Hi Gandhi I also had difficulty building it, and then finally when it built after I tweaked some code in ctakes-temporal, it just returned null content. I figured it was in a state of flux.
But additionally as I discussed with Matthew Vita one of your colleagues, the project could be more useful if there were a way of building and developing with it also outside docker. As currently packaged, it seems optimized for one-off fetch and build from straight to finish. At the moment delegating all the heavy lifting to the shell script which docker-compose invokes means that for each trivial change, the system has to re-do a large amount of downloading and building. On Thu, Jun 14, 2018 at 4:53 PM, Gandhi Rajan Natarajan < gandhi.natara...@arisglobal.com> wrote: > 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. >
