Hi Tim, The MySQL UMLS dictionary requires only config changes and loading the DB with scripts generated from ctake custom dictionary generator GUI. The steps are listed in our last apachecon presentation - https://www.youtube.com/watch?v=pBB4_lycmrw
we can load the MySQL DB and containerize the same. Hope it helps. On Thu, Feb 25, 2021 at 10:18 PM Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > Gandhi, > Is that code public at all? I made a docker container for the REST > server that uses the hsql, but if mysql is even faster and the > dictionary building can be containerized that might be a nice next step > for better performance of the container. > Tim > > > On Thu, 2021-02-25 at 20:33 +0530, gandhi rajan wrote: > > * External Email - Caution * > > > > > > Hi Peter, > > > > Noticed a similar behavior while working on cTAKES REST module. The > > in-memory HSQL in my case was stressing the application server memory > > and > > ended up slowing down the process whereas mysql performed better. > > Also > > the engine you use in MySQL matters as well. > > > > We did a testing on MySQL based UMLS dictionary using multiple pods > > running > > ctakes rest and it was scaling fairly well. But havent explored with > > 100+ > > connections. But i guess with connection pool configurations in MySQL > > DB it > > should be manageable. Hope it helps. > > > > On Thu, Feb 25, 2021 at 7:37 PM Peter Abramowitsch < > > pabramowit...@gmail.com> > > wrote: > > > > > Hi all, > > > > > > As an experiment I extracted my rather large HSQL UMLS dictionary > > > into a > > > local MYSQL instance and ran the equivalent of 3 simultaneous > > > ctakes > > > pipelines with the overlap lookup annotator against it with a set > > > of 1000 > > > notes. > > > > > > Comparing that with the same setup running against the traditional > > > in-memory HSQL database (three separate instances), I was surprised > > > to find > > > that the Mysql implementation it was 30% faster even though it is > > > an out of > > > process DB > > > > > > Has that been anyone else's experience as well? And if so, do you > > > have any > > > experience with a MYSQL based UMLS dictionary with 100+ pipeline > > > connections? > > > > > > Peter > > > > > > > > -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
