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Posted to user@ctakes.apache.org by digital paula <cy...@hotmail.com> on 2013/11/14 20:41:43 UTC
cTakes Document Preprocessor Component Error
Hello cTakes Community, I'm back after hanging out with the UIMA guys :-) for a while, getting a better grasp of the UIMA framework that cTakes sits on. I'm exploring and understanding cTakes components and starting with the Document Preprocessor:https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Document+Preprocessor I loaded the testpatient_cn_1.xml file in the CVD cTakes launcher and loaded the AggregateAE descriptor. It loaded but when I ran it, I got the following 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. I looked in the AggregatorAE descriptor file along with it's dependency CdaCasInitializer.xml and see both have nothing in the Type System tab however I do see a handful of types specified on the Capabilities tab including "org.apache.ctakes.typesystem.type.textspan.Segment" So I added Segment type to the Type System tab. I reran and got this error:
11/14/13 2:23:39 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
org.apache.uima.analysis_engine.AnalysisEngineProcessException: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
Is there a file descriptor already setup maybe in another install with the necessary types/features to run the Document Preprocessor or will I manually have to add all of them? If not, I'd like to use UIMAfit to create the types/features to use with the Document Preprocessor as opposed to manually updating this descriptor with all the types and features needed. Can someone advise? Thanks. Regards,Paula
Re: cTakes Document Preprocessor Component Error
Posted by samir chabou <sa...@yahoo.com>.
Hi,thank you for replying. however, i don't have SVN Client under SVN.thanks
On Wednesday, November 26, 2014 1:25 AM, samir chabou <sa...@yahoo.com> wrote:
I'm trying to install cTAKES in eclipse but i got an error when i try a checkout as maven project from SCM.the error is:
',any help ?Thanks
On Thursday, November 14, 2013 3:38 PM, "Masanz, James J." <Ma...@mayo.edu> wrote:
Try adding
org.apache.ctakes.typesystem.types.TypeSystem
as the type system.
So the source looks like:
<typeSystemDescription>
<imports>
<import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
</imports>
</typeSystemDescription>
Hope that helps
-- James
From: user-return-336-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-336-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of digital paula
Sent: Thursday, November 14, 2013 1:42 PM
To: user@ctakes.apache.org
Subject: cTakes Document Preprocessor Component Error
Hello cTakes Community,
I'm back after hanging out with the UIMA guys :-) for a while, getting a better grasp of the UIMA framework that cTakes sits on. I'm exploring and understanding cTakes components and starting with the Document Preprocessor:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Document+Preprocessor
I loaded the testpatient_cn_1.xml file in the CVD cTakes launcher and loaded the AggregateAE descriptor. It loaded but when I ran it, I got the following 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.
I looked in the AggregatorAE descriptor file along with it's dependency CdaCasInitializer.xml and see both have nothing in the Type System tab however I do see a handful of types specified on the Capabilities tab including "org.apache.ctakes.typesystem.type.textspan.Segment"
So I added Segment type to the Type System tab. I reran and got this error:
11/14/13 2:23:39 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
org.apache.uima.analysis_engine.AnalysisEngineProcessException: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
Is there a file descriptor already setup maybe in another install with the necessary types/features to run the Document Preprocessor or will I manually have to add all of them? If not, I'd like to use UIMAfit to create the types/features to use with the Document Preprocessor as opposed to manually updating this descriptor with all the types and features needed. Can someone advise?
Thanks.
Regards,
Paula
Re: cTakes Document Preprocessor Component Error
Posted by britt fitch <br...@wiredinformatics.com>.
Hi Samir, it looks like you might have the wrong SVN client option specified. If I recall correctly, in Windows it defaults to ‘JavaHL’ and you want to go to:
‘Preferences' > ‘Team' > 'SVN' > 'SVN Client’ and select the ‘SVNKit’ option from the drop down.
