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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]
Date Tue, 02 Jan 2018 15:34:55 GMT
3 cheers Matthew!

-----Original Message-----
From: John Green [mailto:john.travis.green@gmail.com] 
Sent: Sunday, December 31, 2017 9:12 AM
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]

Strong work!  

--- Sent from VMware Boxer

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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