.com
> On Sep 18, 2015, at 11:46 PM, Christopher Baechle <cb...@my.fau.edu> wrote:
>
> I created a new annotator for finding socio-demographic information
> from a clinical note. It works within eclipse, but fails when I run it
> from the packaged distribution created from mvn install.
>
> Caused by: org.apache.uima.cas.CASRuntimeException: JCas type
> "org.apache.ctakes.sociodemo.Age" used in Java code, but was not
> declared in the XML type descriptor.
>
> Age is an Annotation. I didn't follow the normal convention of adding
> it to org.apache.ctakes.typesystem and put it in my package
> org.apache.ctakes.sociodemo.
>
> I added my descriptor xml file to
> AggregatePlaintextFastUMLSProcessor.xml. I think it might be a
> classpath issue (the jvm unable to find my descriptor file). I added
> the full absolute path to runctakesCVD.sh but it still persists.
>
> Any suggestions?