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Posted to dev@ctakes.apache.org by Ben Yu <be...@pharm.utah.edu> on 2016/02/26 21:52:08 UTC
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(LvgAnnotator.java:565)
at edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getTokenProcessingPipeline(ClinicalPipelineFactory.java:132)
at edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getDefaultPipeline(ClinicalPipelineFactory.java:71)
at edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.main(ClinicalPipelineFactory.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
Re: ctakes our existing web application
Posted by "Mattmann, Chris A (3980)" <ch...@jpl.nasa.gov>.
Great to hear! Let me know and please feel free to issue pull
requests, and issues, etc.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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 <be...@pharm.utah.edu>
Reply-To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
Date: Friday, February 26, 2016 at 12:57 PM
To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
Subject: RE: ctakes our existing web application
>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 <be...@pharm.utah.edu>
>Reply-To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
>Date: Friday, February 26, 2016 at 12:52 PM
>To: "dev@ctakes.apache.org" <de...@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(LvgAnn
>>ota
>>tor.java:565)
>> at
>>edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getTokenProces
>>sin
>>gPipeline(ClinicalPipelineFactory.java:132)
>> at
>>edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getDefaultPipe
>>lin
>>e(ClinicalPipelineFactory.java:71)
>> at
>>edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.main(ClinicalP
>>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
>>
>
RE: ctakes our existing web application
Posted by Ben Yu <be...@pharm.utah.edu>.
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 <be...@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 <be...@pharm.utah.edu>
> Reply-To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
> Date: Friday, February 26, 2016 at 12:52 PM
> To: "dev@ctakes.apache.org" <de...@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
> >
>
>
Re: ctakes our existing web application
Posted by Bruce Tietjen <br...@perfectsearchcorp.com>.
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 <be...@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 <be...@pharm.utah.edu>
> Reply-To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
> Date: Friday, February 26, 2016 at 12:52 PM
> To: "dev@ctakes.apache.org" <de...@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(LvgAnn
> >ota
> >tor.java:565)
> > at
> >edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getTokenProces
> >sin
> >gPipeline(ClinicalPipelineFactory.java:132)
> > at
> >edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getDefaultPipe
> >lin
> >e(ClinicalPipelineFactory.java:71)
> > at
> >edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.main(ClinicalP
> >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
> >
>
>
RE: ctakes our existing web application
Posted by Ben Yu <be...@pharm.utah.edu>.
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 <be...@pharm.utah.edu>
Reply-To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
Date: Friday, February 26, 2016 at 12:52 PM
To: "dev@ctakes.apache.org" <de...@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(LvgAnn
>ota
>tor.java:565)
> at
>edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getTokenProces
>sin
>gPipeline(ClinicalPipelineFactory.java:132)
> at
>edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getDefaultPipe
>lin
>e(ClinicalPipelineFactory.java:71)
> at
>edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.main(ClinicalP
>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
>
Re: ctakes our existing web application
Posted by "Mattmann, Chris A (3980)" <ch...@jpl.nasa.gov>.
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 <be...@pharm.utah.edu>
Reply-To: "dev@ctakes.apache.org" <de...@ctakes.apache.org>
Date: Friday, February 26, 2016 at 12:52 PM
To: "dev@ctakes.apache.org" <de...@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(LvgAnnota
>tor.java:565)
> at
>edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getTokenProcessin
>gPipeline(ClinicalPipelineFactory.java:132)
> at
>edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.getDefaultPipelin
>e(ClinicalPipelineFactory.java:71)
> at
>edu.utah.porc.chartreview.ctakes.ClinicalPipelineFactory.main(ClinicalPipe
>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
>