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From Kannan Thiagarajan <kanna...@gmail.com>
Subject Re: cTakes with java web application
Date Tue, 02 Apr 2013 15:47:23 GMT
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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