Re: Help - cTakes with UMLS and Ytex

Vivek Chris and I responded to you about 12 hours ago. On 6/28/16, 10:17 AM, "Vivek Venugopal" wrote: >Hi, > >Regarding my query on cTakes and UMLS : >I haven't got any response. Any info would be helpful. > > >Thanks, >Vivek Venugopal. >

Re: Help - cTakes with UMLS and Ytex

Hi, Regarding my query on cTakes and UMLS : I haven't got any response. Any info would be helpful. Thanks, Vivek Venugopal. On Mon, Jun 27, 2016 at 1:30 PM, Vivek Venugopal wrote: > Hi, > > At the University of Minnesota, We are trying to set up cTakes with UMLS > and see how we can utilize i

Re: running pipeline from command line

Hi Dima Personally I hate Maven because of how it obscures classpaths and dependencies (even though it purports to make that easier). My use case is a little different than yours, but when I launch a little pipeline from the command line, it looks as simple as this: Cd into the top of my applic

running pipeline from command line

Dear cTAKES developers, I ran into new issues running a uimafit pipeline from command line. I am trying to get a basic pipeline to run using this command: mvn exec:java -Dexec.mainClass=“org.apache.ctakes.examples.pipelines.BasicAnnotations" It runs fine in Eclipse, but it stumbles on diction

Re: URI is not hierarchical

On second thought... This might be useful http://stackoverflow.com/questions/18055189/why-my-uri-is-not-hierarchical On 6/28/16, 9:24 AM, "Abramowitsch, Peter" wrote: >Dima > >Although I'm not an expert, I don't think Ctakes relies on any Environment >variables a priori, unless you have a Cta

Re: URI is not hierarchical

Dima Although I'm not an expert, I don't think Ctakes relies on any Environment variables a priori, unless you have a Ctakes extensions that has added a dependency. Depending on your error you may need to look in AE or TypeSystem definition files or in the uimafit types.txt file where search path

Re: URI is not hierarchical

Hi Dima, Might be a red herring - I am not 100% positive that there is an env var in cTAKES that you are missing just that in the past when I’ve had that same bug (in another project), that was the cause. You may try looking for URIs in config file in which the property isn’t being resolved or it

Re: URI is not hierarchical

Thanks, Chris. I didn’t realize cTAKES was relying on environment variables for locating resources. Do you know which environment variable might be the issue? Thanks again for your help, Dima > On Jun 28, 2016, at 10:26, Mattmann, Chris A (3980) > wrote: > > Hi Dima, > > In Apache OODT, wh

Re: URI is not hierarchical

Hi Dima, In Apache OODT, when we do environment variable replacement on a URI, e.g., file://[SOME_ENV]/path, if $SOME_ENV isn’t defined, you get that error like you had below so that was the source of my suggestion sorry for not clarifying. Cheers, Chris +

Re: URI is not hierarchical

Brandon, thank you. I just did a quick mailing archive search and it looks like this is known issue, which presumably was fixed a while ago: http://mail-archives.apache.org/mod_mbox/ctakes-dev/201510.mbox/%3cd8f818ba-50fd-4a08-95ea-4e841ff6f...@childrens.harvard.edu%3E Thanks again, Dima > On

Re: URI is not hierarchical

Hi Chris, Sorry, could you please clarify which environment variable I am missing? Thanks, Dima > On Jun 28, 2016, at 09:49, Mattmann, Chris A (3980) > wrote: > > Looks to me like a missing environment variable.. > > ++ > Chris

Re: URI is not hierarchical

Looks to me like a missing environment variable.. ++ Chris Mattmann, Ph.D. Chief Architect Instrument Software and Science Data Systems Section (398) NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA Office: 168-519, Mailstop: 168

RE: URI is not hierarchical

Hi Dima, I believe this is related to the path of LVG. You can try coping the LVG data folder to the same directory (This is at least how I've gotten around it) when running a compiled jar. You can also search the mailing list for additional discussion on this issue. Thanks, Brandon -Or

URI is not hierarchical

Dear cTAKES developers, I am looking for a simple cTAKEs pipeline that can be run from command line to introduce a group of people to cTAKES. This pipeline: ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java seemed like a good candidate so I

Re: CTakes APIs

Correct, Peter.. ++ Chris Mattmann, Ph.D. Chief Architect Instrument Software and Science Data Systems Section (398) NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA Office: 168-519, Mailstop: 168-527 Email: chris.a.mattm...@nasa