Return-Path: X-Original-To: apmail-ctakes-user-archive@www.apache.org Delivered-To: apmail-ctakes-user-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id D18DEF537 for ; Tue, 2 Apr 2013 14:46:08 +0000 (UTC) Received: (qmail 20175 invoked by uid 500); 2 Apr 2013 14:46:08 -0000 Delivered-To: apmail-ctakes-user-archive@ctakes.apache.org Received: (qmail 20113 invoked by uid 500); 2 Apr 2013 14:46:08 -0000 Mailing-List: contact user-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: user@ctakes.apache.org Delivered-To: mailing list user@ctakes.apache.org Received: (qmail 20088 invoked by uid 99); 2 Apr 2013 14:46:07 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 02 Apr 2013 14:46:07 +0000 X-ASF-Spam-Status: No, hits=1.5 required=5.0 tests=HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (nike.apache.org: domain of girinambari@gmail.com designates 209.85.223.175 as permitted sender) Received: from [209.85.223.175] (HELO mail-ie0-f175.google.com) (209.85.223.175) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 02 Apr 2013 14:46:01 +0000 Received: by mail-ie0-f175.google.com with SMTP id c12so472687ieb.6 for ; Tue, 02 Apr 2013 07:45:40 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=x-received:mime-version:in-reply-to:references:from:date:message-id :subject:to:content-type; bh=8vffNG07uvZZ7LXnlCGEjGDlXySJxlYlP4rNxFTy7E4=; b=jjNllJcFbbwb595gooN+5bK6Llfd7uUx7naRnBLzGgVLS95uYSwHvPRtQ/RQ6o3RUn DSLbJoBG6iNikLh0S4UV+nKVe9rt5RW0DCXswe0FM59fpq7vZvTo0b7SYFsF0ZbbD4Dr RbNIWdCZMK7WscCSd7bv6cDu4NwC66dSmDMbn4fdLn6nYxY9N3w6Fq1PYP//8SBtPpjt Md4+kUZBevd2uTXF9t5zd/pvYpXHN4PHNJVCughSW3NufYi4lOds0BKStoz0cxdj56YF SPhTzAhKVxrxyPAEFsdYA7FcBsaSv+G7HJ8UePhOHWmjFV2RsTG3CIalK8XdCEo9NcfF BDdA== X-Received: by 10.50.57.168 with SMTP id j8mr5232547igq.51.1364913940228; Tue, 02 Apr 2013 07:45:40 -0700 (PDT) MIME-Version: 1.0 Received: by 10.50.16.38 with HTTP; Tue, 2 Apr 2013 07:45:20 -0700 (PDT) In-Reply-To: <924DE05C19409B438EB81DE683A942D9104CFD73@CHEXMBX1A.CHBOSTON.ORG> References: <924DE05C19409B438EB81DE683A942D9104CFC59@CHEXMBX1A.CHBOSTON.ORG> <924DE05C19409B438EB81DE683A942D9104CFD73@CHEXMBX1A.CHBOSTON.ORG> From: giri vara prasad nambari Date: Tue, 2 Apr 2013 10:45:20 -0400 Message-ID: Subject: Re: cTakes with java web application To: user Content-Type: multipart/alternative; boundary=14dae9340ee78e6f5804d961ca1a X-Virus-Checked: Checked by ClamAV on apache.org --14dae9340ee78e6f5804d961ca1a Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable 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 wrote: > Hi Giri,**** > > I presume, essentially, you=92re planning to include the cTAKES lib(s) (v= ia > 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=92s > (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/o= rg/chboston/cnlp/ctakes/gui/service/LauncherService.java > **** > > ** ** > > Essentially, it boils down to a few lines of code:**** > > AnalysisEngine aggregateAE =3D AnalysisEngineFactory.createAggregate(**** > > engines, componentNames, typeSystemDescription, null,**** > > new SofaMapping[0]);**** > > **** > > JCas jcas =3D 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 > wrote:**** > > Hi Giri,**** > > Apache cTAKES is mainly in Java built on top of the UIMA Framework.**** > > Currently, there isn=92t out of the box web application with cTAKES, howe= ver > there is a GUI currently in the sandbox area but isn=92t 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 directio= n. > **** > > UIMA-AS (If you=92re 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**** > > **** > > **** > > ** ** > --14dae9340ee78e6f5804d961ca1a Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
Hi Pei,
=A0
Thanks for your time!=
=A0
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.
=A0=
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?
=A0
The reason is, I wou= ld 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 nee= d to go back re-evaluate the software stack.
=A0
Thank you,
Giri


