Example usage for org.apache.hadoop.fs Path Path

Introduction

In this page you can find the example usage for org.apache.hadoop.fs Path Path.

Prototype

public Path(URI aUri) 

Source Link

Document

Construct a path from a URI

Usage

From source file:BuildPageRankRecords.java

License:Apache License

/**
 * Runs this tool./*from  w w w .  j  a v  a  2s .  c o  m*/
 */
@SuppressWarnings({ "static-access" })
public int run(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("output path").create(OUTPUT));
    options.addOption(
            OptionBuilder.withArgName("num").hasArg().withDescription("number of nodes").create(NUM_NODES));

    CommandLine cmdline;
    CommandLineParser parser = new GnuParser();

    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        return -1;
    }

    if (!cmdline.hasOption(INPUT) || !cmdline.hasOption(OUTPUT) || !cmdline.hasOption(NUM_NODES)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(this.getClass().getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        return -1;
    }

    String inputPath = cmdline.getOptionValue(INPUT);
    String outputPath = cmdline.getOptionValue(OUTPUT);
    int n = Integer.parseInt(cmdline.getOptionValue(NUM_NODES));

    LOG.info("Tool name: " + BuildPageRankRecords.class.getSimpleName());
    LOG.info(" - inputDir: " + inputPath);
    LOG.info(" - outputDir: " + outputPath);
    LOG.info(" - numNodes: " + n);

    Configuration conf = getConf();
    conf.setInt(NODE_CNT_FIELD, n);
    conf.setInt("mapred.min.split.size", 1024 * 1024 * 1024);

    Job job = Job.getInstance(conf);
    job.setJobName(BuildPageRankRecords.class.getSimpleName() + ":" + inputPath);
    job.setJarByClass(BuildPageRankRecords.class);

    job.setNumReduceTasks(0);

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

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

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

    job.setOutputKeyClass(IntWritable.class);
    job.setOutputValueClass(PageRankNode.class);

    job.setMapperClass(MyMapper.class);

    // Delete the output directory if it exists already.
    FileSystem.get(conf).delete(new Path(outputPath), true);

    job.waitForCompletion(true);

    return 0;
}

---

From source file:SleepJobWithArray.java

License:Apache License

public JobConf setupJobConf(int numMapper, int numReducer, long mapSleepTime, int mapSleepCount,
        long reduceSleepTime, int reduceSleepCount) {
    JobConf job = new JobConf(getConf(), SleepJobWithArray.class);
    job.setNumMapTasks(numMapper);/*from   w ww  .  j a  v  a 2 s .c o  m*/
    job.setNumReduceTasks(numReducer);
    job.setMapperClass(SleepJobWithArray.class);
    job.setMapOutputKeyClass(IntWritable.class);
    job.setMapOutputValueClass(NullWritable.class);
    job.setReducerClass(SleepJobWithArray.class);
    job.setOutputFormat(NullOutputFormat.class);
    job.setInputFormat(SleepInputFormat.class);
    job.setPartitionerClass(SleepJobWithArray.class);
    job.setSpeculativeExecution(false);
    FileInputFormat.addInputPath(job, new Path("ignored"));
    job.setLong("sleep.job.map.sleep.time", mapSleepTime);
    job.setLong("sleep.job.reduce.sleep.time", reduceSleepTime);
    job.setInt("sleep.job.map.sleep.count", mapSleepCount);
    job.setInt("sleep.job.reduce.sleep.count", reduceSleepCount);
    return job;
}

---

From source file:Distinct.java

License:Apache License

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: Distinct <in> <out>");
        System.exit(2);//from   w ww  . j a v a  2s  .  com
    }
    Job job = Job.getInstance(conf, "distinct1");
    job.setJarByClass(Distinct.class);
    job.setMapperClass(TokenizerMapper1.class);
    job.setReducerClass(Reducer1.class);
    FileInputFormat.addInputPath(job, new Path(otherArgs[0]));
    FileOutputFormat.setOutputPath(job, new Path(tempDir));
    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(IntWritable.class);
    job.waitForCompletion(true);

    Configuration conf2 = new Configuration();
    Job job2 = Job.getInstance(conf2, "distinct2");
    job2.setJarByClass(Distinct.class);
    job2.setMapperClass(TokenizerMapper2.class);
    job2.setReducerClass(Reducer2.class);
    FileInputFormat.addInputPath(job2, new Path(tempDir));
    FileOutputFormat.setOutputPath(job2, new Path(otherArgs[1]));
    job2.setOutputKeyClass(Text.class);
    job2.setOutputValueClass(IntWritable.class);
    System.exit(job2.waitForCompletion(true) ? 0 : 1);
}