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
Britt.Fitch@wiredinformatics.com
On Nov 26, 2014, at 1:24 AM, samir chabou <sa...@yahoo.com> wrote:
> I'm trying to install cTAKES in eclipse but i got an error when i try a checkout as maven project from SCM.
> the error is:
> <blob.jpeg>
> ',any help ?
> Thanks
>
>
> On Thursday, November 14, 2013 3:38 PM, "Masanz, James J." <Ma...@mayo.edu> wrote:
>
>
> Try adding
>
> org.apache.ctakes.typesystem.types.TypeSystem
>
> as the type system.
>
> So the source looks like:
>
> <typeSystemDescription>
> <imports>
> <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
> </imports>
> </typeSystemDescription>
>
> Hope that helps
> -- James
>
>
> From: user-return-336-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-336-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of digital paula
> Sent: Thursday, November 14, 2013 1:42 PM
> To: user@ctakes.apache.org
> Subject: cTakes Document Preprocessor Component Error
>
> Hello cTakes Community,
>
> I'm back after hanging out with the UIMA guys :-) for a while, getting a better grasp of the UIMA framework that cTakes sits on. I'm exploring and understanding cTakes components and starting with the Document Preprocessor:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Document+Preprocessor
>
> I loaded the testpatient_cn_1.xml file in the CVD cTakes launcher and loaded the AggregateAE descriptor. It loaded but when I ran it, I got the following 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.
>
> I looked in the AggregatorAE descriptor file along with it's dependency CdaCasInitializer.xml and see both have nothing in the Type System tab however I do see a handful of types specified on the Capabilities tab including "org.apache.ctakes.typesystem.type.textspan.Segment"
>
> So I added Segment type to the Type System tab. I reran and got this error:
>
> 11/14/13 2:23:39 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
> org.apache.uima.analysis_engine.AnalysisEngineProcessException: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
> Is there a file descriptor already setup maybe in another install with the necessary types/features to run the Document Preprocessor or will I manually have to add all of them? If not, I'd like to use UIMAfit to create the types/features to use with the Document Preprocessor as opposed to manually updating this descriptor with all the types and features needed. Can someone advise?
>
> Thanks.
>
> Regards,
> Paula
>
>
>
>
>
>
>
> <blob.jpeg>
Re: cTakes Document Preprocessor Component Error
Posted by britt fitch <br...@wiredinformatics.com>.
Hi Samir, it looks like you might have the wrong SVN client option specified. If I recall correctly, in Windows it defaults to ‘JavaHL’ and you want to go to:
‘Preferences' > ‘Team' > 'SVN' > 'SVN Client’ and select the ‘SVNKit’ option from the drop down.
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
Britt.Fitch@wiredinformatics.com
On Nov 26, 2014, at 1:24 AM, samir chabou <sa...@yahoo.com> wrote:
> I'm trying to install cTAKES in eclipse but i got an error when i try a checkout as maven project from SCM.
> the error is:
> <blob.jpeg>
> ',any help ?
> Thanks
>
>
> On Thursday, November 14, 2013 3:38 PM, "Masanz, James J." <Ma...@mayo.edu> wrote:
>
>
> Try adding
>
> org.apache.ctakes.typesystem.types.TypeSystem
>
> as the type system.
>
> So the source looks like:
>
> <typeSystemDescription>
> <imports>
> <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
> </imports>
> </typeSystemDescription>
>
> Hope that helps
> -- James
>
>
> From: user-return-336-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-336-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of digital paula
> Sent: Thursday, November 14, 2013 1:42 PM
> To: user@ctakes.apache.org
> Subject: cTakes Document Preprocessor Component Error
>
> Hello cTakes Community,
>
> I'm back after hanging out with the UIMA guys :-) for a while, getting a better grasp of the UIMA framework that cTakes sits on. I'm exploring and understanding cTakes components and starting with the Document Preprocessor:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Document+Preprocessor
>
> I loaded the testpatient_cn_1.xml file in the CVD cTakes launcher and loaded the AggregateAE descriptor. It loaded but when I ran it, I got the following 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.
