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From Matthew Vita <matthewvit...@gmail.com>
Subject Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Date Sat, 16 Dec 2017 06:01:54 GMT
I should note that my main work item at the moment is getting the
Dictionary GUI tool to write straight to MySQL to make this (and other
solutions) more streamlined. I have read over the code and understand it
pretty well. Just fighting to load in the MySQL driver despite what I
thought was the right approach (
https://github.com/GoTeamEpsilon/ctakes-rest-service/issues/2#issuecomment-351921458).
Going to spend some time on it over the weekend :).

I'm very grateful for Gandhi and you all.

cTAKES + REST = many possibilities as we enter into the new year!

Thanks,

Matthew Vita
www.matthewvita.com

On Fri, Dec 15, 2017 at 9:56 PM, Matthew Vita <matthewvita48@gmail.com>
wrote:

> > could be wrapped in a docker container that would be really powerful,
>
> ​I am on it!​
>
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Fri, Dec 15, 2017 at 6:46 AM, Miller, Timothy <
> Timothy.Miller@childrens.harvard.edu> wrote:
>
>> Great, that's very helpful.
>>
>> I'll be happy to help with extracting the information needed from the
>> CAS the easy way. Sean, am I remembering right that there was an API
>> started for that somewhere? Or maybe that was part of DeepPhe?
>>
>> Tim
>>
>>
>> On Fri, 2017-12-15 at 03:52 +0000, Gandhi Rajan Natarajan wrote:
>> > Hi Tim,
>> >
>> > Thanks for taking time out and having a look at this. As you
>> > mentioned, the dictionary descriptor file contains details specific
>> > to my setup which needs to be changes to 127.0.0.1 by default. Will
>> > make the change accordingly.
>> >
>> > The only reason we went ahead with the approach of parsing XML to
>> > JSON is due to our lack of in-depth knowledge in cTAKES
>> > implementations. If I could get some guidance on how to get the
>> > required JSON details directly from type systems, will be happy to
>> > implement the same as it will be a huge performance gain.
>> >
>> > Also as you said we have two directories names ctakes-web-rest and
>> > ctakes-rest-service. Ctakes-rest-service directory is no longer
>> > active and its obsolete. We are just maintaining it for some
>> > reference for the time being. We will knock it off soon.
>> >
>> > Thanks again for the detailed feedback.
>> >
>> > Regards,
>> > Gandhi
>> >
>> >
>> > -----Original Message-----
>> > From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
>> > Sent: Friday, December 15, 2017 1:25 AM
>> > To: dev@ctakes.apache.org
>> > Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS]
>> > [SUSPICIOUS]
>> >
>> > I looked at this today. Looks like a great start!
>> >
>> > I was able to get as far as deploying to tomcat, seeing the web form,
>> > and submitting, but didn't get correct feedback because I don't have
>> > a mysql dictionary set up, which the default descriptor points at. I
>> > didn't see any instructions for building that and didn't have time to
>> > figure that out.
>> >
>> > I think I mentioned in a different thread that if this whole thing
>> > could be wrapped in a docker container that would be really powerful,
>> > but if not, there are a few things that are obvious to you as
>> > developers but would make it easier for novices (like me) to deploy.
>> >
>> > * download tomcat bin and start with bin/startup.sh (check at
>> > localhost:8080)
>> > * run mvn install on my ctakes installation to populate jar files in
>> > the .m2 directory that were missing
>> > * run mvn package inside the ctakes-web-rest subdirectory
>> > * copy the .war file into the webapps directory in my tomcat
>> > installation.
>> > * While I couldn't get the dictionary to work pointing to mysql, I
>> > noticed that the dictionary descriptor file has a hardcoded IP
>> > address when maybe it should be 127.0.0.1?
>> >
>> > One other thing I noticed in the code is that in sending back JSON it
>> > looks like you're turning the JCas into xml and then parsing it
>> > yourself. It should be easier just to access typesystem objects
>> > directly. Sean may have some API code laying around to simplify that
>> > as well.
>> >
>> > To iterate over signs/symptoms, for example, you would do:
>> >
>> > for(SignSymptomMention ss : JCasUtil.select(jcas,
>> > SignSymptomMention.class)){
>> >   int begin = ss.getBegin(); // begin offset
>> >   int end = ss.getEnd():     // end offset ...
