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Posted to dev@ctakes.apache.org by "Miller, Timothy" <Ti...@childrens.harvard.edu> on 2017/12/14 19:54:57 UTC
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@arisglobal.
> > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
> > > Ta
> > > o&m
> > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarVc3
> > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
> > > Ta
> > > o&m
> > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarVc3
> > > 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@arisglobal.
> > > 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@arisglobal.
> > > 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.apach
> > > e.
> > > org
> > > _jira_browse_CTAKES-
> > > 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd
> > > ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWe
> > > Hr
> > > vVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmkKsbHo
> > > 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.com
> > > > _g
> > > > and
> > > > hirajan_cTAKES_tree_master_SpringUpgrade_ctakes&d=DwIFaQ&c=qS4g
> > > > oW
> > > > BT7
> > > > poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6
> > > > 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.com
> > > > _h
> > > > eal
> > > > thnlp_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r
> > > > =f
> > > > s67
> > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K
> > > > 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 <de...@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.apa
> > > > ch
> > > > e.o
> > > > rg_jira_browse_CTAKES-
> > > > 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
> > > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > Aa
> > > > XwW
> > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmk
> > > > Ks
> > > > bHo
> > > > vDNb4qYLIGA1LFWE&e= [2] -
> > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apa
> > > > 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.apa
> > > > ch
> > > > e.o
> > > > rg_jira_browse_CTAKES-
> > > > 2D188&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
> > > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > Aa
> > > > XwW
> > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=ptUmgt8eoj8hkr7RAFaAhc
> > > > 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=fs67GvlGZstTpyIisCYNYm
> > > > > QC
> > > > > P6r
> > > > > 0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_
> > > > > 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__githu
> > > > > b.
> > > > > com_GoTeamEpsilon_cTAKES-2DFriendly-2DWeb-
> > > > > 2DUI&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r
> > > > > =f
> > > > > s67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l3
> > > > > 0M
> > > > > X0K74_d9uL4nLj63jy45d5x_Y&s=NWjnOk5b4IeAjOCaCiYTS5KlnANsLcZTQ
> > > > > _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__github
> > > > > > .
> > > > > > com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes-
> > > > > > 2DSVN-
> > > > > > 2Dsrc&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxe
> > > > > > FU
> > > > > > &r
> > > > > > =
> > > > > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=cedfmyhdY7P3q
> > > > > > 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.edu]
> > > > > > 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.edu]
> > > > > > 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__github
> > > > > > .
> > > > > > 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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RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
Hi Jeff,
We have now upgraded from Spring 3x to Spring 4.3.12 now.
Since cTAKES was using Spring 3x version only for very few modules in it and not Spring's extensive functionality, we decided to upgrade to the latest version of the Spring rather than Spring Boot.
But as you mentioned, cTAKES REST module will generate one WAR file that can be deployed to any application server.
In fact, plans are already on to dockerize the complete deployment so that everything can be handled by single click.
Regards,
Gandhi
-----Original Message-----
From: Jeff Headley [mailto:jeffunf96@gmail.com]
Sent: Monday, December 18, 2017 12:13 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
My use of ctakes is for a part-time side job and I haven’t been able to read every email in here. Apologies in advance if this idea has come up before.
Spring Boot. It appears that ctakes is already using spring. Older version I think. If ctakes was to use a newer spring and use spring boot, I think people would like the possibilities. You could build a fat jar that could be easily executed with an embedded server to provide these rest endpoints. Built in metrics and all the stuff spring boot brings with it. It could still be deployed as a war to a server and should be easy to deploy in the cloud as well. We use spring boot at my full-time job in an AWS environment and we are quite happy with Spring Boot for our rest services.
Sent from my iPhone
> On Dec 17, 2017, at 11:33 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Cheers all!
>
> -----Original Message-----
> From: Matthew Vita [mailto:matthewvita48@gmail.com]
> Sent: Saturday, December 16, 2017 1:02 AM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS]
> [SUSPICIOUS]
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GoTeamEpsilon_ctakes-2Drest-2Dservice_issues_2-23issuecomment-2D351921458&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SNOWoRw_Hkp1F9ybCI6H8JeisqZQQKapVBXOXwKpy98&s=fAORUifZYDKtiRuE_7TcoYAcw29S-Q6k6uNcyjhfQFI&e=).
