Sounds great, Matthew and Gandhi, thanks for sharing your solution. Tim ________________________________________ From: Matthew Vita <matthewvit...@gmail.com> Sent: Sunday, October 29, 2017 11:59 AM 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.com_GoTeamEpsilon_cTAKES-2DConcept-2DMention-2DParser&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=RsnpR4AiLXd_qcFBYZG7T4_ExzPAkin8TsudEMLyPo8&s=YwuDivFqbAlEMTdeK-uxI2c01mLaq-4TfNwqDnVWUW4&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__github.com_GoTeamEpsilon_cTAKES-2DFriendly-2DWeb-2DUI&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=RsnpR4AiLXd_qcFBYZG7T4_ExzPAkin8TsudEMLyPo8&s=NjO4o8D_b6137joWwzPbit21dfg58a0_BXTikkpMFm8&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.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-H622ZVSJEJcgd8s&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=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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