Dictionary connection error with default clinical pipeline

2018-04-05 Thread Reed Villanueva
Using intellij IDEA to work on a ctakes project. Currently I have added the jars by copying them to some folder and pointing intellij to that folder as a library in the File --> Project Structure. The way I am using the resources/ folder right now is by having it in the same folder as a src folder

Re: How to get XMI output fie from java jcas?

2018-04-10 Thread Reed Villanueva
the link - https://github.com/ > GoTeamEpsilon/ctakes-rest-service/blob/master/ctakes- > web-rest/src/main/java/org/apache/ctakes/rest/service/ > CtakesRestController.java and see if it helps. > > > > *Regards,* > > *Gandhi* > > > > *From:* Reed Villanu

How to get XMI output fie from java jcas?

2018-04-10 Thread Reed Villanueva
How can I get the output of a pipeline built in java as an XMI file similar to how piper files output extracted annotation information in form of XMI files? Eg. I have the code AggregateBuilder builder = new AggregateBuilder(); builder.add( ClinicalPipelineFactory.getDefaultPipeline() );

Re: Documents won't process

2018-04-06 Thread Reed Villanueva
Could you please post an example of the kind of input text you say is causing the error as well as the full stack trace of the error if any is output? > On Apr 4, 2018, at 11:17 AM, Scotty, Erica J > wrote: > > I have some documents I am trying to process,

Re: Sentence extraction from cTAKES XML output.

2018-03-28 Thread Reed Villanueva
Orthopnea (since the CUI correspond to Orthopnea hence the tagged sentence > should comprise the tagged concept as well i.e Orthopnea) > > > > Below is the snippet from the of the raw_text where I have marked the > sentence in red rectangular box which yields “o pnd. ort” instea

Re: Sentence extraction from cTAKES XML output.

2018-03-27 Thread Reed Villanueva
Could you provide an example of the problem your are seeing and a bit more about the kind of output you are trying to end up with? On Tue, Mar 27, 2018 at 3:33 PM, Yadav, Harish wrote: > Hi All, > > > > I am trying to extract the sentence from cTAKES XML output by taking

How do piper files access (non-primitive) analysis engines?

2018-03-24 Thread Reed Villanueva
Having problem where seem to not be able to ADD analysis engines (AEs) in piper files (as described in the docs: https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files). It seems like the main difference, looking at the first few lines of the raw xmi of these AEs (in say google chrome) as

Re: How do piper files access (non-primitive) analysis engines?

2018-03-24 Thread Reed Villanueva
ry [root]. 24 Mar 2018 18:24:37 ERROR PiperFileRunner - MESSAGE LOCALIZATION FAILED: > Can't find resource for bundle java.util.PropertyResourceBundle, key No > Analysis Component found for AggregatePlaintextFastUMLSProcessor ​​ On Sat, Mar 24, 2018 at 6:57 PM, Reed Villanueva &

Re: How do piper files access (non-primitive) analysis engines?

2018-03-25 Thread Reed Villanueva
d in piper files?​ On Sat, Mar 24, 2018 at 7:05 PM, Reed Villanueva <villanuevar...@gmail.com> wrote: > Forgot to add an example of the error message that I am seeing when I try > to use these AEs: > > Here is the error message when trying to use bin/runPiperFile.sh -p > my

Missing resources for using the AggregatePlaintextFastUMLSProcessor?

2018-03-24 Thread Reed Villanueva
Examining the XMI output of the AggregatePlaintextFastUMLSProcessor.xmi file, there is the tag tree: > ​ > http://uima.apache.org/resourceSpecifier > "> > org.apache.uima.java > false > ... > > AggregatePlaintextFastUMLSProcessor > > Runs the complete pipeline for annotating clinical documents

Fwd: User wishing to use version 4.0.1 from developer install for bug fixes, experiencing setup problems

2018-03-22 Thread Reed Villanueva
I am a user experiencing an error when trying to use the simple piper fabricator gui ($CTAKES_HOME/bin/runPiperCreator.sh): > Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at > javax.swing.plaf.synth.SynthTableHeaderUI$HeaderRenderer.get >

Re: Default clinical pipeline does not appear to work as advertised by the docs' graphic showing its use, how to get there?

2018-03-23 Thread Reed Villanueva
“liver”). > “lesions” is negated as indicated by Polarity=-1. > > > > This does not seem error-free to me, still. Could anyone confirm this is > the expected result, please? > > > > Cheers, > > Gundolf. > > > > > > *From: *Reed Villanueva <vi

Why can't we use runClinicalPipeline while ctakesCVD is in use?

2018-03-23 Thread Reed Villanueva
Running bin/runClinicalPipeline.sh the the bin/runctakesCVD.sh is also being used throws a jdbc connection error: > 22 Mar 2018 22:22:40 INFO UmlsUserApprover - Checking UMLS Account at > https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user myuser: > ..22 Mar 2018 22:22:42 INFO