Java tutorial
/** * Software License, Version 1.0 * * Copyright 2003 The Trustees of Indiana University. All rights reserved. * * *Redistribution and use in source and binary forms, with or without *modification, are permitted provided that the following conditions are met: * *1) All redistributions of source code must retain the above copyright notice, * the list of authors in the original source code, this list of conditions and * the disclaimer listed in this license; *2) All redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the disclaimer listed in this license in * the documentation and/or other materials provided with the distribution; *3) Any documentation included with all redistributions must include the * following acknowledgement: * *"This product includes software developed by the Community Grids Lab. For * further information contact the Community Grids Lab at * http://communitygrids.iu.edu/." * * Alternatively, this acknowledgement may appear in the software itself, and * wherever such third-party acknowledgments normally appear. * *4) The name Indiana University or Community Grids Lab or NaradaBrokering, * shall not be used to endorse or promote products derived from this software * without prior written permission from Indiana University. For written * permission, please contact the Advanced Research and Technology Institute * ("ARTI") at 351 West 10th Street, Indianapolis, Indiana 46202. *5) Products derived from this software may not be called NaradaBrokering, * nor may Indiana University or Community Grids Lab or NaradaBrokering appear * in their name, without prior written permission of ARTI. * * * Indiana University provides no reassurances that the source code provided * does not infringe the patent or any other intellectual property rights of * any other entity. Indiana University disclaims any liability to any * recipient for claims brought by any other entity based on infringement of * intellectual property rights or otherwise. * *LICENSEE UNDERSTANDS THAT SOFTWARE IS PROVIDED "AS IS" FOR WHICH NO *WARRANTIES AS TO CAPABILITIES OR ACCURACY ARE MADE. INDIANA UNIVERSITY GIVES *NO WARRANTIES AND MAKES NO REPRESENTATION THAT SOFTWARE IS FREE OF *INFRINGEMENT OF THIRD PARTY PATENT, COPYRIGHT, OR OTHER PROPRIETARY RIGHTS. *INDIANA UNIVERSITY MAKES NO WARRANTIES THAT SOFTWARE IS FREE FROM "BUGS", *"VIRUSES", "TROJAN HORSES", "TRAP DOORS", "WORMS", OR OTHER HARMFUL CODE. *LICENSEE ASSUMES THE ENTIRE RISK AS TO THE PERFORMANCE OF SOFTWARE AND/OR *ASSOCIATED MATERIALS, AND TO THE PERFORMANCE AND VALIDITY OF INFORMATION *GENERATED USING SOFTWARE. */ package cgl.hadoop.apps.runner; import java.io.File; import java.io.IOException; import java.net.URI; import java.net.URISyntaxException; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.filecache.DistributedCache; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.IntWritable; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapreduce.Mapper; /** * @author Thilina Gunarathne (tgunarat@cs.indiana.edu) * * @editor Stephen, TAK-LON WU (taklwu@indiana.edu) */ public class RunnerMap extends Mapper<String, String, IntWritable, Text> { private String localDB = ""; private String localBlastProgram = ""; @Override public void setup(Context context) throws IOException { Configuration conf = context.getConfiguration(); Path[] local = DistributedCache.getLocalCacheArchives(conf); localBlastProgram = local[0].toUri().getPath(); localDB = local[0].toUri().getPath() + File.separator + conf.get(DataAnalysis.DB_ARCHIVE) + File.separator + conf.get(DataAnalysis.DB_NAME); /** Write your code here get two absolute filepath for localDB and localBlastBinary **/ } public void map(String key, String value, Context context) throws IOException, InterruptedException { long startTime = System.currentTimeMillis(); String endTime = ""; Configuration conf = context.getConfiguration(); String programDir = conf.get(DataAnalysis.PROGRAM_DIR); String execName = conf.get(DataAnalysis.EXECUTABLE); String cmdArgs = conf.get(DataAnalysis.PARAMETERS); String outputDir = conf.get(DataAnalysis.OUTPUT_DIR); String workingDir = conf.get(DataAnalysis.WORKING_DIR); System.out.println("the map key : " + key); System.out.println("the value path : " + value.toString()); System.out.println("Local DB : " + this.localDB); // We have the full file names in the value. String localInputFile = ""; String outFile = ""; String stdOutFile = ""; String stdErrFile = ""; String fileNameOnly = ""; fileNameOnly = key; localInputFile = workingDir + File.separator + fileNameOnly; outFile = workingDir + File.separator + fileNameOnly + ".output"; stdErrFile = workingDir + File.separator + fileNameOnly + ".error"; stdOutFile = workingDir + File.separator + fileNameOnly + ".input"; /** Write your code to get localInputFile, outFile, stdOutFile and stdErrFile **/ // download the file from HDFS Path inputFilePath = new Path(value); FileSystem fs = inputFilePath.getFileSystem(conf); fs.copyToLocalFile(inputFilePath, new Path(localInputFile)); // Prepare the arguments to the executable String execCommand = cmdArgs.replaceAll("#_INPUTFILE_#", localInputFile); if (cmdArgs.indexOf("#_OUTPUTFILE_#") > -1) { execCommand = execCommand.replaceAll("#_OUTPUTFILE_#", outFile); } else { outFile = stdOutFile; } endTime = Double.toString(((System.currentTimeMillis() - startTime) / 1000.0)); System.out.println("Before running the executable Finished in " + endTime + " seconds"); execCommand = this.localBlastProgram + File.separator + execName + " " + execCommand + " -db " + this.localDB; //Create the external process startTime = System.currentTimeMillis(); Process p = Runtime.getRuntime().exec(execCommand); OutputHandler inputStream = new OutputHandler(p.getInputStream(), "INPUT", stdOutFile); OutputHandler errorStream = new OutputHandler(p.getErrorStream(), "ERROR", stdErrFile); // start the stream threads. inputStream.start(); errorStream.start(); p.waitFor(); //end time of this procress endTime = Double.toString(((System.currentTimeMillis() - startTime) / 1000.0)); System.out.println("Program Finished in " + endTime + " seconds"); //Upload the results to HDFS startTime = System.currentTimeMillis(); Path outputDirPath = new Path(outputDir); Path outputFileName = new Path(outputDirPath, fileNameOnly); fs.copyFromLocalFile(new Path(outFile), outputFileName); endTime = Double.toString(((System.currentTimeMillis() - startTime) / 1000.0)); System.out.println("Upload Result Finished in " + endTime + " seconds"); } }