Java tutorial
/* * Copyright 2016 YU Jia Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. */ package diamondmapreduce; /** * * @author yujia1986 */ import awshamondsidefunctions.AWSDiamondReducer; import java.net.URI; import java.util.Arrays; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configured; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapreduce.Job; import org.apache.hadoop.mapreduce.lib.input.FileInputFormat; import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat; import org.apache.hadoop.mapreduce.lib.output.TextOutputFormat; import org.apache.hadoop.util.Tool; import org.apache.hadoop.util.ToolRunner; import sharedsidefunctions.CheckArguments; import sharedsidefunctions.CopyFromLocal; import sharedsidefunctions.DeleteHDFSFiles; import sharedsidefunctions.HadoopUser; import sharedsidefunctions.MakeDB; import sharedsidefunctions.MakeHamondHDFSdir; import sharedsidefunctions.SetConf; public class DiamondMapReduce extends Configured implements Tool { public static String QUERY = "query"; public static String DATABASE = "reference"; public static String OUTPUT = "output"; public static String userName; int launchHamond(String[] arguments) throws Exception { //extract diamond, query, reference and output from array String diamond = arguments[0]; String query = arguments[1]; String dataBase = arguments[2]; String outPut = arguments[3]; //set Hadoop configuration Job job = Job.getInstance(getConf(), "DIAMOND"); Configuration conf = job.getConfiguration(); SetConf.setHadoopConf(conf); //get user name userName = HadoopUser.getHadoopUser(); //delete all existing DIAMOND files under current Hadoop user DeleteHDFSFiles.deleteAllFiles(userName); //make Hamond directory on HDFS MakeHamondHDFSdir.makedir(conf, userName); //make DIAMOND database on local then copy to HDFS with query and delete local database MakeDB.makeDB(diamond, dataBase); //copy DIAMOND bin, query and local database file to HDFS CopyFromLocal.copyFromLocal(conf, diamond, query, dataBase, userName); //pass query name and database name to mappers conf.set(QUERY, query); conf.set(DATABASE, dataBase + ".dmnd"); String[] subArgs = Arrays.copyOfRange(arguments, 4, arguments.length); conf.setStrings("DIAMOND-arguments", subArgs); conf.setStrings(OUTPUT, outPut); //add DIAMOND bin and database into distributed cache job.addCacheFile(new URI("/user/" + userName + "/Hamond/diamond")); job.addCacheFile(new URI("/user/" + userName + "/Hamond/" + new Path(dataBase).getName() + ".dmnd")); //set job input and output paths FileInputFormat.addInputPath(job, new Path("/user/" + userName + "/Hamond/" + new Path(query).getName())); FileOutputFormat.setOutputPath(job, new Path("/user/" + userName + "/Hamond/out")); //set job driver and mapper job.setJarByClass(DiamondMapReduce.class); job.setMapperClass(DiamondMapper.class); //set job input format into customized multilines format job.setInputFormatClass(CustomNLineFileInputFormat.class); job.setMapOutputKeyClass(Text.class); job.setMapOutputValueClass(Text.class); job.setOutputFormatClass(TextOutputFormat.class); job.setNumReduceTasks(0); return job.waitForCompletion(true) ? 0 : 1; } int launchHamondAWS(String[] arguments) throws Exception { //extract diamond, query, reference and output from array String diamond = arguments[0]; String query = arguments[1]; String dataBase = arguments[2]; String outPut = arguments[3]; //set Hadoop configuration Job job = Job.getInstance(getConf(), "DIAMOND"); Configuration conf = job.getConfiguration(); SetConf.setHadoopConf(conf); //get user name userName = HadoopUser.getHadoopUser(); //delete all existing DIAMOND files under current Hadoop user DeleteHDFSFiles.deleteAllFiles(userName); //make local Hamond dir awshamondsidefunctions.MakeHamondDir.make(); //copy DIAMOND, query, reference from S3 to master local awshamondsidefunctions.CopyFromS3.copyFromS3(diamond, query, dataBase); //make Hamond directory on HDFS MakeHamondHDFSdir.makedir(conf, userName); //make DIAMOND database on local then copy to HDFS with query and delete local database MakeDB.makeDB("/mnt/Hamond/diamond", "/mnt/Hamond/" + new Path(dataBase).getName()); //copy DIAMOND bin, query and local database file to HDFS CopyFromLocal.copyFromLocal(conf, "/mnt/Hamond/diamond", "/mnt/Hamond/" + new Path(query).getName(), "/mnt/Hamond/" + new Path(dataBase).getName(), userName); //pass query name and database name to mappers conf.set(QUERY, query); conf.set(DATABASE, dataBase); conf.set(OUTPUT, outPut); String[] subArgs = Arrays.copyOfRange(arguments, 4, arguments.length); conf.setStrings("DIAMOND-arguments", subArgs); conf.setStrings(OUTPUT, outPut); //add DIAMOND bin and database into distributed cache job.addCacheFile(new URI("/user/" + userName + "/Hamond/diamond")); job.addCacheFile(new URI("/user/" + userName + "/Hamond/" + new Path(dataBase).getName() + ".dmnd")); //set job input and output paths FileInputFormat.addInputPath(job, new Path("/user/" + userName + "/Hamond/" + new Path(query).getName())); FileOutputFormat.setOutputPath(job, new Path("/user/" + userName + "/Hamond/out")); //set job driver and mapper job.setJarByClass(DiamondMapReduce.class); job.setMapperClass(DiamondMapper.class); job.setReducerClass(AWSDiamondReducer.class); //set job input format into customized multilines format job.setInputFormatClass(CustomNLineFileInputFormat.class); job.setMapOutputKeyClass(Text.class); job.setMapOutputValueClass(Text.class); job.setOutputFormatClass(TextOutputFormat.class); job.setNumReduceTasks(1); return job.waitForCompletion(true) ? 0 : 1; } @Override public int run(String[] args) throws Exception { CheckArguments.check(args); //check whether to invoke regular Hamond or HamondAWS int status = 100; if (!args[0].contains("s3")) { status = launchHamond(args); hamondsidefunctions.CopyToLocal.copyToLocal(args[3]); DeleteHDFSFiles.deleteAllFiles(userName); } else if (args[0].contains("s3")) { status = launchHamondAWS(args); awshamondsidefunctions.CopyToS3.copyToS3(args[3]); DeleteHDFSFiles.deleteAllFiles(userName); awshamondsidefunctions.DeleteLocalFiles.delete(); } return status; } public static void main(String[] argv) throws Exception { int res = ToolRunner.run(new Configuration(), new DiamondMapReduce(), argv); System.exit(res); } }