ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From gandhi rajan <gandhiraja...@gmail.com>
Subject Re: MySQL web rest version unstable (with question) and note about official web rest Dockerfile
Date Thu, 13 Jun 2019 17:04:05 GMT
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 <matthewvita48@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 <matthewvita48@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 <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
> >> !!!"
> >>
> >
>


-- 
Regards,
Gandhi

"The best way to find urself is to lose urself in the service of others !!!"

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message