> 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
> <ma...@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.c
>>>>>>> om
>>>>>>> _G
>>>>>>> oT
>>>>>>> eam
>>>>>>> Epsilon_ctakes-2Drest-
>>>>>>> 2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x
>>>>>>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f
>>>>>>> 7d
>>>>>>> 4g
>>>>>>> Ta
>>>>>>> o&m
>>>>>>> =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQa
>>>>>>> rV
>>>>>>> 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.c
>>>>>>> om
>>>>>>> _G
>>>>>>> oT
>>>>>>> eam
>>>>>>> Epsilon_ctakes-2Drest-
>>>>>>> 2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x
>>>>>>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f
>>>>>>> 7d
>>>>>>> 4g
>>>>>>> Ta
>>>>>>> o&m
>>>>>>> =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQa
>>>>>>> rV
>>>>>>> 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.a
>>>>>>> pa
>>>>>>> ch
>>>>>>> e.
>>>>>>> org
>>>>>>> _jira_browse_CTAKES-
>>>>>>> 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd
>>>>>>> ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Aa
>>>>>>> Xw
>>>>>>> We
>>>>>>> Hr
>>>>>>> vVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmkK
>>>>>>> sb
>>>>>>> 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=fs67GvlGZstTpyIisCYNYm
>>>>>>>> QC
>>>>>>>> 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_3xhKwEW14JZMSdioCoppxe
>>>>>>>> FU
>>>>>>>> &r
>>>>>>>> =f
>>>>>>>> s67
>>>>>>>> GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30
>>>>>>>> MX
>>>>>>>> 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 <de...@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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
>>>>>>>> o&
>>>>>>>> m=
>>>>>>>> Aa
>>>>>>>> XwW
>>>>>>>> eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJ
>>>>>>>> VC
>>>>>>>> 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
>>>>>>>> o&
>>>>>>>> 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
>>>>>>>> o&
>>>>>>>> m=
>>>>>>>> Aa
>>>>>>>> XwW
>>>>>>>> eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=ptUmgt8eoj8hkr7RAF
>>>>>>>> aA
>>>>>>>> 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__gith
>>>>>>>>> ub
>>>>>>>>> .c
>>>>>>>>> om
>>>>>>>>> _Go
>>>>>>>>> TeamEpsilon_cTAKES-2DConcept-2DMention-
>>>>>>>>> 2DParser&d=DwIFaQ&c=qS4goWB
>>>>>>>>> T7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisC
>>>>>>>>> YN
>>>>>>>>> Ym
>>>>>>>>> QC
>>>>>>>>> P6r
>>>>>>>>> 0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45
>>>>>>>>> d5
>>>>>>>>> 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_3xhKwEW14JZMSdioCoppxe
>>>>>>>>> FU
>>>>>>>>> &r
>>>>>>>>> =f
>>>>>>>>> s67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgj
>>>>>>>>> d3
>>>>>>>>> l3
>>>>>>>>> 0M
>>>>>>>>> X0K74_d9uL4nLj63jy45d5x_Y&s=NWjnOk5b4IeAjOCaCiYTS5KlnANsL
>>>>>>>>> cZ
>>>>>>>>> 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__gi
>>>>>>>>>> th
>>>>>>>>>> ub
>>>>>>>>>> .
>>>>>>>>>> com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes
>>>>>>>>>> -
>>>>>>>>>> 2DSVN-
>>>>>>>>>> 2Dsrc&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
>>>>>>>>>> px
>>>>>>>>>> e
>>>>>>>>>> FU
>>>>>>>>>> &r
>>>>>>>>>> =
>>>>>>>>>> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=cedfmyhdY
>>>>>>>>>> 7P
>>>>>>>>>> 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__gi
>>>>>>>>>> th
>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>> This email and any files transmitted with it are
>>>>>>>>>> confidential and intended solely for the use of the
>>>>>>>>>> individual or entity to whom they are
>>>>>>>>> addressed.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> If you are not the named addressee you should not
>>>>>>>>>> disseminate, distribute or copy this e-mail. Please
>>>>>>>>>> notify the sender or system manager by email
>>>>>>>>>> immediately if you have received this e-mail by mistake
>>>>>>>>>> and delete this e- mail from your system.
>>>>>>>>>> If
>>>>>>>>>> you are not the intended recipient you are notified
>>>>>>>>>> that disclosing, copying, distributing or taking any
>>>>>>>>>> action in reliance on the contents of this information
>>>>>>>>>> is strictly prohibited and against the law.
>>>>>>>>>> This email and any files transmitted with it are
>>>>>>>>>> confidential and intended solely for the use of the
>>>>>>>>>> individual or entity to whom they are
>>>>>>>>> addressed.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> If you are not the named addressee you should not
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>>>>>>>> disseminate, distribute or copy this e-mail. Please notify
>>>>>>>> the sender or system manager by email immediately if you
>>>>>>>> have received this e-mail by mistake and delete this e-mail
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>>>>>>>> are notified that disclosing, copying, distributing or
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>>>>>>>> information is strictly prohibited and against the law.