>
> I looked in the AggregatorAE descriptor file along with it's dependency CdaCasInitializer.xml and see both have nothing in the Type System tab however I do see a handful of types specified on the Capabilities tab including "org.apache.ctakes.typesystem.type.textspan.Segment"
>
> So I added Segment type to the Type System tab. I reran and got this error:
>
> 11/14/13 2:23:39 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
> org.apache.uima.analysis_engine.AnalysisEngineProcessException: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
> Is there a file descriptor already setup maybe in another install with the necessary types/features to run the Document Preprocessor or will I manually have to add all of them? If not, I'd like to use UIMAfit to create the types/features to use with the Document Preprocessor as opposed to manually updating this descriptor with all the types and features needed. Can someone advise?
>
> Thanks.
>
> Regards,
> Paula
>
>
>
>
>
>
>
> <blob.jpeg>
Re: cTakes Document Preprocessor Component Error
Posted by samir chabou <sa...@yahoo.com.INVALID>.
I'm trying to install cTAKES in eclipse but i got an error when i try a checkout as maven project from SCM.the error is:
',any help ?Thanks
On Thursday, November 14, 2013 3:38 PM, "Masanz, James J." <Ma...@mayo.edu> wrote:
Try adding
org.apache.ctakes.typesystem.types.TypeSystem
as the type system.
So the source looks like:
<typeSystemDescription>
<imports>
<import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
</imports>
</typeSystemDescription>
Hope that helps
-- James
From: user-return-336-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-336-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of digital paula
Sent: Thursday, November 14, 2013 1:42 PM
To: user@ctakes.apache.org
Subject: cTakes Document Preprocessor Component Error
Hello cTakes Community,
I'm back after hanging out with the UIMA guys :-) for a while, getting a better grasp of the UIMA framework that cTakes sits on. I'm exploring and understanding cTakes components and starting with the Document Preprocessor:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Document+Preprocessor
I loaded the testpatient_cn_1.xml file in the CVD cTakes launcher and loaded the AggregateAE descriptor. It loaded but when I ran it, I got the following 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.
I looked in the AggregatorAE descriptor file along with it's dependency CdaCasInitializer.xml and see both have nothing in the Type System tab however I do see a handful of types specified on the Capabilities tab including "org.apache.ctakes.typesystem.type.textspan.Segment"
So I added Segment type to the Type System tab. I reran and got this error:
11/14/13 2:23:39 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
org.apache.uima.analysis_engine.AnalysisEngineProcessException: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
Is there a file descriptor already setup maybe in another install with the necessary types/features to run the Document Preprocessor or will I manually have to add all of them? If not, I'd like to use UIMAfit to create the types/features to use with the Document Preprocessor as opposed to manually updating this descriptor with all the types and features needed. Can someone advise?
Thanks.
Regards,
Paula
Re: cTakes Document Preprocessor Component Error
Posted by samir chabou <sa...@yahoo.com>.
I'm trying to install cTAKES in eclipse but i got an error when i try a checkout as maven project from SCM.the error is:
',any help ?Thanks
On Thursday, November 14, 2013 3:38 PM, "Masanz, James J." <Ma...@mayo.edu> wrote:
Try adding
org.apache.ctakes.typesystem.types.TypeSystem
as the type system.
So the source looks like:
<typeSystemDescription>
<imports>
<import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
</imports>
</typeSystemDescription>
Hope that helps
-- James
From: user-return-336-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-336-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of digital paula
Sent: Thursday, November 14, 2013 1:42 PM
To: user@ctakes.apache.org
Subject: cTakes Document Preprocessor Component Error
Hello cTakes Community,
I'm back after hanging out with the UIMA guys :-) for a while, getting a better grasp of the UIMA framework that cTakes sits on. I'm exploring and understanding cTakes components and starting with the Document Preprocessor:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Document+Preprocessor
I loaded the testpatient_cn_1.xml file in the CVD cTakes launcher and loaded the AggregateAE descriptor. It loaded but when I ran it, I got the following 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.
