Java Code Examples for org.apache.hadoop.mapreduce.Job#setMapOutputValueClass()

private Path doMapReduce(final String inputFile) throws Exception {
    final FileSystem fileSystem = FileSystem.get(conf);
    final Path inputPath = new Path(inputFile);
    final Path outputPath = fileSystem.makeQualified(new Path("target/out"));
    fileSystem.delete(outputPath, true);

    final Job job = Job.getInstance(conf);
    FileInputFormat.setInputPaths(job, inputPath);

    conf.set(BAMTestNoHeaderOutputFormat.READ_HEADER_FROM_FILE, inputFile);
    job.setInputFormatClass(BAMInputFormat.class);
    job.setMapOutputKeyClass(LongWritable.class);
    job.setMapOutputValueClass(SAMRecordWritable.class);

    job.setOutputFormatClass(BAMTestNoHeaderOutputFormat.class);
    job.setOutputKeyClass(LongWritable.class);
    job.setOutputValueClass(SAMRecordWritable.class);

    job.setNumReduceTasks(0);
    FileOutputFormat.setOutputPath(job, outputPath);

    final boolean success = job.waitForCompletion(true);
    assertTrue(success);

    return outputPath;
}
 

public Job createJob() 
throws IOException {
  Configuration conf = getConf();
  conf.setInt(MRJobConfig.NUM_MAPS, 1);
  Job job = Job.getInstance(conf, "test");
  job.setNumReduceTasks(1);
  job.setJarByClass(CredentialsTestJob.class);
  job.setNumReduceTasks(1);
  job.setMapperClass(CredentialsTestJob.CredentialsTestMapper.class);
  job.setMapOutputKeyClass(IntWritable.class);
  job.setMapOutputValueClass(NullWritable.class);
  job.setReducerClass(CredentialsTestJob.CredentialsTestReducer.class);
  job.setInputFormatClass(SleepJob.SleepInputFormat.class);
  job.setPartitionerClass(SleepJob.SleepJobPartitioner.class);
  job.setOutputFormatClass(NullOutputFormat.class);
  job.setSpeculativeExecution(false);
  job.setJobName("test job");
  FileInputFormat.addInputPath(job, new Path("ignored"));
  return job;
}
 

public static boolean runCalcJob(Configuration conf, Path input, Path outputPath)
    throws Exception {

  Job job = new Job(conf);
  job.setJarByClass(Main.class);
  job.setMapperClass(CalcMapReduce.Map.class);
  job.setReducerClass(CalcMapReduce.Reduce.class);

  job.setInputFormatClass(KeyValueTextInputFormat.class);

  job.setMapOutputKeyClass(CalcMapReduce.TextPair.class);
  job.setMapOutputValueClass(IntWritable.class);

  FileInputFormat.setInputPaths(job, input);
  FileOutputFormat.setOutputPath(job, outputPath);

  return job.waitForCompletion(true);
}
 

@SuppressWarnings("deprecation")
public static boolean runJob(Configuration conf,
    Class<? extends InputFormat<?,?>> inputFormatClass,
    Class<? extends Mapper<?,?,?,?>> mapperClass,
    Class<? extends OutputFormat<?,?>> outputFormatClass) throws IOException,
    InterruptedException, ClassNotFoundException {
  Job job = new Job(conf);
  job.setInputFormatClass(inputFormatClass);
  job.setMapperClass(mapperClass);
  job.setMapOutputKeyClass(Text.class);
  job.setMapOutputValueClass(NullWritable.class);
  job.setOutputFormatClass(outputFormatClass);
  
  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(NullWritable.class);

  boolean ret = job.waitForCompletion(true);

  // Hadoop 1.0 (and 0.20) have nasty bug when job committer is not called in
  // LocalJobRuner
  if (isHadoop1()) {
    callOutputCommitter(job, outputFormatClass);
  }

  return ret;
}
 

public static void main(String[] args) throws Exception {
    Configuration conf = new Configuration();

    String[] otherArgs = new GenericOptionsParser(conf, args).getRemainingArgs();
    Job job = Job.getInstance(conf, "hello world");
    job.setJarByClass(HelloWorld.class);
    
