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From Pei Chen <chen...@apache.org>
Subject Re: cTakes - help please
Date Tue, 20 Oct 2015 15:45:48 GMT
Chris,
Could you confirm if the paths were modified? if so, is it accurate?  In
particular, per error message: des -> desc?
Malformed URL c:/apache-ctakes-3.2.2/*des*/ctakes-chunker/desc

If not, would you mind including the descriptor xml's?
--Pei

On Mon, Oct 19, 2015 at 5:38 PM, Tonner, Chris <Chris.Tonner@ucsf.edu>
wrote:

> Hello:
>
>
>
> I work in the Department of Medicine at the University of California, San
> Francisco.  We are interested in cTakes to extract medical information from
> our EMRs.
>
>
>
> I have been attempting to install and run cTakes, but have had some
> problems.  Would you be able to give us technical help to get cTakes up and
> running.
>
>
>
> Following the instructions on the User Installation Guide.
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide
>
>
>
> I  have modified the two bat files c: bin\runctakesCVD.bat file  and
> CPE.bat… Example of modified code – is this correct?
>
>
>
> @REM set ctakes.umlsuser=[christonner], ctakes.umlspw=[123Start]
>
> @REM or add the properties
>
> @REM -Dctakes.umlsuser=[christonner] -Dctakes.umlspw=[123Start]
>
>
>
> These batch files run and the debugger opens.
>
>
>
> I can load some of the analysis engine, but get errors with the UMLS and
> the negation AE.
>
>
>
> In short we are at a loss on how to troubleshoot this.  Is there a more
> extensive manual on how to install cTakes and how to use cTakes?
>
>
>
> Error Examples.
>
>
>
> SEVERE: Malformed URL
> c:/apache-ctakes-3.2.2/des/ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml
> in import declaration. (Descriptor:
> file:/C:/apache-ctakes-3.2.2/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml)
>
> org.apache.uima.resource.ResourceInitializationException: Malformed URL
> c:/apache-ctakes-3.2.2/des/ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml
> in import declaration.
>
> (Descriptor:
> file:/C:/apache-ctakes-3.2.2/desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml)
>
>
>
> Thanks you,
>
> Chris Tonner
>
> University of California, San Francisco
>
>
>
>
>
>
>

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