Example usage for org.apache.commons.cli HelpFormatter setWidth

List of usage examples for org.apache.commons.cli HelpFormatter setWidth

Introduction

In this page you can find the example usage for org.apache.commons.cli HelpFormatter setWidth.

Prototype

public void setWidth(int width) 

Source Link

Document

Sets the 'width'.

Usage

From source file:edu.umd.gorden2.RunPersonalizedPageRankBasic.java

/**
 * Runs this tool.//from  w ww  . ja va  2s  .co m
 */
@SuppressWarnings({ "static-access" })
public int run(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(new Option(RANGE, "use range partitioner"));

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("base path").create(BASE));
    options.addOption(
            OptionBuilder.withArgName("num").hasArg().withDescription("start iteration").create(START));
    options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("end iteration").create(END));
    options.addOption(
            OptionBuilder.withArgName("num").hasArg().withDescription("number of nodes").create(NUM_NODES));
    options.addOption(
            OptionBuilder.withArgName("sources").hasArg().withDescription("sources").create("sources"));

    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(BASE) || !cmdline.hasOption(START) || !cmdline.hasOption(END)
            || !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 basePath = cmdline.getOptionValue(BASE);
    int n = Integer.parseInt(cmdline.getOptionValue(NUM_NODES));
    int s = Integer.parseInt(cmdline.getOptionValue(START));
    int e = Integer.parseInt(cmdline.getOptionValue(END));
    boolean useRange = cmdline.hasOption(RANGE);
    String m = cmdline.getOptionValue("sources");

    LOG.info("Tool name: RunPageRank");
    LOG.info(" - base path: " + basePath);
    LOG.info(" - num nodes: " + n);
    LOG.info(" - start iteration: " + s);
    LOG.info(" - end iteration: " + e);
    LOG.info(" - user range partitioner: " + useRange);
    LOG.info(" - sources: " + m);

    // Iterate PageRank.
    for (int i = s; i < e; i++) {
        iteratePageRank(i, i + 1, basePath, n, m);
    }

    return 0;
}

From source file:edu.umd.honghongie.RunPersonalizedPageRankBasic.java

/**
 * Runs this tool.//  w  w w  .j a  v  a2s . c o m
 */
@SuppressWarnings({ "static-access" })
public int run(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(new Option(COMBINER, "use combiner"));
    options.addOption(new Option(RANGE, "use range partitioner"));

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("base path").create(BASE));
    options.addOption(
            OptionBuilder.withArgName("num").hasArg().withDescription("start iteration").create(START));
    options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("end iteration").create(END));
    options.addOption(
            OptionBuilder.withArgName("num").hasArg().withDescription("number of nodes").create(NUM_NODES));

    //*** add option of source
    options.addOption(
            OptionBuilder.withArgName("node").hasArg().withDescription("source nodes").create(SOURCE));

    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(BASE) || !cmdline.hasOption(START) || !cmdline.hasOption(END)
            || !cmdline.hasOption(NUM_NODES) || !cmdline.hasOption(SOURCE)) {
        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 basePath = cmdline.getOptionValue(BASE);
    int n = Integer.parseInt(cmdline.getOptionValue(NUM_NODES));
    int s = Integer.parseInt(cmdline.getOptionValue(START));
    int e = Integer.parseInt(cmdline.getOptionValue(END));
    boolean useCombiner = cmdline.hasOption(COMBINER);
    boolean useRange = cmdline.hasOption(RANGE);
    //********
    String nodeid = cmdline.getOptionValue(SOURCE);

    ArrayListOfInts sourceids = new ArrayListOfInts();
    String ss[] = nodeid.split(",");
    for (int i = 0; i < ss.length; i++) {
        sourceids.add(Integer.parseInt(ss[i]));
    }
    System.out.println("***** 1 **** sourceids**** " + sourceids.toString());

    LOG.info("Tool name: RunPageRank");
    LOG.info(" - base path: " + basePath);
    LOG.info(" - num nodes: " + n);
    LOG.info(" - start iteration: " + s);
    LOG.info(" - end iteration: " + e);
    LOG.info(" - use combiner: " + useCombiner);
    LOG.info(" - user range partitioner: " + useRange);
    LOG.info(" - source node: " + nodeid);