    // Map related configuration
    job.setInputFormatClass(DocumentInputFormat.class);
    job.setMapperClass(MyMapper.class);
    job.setMapOutputKeyClass(IntWritable.class);
    job.setMapOutputValueClass(Text.class);
    
    // Reduce related configuration
    job.setReducerClass(MyReducer.class);
    job.setOutputFormatClass(ContentOutputFormat.class);
    job.setOutputKeyClass(DocumentURI.class);
    job.setOutputValueClass(Text.class);

    conf = job.getConfiguration();
    conf.addResource("marklogic-hello-world.xml");
    
    System.exit(job.waitForCompletion(true) ? 0 : 1);
}
 

/**
 * Sets up the actual job.
 * @param args The command line parameters.
 * @return The newly created job.
 * @throws IOException When setting up the job fails.
 */
public Job createSubmittableJob(String[] args) throws IOException {
  Configuration conf = getConf();
  String inputDirs = args[0];
  String tabName = args[1];
  conf.setStrings(TABLES_KEY, tabName);
  conf.set(FileInputFormat.INPUT_DIR, inputDirs);
  Job job =
      Job.getInstance(conf,
        conf.get(JOB_NAME_CONF_KEY, NAME + "_" + EnvironmentEdgeManager.currentTime()));
  job.setJarByClass(MapReduceHFileSplitterJob.class);
  job.setInputFormatClass(HFileInputFormat.class);
  job.setMapOutputKeyClass(ImmutableBytesWritable.class);
  String hfileOutPath = conf.get(BULK_OUTPUT_CONF_KEY);
  if (hfileOutPath != null) {
    LOG.debug("add incremental job :" + hfileOutPath + " from " + inputDirs);
    TableName tableName = TableName.valueOf(tabName);
    job.setMapperClass(HFileCellMapper.class);
    job.setReducerClass(CellSortReducer.class);
    Path outputDir = new Path(hfileOutPath);
    FileOutputFormat.setOutputPath(job, outputDir);
    job.setMapOutputValueClass(MapReduceExtendedCell.class);
    try (Connection conn = ConnectionFactory.createConnection(conf);
        Table table = conn.getTable(tableName);
        RegionLocator regionLocator = conn.getRegionLocator(tableName)) {
      HFileOutputFormat2.configureIncrementalLoad(job, table.getDescriptor(), regionLocator);
    }
    LOG.debug("success configuring load incremental job");

    TableMapReduceUtil.addDependencyJars(job.getConfiguration(),
      org.apache.hbase.thirdparty.com.google.common.base.Preconditions.class);
  } else {
    throw new IOException("No bulk output directory specified");
  }
  return job;
}
 

public int run(String[] args) throws Exception {
        //创建job
        Configuration config = getConf();
        Job job = Job.getInstance(config);
        //通过job设置一些参数
        job.setJarByClass(ParseLogJob.class);
        job.setJobName("parselog");
        job.setMapperClass(LogMapper.class);
        //设置reduce个数为0
//        job.setNumReduceTasks(0);
        job.setReducerClass(LogReducer.class);
        job.setMapOutputKeyClass(LongWritable.class);
        job.setMapOutputValueClass(LogBeanWritable.class);
        job.setOutputValueClass(Text.class);


        //添加输入和输出数据
        FileInputFormat.addInputPath(job, new Path(args[0]));
        Path outputPath = new Path(args[1]);
        FileOutputFormat.setOutputPath(job, outputPath);
        FileSystem fs = FileSystem.get(config);
        if (fs.exists(outputPath)) {
            fs.delete(outputPath, true);
        }


        //运行程序
        if (!job.waitForCompletion(true)) {
            throw new RuntimeException(job.getJobName() + "failed!");
        }
        return 0;
    }
 

public static ScanMetrics runJob(org.apache.hadoop.conf.Configuration hadoopConf,
                                 Class<? extends InputFormat> inputFormat, String jobName,
                                 Class<? extends Mapper> mapperClass)
        throws IOException, InterruptedException, ClassNotFoundException {

    Job job = Job.getInstance(hadoopConf);

