Examples with HelpFormatter org.apache.commons.cli.HelpFormatter used on opensource projects

Example 21 with HelpFormatter

use of org.apache.commons.cli.HelpFormatter in project Cloud9 by lintool.

the class IterateBfs method run.

@SuppressWarnings("static-access")
@Override
public int run(String[] args) throws Exception {
    Options options = new Options();
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("XML dump file").create(INPUT_OPTION));
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("output path").create(OUTPUT_OPTION));
    options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("number of partitions").create(NUM_PARTITIONS_OPTION));
    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_OPTION) || !cmdline.hasOption(OUTPUT_OPTION) || !cmdline.hasOption(NUM_PARTITIONS_OPTION)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(this.getClass().getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        return -1;
    }
    String inputPath = cmdline.getOptionValue(INPUT_OPTION);
    String outputPath = cmdline.getOptionValue(OUTPUT_OPTION);
    int n = Integer.parseInt(cmdline.getOptionValue(NUM_PARTITIONS_OPTION));
    LOG.info("Tool name: " + this.getClass().getName());
    LOG.info(" - inputDir: " + inputPath);
    LOG.info(" - outputDir: " + outputPath);
    LOG.info(" - numPartitions: " + n);
    getConf().set("mapred.child.java.opts", "-Xmx2048m");
    Job job = Job.getInstance(getConf());
    job.setJobName(String.format("IterateBfs[%s: %s, %s: %s, %s: %d]", INPUT_OPTION, inputPath, OUTPUT_OPTION, outputPath, NUM_PARTITIONS_OPTION, n));
    job.setJarByClass(EncodeBfsGraph.class);
    job.setNumReduceTasks(n);
    FileInputFormat.addInputPath(job, new Path(inputPath));
    FileOutputFormat.setOutputPath(job, new Path(outputPath));
    job.setInputFormatClass(SequenceFileInputFormat.class);
    job.setOutputFormatClass(SequenceFileOutputFormat.class);
    job.setMapOutputKeyClass(IntWritable.class);
    job.setMapOutputValueClass(BfsNode.class);
    job.setOutputKeyClass(IntWritable.class);
    job.setOutputValueClass(BfsNode.class);
    job.setMapperClass(MapClass.class);
    job.setReducerClass(ReduceClass.class);
    // Delete the output directory if it exists already.
    FileSystem.get(job.getConfiguration()).delete(new Path(outputPath), true);
    job.waitForCompletion(true);
    return 0;
}

Example 22 with HelpFormatter

use of org.apache.commons.cli.HelpFormatter in project Cloud9 by lintool.

the class AnalyzeBigramCount method main.

@SuppressWarnings({ "static-access" })
public static void main(String[] args) {
    Options options = new Options();
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
    CommandLine cmdline = null;
    CommandLineParser parser = new GnuParser();
    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        System.exit(-1);
    }
    if (!cmdline.hasOption(INPUT)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(AnalyzeBigramCount.class.getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        System.exit(-1);
    }
    String inputPath = cmdline.getOptionValue(INPUT);
    System.out.println("input path: " + inputPath);
    List<PairOfWritables<Text, IntWritable>> bigrams = SequenceFileUtils.readDirectory(new Path(inputPath));
    Collections.sort(bigrams, new Comparator<PairOfWritables<Text, IntWritable>>() {

        public int compare(PairOfWritables<Text, IntWritable> e1, PairOfWritables<Text, IntWritable> e2) {
            if (e2.getRightElement().compareTo(e1.getRightElement()) == 0) {
                return e1.getLeftElement().compareTo(e2.getLeftElement());
            }
            return e2.getRightElement().compareTo(e1.getRightElement());
        }
    });
    int singletons = 0;
    int sum = 0;
    for (PairOfWritables<Text, IntWritable> bigram : bigrams) {
        sum += bigram.getRightElement().get();
        if (bigram.getRightElement().get() == 1) {
            singletons++;
        }
    }
    System.out.println("total number of unique bigrams: " + bigrams.size());
    System.out.println("total number of bigrams: " + sum);
    System.out.println("number of bigrams that appear only once: " + singletons);
    System.out.println("\nten most frequent bigrams: ");
    Iterator<PairOfWritables<Text, IntWritable>> iter = Iterators.limit(bigrams.iterator(), 10);
    while (iter.hasNext()) {
        PairOfWritables<Text, IntWritable> bigram = iter.next();
        System.out.println(bigram.getLeftElement() + "\t" + bigram.getRightElement());
    }
}

Example 23 with HelpFormatter

use of org.apache.commons.cli.HelpFormatter in project Cloud9 by lintool.

the class AnalyzeBigramRelativeFrequencyJson method main.