>> > }
>> >
>> > Using the typesystem directly may help you to speed up that code or
>> > make it easier to read. But maybe there is a reason to write it to
>> > xml that I'm not aware of.
>> >
>> > Finally, I see there are two sub-directories with similar names,
>> > ctakes-rest-service and ctakes-web-rest. If they are duplicates can
>> > you delete the old one?
>> >
>> > I'll keep poking around, but hopefully this is helpful feedback for
>> > you guys. Thanks again for getting this off the ground!
>> >
>> > Tim
>> >
>> >
>> >
>> >
>> > On Thu, 2017-12-07 at 14:16 +0000, Miller, Timothy wrote:
>> > >
>> > > I am really interested in this too, just waiting until I have a few
>> > > free hours to look around. Don't want you to think it's not of
>> > > interest.
>> > > Tim
>> > >
>> > >
>> > > On Tue, 2017-12-05 at 19:18 +0000, Finan, Sean wrote:
>> > > >
>> > > >
>> > > > Hi all,
>> > > >
>> > > > I am trying to clear a backlog at work.  I will most likely not
>> > > > be
>> > > > able to do anything with ctakes for another week.  Hopefully some
>> > > > rest expert out there can prove their worth by testing ...
>> > > >
>> > > > Sean
>> > > >
>> > > > -----Original Message-----
>> > > > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>> > > > Sent: Tuesday, December 05, 2017 1:58 PM
>> > > > To: dev@ctakes.apache.org
>> > > > Subject: Re: cTAKES as REST service [EXTERNAL]
>> > > >
>> > > >
>> > > > Hi Gandhi, Sean, Tim, Alex, James,
>> > > >
>> > > > I'm still getting back into the swing of things after my trip
>> > > > (I'm
>> > > > on business traveling at the moment, here in the states). I will
>> > > > be
>> > > > jumping right back into cTAKES REST development next week
>> > > > personally
>> > > > and with a new team mate from the open source team.
>> > > >
>> > > > I'm so sorry for my silence/lack of updates!!! Very excited to
>> > > > see
>> > > > what Gandhi's updates are looking like and enriching the JSON
>> > > > response payload.
>> > > >
>> > > > Thanks,
>> > > >
>> > > > Matthew Vita
>> > > > www.matthewvita.com
>> > > >
>> > > > On Tue, Dec 5, 2017 at 10:24 AM, Gandhi Rajan Natarajan <
>> > > > Gandhi.Nata rajan@arisglobal.com> wrote:
>> > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > > Could someone help me out on the resources cleanup atleast if
>> > > > > not
>> > > > > review?
>> > > > >
>> > > > > Regards,
>> > > > > Gandhi
>> > > > >
>> > > > >
>> > > > > -----Original Message-----
>> > > > > From: Gandhi Rajan Natarajan [mailto:Gandhi.Natarajan@arisgloba
>> > > > > l.
>> > > > > co
>> > > > > m]
>> > > > > Sent: Monday, December 04, 2017 10:05 PM
>> > > > > To: dev@ctakes.apache.org
>> > > > > Subject: RE: cTAKES as REST service [EXTERNAL]
>> > > > >
>> > > > > Hi Sean, Tim, Alex, Matthew, James and All,
>> > > > >
>> > > > > I have placed the first cut version of cTAKES REST module in
>> > > > > the
>> > > > > following path -
>> > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com
>> > > > > _G
>> > > > > oT
>> > > > > eam
>> > > > > Epsilon_ctakes-2Drest-
>> > > > > 2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x
>> > > > > hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d
>> > > > > 4g
>> > > > > Ta
>> > > > > o&m
>> > > > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarV
>> > > > > c3
>> > > > > BP
>> > > > > MxK
>> > > > > izpqJwoUJtjIJZC8C6iA&e=
>> > > > > master/ctakes-web-rest/
>> > > > >
>> > > > > Things pending in the module:
>> > > > > 1) Index Page to test the rest module using AJAX call
>> > > > > 2) Revamping the final output XML
>> > > > >
>> > > > > Request you all to have a look at this module and provide your
>> > > > > feedback. I would also require expert advice to clean up the
>> > > > > resources folder -
>> > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com
>> > > > > _G
>> > > > > oT
>> > > > > eam
>> > > > > Epsilon_ctakes-2Drest-
>> > > > > 2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x
>> > > > > hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d
>> > > > > 4g
>> > > > > Ta
>> > > > > o&m
>> > > > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarV
>> > > > > c3
>> > > > > BP
>> > > > > MxK
>> > > > > izpqJwoUJtjIJZC8C6iA&e= master/ctakes-web-
>> > > > > rest/src/main/resources/org
>> > > > >
>> > > > > This module can be deployed as a web-app in Tomcat using the
>> > > > > generated WAR file . It can be tested using any REST client
>> > > > > (like
>> > > > > Chrome's Postman app) by accessing the following URL -
>> > > > > http://<hostt_name>:<port>/ctakes-web-rest/service/analyze
>> > > > > and providing the analysis text as request body.