    //job.setJarByClass(HadoopScanMapper.class);
    job.setJarByClass(mapperClass);
    //job.setJobName(HadoopScanMapper.class.getSimpleName() + "[" + scanJob + "]");
    job.setJobName(jobName);
    job.setOutputKeyClass(NullWritable.class);
    job.setOutputValueClass(NullWritable.class);
    job.setMapOutputKeyClass(NullWritable.class);
    job.setMapOutputValueClass(NullWritable.class);
    job.setNumReduceTasks(0);
    //job.setMapperClass(HadoopScanMapper.class);
    job.setMapperClass(mapperClass);
    job.setOutputFormatClass(NullOutputFormat.class);
    job.setInputFormatClass(inputFormat);

    boolean success = job.waitForCompletion(true);

    if (!success) {
        String f;
        try {
            // Just in case one of Job's methods throws an exception
            f = String.format("MapReduce JobID %s terminated abnormally: %s",
                    job.getJobID().toString(), HadoopCompatLoader.DEFAULT_COMPAT.getJobFailureString(job));
        } catch (RuntimeException e) {
            f = "Job failed (unable to read job status programmatically -- see MapReduce logs for information)";
        }
        throw new IOException(f);
    } else {
        return DEFAULT_COMPAT.getMetrics(job.getCounters());
    }
}
 

public int run(String[] args) throws Exception {
	String jobName = "wla_baidu";

	String inputPath = args[0];
	String outputPath = args[1];
	Path path = new Path(outputPath);
	// 删除输出目录
	path.getFileSystem(getConf()).delete(path, true);

	// 1、把所有代码组织到类似于Topology的类中
	Job job = Job.getInstance(getConf(), jobName);

	// 2、一定要打包运行，必须写下面一行代码
	job.setJarByClass(MR_WLA.class);

	// 3、指定输入的hdfs
	FileInputFormat.setInputPaths(job, inputPath);

	// 4、指定map类
	job.setMapperClass(WLA_Mapper.class);

	// 5、指定map输出的<key,value>的类型
	job.setMapOutputKeyClass(Text.class);
	job.setMapOutputValueClass(Text.class);

	// 6、指定reduce类
	job.setReducerClass(WLA_Reducer.class);

	// 7、指定reduce输出的<key,value>的类型
	job.setOutputKeyClass(Text.class);
	job.setOutputValueClass(Text.class);

	// 8、指定输出的hdfs
	FileOutputFormat.setOutputPath(job, new Path(outputPath));

	return job.waitForCompletion(true) ? 0 : 1;
}
 

public static void run() throws IOException, ClassNotFoundException,
		InterruptedException {
	String inputPath = ItemBasedCFDriver.path.get("step5InputPath");
	String outputPath = ItemBasedCFDriver.path.get("step5OutputPath");

	Configuration conf = new Configuration();
	conf.set("mapred.textoutputformat.separator", ":");

	Job job = Job.getInstance(conf);
	HDFS hdfs = new HDFS(conf);
	hdfs.rmr(outputPath);

	job.setMapperClass(Step5_Mapper.class);

	job.setJarByClass(CalculateSimilarityStep5.class);

	job.setMapOutputKeyClass(IntWritable.class);
	job.setMapOutputValueClass(IntWritable.class);

	job.setInputFormatClass(TextInputFormat.class);
	job.setOutputFormatClass(TextOutputFormat.class);

	FileInputFormat.setInputPaths(job, new Path(inputPath));
	FileOutputFormat.setOutputPath(job, new Path(outputPath));

	job.waitForCompletion(true);
}
 

@Override
public int run(String[] args) throws Exception {
	Configuration conf = new Configuration();
	String[] otherArgs = new GenericOptionsParser(conf, args).getRemainingArgs();
	if (otherArgs.length != 2) {
		System.err.println("Usage: MedianAndStandardDeviationCommentLengthByHour <in> <out>");
		ToolRunner.printGenericCommandUsage(System.err);
		System.exit(2);
	}

