ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Kim Ebert <kim.eb...@perfectsearchcorp.com>
Subject Re: cTakes with java web application
Date Tue, 02 Apr 2013 16:10:22 GMT
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
>>>
>>>
>>>
>


Mime
View raw message