>> > > > >
>> > > > > Sample input : "Patient has cancer and nausea. Earlier he has
>> > > > > been
>> > > > > deducted for red eye."
>> > > > > Sample output:
>> > > > >  {
>> > > > >     "DrugChangeStatusAnnotation": [],
>> > > > >     "StrengthAnnotation": [],
>> > > > >     "FractionStrengthAnnotation": [],
>> > > > >     "FrequencyUnitAnnotation": [],
>> > > > >     "CompanyAnnotation": [],
>> > > > >     "DiseaseDisorderMention": [
>> > > > >         "CANCER"
>> > > > >     ],
>> > > > >     "SignSymptomMention": [
>> > > > >         "RED EYE",
>> > > > >         "NAUSEA"
>> > > > >     ],
>> > > > >     "RouteAnnotation": [],
>> > > > >     "DateAnnotation": [],
>> > > > >     "MeasurementAnnotation": [],
>> > > > >     "ProcedureMention": [],
>> > > > >     "TimeMention": [],
>> > > > >     "StrengthUnitAnnotation": []
>> > > > > }
>> > > > >
>> > > > > Regards,
>> > > > > Gandhi
>> > > > >
>> > > > > -----Original Message-----
>> > > > > From: Gandhi Rajan Natarajan [mailto:Gandhi.Natarajan@arisgloba
>> > > > > l.
>> > > > > co
>> > > > > m]
>> > > > > Sent: Sunday, November 19, 2017 1:45 PM
>> > > > > To: dev@ctakes.apache.org
>> > > > > Subject: RE: cTAKES as REST service [EXTERNAL]
>> > > > >
>> > > > > Hi All,
>> > > > >
>> > > > > Have completed cTAKES Spring upgrade changes and checked in the
>> > > > > same to SVN. Please revert in case of any issues.
>> > > > >
>> > > > > @Alex, Thanks a lot for taking time out and providing your
>> > > > > review
>> > > > > comments on Spring upgrade. Really appreciate it.
>> > > > >
>> > > > > Now it will ease our effort in creating ctakes rest module.
>> > > > >
>> > > > > Regards,
>> > > > > Gandhi
>> > > > >
>> > > > >
>> > > > > -----Original Message-----
>> > > > > From: Gandhi Rajan Natarajan [mailto:Gandhi.Natarajan@arisgloba
>> > > > > l.
>> > > > > co
>> > > > > m]
>> > > > > Sent: Sunday, November 19, 2017 4:20 AM
>> > > > > To: dev@ctakes.apache.org
>> > > > > Subject: RE: cTAKES as REST service [EXTERNAL]
>> > > > >
>> > > > > Hi,
>> > > > >
>> > > > > I have attached the patch file for cTAKES Spring upgrade in
>> > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apa
>> > > > > ch
>> > > > > e.
>> > > > > org
>> > > > > _jira_browse_CTAKES-
>> > > > > 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd
>> > > > > ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXw
>> > > > > We
>> > > > > Hr
>> > > > > vVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmkKsb
>> > > > > Ho
>> > > > > vD
>> > > > > Nb4qYLIGA1LFWE&e=  Unfortunately I'm not able to assign this
>> > > > > issue
>> > > > > to me as I don’t have access. Could someone help me out with
>> > > > > the
>> > > > > access?
>> > > > >
>> > > > > For time being I have commented out the DataAnnotatorTest
>> > > > > failure
>> > > > > in the patch.
>> > > > >
>> > > > > Could someone test the patch and let us know so that I can
>> > > > > commit
>> > > > > the changes in SVN?
>> > > > >
>> > > > > This change will lay the foundation for REST module
>> > > > > implementation
>> > > > > in cTAKES.