	Job job = new Job(conf,
			"StackOverflow Median and Standard Deviation Comment Length By Hour");
	job.setJarByClass(MedianAndStandardDeviationCommentLengthByHour.class);
	job.setInputFormatClass(TextInputFormat.class);
	job.setMapperClass(MedianStdDevMapper.class);
	job.setCombinerClass(MedianStdDevCombiner.class);
	job.setReducerClass(MedianStdDevReducer.class);
	job.setMapOutputKeyClass(IntWritable.class);
	job.setMapOutputValueClass(SortedMapWritable.class);
	job.setOutputKeyClass(IntWritable.class);
	job.setOutputValueClass(MedianStdDevTuple.class);
	FileInputFormat.addInputPath(job, new Path(otherArgs[0]));
	FileOutputFormat.setOutputPath(job, new Path(otherArgs[1]));
	boolean success = job.waitForCompletion(true);

	return success ? 0 : 1;
}
 

public static void main(String[] args) throws Exception {
  Configuration conf = HBaseConfiguration.create();
  String[] otherArgs = new GenericOptionsParser(conf, args).getRemainingArgs();
  if (otherArgs.length < 2) {
    System.err.println("Usage: wordcount-hbase <in> [<in>...] <table-name>");
    System.exit(2);
  }

  Job job = Job.getInstance(conf, "word count");

  for (int i = 0; i < otherArgs.length - 1; ++i) {
    FileInputFormat.addInputPath(job, new Path(otherArgs[i]));
  }

  TableName tableName = TableName.valueOf(otherArgs[otherArgs.length - 1]);
  try {
    CreateTable.createTable(tableName, conf,
        Collections.singletonList(Bytes.toString(COLUMN_FAMILY)));
  } catch (Exception e) {
    LOG.error("Could not create the table.", e);
  }

  job.setJarByClass(WordCountHBase.class);
  job.setMapperClass(TokenizerMapper.class);
  job.setMapOutputValueClass(IntWritable.class);

  TableMapReduceUtil.initTableReducerJob(tableName.getNameAsString(), MyTableReducer.class, job);

  System.exit(job.waitForCompletion(true) ? 0 : 1);
}
 

public static void main(String[] args) throws IOException, ClassNotFoundException, InterruptedException {
    Configuration conf = new Configuration();

    Job job = Job.getInstance(conf);

    job.setJarByClass(CommonFriendStep2.class);
    // 设置job的mapper类和reducer类
    job.setMapperClass(CommonFansStep2Mapper.class);
    job.setReducerClass(CommonFansStep2Reducer.class);

    // 设置map阶段输出key:value数据的类型
    job.setMapOutputKeyClass(Text.class);
    job.setMapOutputValueClass(Text.class);

    // 设置reudce阶段输出key:value数据的类型
    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(Text.class);

    // 检测输出目录是否已存在，如果已存在则删除，以免在测试阶段需要反复手动删除输出目录
    FileSystem fs = FileSystem.get(conf);
    Path out = new Path(args[1]);
    if(fs.exists(out)) {
        fs.delete(out, true);
    }

    // 设置数据输入输出目录
    FileInputFormat.setInputPaths(job, new Path(args[0]));
    FileOutputFormat.setOutputPath(job,out);

    // 提交job到yarn或者local runner执行
    job.waitForCompletion(true);

}
 

public int run(String[] args) throws Exception {
    //创建job
    Configuration config = getConf();
    Job job = Job.getInstance(config);
    //通过job设置一些参数
    job.setJarByClass(ParseLogJob.class);
    job.setJobName("parselog");
    job.setMapperClass(LogMapper.class);
    //设置reduce个数为0
    job.setReducerClass(LogReducer.class);
    job.setMapOutputKeyClass(LongWritable.class);
    job.setMapOutputValueClass(LogWritable.class);
    job.setOutputValueClass(Text.class);


    //添加输入和输出数据
    FileInputFormat.addInputPath(job, new Path(args[0]));
    Path outputPath = new Path(args[1]);
    FileOutputFormat.setOutputPath(job, outputPath);

    //设置压缩类型
    FileOutputFormat.setCompressOutput(job, true);
    FileOutputFormat.setOutputCompressorClass(job, LzopCodec.class);

    FileSystem fs = FileSystem.get(config);
    if (fs.exists(outputPath)) {
        fs.delete(outputPath, true);
    }


