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 > !!!" >
