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
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 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() );
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,
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
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
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
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 &
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
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
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
>
“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
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
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