    //运行程序
    if (!job.waitForCompletion(true)) {
        throw new RuntimeException(job.getJobName() + "failed!");
    }
    return 0;
}
 

public static void main(String[] args) throws Exception {
    Configuration conf = new Configuration();
    String[] otherArgs = new GenericOptionsParser(conf, args).getRemainingArgs();
    if (otherArgs.length != 2) {
        System.err.println("Usage: MRSessionize <in> <out>");
        System.exit(2);
    }
    Job job = new Job(conf, "MapReduce Sessionization");
    job.setJarByClass(MRSessionize.class);
    job.setMapperClass(SessionizeMapper.class);
    job.setReducerClass(SessionizeReducer.class);

    // WARNING: do NOT set the Combiner class
    // from the same IP in one place before we can do sessionization
    // Also, our reducer doesn't return the same key,value types it takes
    // It can't be used on the result of a previous reducer

    job.setMapOutputKeyClass(IpTimestampKey.class);
    job.setMapOutputValueClass(Text.class);
    job.setOutputKeyClass(NullWritable.class);
    job.setOutputValueClass(Text.class);

    // We need these for secondary sorting.
    // We need to shuffle the records (between Map and Reduce phases) by using IP address as key, since that is
    // the field we are using for determining uniqueness of users. However, when the records arrive to the reducers,
    // we would like them to be sorted in ascending order of their timestamps. This concept is known as secondary
    // sorting since we are "secondarily" sorting the records by another key (timestamp, in our case) in addition
    // to the shuffle key (also called the "partition" key).

    // So, to get some terminology straight.
    // Natural key (aka Shuffle key or Partition key) is the key we use to shuffle. IP address in our case
    // Secondary Sorting Key is the key we use to sort within each partition that gets sent to the user. Timestamp
    // in our case.
    // Together, the natural key and secondary sorting key form what we call the composite key. This key is called
    // IpTimestampKey in our example.

    // For secondary sorting, even though we are partitioning and shuffling by only the natural key, the map output
    // key and the reduce input key is the composite key. We, however, use a custom partitioner and custom grouping
    // comparator that only uses the natural key part of the composite key to partition and group respectively (both
    // happen during the shuffle phase).

    // However, we have a different sort comparator which also gets used in the shuffle phase but determines how
    // the records are sorted when they enter the reduce phase. This custom sort comparator in our case will make use
    // of the entire composite key.

    // We found http://vangjee.wordpress.com/2012/03/20/secondary-sorting-aka-sorting-values-in-hadoops-mapreduce-programming-paradigm/
    // to be very helpful, if you'd like to read more on the subject.
    job.setPartitionerClass(NaturalKeyPartitioner.class);
    job.setGroupingComparatorClass(NaturalKeyComparator.class);
    job.setSortComparatorClass(CompositeKeyComparator.class);

    FileInputFormat.addInputPath(job, new Path(otherArgs[0]));
    FileOutputFormat.setOutputPath(job, new Path(otherArgs[1]));
    System.exit(job.waitForCompletion(true) ? 0 : 1);
}
 

public static void main( String[] args ) throws IOException, ClassNotFoundException, InterruptedException
  {
  	Configuration conf = new Configuration();	
  	String[] otherArgs = new GenericOptionsParser(conf, args).getRemainingArgs();
StringBuilder sb = new StringBuilder();
  	for (int j = 2; j < otherArgs.length; j++) {
	
  		sb.append(otherArgs[j]);
}
  	
  	LOGGER.debug("Arguments[ " + otherArgs.length+"]"+"and values respectively ["+otherArgs[0]+"], "+
		otherArgs[1]+", ["+otherArgs[2]+"]"+", ["+otherArgs[3]+"],"+
		otherArgs[4]);

String inputpath = otherArgs[0];
String outputpath = "/tmp/jumbune/dvjsonreport"+  new Date().getTime();

String json = otherArgs[1];
String nullCondition = otherArgs[2];
String regex = otherArgs[3];
String dvDir = otherArgs[4];



if(regex.isEmpty()){
	conf.set(JsonDataVaildationConstants.REGEX_ARGUMENT, "");
}else{
	conf.set(JsonDataVaildationConstants.REGEX_ARGUMENT, regex);
}

if(nullCondition.isEmpty()){
	conf.set(JsonDataVaildationConstants.NULL_ARGUMENT, "");
}else{
	conf.set(JsonDataVaildationConstants.NULL_ARGUMENT, nullCondition);
}


conf.set(JsonDataVaildationConstants.SLAVE_DIR, dvDir);
conf.set(JsonDataVaildationConstants.JSON_ARGUMENT, json);
FileSystem fs = FileSystem.get(conf);

