package org.apache.ctakes.assertion.pipelines;
import static org.apache.ctakes.assertion.util.AssertionTreeUtils.extractAboveLeftConceptTree;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.PrintStream;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import org.apache.ctakes.assertion.eval.XMIReader;
import org.apache.ctakes.assertion.util.SemanticClasses;
import org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.utils.tree.SimpleTree;
import org.apache.log4j.Logger;
import org.apache.uima.UIMAException;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
import org.cleartk.util.Options_ImplBase;
import org.kohsuke.args4j.Option;
import org.uimafit.factory.CollectionReaderFactory;
import org.uimafit.pipeline.JCasIterable;
import org.uimafit.util.JCasUtil;
public class GenerateTreeRepresentation{
public static class Options extends Options_ImplBase {
@Option(
name = "--train-dir",
usage = "specify the directory containing the XMI training files (for example, /NLP/Corpus/Relations/mipacq/xmi/train)",
required = true)
public File trainDirectory;
@Option(
name = "--output",
usage = "The file to which the data points be written.",
required = true)
public File outFile;
}
protected static Options options = new Options();
private static SemanticClasses sems = null;
private static PrintStream out = null;
private static Logger log = Logger.getLogger(GenerateTreeRepresentation.class);
/**
* @param args
* @throws IOException
* @throws UIMAException
*/
public static void main(String[] args) throws UIMAException, IOException {
options.parseOptions(args);
out = new PrintStream(options.outFile);
List<File> trainFiles = Arrays.asList(options.trainDirectory.listFiles());
String[] paths = new String[trainFiles.size()];
for (int i = 0; i < paths.length; ++i) {
paths[i] = trainFiles.get(i).getPath();
}
CollectionReader reader = CollectionReaderFactory.createCollectionReader(
XMIReader.class,
XMIReader.PARAM_FILES,
paths);
JCasIterable casIter = new JCasIterable(reader);
while(casIter.hasNext()){
JCas jcas = casIter.next();
processDocument(jcas);
}
out.close();
}
public static void processDocument(JCas jcas) throws ResourceInitializationException, FileNotFoundException {
log.info("Processing document: " + DocumentIDAnnotationUtil.getDocumentID(jcas));
if(sems == null){
sems = new SemanticClasses(FileLocator.locateFile("org/apache/ctakes/assertion/models/semantic_classes").getAbsolutePath());
}
Collection<IdentifiedAnnotation> mentions = JCasUtil.select(jcas, IdentifiedAnnotation.class);
for(IdentifiedAnnotation mention : mentions){
TopTreebankNode orig = AnnotationTreeUtils.getAnnotationTree(jcas, mention);
if(orig == null){
log.warn("Tree for entity mention: " + mention.getCoveredText() + " (" + mention.getBegin() + "-" + mention.getEnd() + ") is null.");
continue;
}
SimpleTree tree = extractAboveLeftConceptTree(jcas, mention, sems);
// if(mention.getPolarity() == CONST.NE_POLARITY_NEGATION_PRESENT){
if(mention.getUncertainty() == CONST.NE_UNCERTAINTY_PRESENT){
out.print("+1 ");
}else{
out.print("-1 ");
}
out.print("|BT| ");
out.print(tree.toString());
out.println(" |ET|");
out.flush();
}
}
}