ctakes-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Kannan Thiagarajan <kanna...@gmail.com>
Subject Re: cTakes with java web application
Date Tue, 02 Apr 2013 20:50:37 GMT
Thanks Kim.


On Tue, Apr 2, 2013 at 2:20 PM, Kim Ebert
<kim.ebert@perfectsearchcorp.com>wrote:

> 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
> >>>>>>
> >>>>>>
> >>>>>>
> >>
> >
>
>


-- 
Best Regards
Kannan Thiagarajan

Mime
View raw message