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.com > > > > _G > > > > oT > > > > eam > > > > Epsilon_ctakes-2Drest- > > > > 2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x > > > > hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d > > > > 4g > > > > Ta > > > > o&m > > > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarV > > > > 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.com > > > > _G > > > > oT > > > > eam > > > > Epsilon_ctakes-2Drest- > > > > 2Dservice_tree_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3x > > > > hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d > > > > 4g > > > > Ta > > > > o&m > > > > =AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=KZ65xiQopzQNQarV > > > > 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.apa > > > > ch > > > > e. > > > > org > > > > _jira_browse_CTAKES- > > > > 2D472&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSd > > > > ioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXw > > > > We > > > > Hr > > > > vVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVCmkKsb > > > > 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=fs67GvlGZstTpyIisCYNYmQC > > > > > 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_3xhKwEW14JZMSdioCoppxeFU > > > > > &r > > > > > =f > > > > > s67 > > > > > GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX > > > > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao& > > > > > m= > > > > > Aa > > > > > XwW > > > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=HiYEkIXpY3OkZyUqWJVC > > > > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao& > > > > > 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=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao& > > > > > m= > > > > > Aa > > > > > XwW > > > > > eHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5x_Y&s=ptUmgt8eoj8hkr7RAFaA > > > > > 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__github > > > > > > .c > > > > > > om > > > > > > _Go > > > > > > TeamEpsilon_cTAKES-2DConcept-2DMention- > > > > > > 2DParser&d=DwIFaQ&c=qS4goWB > > > > > > T7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYN > > > > > > Ym > > > > > > QC > > > > > > P6r > > > > > > 0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3l30MX0K74_d9uL4nLj63jy45d5 > > > > > > 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_3xhKwEW14JZMSdioCoppxeFU > > > > > > &r > > > > > > =f > > > > > > s67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AaXwWeHrvVgjd3 > > > > > > l3 > > > > > > 0M > > > > > > X0K74_d9uL4nLj63jy45d5x_Y&s=NWjnOk5b4IeAjOCaCiYTS5KlnANsLcZ > > > > > > 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__gith > > > > > > > ub > > > > > > > . > > > > > > > com_gandhirajan_cTAKES_tree_master_SpringUpgrade_ctakes- > > > > > > > 2DSVN- > > > > > > > 2Dsrc&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx > > > > > > > e > > > > > > > FU > > > > > > > &r > > > > > > > = > > > > > > > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=cedfmyhdY7P > > > > > > > 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__gith > > > > > > > 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. 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. > > > > > > > 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. > > > > > > > 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. > > > > > > > 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. > > > > > > > > > > > > > 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. > > > > > > > > > > > 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. > > > > > > > > > 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. > > > > 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. > > > > 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. > > > > 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. > 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.
