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From Kim Ebert <kim.eb...@perfectsearchcorp.com>
Subject Re: cTakes with java web application
Date Tue, 02 Apr 2013 19:20:35 GMT
Hi Kannan,

This does not allow pipelines to work. As far as I can tell, if you have
multiple instances of cTAKES, then they can work independently of each
other using the LVG patch, but they cannot currently share the same LVG
instance.

Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/

On 04/02/2013 10:56 AM, Kannan Thiagarajan 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
>>>>>>
>>>>>>
>>>>>>
>>
>


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