Hi Gandhi, Again, sorry for the late reply!
In terms of presenting and comparing outputs with the same phrase and multiple pipelines, I have put together a comprehensive (throw-away) repository that shows and explains the results between the proper cTAKES system and the MySQL REST one. The phrase was: severe bipolar i disorder . I tried to keep the README limited, but informative along with useful commentary. Each result is neatly packaged under its system and pipeline: https://github.com/MatthewVita/cTAKES-Special-Case-QA Please let me know if there are other debugging approaches to try with this issue. I'm not quite sure of how to move forward :). Thanks, Matthew Vita On Wed, Jun 5, 2019 at 11:23 PM Matthew Vita <matthewvit...@gmail.com> wrote: > Sorry for the delay (work is busy) - will report back soon with the > pipelines. > > Thanks, > Matthew Vita > > > > On Mon, Jun 3, 2019 at 8:19 AM gandhi rajan <gandhiraja...@gmail.com> > wrote: > >> Hi Matt, we gotta see what are the types of pipelines used in both cases. >> Did you tried using pipeline=full instead pipeline=default? >> >> Full pipeline can give more information I guess. >> >> On Monday, June 3, 2019, Matthew Vita <matthewvit...@gmail.com> wrote: >> >> > Hi Gandhi and All, >> > >> > (Correction: my previous statement about the MySQL web rest version “not >> > working in its current state” is only partially true. I was able to HTTP >> > POST “Hypertension” and get correct results. However, I’ll be showing >> that >> > it’s not working for all cases below.) >> > >> > My testing/debugging as of today was to set up the following >> environments >> > and compare the XMLs: >> > >> > >> > 1. >> > >> > Environment #1 - cTAKES Web Rest MySQL version @ 1850060 (with output >> > xml on, per Gandhi) with the resource data loaded in via plain SQL >> > 2. >> > >> > Environment #2 - cTAKES proper @ 1850060 with the resources data >> loaded >> > on disk >> > >> > >> > This setup allows for the data to be the same in either MySQL or HSQLDB. >> > >> > >> > >> > >> > Furthermore, I made sure that the MySQL database had these following >> > entries because I chose to use ‘severe bipolar i disorder’ as my test >> > string: >> > >> > - >> > >> > cui_terms(236784,12,13,'severe bipolar i disorder , most recent >> episode >> > mixed , with psychotic features','features') >> > - >> > >> > TUI(236784,48) >> > - >> > >> > PREFTERM(236784,'Severe mixed bipolar I disorder with psychotic >> > features') >> > - >> > >> > SNOMEDCT_US(236784,10981006) >> > >> > >> > >> > >> > Here’s the result of using the regular cTAKES setup with CVD and >> > AggregatePlaintextFastUMLSProcessor: >> > >> > severe_bipolar_i_disorder_cvd.xml - >> > https://gist.github.com/MatthewVita/93000a05a5d0f4ef6a4267359c63b510 >> > >> > Here’s the result of using cTAKES Web Rest MySQL with cURL: >> > >> > curl -X POST \ >> > >> > ' >> http://localhost:8080/ctakes-web-rest/service/analyze?pipeline=Default' >> > \ >> > >> > -H 'cache-control: no-cache' \ >> > >> > -d 'severe bipolar i disorder' >> > >> > severe_bipolar_i_disorder_rest.xml >> > https://gist.github.com/MatthewVita/341f8c9a3552f3db9352917b810a20b0 >> > >> > >> > The results show that the CVD results are much better. Rest doesn’t even >> > pick up on the main disorder. *Any thoughts or more debugging ideas are >> > welcomed!