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>>>>>>> strictly prohibited and against the law.
>>>> This email and any files transmitted with it are confidential and
>>>> intended solely for the use of the individual or entity to whom
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>>>> sender or system manager by email immediately if you have received
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>>
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Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Posted by Jeff Headley <je...@gmail.com>.
My use of ctakes is for a part-time side job and I haven’t been able to read every email in here. Apologies in advance if this idea has come up before.
Spring Boot. It appears that ctakes is already using spring. Older version I think. If ctakes was to use a newer spring and use spring boot, I think people would like the possibilities. You could build a fat jar that could be easily executed with an embedded server to provide these rest endpoints. Built in metrics and all the stuff spring boot brings with it. It could still be deployed as a war to a server and should be easy to deploy in the cloud as well. We use spring boot at my full-time job in an AWS environment and we are quite happy with Spring Boot for our rest services.
Sent from my iPhone
> On Dec 17, 2017, at 11:33 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Cheers all!
>
> -----Original Message-----
> From: Matthew Vita [mailto:matthewvita48@gmail.com]
> Sent: Saturday, December 16, 2017 1:02 AM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
>
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GoTeamEpsilon_ctakes-2Drest-2Dservice_issues_2-23issuecomment-2D351921458&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SNOWoRw_Hkp1F9ybCI6H8JeisqZQQKapVBXOXwKpy98&s=fAORUifZYDKtiRuE_7TcoYAcw29S-Q6k6uNcyjhfQFI&e=).
> 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 <ma...@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.c
>>>>>>> om
>>>>>>> _G
>>>>>>> oT
>>>>>>> eam
>>>>>>> Epsilon_ctakes-2Drest-
>>>>>>> 2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x
>>>>>>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f
>>>>>>> 7d
>>>>>>> 4g
>>>>>>> Ta
>>>>>>> o&m
>>>>>>> =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQa
>>>>>>> rV
>>>>>>> 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.c
>>>>>>> om
>>>>>>> _G
>>>>>>> oT
>>>>>>> eam
>>>>>>> Epsilon_ctakes-2Drest-
>>>>>>> 2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x
>>>>>>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f
>>>>>>> 7d
>>>>>>> 4g
>>>>>>> Ta
>>>>>>> o&m
>>>>>>> =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQa
>>>>>>> rV
>>>>>>> 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.a
>>>>>>> pa
>>>>>>> ch
>>>>>>> e.
>>>>>>> org
>>>>>>> _jira_browse_CTAKES-
>>>>>>> 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd
>>>>>>> ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Aa
>>>>>>> Xw
>>>>>>> We
>>>>>>> Hr
>>>>>>> vVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmkK
>>>>>>> sb
>>>>>>> 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=fs67GvlGZstTpyIisCYNYm
>>>>>>>> QC
>>>>>>>> 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_3xhKwEW14JZMSdioCoppxe
>>>>>>>> FU
>>>>>>>> &r
>>>>>>>> =f
>>>>>>>> s67
>>>>>>>> GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30
>>>>>>>> MX
>>>>>>>> 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 <de...@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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
>>>>>>>> o&
>>>>>>>> m=
>>>>>>>> Aa
>>>>>>>> XwW
>>>>>>>> eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJ
>>>>>>>> VC
>>>>>>>> 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
>>>>>>>> o&
>>>>>>>> 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
>>>>>>>> o&
>>>>>>>> m=
>>>>>>>> Aa
>>>>>>>> XwW
>>>>>>>> eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=ptUmgt8eoj8hkr7RAF
>>>>>>>> aA
>>>>>>>> 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__gith
>>>>>>>>> ub
>>>>>>>>> .c
>>>>>>>>> om
>>>>>>>>> _Go
>>>>>>>>> TeamEpsilon_cTAKES-2DConcept-2DMention-
>>>>>>>>> 2DParser&d=DwIFaQ&c=qS4goWB
>>>>>>>>> T7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisC
>>>>>>>>> YN
>>>>>>>>> Ym
>>>>>>>>> QC
>>>>>>>>> P6r
>>>>>>>>> 0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45
>>>>>>>>> d5
>>>>>>>>> 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_3xhKwEW14JZMSdioCoppxe
>>>>>>>>> FU
>>>>>>>>> &r
>>>>>>>>> =f
>>>>>>>>> s67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgj
>>>>>>>>> d3
>>>>>>>>> l3
>>>>>>>>> 0M
>>>>>>>>> X0K74_d9uL4nLj63jy45d5x_Y&s=NWjnOk5b4IeAjOCaCiYTS5KlnANsL
>>>>>>>>> cZ
>>>>>>>>> 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__gi
>>>>>>>>>> th
>>>>>>>>>> ub
>>>>>>>>>> .
