/*
* 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.bio.readsmappers;
import static com.google.common.base.Preconditions.checkNotNull;
import static fr.ens.biologie.genomique.eoulsan.EoulsanLogger.getLogger;
import java.io.File;
import java.io.IOException;
import java.util.List;
import com.google.common.base.Joiner;
import com.google.common.base.Objects;
import fr.ens.biologie.genomique.eoulsan.bio.readsmappers.BundledMapperExecutor.ProcessResult;
import fr.ens.biologie.genomique.eoulsan.util.FileUtils;
/**
* This class define a mapper executor that executes process found in the PATH
* of the system.
* @author Laurent Jourdren
* @since 2.0
*/
public class PathMapperExecutor implements MapperExecutor {
//
// MapperExecutor methods
//
@Override
public boolean isExecutable(String executable) {
checkNotNull(executable, "executable argument cannot be null");
return FileUtils.checkIfExecutableIsInPATH(executable);
}
@Override
public String install(final String executable) throws IOException {
checkNotNull(executable, "executable argument cannot be null");
return executable;
}
@Override
public Result execute(final List<String> command,
final File executionDirectory, final boolean stdout,
final boolean redirectStderr, final File... fileUsed) throws IOException {
ProcessBuilder builder = new ProcessBuilder(command);
builder.redirectErrorStream(redirectStderr);
// If no redirection of stderr in stdout, redirect stderr to /dev/null
if (!redirectStderr) {
builder.redirectError(new File("/dev/null"));
}
if (executionDirectory != null) {
builder.directory(executionDirectory);
}
getLogger()
.info("Process command: " + Joiner.on(' ').join(builder.command()));
getLogger().info("Process directory: " + builder.directory());
return new ProcessResult(builder.start());
}
//
// Object methods
//
@Override
public String toString() {
return Objects.toStringHelper(this).toString();
}
}