@SuppressWarnings("deprecation")
Job job = new Job(conf, "JSONDataValidation");
job.setJarByClass(JsonDataValidationExecutor.class);

job.setInputFormatClass(JsonFileInputFormat.class);

job.setMapperClass(JsonDataValidationMapper.class);
job.setPartitionerClass(JsonDataValidationPartitioner.class);
job.setReducerClass(JsonDataValidationReducer.class);
job.setNumReduceTasks(5);

job.setMapOutputKeyClass(Text.class);
job.setMapOutputValueClass(FileKeyViolationBean.class);

job.setOutputKeyClass(Text.class);
job.setOutputValueClass(TotalReducerViolationBean.class);
	
job.setOutputFormatClass(SequenceFileOutputFormat.class);

  	Path[] inputPaths = FileUtil.getAllJsonNestedFilePath(job, inputpath);

FileInputFormat.setInputPaths(job, inputPaths);
FileOutputFormat.setOutputPath(job, new Path(outputpath));
		
if(fs.exists(new Path(outputpath)))
{
	fs.delete(new Path(outputpath), true);
}

job.waitForCompletion(true);	

 Map<String, JsonViolationReport> jsonMap = readDataFromHdfs(conf,outputpath);
 final Gson gson= new Gson();
 final String jsonReport = gson.toJson(jsonMap);

 LOGGER.info("Completed DataValidation");
 LOGGER.info(JsonDataVaildationConstants.JSON_DV_REPORT + jsonReport);
  }
 

@Override
protected int run(CommandLine cmd) throws Exception {
    if (!cmd.getArgList().isEmpty()) throw new HalyardExport.ExportException("Unknown arguments: " + cmd.getArgList().toString());
    String source = cmd.getOptionValue('s');
    String queryFiles = cmd.getOptionValue('q');
    String target = cmd.getOptionValue('t');
    if (!target.contains("{0}")) {
        throw new HalyardExport.ExportException("Bulk export target must contain '{0}' to be replaced by stripped filename of the actual SPARQL query.");
    }
    getConf().set(SOURCE, source);
    getConf().set(TARGET, target);
    String driver = cmd.getOptionValue('c');
    if (driver != null) {
        getConf().set(JDBC_DRIVER, driver);
    }
    String props[] = cmd.getOptionValues('p');
    if (props != null) {
        for (int i=0; i<props.length; i++) {
            props[i] = Base64.encodeBase64String(props[i].getBytes(StandardCharsets.UTF_8));
        }
        getConf().setStrings(JDBC_PROPERTIES, props);
    }
    if (cmd.hasOption('i')) getConf().set(HalyardBulkUpdate.ELASTIC_INDEX_URL, cmd.getOptionValue('i'));
    TableMapReduceUtil.addDependencyJars(getConf(),
           HalyardExport.class,
           NTriplesUtil.class,
           Rio.class,
           AbstractRDFHandler.class,
           RDFFormat.class,
           RDFParser.class,
           HTable.class,
           HBaseConfiguration.class,
           AuthenticationProtos.class,
           Trace.class,
           Gauge.class);
    HBaseConfiguration.addHbaseResources(getConf());
    String cp = cmd.getOptionValue('l');
    if (cp != null) {
        String jars[] = cp.split(":");
        StringBuilder newCp = new StringBuilder();
        for (int i=0; i<jars.length; i++) {
            if (i > 0) newCp.append(':');
            newCp.append(addTmpFile(jars[i])); //append clappspath entris to tmpfiles and trim paths from the classpath
        }
        getConf().set(JDBC_CLASSPATH, newCp.toString());
    }
    Job job = Job.getInstance(getConf(), "HalyardBulkExport " + source + " -> " + target);
    job.setJarByClass(HalyardBulkExport.class);
    job.setMaxMapAttempts(1);
    job.setMapperClass(BulkExportMapper.class);
    job.setMapOutputKeyClass(NullWritable.class);
    job.setMapOutputValueClass(Void.class);
    job.setNumReduceTasks(0);
    job.setInputFormatClass(QueryInputFormat.class);
    QueryInputFormat.setQueriesFromDirRecursive(job.getConfiguration(), queryFiles, false, 0);
    job.setOutputFormatClass(NullOutputFormat.class);
    TableMapReduceUtil.initCredentials(job);
    if (job.waitForCompletion(true)) {
        LOG.info("Bulk Export Completed..");
        return 0;
    }
    return -1;
}
 

