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From Andy McMurry <mcmurry.a...@gmail.com>
Subject Re: cTakes with java web application
Date Tue, 02 Apr 2013 19:05:23 GMT
Since we are on the topic of "fronting" the application to a high performance backend cluster,
I invite you all to check out our Apache friends at MAHOUT 

https://cwiki.apache.org/confluence/display/MAHOUT/Algorithms



On Apr 2, 2013, at 9:56 AM, Kannan Thiagarajan <kannanth@gmail.com> wrote:

> Kim,
> 
> Thanks. I remember seeing this JIRA. 
> 
> Is LVG the only component with known thread-safety issue?  Also, I was not clear if the
patch makes LVG fully thread safe and usable within a Web container. 
> 
> Giri - Sorry for hijacking your thread. But for the benefit of those thinking of using
cTAKES in a WebApp, thread safety is a major concern. Hence I brought it up. 
> 
> 
> Thanks
> Kannan
>  
> 
> 
> 
> 
> 
> On Tue, Apr 2, 2013 at 11:25 AM, Kim Ebert <kim.ebert@perfectsearchcorp.com> wrote:
> Adding user@ctakes.apache.org
> 
> Kim Ebert
> 1.801.669.7342
> Perfect Search Corp
> http://www.perfectsearchcorp.com/
> 
> On 04/02/2013 10:10 AM, Kim Ebert wrote:
> > Hi Kannan,
> >
> > Please see:
> >
> > https://issues.apache.org/jira/browse/CTAKES-149
> >
> > I have not yet had time to bring the patches forward to trunk.
> >
> > Kim Ebert
> > 1.801.669.7342
> > Perfect Search Corp
> > http://www.perfectsearchcorp.com/
> >
> > On 04/02/2013 09:47 AM, Kannan Thiagarajan wrote:
> >> Hello,
> >>
> >> I have a similar use-case (for a web-service). However, on a separate
> >> thread I heard that cTAKES is not entirely thread-safe. I'm curious if its
> >> still the case or if this has been resolved.
> >>
> >> Thanks
> >> Kannan
> >>
> >>
> >>
> >>
> >> On Tue, Apr 2, 2013 at 10:28 AM, Tim Miller <
> >> timothy.miller@childrens.harvard.edu> wrote:
> >>
> >>> Gira,
> >>> Your use case is probably one that will become more and more common, and
> >>> cTAKES devs do similar things all the time. I think the hangup to new or
> >>> non-dev users (and probably something we need to document better) is that
> >>> cTAKES is built on top of UIMA, and so the techniques for running pipelines
> >>> and extracting information are actually UIMA and UIMAFit-based, and so
> >>> there is nothing like the traditional javadocs explaining a cTAKES API to
> >>> rely on.
> >>>
> >>> Pei's sample code is basically UIMA and UIMAFit standard code that points
> >>> at cTAKES pipelines, then once that is working the real cTAKES part is
> >>> basically just understanding the type system so you know how to use UIMA
> >>> API calls to extract the information you need. So maybe better
> >>> documentation of the type system (maybe in javadoc style) is something that
> >>> cTAKES should prioritize.
> >>>
> >>> Tim
> >>>
> >>>
> >>> On 04/02/2013 10:45 AM, giri vara prasad nambari wrote:
> >>>
> >>>> Hi Pei,
> >>>> Thanks for your time!
> >>>> Sort of this is what I am looking for. I will do some research on javadoc
> >>>> to see what I could do with the API.
> >>>> May I ask you one more question? Isn't ctakes build to accommodate these
> >>>> types of requirements (like integrating with other application)? Am
I
> >>>> missing something important?
> >>>> The reason is, I would need to read the out put of ctakes and perform
> >>>> some other analysis using WEKA. If ctakes is not yet ready for these
types
> >>>> of requirements I may need to go back re-evaluate the software stack.
> >>>> Thank you,
> >>>> Giri
> >>>>
> >>>>
> >>>> On Tue, Apr 2, 2013 at 10:20 AM, Chen, Pei <Pei.Chen@childrens.harvard.**
> >>>> edu <Pei.Chen@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
> >>>> harvard.edu <Pei.Chen@childrens.harvard.edu>>> wrote:
> >>>>
> >>>>     Hi Giri,
> >>>>
> >>>>     I presume, essentially, you’re planning to include the cTAKES
> >>>>     lib(s) (via mvn?) into your existing app
> >>>>
> >>>>     1)Programmatically configure the pipeline
> >>>>
> >>>>     2)Pass in a document(s) to cTAKES for processing
> >>>>
> >>>>     3)Do XYZ with the output from the jCAS using the UIMA API’s (such
> >>>>
> >>>>     as writing to disk or saving it to a db)
> >>>>
> >>>>     It is not quite prime time ready but, take a look peek at the
