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.