I looked in the AggregatorAE descriptor file along with it's dependency CdaCasInitializer.xml and see both have nothing in the Type System tab however I do see a handful of types specified on the Capabilities tab including "org.apache.ctakes.typesystem.type.textspan.Segment"
So I added Segment type to the Type System tab. I reran and got this error:
11/14/13 2:23:39 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
org.apache.uima.analysis_engine.AnalysisEngineProcessException: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
Is there a file descriptor already setup maybe in another install with the necessary types/features to run the Document Preprocessor or will I manually have to add all of them? If not, I'd like to use UIMAfit to create the types/features to use with the Document Preprocessor as opposed to manually updating this descriptor with all the types and features needed. Can someone advise?
Thanks.
Regards,
Paula
Re: cTakes Document Preprocessor Component Error - SOLVED
Posted by samir chabou <sa...@yahoo.com>.
going well thanks :)
On Thursday, November 14, 2013 4:15:56 PM, digital paula <cy...@hotmail.com> wrote:
I added the full path for the TypeSystem to the CdaCasInitializer descriptor (the only primitive AE in the AggregateAE) and it works now like a charm. Thanks James!
Also, thanks to Samir for responding....how's it going old friend? :-)
> From: Masanz.James@mayo.edu
> To: user@ctakes.apache.org
> Subject: RE: cTakes Document Preprocessor Component Error
> Date: Thu, 14 Nov 2013 20:37:47 +0000
>
> Try adding
>
> org.apache.ctakes.typesystem.types.TypeSystem
>
> as the type system.
>
> So the source looks like:
>
> <typeSystemDescription>
> <imports>
> <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
> </imports>
> </typeSystemDescription>
>
> Hope that helps
> -- James
>
>
> From: user-return-336-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-336-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of digital paula
> Sent: Thursday, November 14, 2013 1:42 PM
> To: user@ctakes.apache.org
> Subject: cTakes Document Preprocessor Component Error
>
> Hello cTakes Community,
>
> I'm back after hanging out with the UIMA guys :-) for a while, getting a better grasp of the UIMA framework that cTakes sits on. I'm exploring and understanding cTakes components and starting with the Document Preprocessor:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Document+Preprocessor
>
> I loaded the testpatient_cn_1.xml file in the CVD cTakes launcher and loaded the AggregateAE descriptor. It loaded but when I ran it, I got the following 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.
>
> I looked in the AggregatorAE descriptor file along with it's dependency CdaCasInitializer.xml and see both have nothing in the Type System tab however I do see a handful of types specified on the Capabilities tab including "org.apache.ctakes.typesystem.type.textspan.Segment"
>
> So I added Segment type to the Type System tab. I reran and got this error:
>
> 11/14/13 2:23:39 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
> org.apache.uima.analysis_engine.AnalysisEngineProcessException: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
> Is there a file descriptor already setup maybe in another install with the necessary types/features to run the Document Preprocessor or will I manually have to add all of them? If not, I'd like to use UIMAfit to create the types/features to use with the Document Preprocessor as opposed to manually updating this descriptor with all the types and features needed. Can someone advise?
>
> Thanks.
>
> Regards,
> Paula
>
>
>
>
>
RE: cTakes Document Preprocessor Component Error - SOLVED
Posted by digital paula <cy...@hotmail.com>.
I added the full path for the TypeSystem to the CdaCasInitializer descriptor (the only primitive AE in the AggregateAE) and it works now like a charm. Thanks James!
Also, thanks to Samir for responding....how's it going old friend? :-)
> From: Masanz.James@mayo.edu
> To: user@ctakes.apache.org
> Subject: RE: cTakes Document Preprocessor Component Error
> Date: Thu, 14 Nov 2013 20:37:47 +0000
>
> Try adding
>
> org.apache.ctakes.typesystem.types.TypeSystem
>
> as the type system.