    // Iterate PageRank. *** add source
    for (int i = s; i < e; i++) {
        iteratePageRank(i, i + 1, basePath, n, sourceids, useCombiner);
    }

    return 0;
}

From source file:bigmodel.AutoCoderLocal.java

/**
 * Runs this tool.//from  w  w  w  .  j a  v a 2  s.  c om
 */
@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 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) + "/part-r-00000";
    String outputPath = cmdline.getOptionValue(OUTPUT);
    String dataPath = cmdline.getOptionValue(INPUT) + "/common";
    //String inputPath = "/home/qiwang321/mapreduce-data/data/in-mingled1-5/part*";
    //String outputPath = "output";
    //String dataPath = "/home/qiwang321/mapreduce-data/data/in-mingled1-5/common";
    int reduceTasks = cmdline.hasOption(NUM_REDUCERS) ? Integer.parseInt(cmdline.getOptionValue(NUM_REDUCERS))
            : 1;

    LOG.info("Tool: " + AutoCoderLocal.class.getSimpleName());
    LOG.info(" - input path: " + inputPath);
    LOG.info(" - output path: " + outputPath);
    LOG.info(" - number of reducers: " + reduceTasks);
    Configuration conf = getConf();
    initialParameters(conf);

    conf.set("dataPath", dataPath);

    Job job = Job.getInstance(conf);
    job.setJobName(AutoCoderLocal.class.getSimpleName());
    job.setJarByClass(AutoCoderLocal.class);
    // set the path of the information of k clusters in this iteration
    job.getConfiguration().set("sidepath", inputPath + "/side_output");
    job.setNumReduceTasks(reduceTasks);

    dataShuffle();

    FileInputFormat.setInputPaths(job, new Path(inputPath));
    FileOutputFormat.setOutputPath(job, new Path(outputPath));
    FileInputFormat.setMinInputSplitSize(job, 1000 * 1024 * 1024);
    FileInputFormat.setMaxInputSplitSize(job, 1000 * 1024 * 1024);

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

    job.setMapOutputKeyClass(IntWritable.class);
    job.setMapOutputValueClass(ModelNode.class);
    job.setOutputKeyClass(NullWritable.class);
    job.setOutputValueClass(SuperModel.class);

    job.setMapperClass(MyMapper.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);
    LOG.info("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds");

    //prepareNextIteration(inputPath0, outputPath,iterations,conf,reduceTasks);

    return 0;
}

From source file:RunPageRankSchimmy.java

/**
 * Runs this tool./* w w  w.  j a  va2  s  . com*/
 */
@SuppressWarnings({ "static-access" })
public int run(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(new Option(COMBINER, "use combiner"));
    options.addOption(new Option(INMAPPER_COMBINER, "user in-mapper combiner"));
    options.addOption(new Option(RANGE, "use range partitioner"));

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("base path").create(BASE));
    options.addOption(
            OptionBuilder.withArgName("num").hasArg().withDescription("start iteration").create(START));
    options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("end iteration").create(END));
    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(BASE) || !cmdline.hasOption(START) || !cmdline.hasOption(END)
            || !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 basePath = cmdline.getOptionValue(BASE);
    int n = Integer.parseInt(cmdline.getOptionValue(NUM_NODES));
    int s = Integer.parseInt(cmdline.getOptionValue(START));
    int e = Integer.parseInt(cmdline.getOptionValue(END));
    boolean useCombiner = cmdline.hasOption(COMBINER);
    boolean useInmapCombiner = cmdline.hasOption(INMAPPER_COMBINER);
    boolean useRange = cmdline.hasOption(RANGE);

    LOG.info("Tool name: RunPageRank");
    LOG.info(" - base path: " + basePath);
    LOG.info(" - num nodes: " + n);
    LOG.info(" - start iteration: " + s);
    LOG.info(" - end iteration: " + e);
    LOG.info(" - use combiner: " + useCombiner);
    LOG.info(" - use in-mapper combiner: " + useInmapCombiner);
    LOG.info(" - user range partitioner: " + useRange);

    // iterate PageRank
    for (int i = s; i < e; i++) {
        iteratePageRank(basePath, i, i + 1, n, useCombiner, useInmapCombiner, useRange);
    }

    return 0;
}

From source file:edu.umd.shrawanraina.RunPersonalizedPageRankBasic.java

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

    options.addOption(new Option(COMBINER, "use combiner"));
    options.addOption(new Option(INMAPPER_COMBINER, "user in-mapper combiner"));
    options.addOption(new Option(RANGE, "use range partitioner"));

