Use modified version of wapiti library in order to execute wapiti task faster

src/main/java/fr/limsi/sourceExtractor/training/ExtractSource.java

@@ -84,7 +84,10 @@ public class ExtractSource extends TrainingUnLabel {
 			WapitiLabeling wapitiPrim = WapitiLabeling.getWapitiInstance(modelPrim);
 			// wapiti label -m modelPrim input=tests_files_one_by_one
 			// output=DIR_BIO_FILES_FOR_CONVERSION_WAPITI_UNLABELED_PRIM -p
-			wapitiPrim.wapitiTest(this.paths.DIR_TEST_FILES_UNLABELED_PRIM, this.paths.DIR_BIO_FILES_FOR_CONVERSION_WAPITI_UNLABELED_PRIM, jubNumber);
+			wapitiPrim.wapitiTest(this.paths.DIR_TEST_FILES_UNLABELED_PRIM, 
+					this.paths.DIR_BIO_FILES_FOR_CONVERSION_WAPITI_UNLABELED_PRIM, jubNumber,
+					modelPrim.getAbsolutePath(),
+					extractorConfig.getDirLib().getAbsolutePath());
 
 			if (searchSecondary) {
 				System.err.println();
@@ -95,7 +98,10 @@ public class ExtractSource extends TrainingUnLabel {
 				// wapiti label -m modelSec input=tests_files_one_by_one
 				// output=DIR_BIO_FILES_FOR_CONVERSION_WAPITI_UNLABELED_Sec
 				// -p
-				wapitiSec.wapitiTest(this.paths.DIR_TEST_FILES_UNLABELED_SEC, this.paths.DIR_BIO_FILES_FOR_CONVERSION_WAPITI_UNLABELED_SEC, jubNumber);
+				wapitiSec.wapitiTest(this.paths.DIR_TEST_FILES_UNLABELED_SEC, 
+						this.paths.DIR_BIO_FILES_FOR_CONVERSION_WAPITI_UNLABELED_SEC, jubNumber, 
+						modelSec.getAbsolutePath(),
+						extractorConfig.getDirLib().getAbsolutePath());
 			}
 
 			System.err.println();

src/main/java/fr/limsi/sourceExtractor/wapiti/WapitiLabeling.java

 package fr.limsi.sourceExtractor.wapiti;
 
+import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStreamReader;
 import java.io.UnsupportedEncodingException;
 import java.util.concurrent.ArrayBlockingQueue;
 import java.util.concurrent.ForkJoinPool;
@@ -9,22 +12,59 @@ import java.util.concurrent.ForkJoinPool;
 import org.apache.commons.lang3.SystemUtils;
 
 import fr.limsi.sourceExtractor.ProcessingThreadFactory;
+import fr.limsi.wapiti.Wapiti;
 
 public abstract class WapitiLabeling {
-	public abstract void label(File input, File outputDir, String filename) 
+	public abstract void label(File input, File outputDir, String filename)
 			throws UnsupportedEncodingException, FileNotFoundException;
-	
-	
+
 	/**
 	 * Méthode permettant d'utiliser wapiti sur les fichiers de tests
-	 * @param input Fichier ou dossier à tester
-	 * @param modelsFile Le modèle wapiti 
-	 * @param outputDir Le dossier de sortie des fichiers 
-	 * @throws FileNotFoundException 
-	 * @throws UnsupportedEncodingException 
-	 * @throws InterruptedException 
+	 * 
+	 * @param input      Fichier ou dossier à tester
+	 * @param modelsFile Le modèle wapiti
+	 * @param outputDir  Le dossier de sortie des fichiers
+	 * @throws FileNotFoundException
+	 * @throws UnsupportedEncodingException
+	 * @throws InterruptedException
 	 */
-	public void wapitiTest(File input, File outputDir, int jobNumber) throws UnsupportedEncodingException, FileNotFoundException, InterruptedException {
+	public void wapitiTest(File inputDir, File outputDir, int jobNumber, 
+			String modelFile, String dirLib)
+			throws UnsupportedEncodingException, FileNotFoundException, InterruptedException {
+		if (!outputDir.exists()) {
+			outputDir.mkdirs();
+		}
+
+		try {
+			String command = String.format("%s/wapiti"
+					+ " label -m "
+					+ "%s "
+					+ "-i %s/ "
+					+ "-o %s/ -p", dirLib, modelFile, inputDir.getAbsolutePath(), outputDir.getAbsolutePath());
+			System.err.println(command);
+			
+			String line;
+			Process p = Runtime.getRuntime().exec(command);
+			BufferedReader bri = new BufferedReader(new InputStreamReader(p.getInputStream()));
+			BufferedReader bre = new BufferedReader(new InputStreamReader(p.getErrorStream()));
+			while ((line = bri.readLine()) != null) {
+				System.out.println(line);
+			}
+			bri.close();
+			while ((line = bre.readLine()) != null) {
+				System.out.println(line);
+			}
+			bre.close();
+			p.waitFor();
+			
+			
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+	
+	public void wapitiTest(File input, File outputDir, int jobNumber)
+			throws UnsupportedEncodingException, FileNotFoundException, InterruptedException {
 		if (!outputDir.exists()) {
 			outputDir.mkdirs();
 		}
@@ -51,39 +91,36 @@ public abstract class WapitiLabeling {
 			throw new RuntimeException();
 		}
 	}
-	
-	public void wapitiLabeled(File input, String fileId, String extension, File outputDir){
+
+	public void wapitiLabeled(File input, String fileId, String extension, File outputDir) {
 		if (!outputDir.exists()) {
 			outputDir.mkdirs();
 		}
-		File inFile = new File(input, fileId+"."+extension);
+		File inFile = new File(input, fileId + "." + extension);
 		WapitiTask task = new WapitiTask(inFile, outputDir, this);
 		task.compute();
 	}
 
-	//Doublon par rapport a WapitiTask
-	/*private static void wapitiLabelFile(File input, File outputDir, WapitiLabeling wapitiLabeler)
-			throws UnsupportedEncodingException, FileNotFoundException {
-		String filename = input.getName();
-
-		int pos = filename.lastIndexOf(".");
-
-		if (pos > 0) {
-			filename = filename.substring(0, pos);
-		}
-		
-		wapitiLabeler.label(input, outputDir, filename);
-	}*/
+	// Doublon par rapport a WapitiTask
+	/*
+	 * private static void wapitiLabelFile(File input, File outputDir,
+	 * WapitiLabeling wapitiLabeler) throws UnsupportedEncodingException,
+	 * FileNotFoundException { String filename = input.getName();
+	 * 
+	 * int pos = filename.lastIndexOf(".");
+	 * 
+	 * if (pos > 0) { filename = filename.substring(0, pos); }
+	 * 
+	 * wapitiLabeler.label(input, outputDir, filename); }
+	 */
 
-	
-	public static WapitiLabeling getWapitiInstance(File modelFile) throws UnsupportedEncodingException, FileNotFoundException {
+	public static WapitiLabeling getWapitiInstance(File modelFile)
+			throws UnsupportedEncodingException, FileNotFoundException {
 		if (org.apache.commons.lang3.SystemUtils.IS_OS_LINUX || SystemUtils.IS_OS_MAC) {
 			return new WapitiLabelingLinux(modelFile);
-		}
-		else if (SystemUtils.IS_OS_WINDOWS) {
+		} else if (SystemUtils.IS_OS_WINDOWS) {
 			return new WapitiLabelingWindows(modelFile);
-		}
-		else {
+		} else {
 			throw new RuntimeException("Unknown OS");
 		}
 	}