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From Ben Yu <ben...@pharm.utah.edu>
Subject RE: ctakes our existing web application
Date Fri, 26 Feb 2016 22:10:17 GMT
Thank you Bruce for the tip. Makes sense! Didn't realize the file was within the jar.
ben

-----Original Message-----
From: Bruce Tietjen [mailto:bruce.tietjen@perfectsearchcorp.com] 
Sent: Friday, February 26, 2016 2:50 PM
To: dev@ctakes.apache.org
Subject: Re: ctakes our existing web application

FYI -- I believe the details of the error is that the Lvg needs to read it's data files from
a flat file (it doesn't support reading resources from a jar). The data file must be available
in a flat file and the configuration needs to point to the correct location for those files.


[image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior Software Engineer
[image: Mobile:] 801.634.1547
bruce.tietjen@imatsolutions.com

On Fri, Feb 26, 2016 at 1:57 PM, Ben Yu <ben.yu@pharm.utah.edu> wrote:

> Oh beautiful! Thank you Chris. Exactly the direction I was going to. 
> I'll dive into it ...
>
> Thanks,
> ben
>
> -----Original Message-----
> From: Mattmann, Chris A (3980) [mailto:chris.a.mattmann@jpl.nasa.gov]
> Sent: Friday, February 26, 2016 1:54 PM
> To: dev@ctakes.apache.org
> Subject: Re: ctakes our existing web application
>
> Hey there,
>
> You may want to look at Shangridocs, which provides cTAKES as a REST 
> service via Tika:
>
> http://github.com/chrismattmann/shangridocs.git
>
> Happy to help get you started.
>
> Cheers,
> Chris
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Chris Mattmann, Ph.D.
> Chief Architect
> Instrument Software and Science Data Systems Section (398) NASA Jet 
> Propulsion Laboratory Pasadena, CA 91109 USA
> Office: 168-519, Mailstop: 168-527
> Email: chris.a.mattmann@nasa.gov
> WWW:  http://sunset.usc.edu/~mattmann/
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Adjunct Associate Professor, Computer Science Department University of 
> Southern California, Los Angeles, CA 90089 USA
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
>
> -----Original Message-----
> From: Ben Yu <ben.yu@pharm.utah.edu>
> Reply-To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
> Date: Friday, February 26, 2016 at 12:52 PM
> To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
> Subject: ctakes our existing web application
>
> >Hi group,
> >We started to look at options to integrate ctakes into our existing 
> >web app and started the experiment on the ClinicalPipelineFactory 
> >class. I can run it with different engine descriptions and see the 
> >outputs without doing any modifications. But when I create my own 
> >class in my web app and follow the same logic, I got this error:
> >Exception in thread "main" java.lang.IllegalArgumentException: URI is 
> >not hierarchical
> >        at java.io.File.<init>(File.java:418)
> >        at
> >org.apache.ctakes.lvg.ae.LvgAnnotator.createAnnotatorDescription(LvgA
> >nn
> >ota
> >tor.java:565)
> >        at
> >edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getTokenProc
> >es
> >sin
> >gPipeline(ClinicalPipelineFactory.java:132)
> >        at
> >edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getDefaultPi
> >pe
> >lin
> >e(ClinicalPipelineFactory.java:71)
> >        at
> >edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.main(Clinica
> >lP
> >ipe
> >lineFactory.java:244)
> >
> >I am very new to ctakes and I realized there are lots of setups need 
> >to be done but not sure if this is related to anything amiss?
> >
> >The web app is a spring/maven project. I've put in all the ctakes 
> >dependencies and got over the compiling. Above was a run time error.
> >
> >Thanks in adance for any help,
> >Ben
> >801-587-7751
> >
>
>
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