Hi Peter, I do understand that the module requires all ctakes dependency in place before building it. But the original plan was to commit this module into ctakes codebase so that it gets built along with other modules of ctakes and the war file will be ready for deployment.
In your case, the null content may be due to some XML parsing failure which was more specific to our requirement. Infact, if required you can send back the XML file returned from ctakes as is from REST service and do further processing based on your requirement. Unfortunately, we are not yet able to close this module completely to check-in the code to ctakes SVN as most of us are slammed with other works. Regards, Gandhi -----Original Message----- From: Peter Abramowitsch [mailto:pabramowit...@gmail.com] Sent: Thursday, June 14, 2018 10:40 PM To: dev@ctakes.apache.org Subject: Re: Run cTAKES continuously 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/cta > > ke > > 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. > 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.
