Hi Gandhi, Sorry if I wasn't clear or my README.md didn't completely make sense.
I tested with both full and default pipelines. The results can be found here: https://github.com/MatthewVita/cTAKES-Special-Case-QA/tree/master/REST%20MySQL%20Results Thanks, Matthew Vita On Thu, Jun 13, 2019 at 1:04 PM gandhi rajan <gandhiraja...@gmail.com> wrote: > Hi Matt, > > As I mentioned earlier, did you tried using full pipeline instead of > default pipeline? Ctakes web rest relies on the output XML of ctakes > engine. > > Only way to figure out the problem is to understand what are the pipers > used in case of both the cases. > > On Thursday, June 13, 2019, Matthew Vita <matthewvit...@gmail.com> wrote: > > > 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 > > >> !!!" > > >> > > > > > > > > -- > Regards, > Gandhi > > "The best way to find urself is to lose urself in the service of others > !!!" >
