Hi Reed,

Just check the PipelineRunner class in the link - 
 and see if it helps.


From: Reed Villanueva [mailto:villanuevar...@gmail.com]
Sent: Tuesday, April 10, 2018 1:15 PM
To: user@ctakes.apache.org
Subject: How to get XMI output fie from java jcas?

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() );
SimplePipeline.runPipeline( jcas, builder.createAggregateDescription() );

But how do I get all of the annotation info in XMI form from the jcas after 
this (like what gets generated in outputDirectory when doing
bin/runClinicalPipeline  -i inputDirectory  --xmiOut outputDirectory  --user 
umlsUsername  --pass umlsPassword
)? Also, what class can be used to read existing XMI output files?
Thank you.
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