ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Matthew Vita <matthewvit...@gmail.com>
Subject Re: MySQL web rest version unstable (with question) and note about official web rest Dockerfile
Date Fri, 14 Jun 2019 01:34:56 GMT
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 <gandhirajan.n@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 <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