* >> > >> > >> > >> > *Sort of unrelated:* I have a good amount of work getting the MySQL >> > version’s README instructions cleaned up and removing some other bugs in >> > the issue tracker. I wonder if it would be Apache license compliant for >> the >> > main SVN web rest to link to this one? Perhaps this repo can be changed >> to >> > “GoTeamEpsilon/ctakes-mysql-rest-service”? >> > >> > >> > Thanks, >> > Matthew Vita >> > >> > >> > >> > On Fri, May 31, 2019 at 10:11 PM gandhi rajan <gandhiraja...@gmail.com> >> > wrote: >> > >> > > Hi Matt, I would check whether the XML output from cTAKES contains the >> > > terms to isolate the issue. >> > > >> > > On Saturday, June 1, 2019, Matthew Vita <matthewvit...@gmail.com> >> wrote: >> > > >> > > > Hi Jeff, >> > > > >> > > > Not sure I ran into that same issue. Sorry. >> > > > >> > > > In terms of MySQL, I suppose it is faster because it's not in-memory >> > > based >> > > > (to be fair, HSQLDB can utilize disks). Another factor is that you >> can >> > > load >> > > > balance multiple servers in a "stateless" way if you had a heavy >> load >> > > > environment because the MySQL stands alone. >> > > > >> > > > >> > > > >> > > > Hi Gandhi, >> > > > >> > > > I'm using trunk@1850060 with the MySQL-based codebase on Github. >> > > > Everything >> > > > builds and it even connects to all of the tables and models, >> however, >> > it >> > > > doesn't pick up terms. >> > > > >> > > > Where do you think is a good place to start, with respect to >> debugging? >> > > The >> > > > frustrating part is there's no errors in the catalina logs :). >> > > > >> > > > Thanks, >> > > > Matthew Vita >> > > > >> > > > >> > > > >> > > > On Thu, May 30, 2019 at 2:52 PM gandhi rajan < >> gandhiraja...@gmail.com> >> > > > wrote: >> > > > >> > > > > Hi Matt, >> > > > > >> > > > > The ctakes web rest module in cTAKES svn trunk is the latest >> which I >> > > > > checked in and later modified by Tim. >> > > > > >> > > > > On Thursday, May 30, 2019, Matthew Vita <matthewvit...@gmail.com> >> > > wrote: >> > > > > >> > > > > > Hi Gandhi, Tim, Sean, and Community, >> > > > > > >> > > > > > I’ve been fixing up some of the README instructions for >> > > > > > https://github.com/GoTeamEpsilon/ctakes-rest-service on my >> local. >> > > > > > Unfortunately, it’s not working in its current state. I'm still >> > > > debugging >> > > > > > it - is svn co https://svn.apache.org/repos/ >> > asf/ctakes/trunk@1850060 >> > > > > > ctakes >> > > > > > still the best version of cTAKES to base web-rest on? >> > > > > > >> > > > > > Also, it looks like the ctakes-web-rest Dockerfile in the >> official >> > > > > > repository is pointing to a broken Tomcat link: >> > > > > > >> > > > > > *“The requested URL >> > > > > > /pub/software/apache/tomcat/tomcat-9/v9.0.14/bin/apache- >> > > > tomcat-9.0.14.zip >> > > > > > was not found on this server.”* >> > > > > > >> > > > > > There appear to be updated releases here: >> > > > > > >> http://mirror.cc.columbia.edu/pub/software/apache/tomcat/tomcat-9/ >> > - >> > > > > hope >> > > > > > that helps. >> > > > > > >> > > > > > >> > > > > > Talk soon, >> > > > > > Matthew >> > > > > > >> > > > > >> > > > > >> > > > > -- >> > > > > Regards, >> > > > > Gandhi >> > > > > >> > > > > "The best way to find urself is to lose urself in the service of >> > others >> > > > > !!!" >> > > > > >> > > > >> > > >> > > >> > > -- >> > > Regards, >> > > Gandhi >> > > >> > > "The best way to find urself is to lose urself in the service of >> others >> > > !!!" >> > > >> > >> >> >> -- >> Regards, >> Gandhi >> >> "The best way to find urself is to lose urself in the service of others >> !!!" >> >
