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From Matthew Vita <matthewvit...@gmail.com>
Subject Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]
Date Sun, 31 Dec 2017 07:16:46 GMT
Just wanted to note that I've made a good bit of progress on the GUI
dictionary piece. I'll post some screenshots when it is further along, but
I am definitely seeing the tables in my MySQL database (tested with CPT and
ICD10).

I'll aim to setup CouchDB for v2 of the ctakes-rest-service. Next step is
to point cTAKES (within the context of the rest service) at MySQL :).

Thanks,

Matthew Vita
www.matthewvita.com

On Mon, Dec 18, 2017 at 1:27 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Matthew,
>
> I've heard of CouchDB but know nothing about it.  At a glance it looks
> like it is pretty versatile.
>
> Sean
>
> -----Original Message-----
> From: Matthew Vita [mailto:matthewvita48@gmail.com]
> Sent: Monday, December 18, 2017 3:52 PM
> To: dev@ctakes.apache.org
> Cc: Sandeep Byatha Gururaja rao; Shane Chesnutt
> Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL
> Progress + 1 Concern [EXTERNAL]
>
> Okay, thanks for that Sean.
>
> I have a CRAZY idea... how about I try it with CouchDB instead? It's a) by
> Apache b) can be ran in Docker c) Has a JDBC connector on Github and d) Is
> 1 of the 2 databases used in OpenEMR so our cTAKES module users wouldn't
> get too confused.
>
> Again, that last item is nice to have, don't read into it too much :).
>
> Thoughts?
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Mon, Dec 18, 2017 at 7:23 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Fantastic!
> >
> > I am glad that you found the issue - that wouldn't have been a
> > straightforward causal to track down.
> >
> > Unfortunately we cannot package and ship any binaries that aren't
> > fully Apache license compliant etc.  However, we can do two different
> things:
> > - We can still grab mysql from maven central for developers to use in
> > a developer environment, just like we do with the default umls
> dictionary.
> > - We can provide an easy means for fetching the library
> > post-installation.  A Dockerfile for ctakes, a downloader that
> > launches when mysql is selected, or a good old fashioned installation
> script.
> > Luckily the mysql library is easily available and we wouldn't need to
> > put together a runtime package like APR.
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__books.google.com_
> > books-3Fid-3DHTo-5FAmTpQPMC-26pg-3DPA14-26&d=DwIFaQ&c=qS4goWBT7poplM69
> > zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
> > Tao&m=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc&s=-fxY4QiBU8SayGVEzX
> > 8LVPEPzmgsYP6ANRsuTUkHkrY&e=
> > lpg=PA14&dq=apache+license+mysql&source=bl&ots=uOpifTcI2E&sig=-qlWP2-
> > pXtEkwPM8BsKd73GvX9g&hl=en&sa=X&ved=0ahUKEwjhqrrX55PYAhVm5YMKHTB2A
> > GM4ChDoAQhMMAY#v=onepage&q=apache%20license%20mysql&f=false
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__apr.apache.org_do
> > wnload.cgi&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs
> > 67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=n53T6SD3EzUyJps9w7LjgVaYGA
> > 5GQjR3h-9GBGppwBc&s=Gm3m03xhcJj7rfD05pZkfM9t5l8-aBOOZCwJVf4as5g&e=
> >
> > I think that we could make a class that searches for mysql in the
> > environment if the mysql option is selected.   ctakes-gui has a
> dependency
> > that makes this easy.  Then a little downloader that throws a driver
> > into the lib/ directory.  If needed we could create a factory that
> > returns a wrapper for the required mysql driver classes, and the
> > factory could contain a class loader that guarantees the jar is
> > discovered post-installation.  That way a restart of the gui wouldn't be
> necessary ...
> > though that may not be a big deal.
> >
> > I am just throwing out some ideas.  There is probably a very nice
> > solution that I haven't considered.
> >
> > Sean
> >
> >
> >
> > -----Original Message-----
> > From: Matthew Vita [mailto:matthewvita48@gmail.com]
> > Sent: Monday, December 18, 2017 1:23 AM
> > To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao; Shane Chesnutt
> > Subject: cTAKES Rest Service Development - Dictionary GUI MySQL
> > Progress +
> > 1 Concern [EXTERNAL]
> >
> > Hi Gandhi, Sean, Tim, Alex, James,
> >
> > Good news, I was able to get MySQL running in the `ctakes-gui` (recall
> > that I am building in a toggle so that folks can create dictionaries
> > using MySQL rather than HSQLDB script files).
> >
> > I found out the source of the issue with bringing in the MySQL
> dependency.
> > This one definitely took me a while and was super subtle! If you visit
> > /ctakes/ctakes-distribution/src/main/assembly/bin.xml,
> > <exclude>mysql:*</exclude>is present because it's a n  non-asf
> > compliant dependency used by ytex.
> >
> > Removing the exclude and addingin
> > <include>mysql:mysql-connector-java</include> gets the correct result:
> >
> > /ctakes/ctakes-distribution/target/apache-ctakes-4.0.1-SNAPSHOT/lib
> > matthew
> > ​​
> > % ls -lash | grep mysql
> >   3912 -rw-r--r--   1 matthew  staff   1.9M Dec 14 20:23
> > mysql-connector-java-6.0.6.jar
> >
> > Just for completeness, this is the exact POM entry:
> >
> >       <dependency>
> >          <groupId>mysql</groupId>
> >          <artifactId>mysql-connector-java</artifactId>
> >          <version>6.0.6</version>
> >      </dependency>
> >
> >
> > Is there anyway we can use MySQL in cTAKES in a way that is compliant
> > with ASF? I wonder if MariaDB or Postgresql would be better because
> > they work with JDBC and are free/open source. Of course, I am biased
> > towards MySQL/MariaDB because the (near) future users of cTAKES Rest
> > Service in the OpenEMR space are going to want MySQL/MariaDB users :).
> > Not a huge deal though.
> >
> > Thanks,
> >
> > Matthew Vita
> > www.matthewvita.com
> >
>

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