Cheers all! -----Original Message----- From: Matthew Vita [mailto:matthewvit...@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 <matthewvit...@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.mil...@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.mil...@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: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.Nata ra...@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: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 >> > > > > > .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: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 >> > > > > > .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.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__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.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__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.fi...@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.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.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.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__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. 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