>>>>>>>>>> com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes
>>>>>>>>>> -
>>>>>>>>>> 2DSVN-
>>>>>>>>>> 2Dsrc&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
>>>>>>>>>> px
>>>>>>>>>> e
>>>>>>>>>> FU
>>>>>>>>>> &r
>>>>>>>>>> =
>>>>>>>>>> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=cedfmyhdY
>>>>>>>>>> 7P
>>>>>>>>>> 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__gi
>>>>>>>>>> th
>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>> This email and any files transmitted with it are
>>>>>>>>>> confidential and intended solely for the use of the
>>>>>>>>>> individual or entity to whom they are
>>>>>>>>> addressed.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> If you are not the named addressee you should not
>>>>>>>>>> disseminate, distribute or copy this e-mail. Please
>>>>>>>>>> notify the sender or system manager by email
>>>>>>>>>> immediately if you have received this e-mail by mistake
>>>>>>>>>> and delete this e- mail from your system.
>>>>>>>>>> If
>>>>>>>>>> you are not the intended recipient you are notified
>>>>>>>>>> that disclosing, copying, distributing or taking any
>>>>>>>>>> action in reliance on the contents of this information
>>>>>>>>>> is strictly prohibited and against the law.
>>>>>>>>>> This email and any files transmitted with it are
>>>>>>>>>> confidential and intended solely for the use of the
>>>>>>>>>> individual or entity to whom they are
>>>>>>>>> addressed.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> If you are not the named addressee you should not
>>>>>>>>>> disseminate, distribute or copy this e-mail. Please
>>>>>>>>>> notify the sender or system manager by email
>>>>>>>>>> immediately if you have received this e-mail by mistake
>>>>>>>>>> and delete this e- mail from your system.
>>>>>>>>>> If
>>>>>>>>>> you are not the intended recipient you are notified
>>>>>>>>>> that disclosing, copying, distributing or taking any
>>>>>>>>>> action in reliance on the contents of this information
>>>>>>>>>> is strictly prohibited and against the law.
>>>>>>>>>> This email and any files transmitted with it are
>>>>>>>>>> confidential and intended solely for the use of the
>>>>>>>>>> individual or entity to whom they are
>>>>>>>>> addressed.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> If you are not the named addressee you should not
>>>>>>>>>> disseminate, distribute or copy this e-mail. Please
>>>>>>>>>> notify the sender or system manager by email
>>>>>>>>>> immediately if you have received this e-mail by mistake
>>>>>>>>>> and delete this e- mail from your system.
>>>>>>>>>> If
>>>>>>>>>> you are not the intended recipient you are notified
>>>>>>>>>> that disclosing, copying, distributing or taking any
>>>>>>>>>> action in reliance on the contents of this information
>>>>>>>>>> is strictly prohibited and against the law.
>>>>>>>>>> This email and any files transmitted with it are
>>>>>>>>>> confidential and intended solely for the use of the
>>>>>>>>>> individual or entity to whom they are
>>>>>>>>> addressed.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> If you are not the named addressee you should not
>>>>>>>>>> disseminate, distribute or copy this e-mail. Please
>>>>>>>>>> notify the sender or system manager by email
>>>>>>>>>> immediately if you have received this e-mail by mistake
>>>>>>>>>> and delete this e- mail from your system.
>>>>>>>>>> If
>>>>>>>>>> you are not the intended recipient you are notified
>>>>>>>>>> that disclosing, copying, distributing or taking any
>>>>>>>>>> action in reliance on the contents of this information
>>>>>>>>>> is strictly prohibited and against the law.
>>>>>>>>> This email and any files transmitted with it are
>>>>>>>>> confidential and intended solely for the use of the
>>>>>>>>> individual or entity to whom they are
>>>>>>>> addressed.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> If you are not the named addressee you should not
>>>>>>>>> disseminate, distribute or copy this e-mail. Please
>>>>>>>>> notify the sender or system manager by email immediately
>>>>>>>>> if you have received this e-mail by mistake and delete
>>>>>>>>> this e-mail from your system.
>>>>>>>>> If
>>>>>>>>> you are not the intended recipient you are notified that
>>>>>>>>> disclosing, copying, distributing or taking any action in
>>>>>>>>> reliance on the contents of this information is strictly
>>>>>>>>> prohibited and against the law.
