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Apache cTAKES Examples

There is a newer version: 6.0.0

package org.apache.ctakes.examples.pipelines;

import java.io.FileWriter;

import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory;
import org.apache.ctakes.examples.ae.ExampleHelloWorldAnnotator;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.uima.jcas.JCas;
import org.apache.uima.fit.factory.AggregateBuilder;
import org.apache.uima.fit.factory.JCasFactory;
import org.apache.uima.fit.pipeline.SimplePipeline;
import org.apache.uima.fit.util.JCasUtil;

/**
 * Example of a running a pipeline programatically w/o uima xml descriptor xml files
 * Adds the default Tokenization pipeline and adding the Example HelloWorld Annotator
 * 
 */

public class ExampleAggregatePipeline {


	public static void main(String[] args) throws Exception {

		String note = "Hello World!";
	    JCas jcas = JCasFactory.createJCas();
	    jcas.setDocumentText(note);
	    
		AggregateBuilder builder = new AggregateBuilder();
		// Get a simple pre-defined existing pipeline for Tokenization
		
		// You can consider using ClinicalPipelineFactory.getDefaultPipeline();
		// Which will include the UMLS Lookup, but you'll need to set your 
		// -Dctakes.umlsuser and -Dctatkes.umlspw in your environment
		builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
		
		//Add the new HelloWorld Example:
		builder.add(ExampleHelloWorldAnnotator.createAnnotatorDescription());
		
		//Run the Aggregate Pipeline
	    SimplePipeline.runPipeline(jcas, builder.createAggregateDescription());
	    
	    //Print out the IdentifiedAnnotation objects
	    for(IdentifiedAnnotation entity : JCasUtil.select(jcas, IdentifiedAnnotation.class)){
	      System.out.println("Entity: " + entity.getCoveredText() + " === Polarity: " + entity.getPolarity());
	    }
	    
	    //Example to save the Aggregate descriptor to an xml file for external
	    //use such as the UIMA CVD/CPE
	    if(args.length > 0)
	      builder.createAggregateDescription().toXML(new FileWriter(args[0]));
	  }

}