/*
* 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;
import static fr.ens.biologie.genomique.eoulsan.EoulsanLogger.getLogger;
import java.io.IOException;
import java.util.Set;
import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.Globals;
import fr.ens.biologie.genomique.eoulsan.annotations.LocalOnly;
import fr.ens.biologie.genomique.eoulsan.annotations.NoOutputDirectory;
import fr.ens.biologie.genomique.eoulsan.annotations.RequiresAllPreviousSteps;
import fr.ens.biologie.genomique.eoulsan.core.Modules;
import fr.ens.biologie.genomique.eoulsan.core.Parameter;
import fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext;
import fr.ens.biologie.genomique.eoulsan.core.TaskContext;
import fr.ens.biologie.genomique.eoulsan.core.TaskResult;
import fr.ens.biologie.genomique.eoulsan.core.TaskStatus;
import fr.ens.biologie.genomique.eoulsan.core.Version;
/**
* This class define a module that execute a shell command. It use the user
* shell to execute the command. The launched command is : $SHELL -c "command"
* @author Laurent Jourdren
*/
@LocalOnly
@RequiresAllPreviousSteps
@NoOutputDirectory
public class ShellModule extends AbstractModule {
private static final String MODULE_NAME = "shell";
private String command;
@Override
public String getName() {
return MODULE_NAME;
}
@Override
public String getDescription() {
return "This module allow to execute shell commands";
}
@Override
public Version getVersion() {
return Globals.APP_VERSION;
}
@Override
public void configure(final StepConfigurationContext context,
final Set<Parameter> stepParameters) throws EoulsanException {
for (Parameter p : stepParameters) {
switch (p.getName()) {
case "command":
this.command = p.getValue();
break;
default:
Modules.unknownParameter(context, p);
}
}
if (this.command == null || this.command.trim().isEmpty()) {
Modules.invalidConfiguration(context, "No command defined");
}
}
@Override
public TaskResult execute(final TaskContext context,
final TaskStatus status) {
try {
// Define the shell interpreter to use
String shellInterpreter = System.getenv("SHELL");
if (shellInterpreter == null) {
shellInterpreter = "/bin/sh";
}
getLogger().info("Execute: " + this.command);
getLogger().info("Shell interpreter: " + shellInterpreter);
final Process p =
new ProcessBuilder(shellInterpreter, "-c", this.command).start();
final int exitCode = p.waitFor();
// If exit code is not 0 throw an exception
if (exitCode != 0) {
throw new IOException("Finish process with exit code: " + exitCode);
}
// Write log file
return status.createTaskResult();
} catch (IOException | InterruptedException e) {
return status.createTaskResult(e, "Error while running command ("
+ this.command + "): " + e.getMessage());
}
}
}