Ctakes web rest module (rest service) is now available as part of ctakes svn codebase. All you gotta do is to use dictionary generator gui to add dictionary of your choice, get the corresponding scripts and load the DB. Then use the custom dictionary xml file in ctakes web rest module to point to the DB.
On Wednesday, January 30, 2019, <jbliss1...@yahoo.com> wrote: > Steve, are you using the ctakes-rest-service https://github.com/ > GoTeamEpsilon/ctakes-rest-service? > > > > If so, do you have any pointers as to how to configure a custom dictionary > (such as for ICD10) after installing the ctakes-rest-service. Because the > ctakes-rest-service installation procedure involves building ctakes from > source, the runCustomDictionary tool does not work…I have logged an issue > here: https://github.com/GoTeamEpsilon/ctakes-rest-service/issues/56 > > > > I was wondering if you had any pointers in this regard, or know anything > about how to implement their suggested solution of creating custom tables > etc. > > > > *From:* Steve Evans <stephen.ev...@duke.edu> > *Sent:* Tuesday, January 29, 2019 10:23 AM > *To:* user@ctakes.apache.org > *Subject:* RE: Processing large batches of files in cTAKES > > > > Leah, > > > > I run my ctakes work load using docker containers. > > > > I have built a container that serves ctakes requests via tomcat > webservices. That’s not for the feint of heart and not for non-programmer > types. But you might be able to install the ctakes software in a container > with the input/output directories on the host and then run in parallel > using file input/output. > > > > I run 10 containers to get the thru put we need (5/second). This is on a > 16 cpu 64GB host (each container consumes about 2GB of ram) > > > > Not a slam dunk type answer but I thought it might help gen ideas > > > > Steve > > > > > > *From:* Baas,Leah <leah.b...@sanfordhealth.org> > *Sent:* Tuesday, January 29, 2019 12:59 PM > *To:* user@ctakes.apache.org > *Subject:* Processing large batches of files in cTAKES > > > > Hi all, > > > > I would like to process a batch of 13,414 files (avg file size 6.2 KB) > using the default clinical pipeline. I am new to cTAKES and computer > programming, and I’m looking for guidance on how to process these files > with maximum time/CPU efficiency. I am currently running my program on an > Ubuntu VM with 3 CPUs. It takes me 28 seconds (real time) to process one > 6.0 KB file. I’m reading up on parallel processing strategies, but would be > grateful for any suggestions, tips, etc. that you might have! > > > > Thanks, > > > > Leah > > > > > > ----------------------------------------------------------------------- > Confidentiality Notice: This e-mail message, including any attachments, > is for the sole use of the intended recipient(s) and may contain > privileged and confidential information. Any unauthorized review, use, > disclosure or distribution is prohibited. If you are not the intended > recipient, please contact the sender by reply e-mail and destroy > all copies of the original message. > -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
