You are viewing a plain text version of this content. The canonical link for it is here.

Posted to dev@ctakes.apache.org by Tim Miller <ti...@childrens.harvard.edu> on 2013/04/02 17:28:53 UTC

Re: cTakes with java web application

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 
> <ma...@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
>
>     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
>     <ma...@gmail.com>]
>     *Sent:* Tuesday, April 02, 2013 10:04 AM
>     *To:* user@ctakes.apache.org <ma...@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
>     <ma...@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/
>
>     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
>
>     There is also a Simple Rest service (but runs in-process):
>
>     UIMA Simple Server
>
>     http://uima.apache.org/sandbox.html#simple-server
>
>     Thanks,
>
>     Pei
>
>     *From:*giri vara prasad nambari [mailto:girinambari@gmail.com
>     <ma...@gmail.com>]
>     *Sent:* Tuesday, April 02, 2013 12:29 AM
>     *To:* ctakes-user@incubator.apache.org
>     <ma...@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
>
>

Re: cTakes with java web application

Posted by Kannan Thiagarajan <ka...@gmail.com>.

Thanks Kim.


On Tue, Apr 2, 2013 at 2:20 PM, Kim Ebert
<ki...@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
> > <ki...@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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
> >>>>>> harvard.edu <Pe...@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
> >>>>>>     <ma...@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
> >>>>>>     <ma...@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

Re: cTakes with java web application

Posted by Kannan Thiagarajan <ka...@gmail.com>.

Thanks Kim.


On Tue, Apr 2, 2013 at 2:20 PM, Kim Ebert
<ki...@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
> > <ki...@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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
> >>>>>> harvard.edu <Pe...@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
> >>>>>>     <ma...@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
> >>>>>>     <ma...@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

Re: cTakes with java web application

Posted by Kim Ebert <ki...@perfectsearchcorp.com>.

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
> <ki...@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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
>>>>>> harvard.edu <Pe...@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
>>>>>>     <ma...@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
>>>>>>     <ma...@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
>>>>>>
>>>>>>
>>>>>>
>>
>

Re: cTakes with java web application

Posted by Kim Ebert <ki...@perfectsearchcorp.com>.

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
> <ki...@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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
>>>>>> harvard.edu <Pe...@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
>>>>>>     <ma...@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
>>>>>>     <ma...@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
>>>>>>
>>>>>>
>>>>>>
>>
>

Re: cTakes with java web application

Posted by Andy McMurry <mc...@gmail.com>.

Since we are on the topic of "fronting" the application to a high performance backend cluster, I invite you all to check out our Apache friends at MAHOUT 

https://cwiki.apache.org/confluence/display/MAHOUT/Algorithms



On Apr 2, 2013, at 9:56 AM, Kannan Thiagarajan <ka...@gmail.com> 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 <ki...@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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
> >>>> harvard.edu <Pe...@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
> >>>>     <ma...@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 <Pe...@childrens.harvard.edu>
> >>>>     <ma...@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
> >>>>     <ma...@gmail.com>**]
> >>>>     *Sent:* Tuesday, April 02, 2013 12:29 AM
> >>>>     *To:* ctakes-user@incubator.apache.**org<ct...@incubator.apache.org>
> >>>>     <ma...@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
>

Re: cTakes with java web application

Posted by Andy McMurry <mc...@gmail.com>.

Since we are on the topic of "fronting" the application to a high performance backend cluster, I invite you all to check out our Apache friends at MAHOUT 

https://cwiki.apache.org/confluence/display/MAHOUT/Algorithms



On Apr 2, 2013, at 9:56 AM, Kannan Thiagarajan <ka...@gmail.com> 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 <ki...@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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
> >>>> harvard.edu <Pe...@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
> >>>>     <ma...@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 <Pe...@childrens.harvard.edu>
> >>>>     <ma...@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
> >>>>     <ma...@gmail.com>**]
> >>>>     *Sent:* Tuesday, April 02, 2013 12:29 AM
> >>>>     *To:* ctakes-user@incubator.apache.**org<ct...@incubator.apache.org>
> >>>>     <ma...@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
>

Re: cTakes with java web application

Posted by Kannan Thiagarajan <ka...@gmail.com>.

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
<ki...@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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
> >>>> harvard.edu <Pe...@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
> >>>>     <ma...@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
> >>>>     <ma...@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

Re: cTakes with java web application

Posted by Kannan Thiagarajan <ka...@gmail.com>.

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
<ki...@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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
> >>>> harvard.edu <Pe...@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
> >>>>     <ma...@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
> >>>>     <ma...@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

Re: cTakes with java web application

Posted by Kim Ebert <ki...@perfectsearchcorp.com>.

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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
>>>> harvard.edu <Pe...@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
>>>>     <ma...@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 <Pe...@childrens.harvard.edu>
>>>>     <ma...@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
>>>>     <ma...@gmail.com>**]
>>>>     *Sent:* Tuesday, April 02, 2013 12:29 AM
>>>>     *To:* ctakes-user@incubator.apache.**org<ct...@incubator.apache.org>
>>>>     <ma...@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
>>>>
>>>>
>>>>

Re: cTakes with java web application

Posted by Kim Ebert <ki...@perfectsearchcorp.com>.