---

From source file:WriteFDFFixedLengthRecord.java

License:Open Source License

public static void main(String[] args) throws Exception {
    FormatDataFile fdf = new FormatDataFile(new Configuration());
    String fileName = "/indextest/testfile1";
    FileSystem.get(new Configuration()).delete(new Path(fileName), true);
    Head head = new Head();
    FieldMap fieldMap = new FieldMap();
    fieldMap.addField(new Field(ConstVar.FieldType_Byte, ConstVar.Sizeof_Byte, (short) 0));
    fieldMap.addField(new Field(ConstVar.FieldType_Short, ConstVar.Sizeof_Byte, (short) 1));
    head.setFieldMap(fieldMap);/*from ww  w  . j  a v a2s.  c om*/
    head.setPrimaryIndex((short) 0);

    fdf.create(fileName, head);
    for (int i = 0; i < 200; i++) {
        Record record = new Record(2);
        record.addValue(new FieldValue((byte) i, (short) 0));
        record.addValue(new FieldValue((byte) i, (short) 1));
        fdf.addRecord(record);
    }
    fdf.close();
}

---

From source file:DocToSeq.java

License:Apache License

public static void main(String args[]) throws Exception {
    if (args.length != 2) {
        System.err.println("Arguments: [input tsv file] [output sequence file]");
        return;//from w w w.  j  a va  2 s.  com
    }
    String inputFileName = args[0];
    String outputDirName = args[1];
    Configuration configuration = new Configuration();
    FileSystem fs = FileSystem.get(configuration);
    Writer writer = new SequenceFile.Writer(fs, configuration, new Path(outputDirName + "/chunk-0"), Text.class,
            Text.class);

    int count = 0;
    BufferedReader reader = new BufferedReader(new FileReader(inputFileName));
    Text key = new Text();
    Text value = new Text();
    while (true) {
        String line = reader.readLine();
        if (line == null) {
            break;
        }
        String[] tokens = line.split("\t", 3);
        if (tokens.length != 3) {
            System.out.println("Skip line: " + line);
            continue;
        }
        String category = tokens[0];
        String id = tokens[1];
        String message = tokens[2];
        key.set("/" + category + "/" + id);
        value.set(message);
        writer.append(key, value);
        count++;
    }
    reader.close();
    writer.close();
    System.out.println("Wrote " + count + " entries.");
}

---

From source file:AnagramJob.java

License:Apache License

/**
 * @param args//  ww w  .  ja  v a2 s.  c om
 */
public static void main(String[] args) throws Exception {
    JobConf conf = new JobConf(AnagramJob.class);
    conf.setJobName("anagramcount");

    conf.setOutputKeyClass(Text.class);
    conf.setOutputValueClass(Text.class);

    conf.setMapperClass(AnagramMapper.class);
    // conf.setCombinerClass(AnagramReducer.class);
    conf.setReducerClass(AnagramReducer.class);

    conf.setInputFormat(TextInputFormat.class);
    conf.setOutputFormat(TextOutputFormat.class);

    FileInputFormat.setInputPaths(conf, new Path(args[0]));
    FileOutputFormat.setOutputPath(conf, new Path(args[1]));

    JobClient.runJob(conf);

}

---

From source file:BigBWA.java

License:Open Source License

@Override
public int run(String[] args) throws Exception {
    Configuration conf = this.getConf();

    for (String argumento : args) {
        LOG.info("Arg: " + argumento);
    }/* w ww.j  a  va  2  s.c om*/

    String inputPath = "";
    String outputPath = "";

    boolean useReducer = false;

    BwaOptions options = new BwaOptions(args);

    //We set the timeout and stablish the bwa library to call BWA methods
    conf.set("mapreduce.task.timeout", "0");
    conf.set("mapreduce.map.env", "LD_LIBRARY_PATH=./bwa.zip/");

    //==================Algorithm election==================
    //One of the algorithms is going to be in use, because tge default is always specified.
    if (options.isMemAlgorithm()) {
        //Case of the mem algorithm
        conf.set("mem", "true");
        conf.set("aln", "false");
        conf.set("bwasw", "false");
    }

    else if (options.isAlnAlgorithm()) {
        // Case of aln algorithm
        conf.set("mem", "false");
        conf.set("aln", "true");
        conf.set("bwasw", "false");
    }

    else if (options.isBwaswAlgorithm()) {
        // Case of bwasw algorithm
        conf.set("mem", "false");
        conf.set("aln", "false");
        conf.set("bwasw", "true");
    }

    //==================Index election==================
    if (options.getIndexPath() != "") {
        conf.set("indexRoute", options.getIndexPath());
    } else {
        System.err.println("No index has been found. Aborting.");
        System.exit(1);
    }

    //==================Type of reads election==================
    //There is always going to be a type of reads, because default is paired
    if (options.isPairedReads()) {
        conf.set("paired", "true");
        conf.set("single", "false");
    } else if (options.isSingleReads()) {
        conf.set("paired", "false");
        conf.set("single", "true");
    }

    //==================Use of reducer==================
    if (options.isUseReducer()) {
        useReducer = true;
        conf.set("useReducer", "true");
    } else {
        conf.set("useReducer", "false");
    }

    //==================Number of threads per map==================
    if (options.getNumThreads() != "0") {
        conf.set("bwathreads", options.getNumThreads());
    }

    //==================RG Header===================
    if (options.getReadgroupHeader() != "") {
        conf.set("rgheader", options.getReadgroupHeader());
    }