>
> So the source looks like:
>
> <typeSystemDescription>
> <imports>
> <import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
> </imports>
> </typeSystemDescription>
>
> Hope that helps
> -- James
>
>
> From: user-return-336-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-336-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of digital paula
> Sent: Thursday, November 14, 2013 1:42 PM
> To: user@ctakes.apache.org
> Subject: cTakes Document Preprocessor Component Error
>
> Hello cTakes Community,
>
> I'm back after hanging out with the UIMA guys :-) for a while, getting a better grasp of the UIMA framework that cTakes sits on. I'm exploring and understanding cTakes components and starting with the Document Preprocessor:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Document+Preprocessor
>
> I loaded the testpatient_cn_1.xml file in the CVD cTakes launcher and loaded the AggregateAE descriptor. It loaded but when I ran it, I got the following 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.
>
> I looked in the AggregatorAE descriptor file along with it's dependency CdaCasInitializer.xml and see both have nothing in the Type System tab however I do see a handful of types specified on the Capabilities tab including "org.apache.ctakes.typesystem.type.textspan.Segment"
>
> So I added Segment type to the Type System tab. I reran and got this error:
>
> 11/14/13 2:23:39 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
> org.apache.uima.analysis_engine.AnalysisEngineProcessException: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
> Is there a file descriptor already setup maybe in another install with the necessary types/features to run the Document Preprocessor or will I manually have to add all of them? If not, I'd like to use UIMAfit to create the types/features to use with the Document Preprocessor as opposed to manually updating this descriptor with all the types and features needed. Can someone advise?
>
> Thanks.
>
> Regards,
> Paula
>
>
>
>
>
RE: cTakes Document Preprocessor Component Error
Posted by "Masanz, James J." <Ma...@mayo.edu>.
Try adding
org.apache.ctakes.typesystem.types.TypeSystem
as the type system.
So the source looks like:
<typeSystemDescription>
<imports>
<import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
</imports>
</typeSystemDescription>
Hope that helps
-- James
From: user-return-336-Masanz.James=mayo.edu@ctakes.apache.org [mailto:user-return-336-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of digital paula
Sent: Thursday, November 14, 2013 1:42 PM
To: user@ctakes.apache.org
Subject: cTakes Document Preprocessor Component Error
Hello cTakes Community,
I'm back after hanging out with the UIMA guys :-) for a while, getting a better grasp of the UIMA framework that cTakes sits on. I'm exploring and understanding cTakes components and starting with the Document Preprocessor:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Document+Preprocessor
I loaded the testpatient_cn_1.xml file in the CVD cTakes launcher and loaded the AggregateAE descriptor. It loaded but when I ran it, I got the following 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.
I looked in the AggregatorAE descriptor file along with it's dependency CdaCasInitializer.xml and see both have nothing in the Type System tab however I do see a handful of types specified on the Capabilities tab including "org.apache.ctakes.typesystem.type.textspan.Segment"
So I added Segment type to the Type System tab. I reran and got this error:
11/14/13 2:23:39 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
org.apache.uima.analysis_engine.AnalysisEngineProcessException: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
Is there a file descriptor already setup maybe in another install with the necessary types/features to run the Document Preprocessor or will I manually have to add all of them? If not, I'd like to use UIMAfit to create the types/features to use with the Document Preprocessor as opposed to manually updating this descriptor with all the types and features needed. Can someone advise?
Thanks.
Regards,
Paula
Re: cTakes Document Preprocessor Component Error
Posted by samir chabou <sa...@yahoo.com>.
try to rerun the jCasGen in the TypeSytem tab
On Thursday, November 14, 2013 2:42:13 PM, digital paula <cy...@hotmail.com> wrote:
Hello cTakes Community,
I'm back after hanging out with the UIMA guys :-) for a while, getting a better grasp of the UIMA framework that cTakes sits on. I'm exploring and understanding cTakes components and starting with the Document Preprocessor:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Document+Preprocessor
I loaded the testpatient_cn_1.xml file in the CVD cTakes launcher and loaded the AggregateAE descriptor. It loaded but when I ran it, I got the following 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.
