package org.apache.ctakes.clinicalpipeline.runtime;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.PrintStream;
import java.lang.reflect.ParameterizedType;
import java.util.Collection;
import org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader;
import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.factory.CollectionReaderFactory;
import org.uimafit.pipeline.JCasIterable;
import org.uimafit.util.JCasUtil;
public abstract class BagOfAnnotationsGenerator<T extends Annotation,K> {
private String outputDir = null;
private CollectionReader reader = null;
private AnalysisEngine ae = null;
private static final String defaultAEPath = "desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml";
private Class<T> classOfT;
/**
* @param args
* @throws IOException
* @throws UIMAException
*/
public BagOfAnnotationsGenerator(String inputDir, String outputDir) throws UIMAException, IOException{
this(inputDir, outputDir, null);
}
public BagOfAnnotationsGenerator(String inputDir, String outputDir, String aePath) throws UIMAException, IOException {
reader = CollectionReaderFactory.createCollectionReaderFromPath("../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml",
FilesInDirectoryCollectionReader.PARAM_INPUTDIR, inputDir);
this.ae = AnalysisEngineFactory.createAnalysisEngineFromPath(aePath == null ? defaultAEPath : aePath);
this.outputDir = outputDir;
this.classOfT = getClassOfT();
}
public void process() throws UIMAException, IOException{
JCasIterable casIter = new JCasIterable(reader, ae);
while(casIter.hasNext()){
JCas jcas = casIter.next();
String docId = DocumentIDAnnotationUtil.getDocumentID(jcas);
// extract info from cas
processCas(jcas, outputDir + File.separator + docId);
}
ae.destroy();
}
private void processCas(JCas jcas, String outputFilename) throws FileNotFoundException {
PrintStream out = new PrintStream(outputFilename);
Collection<T> annotations = JCasUtil.select(jcas, classOfT);
for(T annot : annotations){
K output = extractInformation(annot);
if(output != null) out.println(output);
}
out.close();
}
protected abstract K extractInformation(T t);
private Class<T> getClassOfT() {
ParameterizedType superclass = (ParameterizedType) getClass().getGenericSuperclass();
return (Class<T>) superclass.getActualTypeArguments()[0];
}
}