Hi Ted, Try building 'ctakes-web-rest' module in https://github.com/GoTeamEpsilon/ctakes-rest-service . Please let me know what's the issue you are facing.
Please have a look at readme file once. You need to have all the ctakes dependency jars before building this module. Regards, Gandhi -----Original Message----- From: Ted Pikul [mailto:tedpik...@gmail.com] Sent: Thursday, June 14, 2018 8:12 PM To: dev@ctakes.apache.org Subject: Re: Run cTAKES continuously 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/ctake > s- > 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. > 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.