public void runJob(Job job, EntityStore entityStore) throws IOException, AccumuloSecurityException, ClassNotFoundException, InterruptedException, TableExistsException, AccumuloException, TableNotFoundException {
    File dir = temporaryFolder.newFolder("input");

    FileOutputStream fileOutputStream = new FileOutputStream(new File(dir,"uuids.txt"));
    PrintWriter printWriter = new PrintWriter(fileOutputStream);
    int countTotalResults = 1000;
    try {
        for (int i = 0; i < countTotalResults; i++) {
            printWriter.println(i+"");
        }
    } finally {
        printWriter.flush();
        fileOutputStream.close();
    }

    Configuration conf = new Configuration();
    FileSystem fs = FileSystem.getLocal(conf);
    fs.setWorkingDirectory(new Path(dir.getAbsolutePath()));

    Path inputPath = fs.makeQualified(new Path(dir.getAbsolutePath()));  // local path


    EntityOutputFomat.setZooKeeperInstance(job, accumuloMiniClusterDriver.getClientConfiguration());
    EntityOutputFomat.setConnectorInfo(job, PRINCIPAL, new PasswordToken(accumuloMiniClusterDriver.getRootPassword()));

    job.setJarByClass(getClass());
    job.setMapperClass(TestMapper.class);

    job.setInputFormatClass(TextInputFormat.class);
    job.setMapOutputKeyClass(Text.class);
    job.setMapOutputValueClass(EntityWritable.class);
    job.setOutputFormatClass(EntityOutputFomat.class);

    FileInputFormat.setInputPaths(job, inputPath);

    job.submit();
    job.waitForCompletion(true);

    Node query = QueryBuilder.create().and().eq(KEY_1, VAL_1).end().build();

    Iterable<Entity> itr = entityStore.query(Collections.singleton(TYPE), query, null, new Auths("A"));

    List<Entity> queryResults = Lists.newArrayList(itr);
    assertEquals(countTotalResults,queryResults.size());
}
 

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

  if (args.length != 5) {
    throw new IllegalArgumentException("Usage : " + MRTester.class.getName() + " <user> <pass> <table> <instanceName> <edge?>");
  }

  String user = args[0];
  String pass = args[1];
  String table = args[2];

  String instanceName = args[3];

  setConf(new Configuration());
  // getConf().set("mapred.job.tracker", "local");
  getConf().set("fs.default.name", "local");

  Job job = Job.getInstance(getConf(), this.getClass().getSimpleName() + "_" + System.currentTimeMillis());
  job.setJarByClass(this.getClass());
  AccumuloGraphConfiguration cfg = new AccumuloGraphConfiguration().setInstanceName(instanceName).setUser(user).setPassword(pass.getBytes())
      .setGraphName(table).setInstanceType(InstanceType.Mock).setCreate(true);
  if (Boolean.parseBoolean(args[4])) {

    job.setInputFormatClass(EdgeInputFormat.class);

    EdgeInputFormat.setAccumuloGraphConfiguration(job, cfg);

    job.setMapperClass(TestEdgeMapper.class);
  } else {
    job.setInputFormatClass(VertexInputFormat.class);

