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From Kim Ebert <kim.eb...@perfectsearchcorp.com>
Subject Re: cTakes with java web application
Date Tue, 02 Apr 2013 16:25:27 GMT
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
>>>>
>>>>
>>>>


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