>> > > > >
>> > > > > Regards,
>> > > > > Gandhi
>> > > > >
>> > > > >
>> > > > > -----Original Message-----
>> > > > > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>> > > > > Sent: Wednesday, November 01, 2017 8:24 AM
>> > > > > To: dev@ctakes.apache.org
>> > > > > Subject: Re: cTAKES as REST service [EXTERNAL]
>> > > > >
>> > > > > Alex,
>> > > > >
>> > > > > Gandhi covered everything we are working on. Please do mail me
>> > > > > if
>> > > > > you'd like to join in and I can give you some open tasks.
>> > > > >
>> > > > > Thanks,
>> > > > >
>> > > > > Matthew Vita
>> > > > > www.matthewvita.com
>> > > > >
>> > > > > On Mon, Oct 30, 2017 at 8:46 PM, Gandhi Rajan Natarajan <
>> > > > > Gandhi.Natarajan@arisglobal.com> wrote:
>> > > > >
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > > Hi Alex and Sean,
>> > > > > >
>> > > > > > Thanks for the acknowledgement.
>> > > > > >
>> > > > > > As mentioned earlier in the thread, I have sent the github
>> > > > > > link
>> > > > > > -
>> > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.c
>> > > > > > om
>> > > > > > _g
>> > > > > > and
>> > > > > > hirajan_cTAKES_tree_master_SpringUpgrade_ctakes&d=DwIFaQ&c=qS
>> > > > > > 4g
>> > > > > > oW
>> > > > > > BT7
>> > > > > > poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQC
>> > > > > > P6
>> > > > > > r0
>> > > > > > bcp
>> > > > > > KGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=
>> > > > > > 1x
>> > > > > > SD
>> > > > > > OHa
>> > > > > > gul92nHBoUl91ypDC-C6yasvlqvnLnavgZeQ&e=
>> > > > > > - SVN-src  that contains changes to be made to upgrade cTAKES
>> > > > > > to
>> > > > > > Spring4x.
>> > > > > > I have done it on my local sandbox and it works. But as I
>> > > > > > mentioned earlier, I was not able to test ytex module changes
>> > > > > > as
>> > > > > > I'm not aware of those modules. Matthew is already testing
>> > > > > > the
>> > > > > > spring upgrade changes and hopefully we will able be close
>> > > > > > it.
>> > > > > > If you could test the ytex modules, it will be of great help
>> > > > > > I
>> > > > > > guess.
>> > > > > >
>> > > > > > Regarding docker works on cTAKES, hats off to Matthew. We can
>> > > > > > assist him if he needs any help out there.
>> > > > > >
>> > > > > > Regarding REST API, we are planning to use Spring REST
>> > > > > > service
>> > > > > > as introducing Jersey container may be an overhead I feel.
>> > > > > > Also
>> > > > > > regarding your idea on new module, I too agree with you. But
>> > > > > > in
>> > > > > > the new module, we can improvise Chei Pen's work in this link
>> > > > > > -
>> > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.c
>> > > > > > om
>> > > > > > _h
>> > > > > > eal
>> > > > > > thnlp_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
>> > > > > > &r
>> > > > > > =f
>> > > > > > s67
>> > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX
>> > > > > > 0K
>> > > > > > 74
>> > > > > > _d9
>> > > > > > uL4nLj63jy45d5x_Y&s=KiyQy6xcOxO862P4LteL-
>> > > > > > 5kE5AO0OnwUhXbeAi5ierY&e=
>> > > > > > examples/tree/master/ctakes-temporal-demo and name it as
>> > > > > > 'ctakes-
>> > > > > > web'
>> > > > > > or 'ctakes-web-rest' so that the module can be used to build
>> > > > > > cTAKES as both traditional web app as well as expose it as an
>> > > > > > REST service.
>> > > > > > It's
>> > > > > just a thought from my side which we can discuss upon.
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > > Once the web-rest module is ready, I feel it will take cTAKES
>> > > > > > to
>> > > > > > a whole new level as you can even plug it with mobile
>> > > > > > applications that can send the clinical text for analysis and
>> > > > > > get JSON response that can be rendered on mobile app UI.
>> > > > > >
>> > > > > > Suggestions are welcome. Cheers.