    VertexInputFormat.setAccumuloGraphConfiguration(job, cfg);
    job.setMapperClass(TestVertexMapper.class);
  }

  job.setMapOutputKeyClass(NullWritable.class);
  job.setMapOutputValueClass(NullWritable.class);
  job.setOutputFormatClass(NullOutputFormat.class);

  job.setNumReduceTasks(0);

  job.waitForCompletion(true);

  return job.isSuccessful() ? 0 : 1;
}
 

protected int runHalvadeJob(Configuration halvadeConf, String tmpOutDir, int jobType) throws IOException, URISyntaxException, InterruptedException, ClassNotFoundException {
    String pipeline = "";
    if(jobType == HalvadeResourceManager.RNA_SHMEM_PASS2) {
        HalvadeConf.setIsPass2(halvadeConf, true);
        HalvadeResourceManager.setJobResources(halvadeOpts, halvadeConf, jobType, false, halvadeOpts.useBamInput);
        pipeline = RNA_PASS2;
    } else if(jobType == HalvadeResourceManager.DNA) {
        HalvadeResourceManager.setJobResources(halvadeOpts, halvadeConf, jobType, false, halvadeOpts.useBamInput);
        pipeline = DNA; 
    }
    halvadeOpts.splitChromosomes(halvadeConf, 0);
    HalvadeConf.setOutDir(halvadeConf, tmpOutDir);
    FileSystem outFs = FileSystem.get(new URI(tmpOutDir), halvadeConf);
    if (outFs.exists(new Path(tmpOutDir))) {
        Logger.INFO("The output directory \'" + tmpOutDir + "\' already exists.");
        Logger.INFO("ERROR: Please remove this directory before trying again.");
        System.exit(-2);
    }
    if(halvadeOpts.useBamInput)
        setHeaderFile(halvadeOpts.in, halvadeConf);     
    if(halvadeOpts.rnaPipeline)
        HalvadeConf.setPass2Suffix(halvadeConf, pass2suffix);
    
    Job halvadeJob = Job.getInstance(halvadeConf, "Halvade" + pipeline);
    halvadeJob.addCacheArchive(new URI(halvadeOpts.halvadeBinaries));
    halvadeJob.setJarByClass(be.ugent.intec.halvade.hadoop.mapreduce.HalvadeMapper.class);
    addInputFiles(halvadeOpts.in, halvadeConf, halvadeJob);
    FileOutputFormat.setOutputPath(halvadeJob, new Path(tmpOutDir));

    if(jobType == HalvadeResourceManager.RNA_SHMEM_PASS2) {
        halvadeJob.setMapperClass(be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.class);
        halvadeJob.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.RnaGATKReducer.class);
    } else if(jobType == HalvadeResourceManager.DNA){ 
        halvadeJob.setMapperClass(halvadeOpts.alignmentTools[halvadeOpts.aln]);
        halvadeJob.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.DnaGATKReducer.class);
    }
    
    
    halvadeJob.setMapOutputKeyClass(ChromosomeRegion.class);
    halvadeJob.setMapOutputValueClass(SAMRecordWritable.class);
    halvadeJob.setInputFormatClass(HalvadeTextInputFormat.class);
    halvadeJob.setOutputKeyClass(Text.class);
    if(halvadeOpts.mergeBam) {
        halvadeJob.setSortComparatorClass(SimpleChrRegionComparator.class);
        halvadeJob.setOutputValueClass(SAMRecordWritable.class);
    }else {
        halvadeJob.setPartitionerClass(ChrRgPartitioner.class);
        halvadeJob.setSortComparatorClass(ChrRgSortComparator.class);
        halvadeJob.setGroupingComparatorClass(ChrRgGroupingComparator.class);
        halvadeJob.setOutputValueClass(VariantContextWritable.class);
    }

    if(halvadeOpts.justAlign && !halvadeOpts.mergeBam)
        halvadeJob.setNumReduceTasks(0);
    else if (halvadeOpts.mergeBam) {
        halvadeJob.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.BamMergeReducer.class);
        halvadeJob.setNumReduceTasks(1);
    } else {
        halvadeJob.setNumReduceTasks(halvadeOpts.reduces); 
        if(halvadeOpts.countOnly) {
            halvadeJob.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.CountReadsReducer.class);
            halvadeJob.setOutputValueClass(LongWritable.class);
        }
    }
    
    if(halvadeOpts.useBamInput) {
        halvadeJob.setMapperClass(be.ugent.intec.halvade.hadoop.mapreduce.AlignedBamMapper.class);
        halvadeJob.setInputFormatClass(BAMInputFormat.class);
    }
    
    return runTimedJob(halvadeJob, "Halvade Job");
}