/*
* Eoulsan development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public License version 2.1 or
* later and CeCILL-C. This should be distributed with the code.
* If you do not have a copy, see:
*
* http://www.gnu.org/licenses/lgpl-2.1.txt
* http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
*
* Copyright for this code is held jointly by the Genomic platform
* of the Institut de Biologie de l'École normale supérieure and
* the individual authors. These should be listed in @author doc
* comments.
*
* For more information on the Eoulsan project and its aims,
* or to join the Eoulsan Google group, visit the home page
* at:
*
* http://outils.genomique.biologie.ens.fr/eoulsan
*
*/
package fr.ens.biologie.genomique.eoulsan.modules.fastqc;
import java.awt.image.BufferedImage;
import java.io.IOException;
import javassist.CannotCompileException;
import javassist.ClassClassPath;
import javassist.ClassPool;
import javassist.CtClass;
import javassist.CtMethod;
import javassist.CtNewMethod;
import javassist.NotFoundException;
import javax.imageio.ImageIO;
import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import uk.ac.babraham.FastQC.Modules.QCModule;
import uk.ac.babraham.FastQC.Utilities.ImageToBase64;
/**
* This class to patch FastQC to be compatible with Hadoop.
* @author Laurent Jourdren
* @since 2.0
*/
public class FastQCRuntimePatcher {
private static final String CLASS_NAME =
"uk.ac.babraham.FastQC.Report.HTMLReportArchive";
/**
* Patch FastQC for hadoop mode.
* @throws EoulsanException if an error occurs while patching FASTQC
*/
public static synchronized void patchFastQC() throws EoulsanException {
try {
// Create the ClassPool and add the FastQC jar classpath in the ClassPool
// classpath using a random class of the jar
final ClassClassPath ccpath = new ClassClassPath(QCModule.class);
final ClassPool pool = ClassPool.getDefault();
pool.insertClassPath(ccpath);
// Get the class to modify
final CtClass cc = pool.get(CLASS_NAME);
// Check if the class is not frozen
if (cc != null && !cc.isFrozen()) {
// Remove the old base64ForIcon method
final CtMethod oldBase64ForIconMethod =
cc.getDeclaredMethod("base64ForIcon");
cc.removeMethod(oldBase64ForIconMethod);
// Create the new base64ForIcon method
final CtMethod newBase64ForIconMethod =
CtNewMethod.make("private String base64ForIcon (String path) { "
+ " return fr.ens.biologie.genomique.eoulsan.modules.fastqc."
+ "FastQCRuntimePatcher.base64ForIcon(path, this.getClass());"
+ " } ", cc);
cc.addMethod(newBase64ForIconMethod);
// Load the class by the ClassLoader
cc.toClass();
}
} catch (NotFoundException | CannotCompileException e) {
throw new EoulsanException(e);
}
}
/**
* This method replace the HTMLReportArchive.base64ForIcon() method.
* @param path path of the resource to load
* @param clazz the class that call the method
* @return an image encoded in base64
*/
public static String base64ForIcon(String path,
@SuppressWarnings("rawtypes") Class clazz) {
try {
BufferedImage b =
ImageIO.read(clazz.getResourceAsStream("/Templates/" + path));
return (ImageToBase64.imageToBase64(b));
} catch (IOException ioe) {
ioe.printStackTrace();
return "Failed";
}
}
}