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From Matthew Vita <matthewvit...@gmail.com>
Subject Re: MySQL web rest version unstable (with question) and note about official web rest Dockerfile
Date Thu, 06 Jun 2019 03:23:58 GMT
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 <gandhirajan.n@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 <matthewvita48@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 <gandhirajan.n@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 <matthewvita48@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 <
> gandhirajan.n@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 <matthewvita48@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
> !!!"
>

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