I've added a section[1] to the User Install Guide describing how to convert an HSQLDB from hsqldb 1.8 to 2.3.4 for cTAKES 4.0
[1] https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide#cTAKES4.0UserInstallGuide-ConvertDictionariesYou'vePreviouslyCreatedtobeCompatiblewithcTAKES4.0 On Sun, Apr 23, 2017 at 10:03 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Thank you James - great explanation and information. > > Hi David, > There is a new version of the dictionary creator gui distributed with > ctakes 4.0. It is 99% the same as the version in sandbox. One important > difference is that it now produces a database in hsqldb 2.3.4 - compatible > with ctakes 4.0. > Another difference (important to you) is that there is an exclusion list > in a data file that lists cui / term combinations that can be excluded. By > default the medications "toDAY" and "ToMORROW" are in that list. It is > obviously done to prevent the frequent false positives that you spoke of in > your Amia presentation. For non-vet use these exclusions are pretty > valid. Since you are interested in a vet dictionary fi you use the new > dictionary creator you can decide whether or not you want them to be > included. > > Sean > > -----Original Message----- > From: James Masanz [mailto:masanz.ja...@gmail.com] > Sent: Saturday, April 22, 2017 11:32 PM > To: dev@ctakes.apache.org > Subject: Re: cTAKES 4.0rc3 - custom dictionary needs rebuilding? > > Dave, > > It's an oversight that we didn't document that. Thanks for pointing that > out! I'll update the documentation tomorrow and post again with proper > details of the command to use. > > The short answer is that hsqldb jar includes a GUI. You use the 2.3.4 > version of that jar, which is included with the cTAKES 4.0 convenience > binary, to open your database. Then you close (shutdown) your DB and it > gets converted to 2.3.4 for you. But if the .properties file for your DB > indicates it's readonly, you need to have edited the properties file first > to remove that. That gives you the idea. I'll write it up properly tomorrow. > > Thanks for testing, > -- James > > > *Sent from my phone.* > > On Apr 22, 2017 9:39 PM, "David Kincaid" <kincaid.d...@gmail.com> wrote: > > I finally had some time this weekend to give 4.0.0rc3 a run. The install > and configuration instructions worked perfectly on my Linux laptop and I > was able to use CVD to run the clinical pipeline successfully against some > of the clinical notes I have here. > > However, I ran into a problem when I tried running my own customized > pipeline that includes a custom dictionary that I create (to include the > SNOMED veterinary extension). I get an exception while it's loading that > the dictionary is not the correct version. So, I assume I just need to > recreate that custom database? Or is there a migration utility from the old > database version to the new version? > > I don't remember seeing mention of this, but certainly could have missed > it. If it's not in the release notes or install/upgrade instructions it > probably should be there. > > Thanks to everyone for pulling this release together and getting it out > the door! > > - Dave >