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("base path").create(BASE));
    options.addOption(
            OptionBuilder.withArgName("num").hasArg().withDescription("start iteration").create(START));
    options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("end iteration").create(END));
    options.addOption(
            OptionBuilder.withArgName("num").hasArg().withDescription("number of nodes").create(NUM_NODES));
    options.addOption(
            OptionBuilder.withArgName("node").hasArg().withDescription("source nodes").create(SOURCES));

    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(BASE) || !cmdline.hasOption(START) || !cmdline.hasOption(END)
            || !cmdline.hasOption(NUM_NODES) || !cmdline.hasOption(SOURCES)) {
        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 basePath = cmdline.getOptionValue(BASE);
    int n = Integer.parseInt(cmdline.getOptionValue(NUM_NODES));
    int s = Integer.parseInt(cmdline.getOptionValue(START));
    int e = Integer.parseInt(cmdline.getOptionValue(END));
    String sources = cmdline.getOptionValue(SOURCES);
    boolean useCombiner = cmdline.hasOption(COMBINER);
    boolean useInmapCombiner = cmdline.hasOption(INMAPPER_COMBINER);
    boolean useRange = cmdline.hasOption(RANGE);

    LOG.info("Tool name: RunPageRank");
    LOG.info(" - base path: " + basePath);
    LOG.info(" - num nodes: " + n);
    LOG.info(" - start iteration: " + s);
    LOG.info(" - end iteration: " + e);
    LOG.info(" - sources: " + Arrays.asList(sources.split("\\s*(,)\\s*")));
    LOG.info(" - use combiner: " + useCombiner);
    LOG.info(" - use in-mapper combiner: " + useInmapCombiner);
    LOG.info(" - user range partitioner: " + useRange);

    Configuration conf = getConf();
    conf.setStrings("sources", sources);
    // Iterate PageRank.
    for (int i = s; i < e; i++) {
        iteratePageRank(sources, i, i + 1, basePath, n, useCombiner, useInmapCombiner);
    }

    return 0;
}

From source file:com.comcast.oscar.cli.CommandRun.java

/**
 * Checks all the commands from the user. Order is IMPORTANT. Do not rearrange without full understanding.
 * @param args/*from ww  w.  j  a v a2 s.  c  o m*/
 */
public void run(String[] args) {
    BasicParser parser = new BasicParser();
    Options options = new Options();
    BuildOptions.run(options);

    try {
        CommandLine line = parser.parse(options, args);
        HelpFormatter hf = new HelpFormatter();
        hf.setWidth(180);
        hf.setLeftPadding(5);
        hf.setDescPadding(5);

        if (line.hasOption("h")) {
            hf.printHelp(Constants.OSCAR_CLI_USAGE, options);
        }

        if (line.hasOption("version")) {
            System.out.println(Constants.APACHE_20_LICENCE_DISCLAIMER);
            System.out.println(Constants.OSCAR_VERSION);
        }

        if (line.hasOption("s")) {
            comSpecification.setValues(line.getOptionValues("s"));

            if (comSpecification.getConfigurationFileType() == -1) {
                System.err.println(Specification.ERROR);
                System.exit(1);
            }

            if (comSpecification.getTlvDisassemble() == null) {
                System.err.println(Specification.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("i")) {
            comInput = new Input(line.getOptionValues("i"));

            if (!comInput.hasInput()) {
                System.err.println(Input.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("o")) {
            comOutput = new Output(line.getOptionValues("o"));
        }

        if (line.hasOption("k")) {
            comKey.setKey(line.getOptionValues("k"));
        }

        if (line.hasOption("mbb")) {
            comMergeBulk = new MergeBulk(line.getOptionValues("mbb"));

            if (comMergeBulk.hasInputDir()) {
                comMergeBulk.mergeFiles(comSpecification.getConfigurationFileType(), comKey.getKey());
            } else {
                System.err.println(MergeBulk.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("f")) {
            comFirmware = new Firmware(line.getOptionValues("f"));
        }

        if (line.hasOption("T")) {
            comTFTPServer = new TFTPServer(line.getOptionValues("T"));

            if (!comTFTPServer.hasAddress()) {
                System.err.println(TFTPServer.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("m")) {
            comMaxCPE = new MaxCPE(line.getOptionValues("m"));
        }

        if (line.hasOption("df")) {
            comDownstreamFrequency = new DownstreamFrequency(line.getOptionValues("df"));
        }

        if (line.hasOption("cvc")) {
            comCVC = new CVC(line.getOptionValues("cvc"));

            if (!comCVC.hasCVC()) {
                System.err.println(CVC.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("t")) {
            comTLV = new TLV(line.getOptionValues("t"));
        }