@SuppressWarnings({ "static-access" })
public static void main(String[] args) {
    Options options = new Options();
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
    CommandLine cmdline = null;
    CommandLineParser parser = new GnuParser();
    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        System.exit(-1);
    }
    if (!cmdline.hasOption(INPUT)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(AnalyzeBigramRelativeFrequencyJson.class.getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        System.exit(-1);
    }
    String inputPath = cmdline.getOptionValue(INPUT);
    System.out.println("input path: " + inputPath);
    List<PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable>> pairs = SequenceFileUtils.readDirectory(new Path(inputPath));
    List<PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable>> list1 = Lists.newArrayList();
    List<PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable>> list2 = Lists.newArrayList();
    for (PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable> p : pairs) {
        BigramRelativeFrequencyJson.MyTuple bigram = p.getLeftElement();
        if (bigram.getJsonObject().get("Left").getAsString().equals("light")) {
            list1.add(p);
        }
        if (bigram.getJsonObject().get("Left").getAsString().equals("contain")) {
            list2.add(p);
        }
    }
    Collections.sort(list1, new Comparator<PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable>>() {

        public int compare(PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable> e1, PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable> e2) {
            if (e1.getRightElement().compareTo(e2.getRightElement()) == 0) {
                return e1.getLeftElement().compareTo(e2.getLeftElement());
            }
            return e2.getRightElement().compareTo(e1.getRightElement());
        }
    });
    Iterator<PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable>> iter1 = Iterators.limit(list1.iterator(), 10);
    while (iter1.hasNext()) {
        PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable> p = iter1.next();
        BigramRelativeFrequencyJson.MyTuple bigram = p.getLeftElement();
        System.out.println(bigram + "\t" + p.getRightElement());
    }
    Collections.sort(list2, new Comparator<PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable>>() {

        public int compare(PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable> e1, PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable> e2) {
            if (e1.getRightElement().compareTo(e2.getRightElement()) == 0) {
                return e1.getLeftElement().compareTo(e2.getLeftElement());
            }
            return e2.getRightElement().compareTo(e1.getRightElement());
        }
    });
    Iterator<PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable>> iter2 = Iterators.limit(list2.iterator(), 10);
    while (iter2.hasNext()) {
        PairOfWritables<BigramRelativeFrequencyJson.MyTuple, FloatWritable> p = iter2.next();
        BigramRelativeFrequencyJson.MyTuple bigram = p.getLeftElement();
        System.out.println(bigram + "\t" + p.getRightElement());
    }
}

Example 24 with HelpFormatter

use of org.apache.commons.cli.HelpFormatter in project Cloud9 by lintool.

the class SequentialPersonalizedPageRank method main.

