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.natara...@arisglobal.com] 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://issues.apache.org/jira/browse/CTAKES-472 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:matthewvit...@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.natara...@arisglobal.com> wrote: > Hi Alex and Sean, > > Thanks for the acknowledgement. > > As mentioned earlier in the thread, I have sent the github link - > https://github.com/gandhirajan/cTAKES/tree/master/SpringUpgrade/ctakes > - 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://github.com/healthnlp/ > 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:zbarce...@gmail.com] > Sent: Monday, October 30, 2017 6:07 PM > To: Apache cTAKES Dev <dev@ctakes.apache.org> > Subject: Re: cTAKES as REST service [EXTERNAL] > > Gandhi and Matthew, thank you for your hard work. > > I was working on upgrading libraries and fixing dependencies too. I > would love to help with Spring dependency. For that reason, I have created > issue: > "upgrade Spring dependency from 3.1.2 to 4.x" (CTAKES-472 [1]). > > Another great idea is the REST service, for that reason I created > CTAKES-473 [2]. It was also requested by Chei Pen in CTAKES-188 [3]. I > would like to know if you settled already to any framework (e.g. > Jersey vs > CXF) and if you also manage the dictionaries and different profiles > through the API. > > The last important idea I get is the Dockerfile, which sounds great > for the community to just test and play with cTAKES without the need > of building and exploring the source code. I was testing your work > Matthew, and I think it is a great start. > > What is the community practice in code for features that require a > longer time to be developed? Would it use a branch until it gets > stable, or it is preferred to have it in trunk for a faster > integration. The REST API feature, it will require a new module. Does > the community prefers a name for it (i.e ctakes-rest-api) ? > > Alex > > [1] - https://issues.apache.org/jira/browse/CTAKES-472 > [2] - https://issues.apache.org/jira/browse/CTAKES-473 > [3] - https://issues.apache.org/jira/browse/CTAKES-188 > > > On Sun, Oct 29, 2017 at 11:36 PM, Gandhi Rajan Natarajan < > gandhi.natara...@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:matthewvit...@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://github.com/GoTeamEpsilon/cTAKES-Concept-Mention-Parser 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://github.com/GoTeamEpsilon/cTAKES-Friendly-Web-UI > > 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.fi...@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.natara...@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_3xhKwEW14JZMSdioCoppxeFU > > > &r > > > = > > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=cedfmyhdY7P3qZdiVB- > > > gp0T0WinfllT61pLMqbP_Jyw&s=eMYiHpgQwJ5Zjc7-gW6qyAJ3AS3-H622ZVSJEJc > > > 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.fi...@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.natara...@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.natara...@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.fi...@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.natara...@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=DwIF > > > 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. 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