Great Work Matthew. This will be very handy for cTAKEs MySQL integration. Cheers.
Regards, Gandhi -----Original Message----- From: Matthew Vita [mailto:matthewvit...@gmail.com] Sent: Sunday, December 31, 2017 12:47 PM To: dev@ctakes.apache.org Cc: Sandeep Byatha Gururaja rao <sandeep...@arisglobal.com>; Shane Chesnutt <shanechesn...@gmail.com> Subject: Re: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL] 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.fi...@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:matthewvit...@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.fi...@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.co > > m_ > > books-3Fid-3DHTo-5FAmTpQPMC-26pg-3DPA14-26&d=DwIFaQ&c=qS4goWBT7poplM > > 69 > > zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d > > 4g > > Tao&m=n53T6SD3EzUyJps9w7LjgVaYGA5GQjR3h-9GBGppwBc&s=-fxY4QiBU8SayGVE > > zX > > 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=n53T6SD3EzUyJps9w7LjgVaY > > GA > > 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:matthewvit...@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 > > > This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