>>>>>>>> This email and any files transmitted with it are
>>>>>>>> confidential and intended solely for the use of the
>>>>>>>> individual or entity to whom they are
>>>>>>> addressed.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> If you are not the named addressee you should not
>>>>>>>> disseminate, distribute or copy this e-mail. Please notify
>>>>>>>> the sender or system manager by email immediately if you
>>>>>>>> have received this e-mail by mistake and delete this e-mail
>>>>>>>> from your system. If you are not the intended recipient you
>>>>>>>> are notified that disclosing, copying, distributing or
>>>>>>>> taking any action in reliance on the contents of this
>>>>>>>> information is strictly prohibited and against the law.
>>>>>>> This email and any files transmitted with it are confidential
>>>>>>> and intended solely for the use of the individual or entity
>>>>>>> to whom they are addressed.
>>>>>>> If you are not the named addressee you should not
>>>>>>> disseminate, distribute or copy this e-mail. Please notify
>>>>>>> the sender or system manager by email immediately if you have
>>>>>>> received this e-mail by mistake and delete this e-mail from
>>>>>>> your system. If you are not the intended recipient you are
>>>>>>> notified that disclosing, copying, distributing or taking any
>>>>>>> action in reliance on the contents of this information is
>>>>>>> strictly prohibited and against the law.
>>>>>>> This email and any files transmitted with it are confidential
>>>>>>> and intended solely for the use of the individual or entity
>>>>>>> to whom they are addressed.
>>>>>>> If you are not the named addressee you should not
>>>>>>> disseminate, distribute or copy this e-mail. Please notify
>>>>>>> the sender or system manager by email immediately if you have
>>>>>>> received this e-mail by mistake and delete this e-mail from
>>>>>>> your system. If you are not the intended recipient you are
>>>>>>> notified that disclosing, copying, distributing or taking any
>>>>>>> action in reliance on the contents of this information is
>>>>>>> strictly prohibited and against the law.
>>>>>>> This email and any files transmitted with it are confidential
>>>>>>> and intended solely for the use of the individual or entity
>>>>>>> to whom they are addressed.
>>>>>>> If you are not the named addressee you should not
>>>>>>> disseminate, distribute or copy this e-mail. Please notify
>>>>>>> the sender or system manager by email immediately if you have
>>>>>>> received this e-mail by mistake and delete this e-mail from
>>>>>>> your system. If you are not the intended recipient you are
>>>>>>> notified that disclosing, copying, distributing or taking any
>>>>>>> action in reliance on the contents of this information is
>>>>>>> strictly prohibited and against the law.
>>>>>>> This email and any files transmitted with it are confidential
>>>>>>> and intended solely for the use of the individual or entity
>>>>>>> to whom they are addressed.
>>>>>>> If you are not the named addressee you should not
>>>>>>> disseminate, distribute or copy this e-mail. Please notify
>>>>>>> the sender or system manager by email immediately if you have
>>>>>>> received this e-mail by mistake and delete this e-mail from
>>>>>>> your system. If you are not the intended recipient you are
>>>>>>> notified that disclosing, copying, distributing or taking any
>>>>>>> action in reliance on the contents of this information is
>>>>>>> strictly prohibited and against the law.
>>>> This email and any files transmitted with it are confidential and
>>>> intended solely for the use of the individual or entity to whom
>>>> they are addressed. If you are not the named addressee you should
>>>> not disseminate, distribute or copy this e-mail. Please notify the
>>>> sender or system manager by email immediately if you have received
>>>> this e- mail by mistake and delete this e-mail from your system. If
>>>> you are not the intended recipient you are notified that
>>>> disclosing, copying, distributing or taking any action in reliance
>>>> on the contents of this information is strictly prohibited and against the law.
>>
>>
RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Cheers all!
-----Original Message-----
From: Matthew Vita [mailto:matthewvita48@gmail.com]
Sent: Saturday, December 16, 2017 1:02 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GoTeamEpsilon_ctakes-2Drest-2Dservice_issues_2-23issuecomment-2D351921458&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SNOWoRw_Hkp1F9ybCI6H8JeisqZQQKapVBXOXwKpy98&s=fAORUifZYDKtiRuE_7TcoYAcw29S-Q6k6uNcyjhfQFI&e=).
