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:matthewvit...@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.natara...@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.natara...@arisglobal.com] > 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_GoTeam > Epsilon_ctakes-2Drest-2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x > hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarVc3BPMxK > 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_GoTeam > Epsilon_ctakes-2Drest-2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x > hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarVc3BPMxK > 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.natara...@arisglobal.com] > 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.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://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org > _jira_browse_CTAKES-2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd > ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmkKsbHovDNb4qYLIGA1LFWE&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: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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_gand > > hirajan_cTAKES_tree_master_SpringUpgrade_ctakes&d=DwIFaQ&c=qS4goWBT7 > > poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcp > > KGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=1xSDOHa > > 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_heal > > thnlp_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67 > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_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: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://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o > > rg_jira_browse_CTAKES-2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwW > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmkKsbHo > > vDNb4qYLIGA1LFWE&e= [2] - > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o > > rg_jira_browse_CTAKES-2D473&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwW > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=amE_Q3-yRQqb3YlCrjqEMO6oyco > > bMTJCydPlOFyi6PA&e= [3] - > > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o > > rg_jira_browse_CTAKES-2D188&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J > > ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwW > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=ptUmgt8eoj8hkr7RAFaAhc7XXCD > > QlTANvb2YasbcToQ&e= > > > > > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Go > > > TeamEpsilon_cTAKES-2DConcept-2DMention-2DParser&d=DwIFaQ&c=qS4goWB > > > T7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r > > > 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__github.com_GoTeamEpsilon_cTAKES-2DFriendly-2DWeb-2DUI&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=NWjnOk5b4IeAjOCaCiYTS5KlnANsLcZTQ_TRneZCtxg&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_3xhKwEW14JZMSdioCoppxe > > > > FU > > > > &r > > > > = > > > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=cedfmyhdY7P3qZdiVB > > > > - > > > > 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.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=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. 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