>> > > > > >
>> > > > > > Regards,
>> > > > > > Gandhi
>> > > > > >
>> > > > > >
>> > > > > > -----Original Message-----
>> > > > > > From: Alexandru Zbarcea [mailto:zbarcea.a@gmail.com]
>> > > > > > Sent: Monday, October 30, 2017 6:07 PM
>> > > > > > To: Apache cTAKES Dev <dev@ctakes.apache.org>
>> > > > > > Subject: Re: cTAKES as REST service [EXTERNAL]
>> > > > > >
>> > > > > > Gandhi and Matthew, thank you for your hard work.
>> > > > > >
>> > > > > > I was working on upgrading libraries and fixing dependencies
>> > > > > > too.
>> > > > > > I
>> > > > > > would love to help with Spring dependency. For that reason, I
>> > > > > > have
>> > > > > created issue:
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > > "upgrade Spring dependency from 3.1.2 to 4.x" (CTAKES-472
>> > > > > > [1]).
>> > > > > >
>> > > > > > Another great idea is the REST service, for that reason I
>> > > > > > created
>> > > > > > CTAKES-473 [2]. It was also requested by Chei Pen in CTAKES-
>> > > > > > 188
>> > > > > > [3].
>> > > > > > I would like to know if you settled already to any framework
>> > > > > > (e.g.
>> > > > > > Jersey vs
>> > > > > > CXF) and if you also manage the dictionaries and different
>> > > > > > profiles through the API.
>> > > > > >
>> > > > > > The last important idea I get is the Dockerfile, which sounds
>> > > > > > great for the community to just test and play with cTAKES
>> > > > > > without the need of building and exploring the source code. I
>> > > > > > was testing your work Matthew, and I think it is a great
>> > > > > > start.
>> > > > > >
>> > > > > > What is the community practice in code for features that
>> > > > > > require
>> > > > > > a longer time to be developed? Would it use a branch until it
>> > > > > > gets stable, or it is preferred to have it in trunk for a
>> > > > > > faster
>> > > > > > integration. The REST API feature, it will require a new
>> > > > > > module.
>> > > > > > Does the community prefers a name for it (i.e ctakes-rest-
>> > > > > > api) ?
>> > > > > >
>> > > > > > Alex
>> > > > > >
>> > > > > > [1] -
>> > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.a
>> > > > > > pa
>> > > > > > ch
>> > > > > > e.o
>> > > > > > rg_jira_browse_CTAKES-
>> > > > > > 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
>> > > > > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&
>> > > > > > m=
>> > > > > > Aa
>> > > > > > XwW
>> > > > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVC
>> > > > > > mk
>> > > > > > Ks
>> > > > > > bHo
>> > > > > > vDNb4qYLIGA1LFWE&e= [2] -
>> > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.a
>> > > > > > pa
>> > > > > > ch
>> > > > > > e.o
>> > > > > > rg_jira_browse_CTAKES-
>> > > > > > 2D473&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
>> > > > > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&
>> > > > > > m=
>> > > > > > Aa
>> > > > > > XwW
>> > > > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=amE_Q3-
>> > > > > > yRQqb3YlCrjqEMO6oyco
>> > > > > > bMTJCydPlOFyi6PA&e= [3] -
>> > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.a
>> > > > > > pa
>> > > > > > ch
>> > > > > > e.o
>> > > > > > rg_jira_browse_CTAKES-
>> > > > > > 2D188&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
>> > > > > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&
>> > > > > > m=
>> > > > > > Aa
>> > > > > > XwW
>> > > > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=ptUmgt8eoj8hkr7RAFaA
>> > > > > > hc
>> > > > > > 7X
>> > > > > > XCD
>> > > > > > QlTANvb2YasbcToQ&e=
>> > > > > >
>> > > > > >
>> > > > > > On Sun, Oct 29, 2017 at 11:36 PM, Gandhi Rajan Natarajan <
>> > > > > > Gandhi.Natarajan@arisglobal.com> wrote:
>> > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > > > Matthew,
>> > > > > > >
>> > > > > > > Looking forward to hear from you. Please let me know if
>> > > > > > > there
>> > > > > > > are any changes required to make the rest service more
>> > > > > > > superior and performance effective. Cheers.