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 <ma...@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.c
>> > > > > om
>> > > > > _G
>> > > > > oT
>> > > > > eam
>> > > > > Epsilon_ctakes-2Drest-
>> > > > > 2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x
>> > > > > hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f
>> > > > > 7d
>> > > > > 4g
>> > > > > Ta
>> > > > > o&m
>> > > > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQa
>> > > > > rV
>> > > > > 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.c
>> > > > > om
>> > > > > _G
>> > > > > oT
>> > > > > eam
>> > > > > Epsilon_ctakes-2Drest-
>> > > > > 2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x
>> > > > > hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f
>> > > > > 7d
>> > > > > 4g
>> > > > > Ta
>> > > > > o&m
>> > > > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQa
>> > > > > rV
>> > > > > 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.a
>> > > > > pa
>> > > > > ch
>> > > > > e.
>> > > > > org
>> > > > > _jira_browse_CTAKES-
>> > > > > 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd
>> > > > > ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Aa
>> > > > > Xw
>> > > > > We
>> > > > > Hr
>> > > > > vVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmkK
>> > > > > sb
>> > > > > 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=fs67GvlGZstTpyIisCYNYm
>> > > > > > QC
>> > > > > > 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_3xhKwEW14JZMSdioCoppxe
>> > > > > > FU
>> > > > > > &r
>> > > > > > =f
>> > > > > > s67
>> > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30
>> > > > > > MX
>> > > > > > 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 <de...@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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
>> > > > > > o&
>> > > > > > m=
>> > > > > > Aa
>> > > > > > XwW
>> > > > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJ
>> > > > > > VC
>> > > > > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
>> > > > > > o&
>> > > > > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
>> > > > > > o&
>> > > > > > m=
>> > > > > > Aa
>> > > > > > XwW
>> > > > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=ptUmgt8eoj8hkr7RAF
>> > > > > > aA
>> > > > > > 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__gith
>> > > > > > > ub
>> > > > > > > .c
>> > > > > > > om
>> > > > > > > _Go
>> > > > > > > TeamEpsilon_cTAKES-2DConcept-2DMention-
>> > > > > > > 2DParser&d=DwIFaQ&c=qS4goWB
>> > > > > > > T7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisC
>> > > > > > > YN
>> > > > > > > Ym
>> > > > > > > QC
>> > > > > > > P6r
>> > > > > > > 0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45
>> > > > > > > d5
>> > > > > > > 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_3xhKwEW14JZMSdioCoppxe
>> > > > > > > FU
>> > > > > > > &r
>> > > > > > > =f
>> > > > > > > s67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgj
>> > > > > > > d3
>> > > > > > > l3
>> > > > > > > 0M
>> > > > > > > X0K74_d9uL4nLj63jy45d5x_Y&s=NWjnOk5b4IeAjOCaCiYTS5KlnANsL
>> > > > > > > cZ
>> > > > > > > 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__gi
>> > > > > > > > th
>> > > > > > > > ub
>> > > > > > > > .
>> > > > > > > > com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes
>> > > > > > > > -
>> > > > > > > > 2DSVN-
>> > > > > > > > 2Dsrc&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
>> > > > > > > > px
>> > > > > > > > e
>> > > > > > > > FU
>> > > > > > > > &r
>> > > > > > > > =
>> > > > > > > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=cedfmyhdY
>> > > > > > > > 7P
>> > > > > > > > 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__gi
>> > > > > > > > th
>> > > > > > > > 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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>
Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Posted by Matthew Vita <ma...@gmail.com>.
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 <ma...@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 <de...@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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>
Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Posted by Matthew Vita <ma...@gmail.com>.
> 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 <de...@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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RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Tim,
There is code scattered all throughout ctakes to handle various easy ways, starting or stopping at different levels of information - I think that you may have actually created some of the best of it (ctakes to anafora maybe?).
I started working on a document bundle created from discovered mentions, placing relations (including coref) in arrays of object references. This is different than the DeepPhe approach which uses a coalescence of ctakes types to represent a single concept. It would be nice to (at some point) migrate that into ctakes, perhaps after the next DeepPhe release.
It should be able to produce both json and xml output. I will place it in sandbox (later) for you and Gandhi and anybody else that wants to take a look.
Sean
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Friday, December 15, 2017 9:47 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
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 <de...@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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Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
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 <de...@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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RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
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@arisglobal.
> > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
> > > Ta
> > > o&m
> > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarVc3
> > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
> > > Ta
> > > o&m
> > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarVc3
> > > 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@arisglobal.
> > > 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@arisglobal.
> > > 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.apach
> > > e.