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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
>>>> harvard.edu <Pe...@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
>>>>     <ma...@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 <Pe...@childrens.harvard.edu>
>>>>     <ma...@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
>>>>     <ma...@gmail.com>**]
>>>>     *Sent:* Tuesday, April 02, 2013 12:29 AM
>>>>     *To:* ctakes-user@incubator.apache.**org<ct...@incubator.apache.org>
>>>>     <ma...@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
>>>>
>>>>
>>>>

Re: cTakes with java web application

Posted by Kim Ebert <ki...@perfectsearchcorp.com>.

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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
>>> harvard.edu <Pe...@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
>>>     <ma...@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 <Pe...@childrens.harvard.edu>
>>>     <ma...@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
>>>     <ma...@gmail.com>**]
>>>     *Sent:* Tuesday, April 02, 2013 12:29 AM
>>>     *To:* ctakes-user@incubator.apache.**org<ct...@incubator.apache.org>
>>>     <ma...@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
>>>
>>>
>>>
>

Re: cTakes with java web application

Posted by Kannan Thiagarajan <ka...@gmail.com>.

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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
>> harvard.edu <Pe...@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
>>     <ma...@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 <Pe...@childrens.harvard.edu>
>>     <ma...@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
>>     <ma...@gmail.com>**]
>>     *Sent:* Tuesday, April 02, 2013 12:29 AM
>>     *To:* ctakes-user@incubator.apache.**org<ct...@incubator.apache.org>
>>     <ma...@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

Re: cTakes with java web application

Posted by giri vara prasad nambari <gi...@gmail.com>.

Hi Tim and Team,

I see. Now I am getting more clarity on the way I need to spend my time.

cTakes is more on defining type systems and pipeline. UIMA/UIMA-Fit is the
code which really process the text based on cTakes definitions to extract
information. Am I correct?

I know your time is valuable, but, could some one help me with any
documentation for UIMA-Fit client code (and/or) related documentation? (I
just started on this domain, so any pointers would be really helpful).

Thanks for your time.

Thank you,
Giri


On Tue, Apr 2, 2013 at 11:28 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
> > 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
>>
>>
>>
>> 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]
>> *Sent:* Tuesday, April 02, 2013 10:04 AM
>> *To:* 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 <Pe...@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/
>>
>>
>>
>> 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
>>
>>
>>
>> There is also a Simple Rest service (but runs in-process):
>>
>> UIMA Simple Server
>>
>> http://uima.apache.org/sandbox.html#simple-server
>>
>>
>>
>> Thanks,
>>
>> Pei
>>
>>
>>
>> *From:* giri vara prasad nambari [mailto:girinambari@gmail.com]
>> *Sent:* Tuesday, April 02, 2013 12:29 AM
>> *To:* 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
>>
>>
>>
>>
>>
>>
>>
>
>
>

Re: cTakes with java web application

Posted by giri vara prasad nambari <gi...@gmail.com>.

Hi Tim and Team,

I see. Now I am getting more clarity on the way I need to spend my time.

cTakes is more on defining type systems and pipeline. UIMA/UIMA-Fit is the
code which really process the text based on cTakes definitions to extract
information. Am I correct?

I know your time is valuable, but, could some one help me with any
documentation for UIMA-Fit client code (and/or) related documentation? (I
just started on this domain, so any pointers would be really helpful).

Thanks for your time.

Thank you,
Giri


On Tue, Apr 2, 2013 at 11:28 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
> > 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
>>
>>
>>
>> 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]
>> *Sent:* Tuesday, April 02, 2013 10:04 AM
>> *To:* 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 <Pe...@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/
>>
>>
>>
>> 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
>>
>>
>>
>> There is also a Simple Rest service (but runs in-process):
>>
>> UIMA Simple Server
>>
>> http://uima.apache.org/sandbox.html#simple-server
>>
>>
>>
>> Thanks,
>>
>> Pei
>>
>>
>>
>> *From:* giri vara prasad nambari [mailto:girinambari@gmail.com]
>> *Sent:* Tuesday, April 02, 2013 12:29 AM
>> *To:* 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
>>
>>
>>
>>
>>
>>
>>
>
>
>

Re: cTakes with java web application

Posted by Kannan Thiagarajan <ka...@gmail.com>.

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 <Pe...@childrens.harvard.edu> <mailto:Pei.Chen@childrens.**
>> harvard.edu <Pe...@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
>>     <ma...@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 <Pe...@childrens.harvard.edu>
>>     <ma...@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
>>     <ma...@gmail.com>**]
>>     *Sent:* Tuesday, April 02, 2013 12:29 AM
>>     *To:* ctakes-user@incubator.apache.**org<ct...@incubator.apache.org>
>>     <ma...@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