>> > > > > > >
>> > > > > > > Regards,
>> > > > > > > Gandhi
>> > > > > > >
>> > > > > > >
>> > > > > > > -----Original Message-----
>> > > > > > > From: Matthew Vita [mailto:matthewvita48@gmail.com]
>> > > > > > > Sent: Sunday, October 29, 2017 9:30 PM
>> > > > > > > To: dev@ctakes.apache.org
>> > > > > > > Subject: Re: cTAKES as REST service [EXTERNAL]
>> > > > > > >
>> > > > > > > Sean,
>> > > > > > >
>> > > > > > > Ghandi and I have met and we both agreed that his solution
>> > > > > > > is
>> > > > > > > superior to the one I was working on. Therefore, I will be
>> > > > > > > helping to see this project through to the end so we can
>> > > > > > > get
>> > > > > > > it into the
>> > > > > codebase!
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > > > Here are the remaining work items that I will be spending
>> > > > > > > time
>> > > > > > > on:
>> > > > > > >
>> > > > > > >    1. Get it running (I'm using Linux Mint)
>> > > > > > >    2. Test it out (including stress tests)
>> > > > > > >    3. Automate it to run in Docker (just need UMLS
>> > > > > > > credentials)
>> > > > > > >    4. Make a call to
>> > > > > > >
>> > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github
>> > > > > > > .c
>> > > > > > > om
>> > > > > > > _Go
>> > > > > > > TeamEpsilon_cTAKES-2DConcept-2DMention-
>> > > > > > > 2DParser&d=DwIFaQ&c=qS4goWB
>> > > > > > > T7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYN
>> > > > > > > Ym
>> > > > > > > QC
>> > > > > > > P6r
>> > > > > > > 0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5
>> > > > > > > x_
>> > > > > > > Y&
>> > > > > > > s=n
>> > > > > > > mNH9xHjD0NbybZpcz8-3bZSyfs9_DmemXiZlC_N6js&e= to
>> > > > > > get a
>> > > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > > >    nice JSON payload that is easy to traverse (this can be
>> > > > > > > an
>> > > > > > > optional switch,
>> > > > > > >    of course - I believe it may be best to rewrite this in
>> > > > > > > Java should this be
>> > > > > > >    included with the solution)
>> > > > > > >    5. Test the output in my web viewer:
>> > > > > > >    https://urldefense.proofpoint.com/v2/url?u=https-3A__git
>> > > > > > > hu
>> > > > > > > b.
>> > > > > > > com_GoTeamEpsilon_cTAKES-2DFriendly-2DWeb-
>> > > > > > > 2DUI&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
>> > > > > > > &r
>> > > > > > > =f
>> > > > > > > s67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3
>> > > > > > > l3
>> > > > > > > 0M
>> > > > > > > X0K74_d9uL4nLj63jy45d5x_Y&s=NWjnOk5b4IeAjOCaCiYTS5KlnANsLcZ
>> > > > > > > TQ
>> > > > > > > _T
>> > > > > > > RneZCtxg&e=
>> > > > > > >    6. Work on preparing the solution for the cTAKES core
>> > > > > > > codebase.
>> > > > > > > I
>> > > > > will
>> > > > > >
>> > > > > >
>> > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > > >
>> > > > > > >    prepare it with a very rich README.
>> > > > > > >
>> > > > > > > I will provide my updates over the coming days.
>> > > > > > >
>> > > > > > > Thanks,
>> > > > > > >
>> > > > > > > Matthew Vita
>> > > > > > > www.matthewvita.com
>> > > > > > >
>> > > > > > > On Sun, Oct 29, 2017 at 7:47 AM, Finan, Sean <
>> > > > > > > Sean.Finan@childrens.harvard.edu> wrote:
>> > > > > > >
>> > > > > > > >
>> > > > > > > >
>> > > > > > > >
>> > > > > > > > Hi Gandhi,
>> > > > > > > >
>> > > > > > > > Thank you for the additional information.  Having a
>> > > > > > > > reliable
>> > > > > > > > rest service included with ctakes would be a boon for
>> > > > > > > > everybody interested in web access.  I look forward to
>> > > > > > > > checking out the info in github as soon as I am able.
>> > > > > > > >
>> > > > > > > > Thanks to you and Mathew both!
>> > > > > > > >
>> > > > > > > > Sean
>> > > > > > > >
>> > > > > > > >
>> > > > > > > > -----Original Message-----
>> > > > > > > > From: Gandhi Rajan Natarajan
>> > > > > > > > [mailto:Gandhi.Natarajan@arisglobal.com]
>> > > > > > > > Sent: Sunday, October 29, 2017 5:44 AM
>> > > > > > > > To: dev@ctakes.apache.org
>> > > > > > > > Subject: RE: cTAKES as REST service [EXTERNAL]
>> > > > > > > >
>> > > > > > > > Hi Sean,
>> > > > > > > >
>> > > > > > > > I feel it's better to upgrade cTAKES Spring version to 4x
>> > > > > > > > so
>> > > > > > > > that exposing it as rest service becomes seamless. Please
>> > > > > > > > find the github link that contains the proposed changes
>> > > > > > > > for
>> > > > > > > > Spring upgrade in cTAKES,
>> > > > > > > >
>> > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__gith
>> > > > > > > > ub
>> > > > > > > > .