> > > org
> > > _jira_browse_CTAKES-
> > > 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd
> > > ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWe
> > > Hr
> > > vVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmkKsbHo
> > > 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.com
> > > > _g
> > > > and
> > > > hirajan_cTAKES_tree_master_SpringUpgrade_ctakes&d=DwIFaQ&c=qS4g
> > > > oW
> > > > BT7
> > > > poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6
> > > > 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.com
> > > > _h
> > > > eal
> > > > thnlp_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r
> > > > =f
> > > > s67
> > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K
> > > > 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 <de...@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.apa
> > > > ch
> > > > e.o
> > > > rg_jira_browse_CTAKES-
> > > > 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
> > > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > Aa
> > > > XwW
> > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmk
> > > > Ks
> > > > bHo
> > > > vDNb4qYLIGA1LFWE&e= [2] -
> > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apa
> > > > 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.apa
> > > > ch
> > > > e.o
> > > > rg_jira_browse_CTAKES-
> > > > 2D188&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
> > > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > Aa
> > > > XwW
> > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=ptUmgt8eoj8hkr7RAFaAhc
> > > > 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=fs67GvlGZstTpyIisCYNYm
> > > > > QC
> > > > > P6r
> > > > > 0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_
> > > > > 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__githu
> > > > > b.
> > > > > com_GoTeamEpsilon_cTAKES-2DFriendly-2DWeb-
> > > > > 2DUI&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r
> > > > > =f
> > > > > s67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l3
> > > > > 0M
> > > > > X0K74_d9uL4nLj63jy45d5x_Y&s=NWjnOk5b4IeAjOCaCiYTS5KlnANsLcZTQ
> > > > > _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__github
> > > > > > .
> > > > > > com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes-
> > > > > > 2DSVN-
> > > > > > 2Dsrc&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxe
> > > > > > FU
> > > > > > &r
> > > > > > =
> > > > > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=cedfmyhdY7P3q
> > > > > > 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.edu]
> > > > > > 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.edu]
> > > > > > 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__github
> > > > > > .
> > > > > > 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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RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Tim,
The pipelines will soon be preloaded.
Sean
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Thursday, December 14, 2017 3:58 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Another thought I just had is that it seems to load the pipeline when the first call is made -- without knowing the REST APIs that well, is it possible to load the pipelines when the war is deployed? With some of our larger pipelines the first call may take quite a while. Would every call re-load the pipeline?
Tim
On Thu, 2017-12-14 at 20:16 +0000, Finan, Sean wrote:
> Hi Tim,
>
> Many thanks for testing the new rest service! And double that for the
> setup instructions!
>
> >
> > if this whole thing could be wrapped in a docker container that
> > would be really powerful
> - Matthew and I have had a short discussion or two on a docker that he
> is working on. It was working, but performed a lot of the spring
> updates and some workarounds that should no longer be needed. The
> next iteration should be cleaner and simpler. We have also talked
> about making the container more compact. He is busy with real work,
> but I think that this is definitely just over the horizon.
>
> >
> > 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.
> - I am actually looking at the rest/util/XmlParser and had the very
> same thought. It is a great start though, and as far as I know it is
> the first publicly available ctakes json writer. If anybody else out
> there already has or knows of another, please share!
>
>
> Cheers all,
> Sean
>
>
> -----Original Message-----
> From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
> Sent: Thursday, December 14, 2017 2:55 PM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS]
> [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 <de...@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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RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS] [SUSPICIOUS]
Posted by Gandhi Rajan Natarajan <Ga...@arisglobal.com>.
Hi Tim,
As you mentioned, the pipeline will be loaded only on the very first request to the REST service currently. But it can be changed to load the pipelines on server start too. Every call will not re-load the pipeline. Will incorporate the change to load the pipelines on server start.
Regards,
Gandhi
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Friday, December 15, 2017 2:28 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Another thought I just had is that it seems to load the pipeline when the first call is made -- without knowing the REST APIs that well, is it possible to load the pipelines when the war is deployed? With some of our larger pipelines the first call may take quite a while. Would every call re-load the pipeline?
Tim
On Thu, 2017-12-14 at 20:16 +0000, Finan, Sean wrote:
> Hi Tim,
>
> Many thanks for testing the new rest service! And double that for the
> setup instructions!
>
> >
> > if this whole thing could be wrapped in a docker container that
> > would be really powerful
> - Matthew and I have had a short discussion or two on a docker that he
> is working on. It was working, but performed a lot of the spring
> updates and some workarounds that should no longer be needed. The
> next iteration should be cleaner and simpler. We have also talked
> about making the container more compact. He is busy with real work,
> but I think that this is definitely just over the horizon.
>
> >
> > 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.
> - I am actually looking at the rest/util/XmlParser and had the very
> same thought. It is a great start though, and as far as I know it is
> the first publicly available ctakes json writer. If anybody else out
> there already has or knows of another, please share!