On Tue, Apr 2, 2013 at 10:20 AM,= Chen, Pei <Pei.Chen@childrens.harvard.edu> wro= te:

Hi Giri,

I presume, essential= ly, you=92re planning to include the cTAKES lib(s) (via mvn?) into your exi= sting app

1)Programmaticall= y configure the pipeline

2)Pass in a docum= ent(s) to cTAKES for processing

3)Do XYZ with the= output from the jCAS using the UIMA API=92s (such as writing to disk or sa= ving it to a db)

It is not quite prime time ready but, take a look pe= ek at the below (It uses uimaFIT to do the above):

http://svn.apache.org/repos/asf/ctakes/san= dbox/ctakes-gui/src/main/java/org/chboston/cnlp/ctakes/gui/service/Launcher= Service.java

=A0

Essentially, it boil= s down to a few lines of code:

AnalysisEngine aggregateAE =3D AnalysisEngineFactory.createA= ggregate(

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 engines, componen= tNames, typeSystemDescription, null,

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 new SofaMapping[0= ]);

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0

JCas jcas =3D aggregateAE.newJCas();

jcas.setDocumentText(doc.getText());

aggregateAE.process(jcas);

=A0

=A0

From: giri vara pr= asad 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

=A0

Hi Pei,

=A0

Thanks for your time on answering this.

=A0

Actually I am not looking for pre built web applicat= ion (or) GUI. I was expecting something like "include ctakes jars in m= y 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?=

=A0

I am not moving towards any SOA (or) pre-built GUI.<= u>

=A0

=A0

I would be happy to contribute to GUI, but first I n= eed to finish this ctakes integration task into my web application ASAP.=

=A0

I hope this time my question is more clear.

=A0

Thank you,

Giri

On Tue, Apr 2, 2013 at 9:51 AM, Chen, Pei <Pei.Chen@chil= drens.harvard.edu> wrote:

Hi Giri,

Apache cTAKES is mainly in Java built on top of the UIMA Framework.

Currently, there isn=92t out of the box web application with cTAKES, how= ever there is a GUI currently in the sandbox area but isn=92t quite ready f= or prime time yet.=A0 Is this something that you might be interested in con= tributing to?

http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/=

=A0

There are also some UIMA options that may point you in the right directi= on.

UIMA-AS (If you=92re gearing towards a S= ervice Architecture for your web app.)

http://uima.apache.org/d/uima-as-2.4.0/uima_async_sca= leout.html

=A0

There is also a Simple Rest service (but= runs in-process):

UIMA Simple Server<= /p>

http://uima.apache.org/sandbox.html#simple-server=

=A0

Thanks,

Pei

=A0

From: giri vara prasad nambari [mailto= :girinambari@gma= il.com]
Sent: Tuesday, April 02, 2013 12:29 AM
To: ctakes-user@incubator.apache.org
Subject: Fwd: cTakes with java web application<= /p>

=A0

=A0

Hi Community,

=A0

I did lot of google for sample java code to integrate cTakes into web ap= plication, can some one please point me in right direction.

=A0

I would like to use clinical pipeline with plain text instead of XML doc= uments.

=A0

Any help would be appreciated.

=A0

Thank you,

Giri

=A0

=A0

=A0


--14dae9340ee78e6f5804d961ca1a--