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 < [email protected]> 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:[email protected]] > Sent: Monday, October 30, 2017 6:07 PM > To: Apache cTAKES Dev <[email protected]> > 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 < > [email protected]> 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:[email protected]] > > Sent: Sunday, October 29, 2017 9:30 PM > > To: [email protected] > > 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 < > > [email protected]> 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:[email protected]] > > > Sent: Sunday, October 29, 2017 5:44 AM > > > To: [email protected] > > > 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-H622ZVSJEJcgd > > > 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:[email protected]] > > > Sent: Friday, October 27, 2017 12:53 AM > > > To: [email protected] > > > 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:[email protected]] > > > Sent: Thursday, October 26, 2017 3:02 PM > > > To: [email protected] > > > 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:[email protected]] > > > Sent: Wednesday, October 25, 2017 7:33 PM > > > To: [email protected] > > > 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:[email protected]] > > > Sent: Wednesday, October 25, 2017 7:28 PM > > > To: [email protected] > > > 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:[email protected]] > > > Sent: Wednesday, October 25, 2017 9:20 AM > > > To: [email protected] > > > 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=DwIFAg > > > &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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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. >