>
>
> Cheers all,
> Sean
>
>
> -----Original Message-----
> From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
> Sent: Thursday, December 14, 2017 2:55 PM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS]
> [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 <de...@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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Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS] [SUSPICIOUS]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Another thought I just had is that it seems to load the pipeline when
the first call is made -- without knowing the REST APIs that well, is
it possible to load the pipelines when the war is deployed? With some
of our larger pipelines the first call may take quite a while. Would
every call re-load the pipeline?
Tim
On Thu, 2017-12-14 at 20:16 +0000, Finan, Sean wrote:
> Hi Tim,
>
> Many thanks for testing the new rest service! And double that for
> the setup instructions!
>
> >
> > if this whole thing could be wrapped in a docker container that
> > would be really powerful
> - Matthew and I have had a short discussion or two on a docker that
> he is working on. It was working, but performed a lot of the spring
> updates and some workarounds that should no longer be needed. The
> next iteration should be cleaner and simpler. We have also talked
> about making the container more compact. He is busy with real work,
> but I think that this is definitely just over the horizon.
>
> >
> > 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.
> - I am actually looking at the rest/util/XmlParser and had the very
> same thought. It is a great start though, and as far as I know it is
> the first publicly available ctakes json writer. If anybody else out
> there already has or knows of another, please share!
>
>
> Cheers all,
> Sean
>
>
> -----Original Message-----
> From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
> Sent: Thursday, December 14, 2017 2:55 PM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS]
> [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 <de...@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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RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Tim,
Many thanks for testing the new rest service! And double that for the setup instructions!
> if this whole thing could be wrapped in a docker container that would be really powerful
- Matthew and I have had a short discussion or two on a docker that he is working on. It was working, but performed a lot of the spring updates and some workarounds that should no longer be needed. The next iteration should be cleaner and simpler. We have also talked about making the container more compact. He is busy with real work, but I think that this is definitely just over the horizon.
> 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.
- I am actually looking at the rest/util/XmlParser and had the very same thought. It is a great start though, and as far as I know it is the first publicly available ctakes json writer. If anybody else out there already has or knows of another, please share!
Cheers all,
Sean
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Thursday, December 14, 2017 2:55 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [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@arisglobal.
> > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
> > > Ta
> > > o&m
> > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarVc3
> > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
> > > Ta
> > > o&m
> > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarVc3
> > > 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@arisglobal.
> > > 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@arisglobal.
> > > 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.apach
> > > e.
> > > org
> > > _jira_browse_CTAKES-
> > > 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd
> > > ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWe
> > > Hr
> > > vVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmkKsbHo
> > > 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.com
> > > > _g
> > > > and
> > > > hirajan_cTAKES_tree_master_SpringUpgrade_ctakes&d=DwIFaQ&c=qS4g
> > > > oW
> > > > BT7
> > > > poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6
> > > > 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.com
> > > > _h
> > > > eal
> > > > thnlp_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r
> > > > =f
> > > > s67
> > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K
> > > > 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 <de...@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.apa
> > > > ch
> > > > e.o
> > > > rg_jira_browse_CTAKES-
> > > > 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
> > > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > Aa
> > > > XwW
> > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmk
> > > > Ks
> > > > bHo
> > > > vDNb4qYLIGA1LFWE&e= [2] -
> > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apa
> > > > 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.apa
> > > > ch
> > > > e.o
> > > > rg_jira_browse_CTAKES-
> > > > 2D188&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
> > > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > > > Aa
> > > > XwW
> > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=ptUmgt8eoj8hkr7RAFaAhc
> > > > 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=fs67GvlGZstTpyIisCYNYm
> > > > > QC
> > > > > P6r
> > > > > 0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_
> > > > > 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__githu
> > > > > b.
> > > > > com_GoTeamEpsilon_cTAKES-2DFriendly-2DWeb-
> > > > > 2DUI&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r
> > > > > =f
> > > > > s67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l3
> > > > > 0M
> > > > > X0K74_d9uL4nLj63jy45d5x_Y&s=NWjnOk5b4IeAjOCaCiYTS5KlnANsLcZTQ
> > > > > _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__github
> > > > > > .
> > > > > > com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes-
> > > > > > 2DSVN-
> > > > > > 2Dsrc&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxe
> > > > > > FU
> > > > > > &r
> > > > > > =
> > > > > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=cedfmyhdY7P3q
> > > > > > 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.edu]
> > > > > > 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.edu]
> > > > > > 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__github
> > > > > > .
> > > > > > 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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