I looked in the AggregatorAE descriptor file along with it's dependency CdaCasInitializer.xml and see both have nothing in the Type System tab however I do see a handful of types specified on the Capabilities tab including "org.apache.ctakes.typesystem.type.textspan.Segment"
So I added Segment type to the Type System tab. I reran and got this error:
11/14/13 2:23:39 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
org.apache.uima.analysis_engine.AnalysisEngineProcessException: Feature "id" is not defined for type "org.apache.ctakes.typesystem.type.textspan.Segment".
Is there a file descriptor already setup maybe in another install with the necessary types/features to run the Document Preprocessor or will I manually have to add all of them? If not, I'd like to use UIMAfit to create the types/features to use with the Document Preprocessor as opposed to manually updating this descriptor with all the types and features needed. Can someone advise?
Thanks.
Regards,
Paula
Re: cTakes Document Preprocessor Component Error
Posted by Pei Chen <pe...@wiredinformatics.com>.
Paula,
Which AggregateAE descriptor are you using? If it includes:
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/SimpleSegmentAnnotator.xml
In particular, ensure that this is included:
<typeSystemDescription>
<imports>
<import name="org.apache.ctakes.typesystem.types.TypeSystem"/>
</imports>
</typeSystemDescription>
If you plan to use uimaFIT, all you would need is to include the
ctakes-type-system project, it uses automatic type system detection via:
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.apache.uima.fit/types.txt
See example pipeline using uimaFIT:
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-examples/src/main/java/org/apache/ctakes/examples/pipelines/ExampleAggregatePipeline.java
Hope that helps...
Pei Chen
Wired Informatics <http://www.wiredinformatics.com>
265 Franklin St Ste 1702
Boston, MA 02110
tel: (617) 433-7544
Pei.Chen@wiredinformatics.com
On Wed, Nov 26, 2014 at 11:27 PM, Pei Chen <ch...@apache.org> wrote:
>
> ---------- Forwarded message ----------
> From: digital paula <cy...@hotmail.com>
> Date: Thu, Nov 14, 2013 at 2:41 PM
> Subject: cTakes Document Preprocessor Component Error
> To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
>
>
> Hello cTakes Community,
>
> I'm back after hanging out with the UIMA guys :-) for a while, getting a
> better grasp of the UIMA framework that cTakes sits on. I'm exploring
> and understanding cTakes components and starting with the Document
> Preprocessor:
>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Document+Preprocessor
>
> I loaded the testpatient_cn_1.xml file in the CVD cTakes launcher and
> loaded the AggregateAE descriptor. It loaded but when I ran it, I got the
> following 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.
>
> I looked in the AggregatorAE descriptor file along with it's dependency CdaCasInitializer.xml
> and see both have nothing in the Type System tab however I do see a handful
> of types specified on the Capabilities tab including
> "org.apache.ctakes.typesystem.type.textspan.Segment"
>
> So I added Segment type to the Type System tab. I reran and got this
> error:
>
> 11/14/13 2:23:39 PM - 14:
> org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Feature
> "id" is not defined for type
> "org.apache.ctakes.typesystem.type.textspan.Segment".
> org.apache.uima.analysis_engine.AnalysisEngineProcessException: Feature
> "id" is not defined for type
> "org.apache.ctakes.typesystem.type.textspan.Segment".
> Is there a file descriptor already setup maybe in another install with the
> necessary types/features to run the Document Preprocessor or will I
> manually have to add all of them? If not, I'd like to use UIMAfit to
> create the types/features to use with the Document Preprocessor as opposed
> to manually updating this descriptor with all the types and features
> needed. Can someone advise?
>
> Thanks.
>
> Regards,
> Paula
>
>
>
>
>
>
>