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.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: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 > > >
