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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject groovy script(s) for running equivalent of AggregatePlaintextUMLSProcessor.xml
Date Tue, 24 Dec 2013 19:48:08 GMT

I checked in 2 groovy scripts under
ctakes-core\scripts\groovy\
I checked into trunk. Will gladly move or remove if needed.

They do not do automatic downloads of ctakes, instead they rely on user to already have downloaded
a convenience binary and the separately downloadable resources, and to have extracted both
of those.

They run the same as what's defined in AggregatePlaintextUMLSProcessor.xml except I haven't
included the semantic role labeler or the dependency parser yet (just for lack of time today).
 Right now the script uses XML descriptors for some parts and uimaFIT without using XML descriptor
files for other parts of the pipeline.

I have a few other TODOs but the scripts are ready for others to look at.

Feedback welcome and encouraged!

To run:
Install groovy
Have groovy on your path.
Within run_cTAKES.groovy, you need to set the values of
cTAKES_HOME
EXTERNAL_RESOURCE_PATH

Set  JAVA_OPTS env variable as follows
-Dctakes.umlsuser=YOUR_USERID  -Dctakes.umlspw=YOUR_PWD

Then to run, enter this, with inputDirName being wherever you have your input text files.

groovy run_cTAKES.groovy inputDirName

-- James


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