>> > > > > > > > com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes-
>> > > > > > > > 2DSVN-
>> > > > > > > > 2Dsrc&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx
>> > > > > > > > e
>> > > > > > > > FU
>> > > > > > > > &r
>> > > > > > > > =
>> > > > > > > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=cedfmyhdY7P
>> > > > > > > > 3q
>> > > > > > > > Zd
>> > > > > > > > iVB
>> > > > > > > > -
>> > > > > > > > gp0T0WinfllT61pLMqbP_Jyw&s=eMYiHpgQwJ5Zjc7-gW6qyAJ3AS3-
>> > > > > > > > H622ZVSJE
>> > > > > > > > Jc
>> > > > > > > > gd
>> > > > > > > > 8s
>> > > > > > > > &e=
>> > > > > > > >
>> > > > > > > > I have not tested the changes in ytex modules as I'm not
>> > > > > > > > sure how to go about that.
>> > > > > > > >
>> > > > > > > > Matthew Vita will be reviewing the changes. He is also
>> > > > > > > > reviewing and testing my rest service changes. He will
>> > > > > > > > provide more info to us once we are done with our
>> > > > > > > > testing.
>> > > > > > > > So that we can discuss about productizing the same.
>> > > > > > > >
>> > > > > > > > Regards,
>> > > > > > > > Gandhi
>> > > > > > > >
>> > > > > > > >
>> > > > > > > > -----Original Message-----
>> > > > > > > > From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.ed
>> > > > > > > > u]
>> > > > > > > > Sent: Friday, October 27, 2017 12:53 AM
>> > > > > > > > To: dev@ctakes.apache.org
>> > > > > > > > Subject: RE: cTAKES as REST service [EXTERNAL]
>> > > > > > > >
>> > > > > > > > Hi Gandhi,
>> > > > > > > >
>> > > > > > > > That sounds really great!  Thank you for sharing the
>> > > > > > > > process!
>> > > > > > > >
>> > > > > > > > Sean
>> > > > > > > >
>> > > > > > > > -----Original Message-----
>> > > > > > > > From: Gandhi Rajan Natarajan
>> > > > > > > > [mailto:Gandhi.Natarajan@arisglobal.com]
>> > > > > > > > Sent: Thursday, October 26, 2017 3:02 PM
>> > > > > > > > To: dev@ctakes.apache.org
>> > > > > > > > Subject: RE: cTAKES as REST service [EXTERNAL]
>> > > > > > > >
>> > > > > > > > Hi Sean,
>> > > > > > > >
>> > > > > > > > I'm glad to inform that I was able to upgrade cTAKES to
>> > > > > > > > Spring 4 in my sandbox. As you have mentioned, it is used
>> > > > > > > > by
>> > > > > > > > uima fit for firing some queries.
>> > > > > > > >
>> > > > > > > > To brief it, I did the following changes:
>> > > > > > > >
>> > > > > > > > 1) Changing SimpleJdbcTemplate to JdbcTemplate in uima
>> > > > > > > > modules
>> > > > > > > > 2) Changing Spring version in cTAKES root pom.xml
>> > > > > > > > 3) Adding Spring versions in ctakes type system, ctakes
>> > > > > > > > assertion, ctakes ytex and ctakes ytex web modules.
>> > > > > > > >
>> > > > > > > > Now I'm able to expose cTAKES as a rest service which
>> > > > > > > > takes
>> > > > > > > > the clinical text as Input and outputs the result.
>> > > > > > > >
>> > > > > > > >  Hope it helps someone.
