EntityAnnotator.java

package edu.isistan.uima.unified.analysisengines.opennlp;

import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;

import opennlp.tools.namefind.NameFinderME;
import opennlp.tools.namefind.TokenNameFinderModel;
import opennlp.tools.util.Span;

import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.text.AnnotationIndex;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.apache.uima.resource.ResourceInitializationException;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.SubProgressMonitor;
import org.uimafit.component.JCasAnnotator_ImplBase;
import org.uimafit.descriptor.ConfigurationParameter;
import org.uimafit.descriptor.ExternalResource;

import edu.isistan.uima.unified.analysisengines.AnnotationGenerator;
import edu.isistan.uima.unified.sharedresources.ProgressMonitorResource;
import edu.isistan.uima.unified.typesystems.nlp.Sentence;
import edu.isistan.uima.unified.typesystems.nlp.Token;

public class EntityAnnotator extends JCasAnnotator_ImplBase {
	@ConfigurationParameter(name="model")
	private String modelName;
	@ConfigurationParameter(name="tag")
	private String tagName;
	//
	protected TokenNameFinderModel model;
	protected NameFinderME namefinder;
	//
	@ExternalResource(key="monitor")
	private ProgressMonitorResource monitorResource;
	private IProgressMonitor subMonitor;
	
	@Override
	public void initialize(UimaContext aContext) throws ResourceInitializationException {
		super.initialize(aContext);
		InputStream in = null;
		try {
			//modelName = (String) aContext.getConfigParameterValue("model");
			in = new FileInputStream(modelName);
			model = new TokenNameFinderModel(in);
			namefinder = new NameFinderME(model);
			//
			//tagName = (String) aContext.getConfigParameterValue("tag");
		}
		catch (Exception e) { 
			e.printStackTrace();
		}
		finally {
			if (in != null) {
				try {
					in.close();
				}
				catch (IOException e) {
				}
			}
		}
	}
	
	public void process(JCas aJCas) throws AnalysisEngineProcessException {
		if(namefinder == null)
			return;
		//
		subMonitor = new SubProgressMonitor(monitorResource.getMonitor(), 1, SubProgressMonitor.PREPEND_MAIN_LABEL_TO_SUBTASK);
		subMonitor.subTask("Annotating entities (OpenNLP)");
		//
		//String docText = aJCas.getDocumentText();
		AnnotationIndex<Annotation> sAnnotations = aJCas.getAnnotationIndex(Sentence.type);
		AnnotationIndex<Annotation> tAnnotations = aJCas.getAnnotationIndex(Token.type);
		//
		subMonitor.beginTask(this.getClass().getSimpleName(), sAnnotations.size());
		//
		for(Annotation sAnnotation : sAnnotations) {
			//Sentence sentenceAnnotation = (Sentence) sAnnotation;
			//String sentence = sAnnotation.getCoveredText();
			
			Iterator<Annotation> tokenIterator = tAnnotations.subiterator(sAnnotation);
			List<Token> tokenList = new LinkedList<Token>();
			while(tokenIterator.hasNext()) {
				Annotation tAnnotation = tokenIterator.next();
				tokenList.add((Token)tAnnotation);
			}			
			Token[] tokenAnnotations = new Token[tokenList.size()];
			for(int i = 0; i < tokenList.size(); i++)
				tokenAnnotations[i] = tokenList.get(i);
			String[] tokens = new String[tokenAnnotations.length];
			for(int i = 0; i < tokenAnnotations.length; i++)
				tokens[i] = tokenAnnotations[i].getCoveredText();
			
			Span[] entities = namefinder.find(tokens);
			for(int entityNumber = 0; entityNumber < entities.length; entityNumber++) {
				Span entity = entities[entityNumber];
				int spanBegin = -1;
				int spanEnd = -1;

				int spanNumber = 0;
				while(spanNumber < entity.getEnd()) {
					Token tokenAnnotation = tokenAnnotations[spanNumber];
					//String token = tokens[spanNumber];
					
					if(spanNumber < entity.getStart()) {
						
					}
					else if(spanNumber == entity.getStart()) {
						spanBegin = tokenAnnotation.getBegin();
						spanEnd = tokenAnnotation.getEnd();
					}
					else if(spanNumber == entity.getEnd() - 1) {
						spanEnd = tokenAnnotation.getEnd();
					}
					
					spanNumber++;
				}

				AnnotationGenerator.generateEntity(spanBegin, spanEnd, tagName, aJCas);
			}
			//
			subMonitor.worked(1);
		}
		//
		subMonitor.done();
	}
	
	@Override
	public void destroy() {
		model = null;
		namefinder = null;
		super.destroy();
	}
}