    //==================Input and output paths==================
    inputPath = options.getInputPath();
    outputPath = options.getOutputPath();

    conf.set("outputGenomics", outputPath);

    //==================Partition number==================
    if (options.getPartitionNumber() != 0) {
        try {
            FileSystem fs = FileSystem.get(conf);

            Path inputFilePath = new Path(inputPath);

            ContentSummary cSummary = fs.getContentSummary(inputFilePath);

            long length = cSummary.getLength();

            fs.close();

            conf.set("mapreduce.input.fileinputformat.split.maxsize",
                    String.valueOf((length) / options.getPartitionNumber()));
            conf.set("mapreduce.input.fileinputformat.split.minsize",
                    String.valueOf((length) / options.getPartitionNumber()));
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
            LOG.error(e.toString());

            System.exit(1);
        }

    }

    //Job job = new Job(conf,"BigBWA_"+outputPath);
    Job job = Job.getInstance(conf, "BigBWA_" + outputPath);

    job.setJarByClass(BigBWA.class);
    job.setMapperClass(BigBWAMap.class);
    //job.setCombinerClass(BigBWACombiner.class);

    if (useReducer) {
        job.setReducerClass(BigBWAReducer.class);

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

        job.setNumReduceTasks(1);
    } else {
        job.setNumReduceTasks(0);
    }

    job.setOutputKeyClass(NullWritable.class);
    job.setOutputValueClass(Text.class);

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

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

---

From source file:CountHistogram.java

License:Open Source License

@Override
public int run(String[] args) throws Exception {
    try {/*from   w  w w . j  ava  2  s  .co  m*/
        JobClient client = new JobClient();
        JobConf job = new JobConf(getConf(), CountHistogram.class);
        job.setJobName("CountHistogram");

        job.setOutputKeyClass(IntWritable.class);
        job.setOutputValueClass(IntWritable.class);

        job.setMapperClass(Map.class);
        job.setReducerClass(Reduce.class);

        job.setInputFormat(TextInputFormat.class);
        job.setOutputFormat(TextOutputFormat.class);

        FileInputFormat.setInputPaths(job, new Path(args[0]));
        FileOutputFormat.setOutputPath(job, new Path(args[1]));

        client.setConf(job);
        JobClient.runJob(job);
    } catch (Exception e) {
        e.printStackTrace();
        throw e;
    }
    return 0;
}

---

From source file:BigramRelativeFrequencyTuple.java

License:Apache License

/**
 * Runs this tool.//from www . jav  a  2  s .  c  o m
 */
public int run(String[] args) throws Exception {
    if (args.length != 3) {
        printUsage();
        return -1;
    }

    String inputPath = args[0];
    String outputPath = args[1];
    int reduceTasks = Integer.parseInt(args[2]);

    LOG.info("Tool name: " + BigramRelativeFrequencyTuple.class.getSimpleName());
    LOG.info(" - input path: " + inputPath);
    LOG.info(" - output path: " + outputPath);
    LOG.info(" - num reducers: " + reduceTasks);

    Job job = Job.getInstance(getConf());
    job.setJobName(BigramRelativeFrequencyTuple.class.getSimpleName());
    job.setJarByClass(BigramRelativeFrequencyTuple.class);

    job.setNumReduceTasks(reduceTasks);

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

    job.setMapOutputKeyClass(BinSedesTuple.class);
    job.setMapOutputValueClass(FloatWritable.class);
    job.setOutputKeyClass(BinSedesTuple.class);
    job.setOutputValueClass(FloatWritable.class);
    job.setOutputFormatClass(SequenceFileOutputFormat.class);

    job.setMapperClass(MyMapper.class);
    job.setCombinerClass(MyCombiner.class);
    job.setReducerClass(MyReducer.class);
    job.setPartitionerClass(MyPartitioner.class);

    // Delete the output directory if it exists already.
    Path outputDir = new Path(outputPath);
    FileSystem.get(getConf()).delete(outputDir, true);

    long startTime = System.currentTimeMillis();
    job.waitForCompletion(true);
    System.out.println("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds");

    return 0;
}

---

From source file:WordCountA.java

License:Apache License

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: wordcount <in> [<in>...] <out>");
        System.exit(2);// ww  w .  j  a  v  a2  s .  com
    }
    Job job = Job.getInstance(conf, "word count");
    job.setJarByClass(WordCountA.class);
    job.setMapperClass(TokenizerMapper.class);
    // Disable the combiner
    // job.setCombinerClass(IntSumReducer.class);
    // Setup the Partitioner
    job.setPartitionerClass(Letterpartitioner.class);
    job.setReducerClass(IntSumReducer.class);
    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(IntWritable.class);
    for (int i = 0; i < otherArgs.length - 1; ++i) {
        FileInputFormat.addInputPath(job, new Path(otherArgs[i]));
    }
    FileOutputFormat.setOutputPath(job, new Path(otherArgs[otherArgs.length - 1]));
    System.exit(job.waitForCompletion(true) ? 0 : 1);
}

---

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