>> > > > > > > >
>> > > > > > > > Regards,
>> > > > > > > > Gandhi
>> > > > > > > >
>> > > > > > > > -----Original Message-----
>> > > > > > > > From: Gandhi Rajan Natarajan
>> > > > > > > > [mailto:Gandhi.Natarajan@arisglobal.com]
>> > > > > > > > Sent: Wednesday, October 25, 2017 7:33 PM
>> > > > > > > > To: dev@ctakes.apache.org
>> > > > > > > > Subject: RE: cTAKES as REST service [EXTERNAL]
>> > > > > > > >
>> > > > > > > > Hi Sean,
>> > > > > > > >
>> > > > > > > > Thanks for the instant response. Will try to upgrade to
>> > > > > > > > Spring 4 and keep you posted about the progress.
>> > > > > > > >
>> > > > > > > > Regards,
>> > > > > > > > Gandhi
>> > > > > > > >
>> > > > > > > >
>> > > > > > > > -----Original Message-----
>> > > > > > > > From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.ed
>> > > > > > > > u]
>> > > > > > > > Sent: Wednesday, October 25, 2017 7:28 PM
>> > > > > > > > To: dev@ctakes.apache.org
>> > > > > > > > Subject: RE: cTAKES as REST service [EXTERNAL]
>> > > > > > > >
>> > > > > > > > Hi Gandhi,
>> > > > > > > >
>> > > > > > > > You can always build ctakes in your sandbox with spring 4
>> > > > > > > > and see if it works.  This may require some "maven
>> > > > > > > > magic"(overrides)
>> > > > > > > > on your part.  If it does seem to work please create a
>> > > > > > > > jira
>> > > > > > > > item to upgrade the
>> > > > > > > spring version.
>> > > > > > > >
>> > > > > > > >
>> > > > > > > >
>> > > > > > > > Then hopefully before the next release somebody will
>> > > > > > > > thoroughly test an update.
>> > > > > > > >
>> > > > > > > > Offhand I don't know if or why spring is needed for
>> > > > > > > > ctakes
>> > > > > > > > itself.
>> > > > > > > > At a quick search it looks like uimafit requires
>> > > > > > > > it.  Does
>> > > > > > > > anybody out there know what spring capabilities are used,
>> > > > > > > > directly or indirectly, by ctakes modules?
>> > > > > > > >
>> > > > > > > > Thanks,
>> > > > > > > > Sean
>> > > > > > > >
>> > > > > > > > -----Original Message-----
>> > > > > > > > From: Gandhi Rajan Natarajan
>> > > > > > > > [mailto:Gandhi.Natarajan@arisglobal.com]
>> > > > > > > > Sent: Wednesday, October 25, 2017 9:20 AM
>> > > > > > > > To: dev@ctakes.apache.org
>> > > > > > > > Subject: cTAKES as REST service [EXTERNAL]
>> > > > > > > >
>> > > > > > > > Hi All,
>> > > > > > > >
>> > > > > > > > We have extended the cTAKES web application available
>> > > > > > > > under
>> > > > > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__gith
>> > > > > > > > ub
>> > > > > > > > .
>> > > > > > > > com_healthnlp_examples_tree_master_ctakes-2Dtemporal-
>> > > > > > > > 2Ddemo&d=Dw
>> > > > > > > > IF Ag &c = qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
>> > > > > > > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=e5GMRO_
>> > > > > > > > 5OwQhQrkfpV5fwBp7uG07tZVd1u_xJRo9wDs&s=meOj7MzEliqIQEhU_
>> > > > > > > > FeQwEnsUrWFSzgk5ihSEzoGRCI&e= and added our custom
>> > > > > > > > annotator.
>> > > > > > > > We
>> > > > > > > > have tested the same and it works fine with CVD. But we
>> > > > > > > > are
>> > > > > > > > facing problems while trying to expose this as rest
>> > > > > > > > service.
>> > > > > > > >
>> > > > > > > > cTAKES uses Spring 3.1.2 version internally which don't
>> > > > > > > > have
>> > > > > > > > out of the box support for rest controller. Can we go
>> > > > > > > > ahead
>> > > > > > > > and update the spring version to 4x in cTAKES? Will it
>> > > > > > > > have
>> > > > > > > > any impact in the cTAKES
>> > > > > > > behavior?
>> > > > > > > >
>> > > > > > > >
>> > > > > > > >
>> > > > > > > > Also is there a better way to expose cTAKES as rest
>> > > > > > > > service
>> > > > > > > > apart from spring?
>> > > > > > > >
>> > > > > > > > Please advise.
>> > > > > > > >
>> > > > > > > > Regards,
>> > > > > > > > Gandhi
>> > > > > > > >
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>
>

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