Return-Path: X-Original-To: apmail-ctakes-dev-archive@www.apache.org Delivered-To: apmail-ctakes-dev-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 8FC4FF01F for ; Tue, 2 Apr 2013 20:51:06 +0000 (UTC) Received: (qmail 51851 invoked by uid 500); 2 Apr 2013 20:51:06 -0000 Delivered-To: apmail-ctakes-dev-archive@ctakes.apache.org Received: (qmail 51799 invoked by uid 500); 2 Apr 2013 20:51:06 -0000 Mailing-List: contact dev-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@ctakes.apache.org Delivered-To: mailing list dev@ctakes.apache.org Received: (qmail 51783 invoked by uid 99); 2 Apr 2013 20:51:06 -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 20:51:06 +0000 X-ASF-Spam-Status: No, hits=2.5 required=5.0 tests=FREEMAIL_REPLY,HTML_MESSAGE,RCVD_IN_DNSWL_LOW,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (nike.apache.org: domain of kannanth@gmail.com designates 209.85.128.176 as permitted sender) Received: from [209.85.128.176] (HELO mail-ve0-f176.google.com) (209.85.128.176) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 02 Apr 2013 20:50:59 +0000 Received: by mail-ve0-f176.google.com with SMTP id ox1so1068657veb.21 for ; Tue, 02 Apr 2013 13:50:38 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:x-received:in-reply-to:references:date:message-id :subject:from:to:cc:content-type; bh=EML1pceZAkPOmWJte0lzakx4mF7K9f2g3JRO2EcCpCY=; b=hAQAPj5fcRLhSlyoC7tHiqWzcfB/512djM72Z+I2Ykl1+QbqfanqsshLIcFYSpa0lR kxIxT/6kW9DGz4Ac4DJT7/WK5C8Rs8sz7BUPl/+G2T6w6nNCZJ6VQMslBvytaS7L4oYP wuyFUVPqJ9uWxL5POEkD+QSCZAkobEz+KuSi2nk4f9c2u/DsgJ7ecRGYvOl/Ix61Xf2I lugaoKldzhzpFgXsSFE1A8yFTUfgDijQiJauUwuCMD1XuvNv+BzDPfjTDGU6BtQgQS8Z SGuAbUV6Kg+bQZW/VSmWqidsfSSzKoWnwOxaOxNXrktXRPGCP2vWSXpPi4miznlSzxji cKaA== MIME-Version: 1.0 X-Received: by 10.52.155.5 with SMTP id vs5mr11753414vdb.24.1364935838344; Tue, 02 Apr 2013 13:50:38 -0700 (PDT) Received: by 10.59.1.200 with HTTP; Tue, 2 Apr 2013 13:50:37 -0700 (PDT) In-Reply-To: <515B2F83.9020104@perfectsearchcorp.com> References:

<924DE05C19409B438EB81DE683A942D9104CFC59@CHEXMBX1A.CHBOSTON.ORG> <924DE05C19409B438EB81DE683A942D9104CFD73@CHEXMBX1A.CHBOSTON.ORG> <515AF935.1020308@childrens.harvard.edu> <515B02EE.2030705@perfectsearchcorp.com> <515B0677.9090700@perfectsearchcorp.com> <515B2F83.9020104@perfectsearchcorp.com> Date: Tue, 2 Apr 2013 15:50:37 -0500 Message-ID: Subject: Re: cTakes with java web application From: Kannan Thiagarajan To: user@ctakes.apache.org Cc: dev@ctakes.apache.org Content-Type: multipart/alternative; boundary=089e01633a94c95f1e04d966e357 X-Virus-Checked: Checked by ClamAV on apache.org --089e01633a94c95f1e04d966e357 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Thanks Kim. On Tue, Apr 2, 2013 at 2:20 PM, Kim Ebert 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 > > 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 separat= e > >>>> 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 n= ew > >> or > >>>>> non-dev users (and probably something we need to document better) i= s > >> 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)? A= m > 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 the= se > >> 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 > >> >>>>>> edu >>>>>> harvard.edu >> wrote: > >>>>>> > >>>>>> Hi Giri, > >>>>>> > >>>>>> I presume, essentially, you=92re planning to include the cTAKE= S > >>>>>> 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=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/org/chboston/**cnlp/ctakes/gui/service/** > >>>>>> LauncherService.java< > >> > 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 > >>>>>> 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=92t out of the box web application with > cTAKES, > >>>>>> however 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/< > >> http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/> > >>>>>> There are also some UIMA options that may point you in the rig= ht > >>>>>> direction. > >>>>>> > >>>>>> UIMA-AS (If you=92re gearing towards a Service Architecture fo= r > 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 > >>>>>> **] > >>>>>> *Sent:* Tuesday, April 02, 2013 12:29 AM > >>>>>> *To:* ctakes-user@incubator.apache.**org< > >> 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 > >>>>>> > >>>>>> > >>>>>> > >> > > > > --=20 Best Regards Kannan Thiagarajan --089e01633a94c95f1e04d966e357--