LungDriver.java Source code

Introduction

Here is the source code for LungDriver.java

Source

/*******************************************************************************
 * Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
 * 
 * Copyright (c) 2014 Marco Aurelio Barbosa Fagnani Gomes Lotz (marcolotz.com)
 * 
 * The source code in this document is licensed under Creative Commons
 * Attribution-NonCommercial-ShareAlike 4.0 International License. You must 
 * credit the author of the source code in the way specified by the author or
 * licenser (but not in a way to suggest that the author or licenser has given 
 * you allowance to you or to your use of the source code). If you modify,
 * transform or create using this source code as basis, you can only distribute
 * the new source code under the same license or a similar license to this one.
 * 
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 * 
 * To see a copy of the license, access:
 * creativecommons.org/licenses/by-nc-sa/4.0/legalcode
 ******************************************************************************/
import java.io.IOException;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.conf.Configured;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;

/**
 * Main Launcher for the Hadoop Application. The XML file with the
 * configurations is added here.
 * 
 * @author Marco Aurelio Lotz
 * 
 */
public class LungDriver extends Configured implements Tool {

    /* Block executed when the class is created */
    static {
        /*
         * The lungConfiguration.xml contains all the user defined
         * configurations desired for a Hadoop job Don't forget to include it on
         * the class path
         */
        Configuration.addDefaultResource("./lungConfiguration.xml");
    }

    @Override
    public int run(String[] args) throws Exception {

        Configuration conf = getConf();

        String author = conf.get("com.marcolotz.author");
        String jobName = conf.get("mapreduce.job.name");
        String inputPath = conf.get("mapred.input.dir");
        String outputPath = conf.get("mapred.output.dir");

        System.out.println("\nApplication author: " + author + "\n");

        System.out.println("Configurations stored at: conf/lungConfiguration.xml");
        System.out.println("Input path: " + inputPath);
        System.out.println("Output path: " + outputPath);

        /* For non-standard operation (i.e. with arguments) */
        if (args.length != 0) {

            /* terminates the program if there is an incorrect input */
            if (processInputs(args, conf) != 0) {
                return 1;
            }
        }

        System.out.println("Bottom Threshold for nodules candidates detection:"
                + conf.getInt("com.marcolotz.grayNoduleCandidates.bottomThreshold", 110));
        System.out.println("Top Threshold for nodules candidates detection:"
                + conf.getInt("com.marcolotz.grayNoduleCandidates.topThreshold", 120));

        System.out.print("Cleaning output path: ");
        cleanOutputPath(conf, outputPath);

        System.out.print("Configuring the job " + jobName + ": ");

        /* Makes a new job */
        // The classic Job constructor is deprecated.
        Job job = Job.getInstance(conf);

        /*
         * This method sets the jar file in which each node will look for the
         * Mapper and Reducer classes.
         */
        job.setJarByClass(this.getClass());

        System.out.println("[DONE]\n");

        // Submits the job to the cluster
        System.out.println("Distributing the job:");
        return job.waitForCompletion(true) ? 0 : 1;
    }

    /***
     * Method only called by the application when arguments are used
     * 
     * @param args
     * @param conf
     * @return the System status
     */
    private int processInputs(String[] args, Configuration conf) {
        if (args.length != 2) {
            printUsage();
            return 1;
        }

        int bottomThreshold = Integer.parseInt(args[0]);
        int topThreshold = Integer.parseInt(args[1]);

        if (bottomThreshold > topThreshold) {
            System.err.println("Wrong treshold usage. The bottom limit must be under the top timit.");
            printUsage();
            return 1;
        }

        conf.setInt("com.marcolotz.grayNoduleCandidates.bottomThreshold", bottomThreshold);
        conf.setInt("com.marcolotz.grayNoduleCandidates.topThreshold", topThreshold);

        return 0;
    }

    private void printUsage() {
        System.err
                .println("Wrong usage. One can use the no arguments calling for 110-120 gray threshold values or:");
        System.err.println(LungDriver.class.getSimpleName() + " [bottom Gray threshold] [top GrayThreshold]");

    }

    private void cleanOutputPath(Configuration conf, String outputPath) {
        try {
            FileSystem fs = FileSystem.get(conf);
            Path output = new Path(outputPath);
            fs.delete(output, true);
        } catch (IOException e) {
            System.err.println("Failed to delete temporary path");
            e.printStackTrace();
        }

        System.out.println("[DONE]\n");
    }

    public static void main(String[] args) throws Exception {
        int exitCode = ToolRunner.run(new LungDriver(), args);
        System.exit(exitCode);
    }
}