Thank you Peter and Gandhi. I’ve not been able to get the ctakes-rest-service to run successfully (using docker). I’m also not sure it supports UMLS credentials and it looks like the UMLS database is a local copy although I could be misunderstanding that. Due to the license confusion around running a local copy of UMLS database I’d rather just avoid that.
I’ll try the implementation suggested by Peter. I also found that Tika has a cTAKES REST API, but unfortunately it loads the model on each request. On Wednesday, June 13, 2018, Gandhi Rajan Natarajan < gandhi.natara...@arisglobal.com> wrote: > Hi Ted, > > The implementation suggested by Peter is already available in > https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes- > web-rest > > Building this project will give you a WAR file which you need to deploy in > Tomcat. > > Regards, > Gandhi > > -----Original Message----- > From: Peter Abramowitsch [mailto:pabramowit...@gmail.com] > Sent: Wednesday, June 13, 2018 2:40 AM > To: dev@ctakes.apache.org > Subject: Re: Run cTAKES continuously > > Sorry, The mail sent before I was ready This is pseudocode > > // __aae is your analysis engine (there could be multiple) > while(more notes) { > jcas.setDocumentText(note.getFree_text()); > _aae.process(jcas); > // do something with the jcas contents here > jcas.reset() > } > > On Tue, Jun 12, 2018 at 11:06 PM, Peter Abramowitsch < > pabramowit...@gmail.com> wrote: > > > The best solution would be to put it in a server framework. I was not > > able to get the EpsilonTeam server to work, but there's another tiny > > server version written in Scala which you can try. I ended up doing one > using the > > Spark REST framework. You can build a non server / non UI version which > > does run at the command line by coding it up (in Java) to create the > > pipeline or using a piper, then create a jCas which you > > use/reset/reuse > > > > The core of it would be a loop like this > > > > jcas.setDocumentText(note.getFree_text()); > > _aae.process(jcas); > > > > On Tue, Jun 12, 2018 at 8:05 PM, Ted Pikul <tedpik...@gmail.com> wrote: > > > >> Hi- I’ve been able to successfully run cTAKES from the command line > >> as documented here: > >> https://cwiki.apache.org/confluence/display/ctakes/default+ > >> clinical+pipeline > >> > >> This works great, but each time it runs it has to make the database > >> connection using jdbc and load the model, which takes 15 seconds or so. > >> > >> Is there another script besides the runClinicalPipeline.sh that I can > >> run to just keep this running and send new notes to it rather than > >> getting the db connection and loading the model each time? > >> > >> I know there is the cTAKES rest server project: > >> https://github.com/GoTeamEpsilon/ctakes-rest-service which I think > >> might do what I’m looking to do. but as it’s still in alpha stage, > >> especially the docker piece of it, and I don’t really need a server I > >> can just run from command line, I’m not sure this is the right > >> solution for me. > >> > >> I tried looking at how the runctakesCVD.sh script works, as it does > >> what I need but with the CVD UI, but I couldn’t quite figure it out > >> from looking at the UIMA code. > >> > >> Any guidance here is greatly appreciated. Thank you > >> > > > > > 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. >
