/*
* 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.actions;
import static com.google.common.base.Preconditions.checkNotNull;
import static fr.ens.biologie.genomique.eoulsan.EoulsanLogger.getLogger;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.List;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.GnuParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import com.google.common.collect.Lists;
import fr.ens.biologie.genomique.eoulsan.Common;
import fr.ens.biologie.genomique.eoulsan.Globals;
import fr.ens.biologie.genomique.eoulsan.Main;
import fr.ens.biologie.genomique.eoulsan.core.Module;
import fr.ens.biologie.genomique.eoulsan.core.workflow.Executor;
import fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments;
import fr.ens.biologie.genomique.eoulsan.data.DataFile;
import fr.ens.biologie.genomique.eoulsan.modules.TerminalModule;
import fr.ens.biologie.genomique.eoulsan.modules.mgmt.AWSElasticMapReduceExecModule;
import fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.LocalUploadModule;
import fr.ens.biologie.genomique.eoulsan.util.StringUtils;
/**
* This class define an action that execute Eoulsan on AWS Elastic MapReduce.
* @since 1.0
* @author Laurent Jourdren
*/
public class EMRExecAction extends AbstractAction {
/** Action name. */
static final String ACTION_NAME = "emrexec";
@Override
public String getName() {
return ACTION_NAME;
}
@Override
public String getDescription() {
return "execute eoulsan on Amazon Elastic MapReduce service.";
}
@Override
public boolean isCurrentArchCompatible() {
return true;
}
@Override
public void action(final List<String> arguments) {
System.err.println("WARNING: the action \""
+ getName()
+ "\" is currently under development for the next version of "
+ Globals.APP_NAME + " and may actually not work.");
final Options options = makeOptions();
final CommandLineParser parser = new GnuParser();
String jobDescription = null;
int argsOptions = 0;
try {
// parse the command line arguments
final CommandLine line = parser.parse(options,
arguments.toArray(new String[arguments.size()]), true);
// Help option
if (line.hasOption("help")) {
help(options);
}
if (line.hasOption("d")) {
jobDescription = line.getOptionValue("d");
argsOptions += 2;
}
} catch (ParseException e) {
Common.errorExit(e,
"Error while parsing command line arguments: " + e.getMessage());
}
if (arguments.size() != argsOptions + 3) {
help(options);
}
final File paramFile = new File(arguments.get(argsOptions));
final File designFile = new File(arguments.get(argsOptions + 1));
final DataFile s3Path = new DataFile(StringUtils
.replacePrefix(arguments.get(argsOptions + 2), "s3:/", "s3n:/"));
// Execute program in AWS mode
run(paramFile, designFile, s3Path, jobDescription);
}
//
// Command line parsing
//
/**
* Create options for command line
* @return an Options object
*/
@SuppressWarnings("static-access")
private static Options makeOptions() {
// create Options object
final Options options = new Options();
// Help option
options.addOption("h", "help", false, "display this help");
// Description option
options.addOption(OptionBuilder.withArgName("description").hasArg()
.withDescription("job description").withLongOpt("desc").create('d'));
return options;
}
/**
* Show command line help.
* @param options Options of the software
*/
private static void help(final Options options) {
// Show help message
final HelpFormatter formatter = new HelpFormatter();
formatter.printHelp(Globals.APP_NAME_LOWER_CASE
+ ".sh " + ACTION_NAME
+ " [options] workflow.xml design.txt s3://mybucket/test", options);
Common.exit(0);
}
//
// Execution
//
/**
* Run Eoulsan in hadoop mode.
* @param workflowFile workflow file
* @param designFile design file
* @param s3Path path of data on S3 file system
* @param jobDescription job description
*/
private static void run(final File workflowFile, final File designFile,
final DataFile s3Path, final String jobDescription) {
checkNotNull(workflowFile, "paramFile is null");
checkNotNull(designFile, "designFile is null");
checkNotNull(s3Path, "s3Path is null");
getLogger().info("Parameter file: " + workflowFile);
getLogger().info("Design file: " + designFile);
final String desc;
if (jobDescription == null) {
desc = "no job description";
} else {
desc = jobDescription.trim();
}
try {
// Test if workflow file exists
if (!workflowFile.exists()) {
throw new FileNotFoundException(workflowFile.toString());
}
// Test if design file exists
if (!designFile.exists()) {
throw new FileNotFoundException(designFile.toString());
}
// Create ExecutionArgument object
final ExecutorArguments arguments =
new ExecutorArguments(workflowFile, designFile);
arguments.setJobDescription(desc);
// Create the log File
Main.getInstance().createLogFiles(arguments.logPath(Globals.LOG_FILENAME),
arguments.logPath(Globals.OTHER_LOG_FILENAME));
// Create executor
final Executor e = new Executor(arguments);
// Launch executor
e.execute(Lists.newArrayList((Module) new LocalUploadModule(s3Path),
new AWSElasticMapReduceExecModule(), new TerminalModule()), null);
} catch (FileNotFoundException e) {
Common.errorExit(e, "File not found: " + e.getMessage());
} catch (Throwable e) {
Common.errorExit(e, "Error while executing "
+ Globals.APP_NAME_LOWER_CASE + ": " + e.getMessage());
}
}
}