> >>>>     below (It uses uimaFIT to do the above):
> >>>>
> >>>>     http://svn.apache.org/repos/**asf/ctakes/sandbox/ctakes-gui/**
> >>>> src/main/java/org/chboston/**cnlp/ctakes/gui/service/**
> >>>> LauncherService.java<http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/src/main/java/org/chboston/cnlp/ctakes/gui/service/LauncherService.java>
> >>>>
> >>>>     Essentially, it boils down to a few lines of code:
> >>>>
> >>>>     AnalysisEngine aggregateAE = AnalysisEngineFactory.**createAggregate(
> >>>>
> >>>>                    engines, componentNames, typeSystemDescription, null,
> >>>>
> >>>>                    new SofaMapping[0]);
> >>>>
> >>>>     JCas jcas = aggregateAE.newJCas();
> >>>>
> >>>>     jcas.setDocumentText(doc.**getText());
> >>>>
> >>>>     aggregateAE.process(jcas);
> >>>>
> >>>>     *From:*giri vara prasad nambari [mailto:girinambari@gmail.com
> >>>>     <mailto:girinambari@gmail.com>**]
> >>>>     *Sent:* Tuesday, April 02, 2013 10:04 AM
> >>>>     *To:* user@ctakes.apache.org <mailto:user@ctakes.apache.org**>
> >>>>     *Subject:* Re: cTakes with java web application
> >>>>
> >>>>
> >>>>     Hi Pei,
> >>>>
> >>>>     Thanks for your time on answering this.
> >>>>
> >>>>     Actually I am not looking for pre built web application (or) GUI.
> >>>>     I was expecting something like "include ctakes jars in my web
> >>>>     application ((or) even for the matter any client java program)"
> >>>>     and start using ctakes API. Is this possible with ctakes api? If
> >>>>     so, any sample ctakes client code available?
> >>>>
> >>>>     I am not moving towards any SOA (or) pre-built GUI.
> >>>>
> >>>>     I would be happy to contribute to GUI, but first I need to finish
> >>>>     this ctakes integration task into my web application ASAP.
> >>>>
> >>>>     I hope this time my question is more clear.
> >>>>
> >>>>     Thank you,
> >>>>
> >>>>     Giri
> >>>>
> >>>>     On Tue, Apr 2, 2013 at 9:51 AM, Chen, Pei
> >>>>     <Pei.Chen@childrens.harvard.**edu <Pei.Chen@childrens.harvard.edu>
> >>>>     <mailto:Pei.Chen@childrens.**harvard.edu<Pei.Chen@childrens.harvard.edu>>>
> >>>> wrote:
> >>>>
> >>>>     Hi Giri,
> >>>>
> >>>>     Apache cTAKES is mainly in Java built on top of the UIMA Framework.
> >>>>
> >>>>     Currently, there isn’t out of the box web application with cTAKES,
> >>>>     however there is a GUI currently in the sandbox area but isn’t
> >>>>     quite ready for prime time yet.  Is this something that you might
> >>>>     be interested in contributing to?
> >>>>
> >>>>     http://svn.apache.org/repos/**asf/ctakes/sandbox/ctakes-gui/<http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/>
> >>>>
> >>>>     There are also some UIMA options that may point you in the right
> >>>>     direction.
> >>>>
> >>>>     UIMA-AS (If you’re gearing towards a Service Architecture for
your
> >>>>     web app.)
> >>>>
> >>>>     http://uima.apache.org/d/uima-**as-2.4.0/uima_async_scaleout.**html<http://uima.apache.org/d/uima-as-2.4.0/uima_async_scaleout.html>
> >>>>
> >>>>     There is also a Simple Rest service (but runs in-process):
> >>>>
> >>>>     UIMA Simple Server
> >>>>
> >>>>     http://uima.apache.org/**sandbox.html#simple-server<http://uima.apache.org/sandbox.html#simple-server>
> >>>>
> >>>>     Thanks,
> >>>>
> >>>>     Pei
> >>>>
> >>>>     *From:*giri vara prasad nambari [mailto:girinambari@gmail.com
> >>>>     <mailto:girinambari@gmail.com>**]
> >>>>     *Sent:* Tuesday, April 02, 2013 12:29 AM
> >>>>     *To:* ctakes-user@incubator.apache.**org<ctakes-user@incubator.apache.org>
> >>>>     <mailto:ctakes-user@incubator.**apache.org<ctakes-user@incubator.apache.org>
> >>>>     *Subject:* Fwd: cTakes with java web application
> >>>>
> >>>>
> >>>>     Hi Community,
> >>>>
> >>>>     I did lot of google for sample java code to integrate cTakes into
> >>>>     web application, can some one please point me in right direction.
> >>>>
> >>>>     I would like to use clinical pipeline with plain text instead of
> >>>>     XML documents.
> >>>>
> >>>>     Any help would be appreciated.
> >>>>
> >>>>     Thank you,
> >>>>
> >>>>     Giri
> >>>>
> >>>>
> >>>>
> 
> 
> 
> 
> -- 
> Best Regards
> Kannan Thiagarajan
> 


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