@SuppressWarnings({ "static-access" })
public static void main(String[] args) throws IOException {
    Options options = new Options();
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
    options.addOption(OptionBuilder.withArgName("val").hasArg().withDescription("random jump factor").create(JUMP));
    options.addOption(OptionBuilder.withArgName("node").hasArg().withDescription("source node (i.e., destination of the random jump)").create(SOURCE));
    CommandLine cmdline = null;
    CommandLineParser parser = new GnuParser();
    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        System.exit(-1);
    }
    if (!cmdline.hasOption(INPUT) || !cmdline.hasOption(SOURCE)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(SequentialPersonalizedPageRank.class.getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        System.exit(-1);
    }
    String infile = cmdline.getOptionValue(INPUT);
    final String source = cmdline.getOptionValue(SOURCE);
    float alpha = cmdline.hasOption(JUMP) ? Float.parseFloat(cmdline.getOptionValue(JUMP)) : 0.15f;
    int edgeCnt = 0;
    DirectedSparseGraph<String, Integer> graph = new DirectedSparseGraph<String, Integer>();
    BufferedReader data = new BufferedReader(new InputStreamReader(new FileInputStream(infile)));
    String line;
    while ((line = data.readLine()) != null) {
        line.trim();
        String[] arr = line.split("\\t");
        for (int i = 1; i < arr.length; i++) {
            graph.addEdge(new Integer(edgeCnt++), arr[0], arr[i]);
        }
    }
    data.close();
    if (!graph.containsVertex(source)) {
        System.err.println("Error: source node not found in the graph!");
        System.exit(-1);
    }
    WeakComponentClusterer<String, Integer> clusterer = new WeakComponentClusterer<String, Integer>();
    Set<Set<String>> components = clusterer.transform(graph);
    int numComponents = components.size();
    System.out.println("Number of components: " + numComponents);
    System.out.println("Number of edges: " + graph.getEdgeCount());
    System.out.println("Number of nodes: " + graph.getVertexCount());
    System.out.println("Random jump factor: " + alpha);
    // Compute personalized PageRank.
    PageRankWithPriors<String, Integer> ranker = new PageRankWithPriors<String, Integer>(graph, new Transformer<String, Double>() {

        @Override
        public Double transform(String vertex) {
            return vertex.equals(source) ? 1.0 : 0;
        }
    }, alpha);
    ranker.evaluate();
    // Use priority queue to sort vertices by PageRank values.
    PriorityQueue<Ranking<String>> q = new PriorityQueue<Ranking<String>>();
    int i = 0;
    for (String pmid : graph.getVertices()) {
        q.add(new Ranking<String>(i++, ranker.getVertexScore(pmid), pmid));
    }
    // Print PageRank values.
    System.out.println("\nPageRank of nodes, in descending order:");
    Ranking<String> r = null;
    while ((r = q.poll()) != null) {
        System.out.println(r.rankScore + "\t" + r.getRanked());
    }
}

Example 25 with HelpFormatter

use of org.apache.commons.cli.HelpFormatter in project Cloud9 by lintool.

the class ComputeCooccurrenceMatrixStripes method run.

/**
   * Runs this tool.
   */
@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("window size").create(WINDOW));
    options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("number of reducers").create(NUM_REDUCERS));
    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)) {
        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 reduceTasks = cmdline.hasOption(NUM_REDUCERS) ? Integer.parseInt(cmdline.getOptionValue(NUM_REDUCERS)) : 1;
    int window = cmdline.hasOption(WINDOW) ? Integer.parseInt(cmdline.getOptionValue(WINDOW)) : 2;
    LOG.info("Tool: " + ComputeCooccurrenceMatrixStripes.class.getSimpleName());
    LOG.info(" - input path: " + inputPath);
    LOG.info(" - output path: " + outputPath);
    LOG.info(" - window: " + window);
    LOG.info(" - number of reducers: " + reduceTasks);
    Job job = Job.getInstance(getConf());
    job.setJobName(ComputeCooccurrenceMatrixStripes.class.getSimpleName());
    job.setJarByClass(ComputeCooccurrenceMatrixStripes.class);
    // Delete the output directory if it exists already.
    Path outputDir = new Path(outputPath);
    FileSystem.get(getConf()).delete(outputDir, true);
    job.getConfiguration().setInt("window", window);
    job.setNumReduceTasks(reduceTasks);
    FileInputFormat.setInputPaths(job, new Path(inputPath));
    FileOutputFormat.setOutputPath(job, new Path(outputPath));
    job.setMapOutputKeyClass(Text.class);
    job.setMapOutputValueClass(HMapStIW.class);
    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(HMapStIW.class);
    job.setMapperClass(MyMapper.class);
    job.setCombinerClass(MyReducer.class);
    job.setReducerClass(MyReducer.class);
    long startTime = System.currentTimeMillis();
    job.waitForCompletion(true);
    System.out.println("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds");
    return 0;
}