        if (line.hasOption("dm")) {
            comDigitmapInsert = new DigitmapInsert(line.getOptionValues("dm"));

            if (!comDigitmapInsert.hasDigitmap()) {
                System.err.println(DigitmapInsert.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("O")) {
            comOID = new OID(line.getOptionValues("O"));

            if (!comOID.hasOID()) {
                System.err.println(OID.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("d")) {
            comDecompile = new Decompile(line.getOptionValues("d"));
            decompile();
        }

        if (line.hasOption("c")) {
            compile();
        }

        if (line.hasOption("b")) {
            String[] optionValues = line.getOptionValues("b");

            if (optionValues.length >= 3) {
                bulkBuild(optionValues[0]);
                bulkBuildCommand(new File(optionValues[1]), new File(optionValues[2]));
            } else if (optionValues.length >= 2) {
                bulkBuild(optionValues[0]);
                bulkBuildCommand(new File(optionValues[1]));
            } else {
                System.err.println(Constants.ERR_MIS_PAR);
                hf.printHelp(Constants.OSCAR_CLI_USAGE, options);
            }
        }

        if (line.hasOption("ftd")) {
            comFullTLVDisplay.printFullTLVDisplay(comSpecification.getConfigurationFileType());
        }

        if (line.hasOption("x")) {
            comHexDisplay = new HexDisplay(line.getOptionValues("x"));

            if (comInput.hasInput()) {
                if (comInput.isBinary()) {
                    comHexDisplay.printHexDisplayFromBinary(comInput.getInput());
                } else {
                    comHexDisplay.printHexDisplayFromText(comInput.getInput(),
                            comSpecification.getConfigurationFileType());
                }
            } else {
                System.err.println(Input.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("j")) {
            if (comInput.hasInput()) {
                if (comInput.isBinary()) {
                    comJSONDisplay.printJSONDisplayFromBinary(comInput.getInput(),
                            comSpecification.getTlvDisassemble(), comSpecification.getConfigurationFileType());
                } else {
                    comJSONDisplay.printJSONDisplayFromText(comInput.getInput(),
                            comSpecification.getTlvDisassemble());
                }
            } else {
                System.err.println(Input.ERROR);
                System.exit(1);
            }
        }

        if (line.hasOption("ddm")) {
            if (comInput.hasInput()) {
                if (comInput.isBinary()) {
                    comDigitmapDisplay.printDigitmapDisplayFromBinary(comInput.getInput());
                } else {
                    comDigitmapDisplay.printDigitmapDisplayFromText(comInput.getInput());
                }
            }
        }

        if (line.hasOption("j2t")) {
            comJSONtoTLV = new JSONtoTLV(line.getOptionValues("j2t"));

            if (comJSONtoTLV.fileExists()) {
                comJSONtoTLV.printTLV();
            } else {
                System.err.println(JSONtoTLV.ERROR);
            }
        }

        if (line.hasOption("t2j")) {
            comTLVtoJSON = new TLVtoJSON(line.getOptionValues("t2j"));
            comTLVtoJSON.printJSON(comSpecification.getTlvDisassemble());
        }

        if (line.hasOption("td")) {
            comTLVDescription = new TLVDescription(line.getOptionValues("td"));
            comTLVDescription.printTLVDescription(comSpecification.getConfigurationFileType());
        }

        if (line.hasOption("tr")) {
            comTranslate = new Translate(line.getOptionValues("tr"));
            comTranslate.translate();
        }
    } catch (ParseException exp) {
        System.err.println("Parsing failed. Reason: " + exp.getMessage());
    }
}

From source file:be.ugent.intec.halvade.HalvadeOptions.java

public int GetOptions(String[] args, Configuration hConf) throws IOException, URISyntaxException {
    try {//w w  w  . j  av a 2 s.co  m
        boolean result = parseArguments(args, hConf);
        if (!result) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.setWidth(80);
            formatter.printHelp("hadoop jar HalvadeWithLibs.jar -I <IN> -O <OUT> "
                    + "-R <REF> -D <SITES> -B <BIN> -N <nodes> -M <mem> -C <cores> [options]", options);
            return 1;
        }
        onedec = new DecimalFormat("###0.0");
        // add parameters to configuration:
        HalvadeConf.setRefDirIsSet(hConf, localRefDir != null);
        if (localRefDir == null) {
            localRefDir = tmpDir;
        }
        HalvadeConf.setScratchTempDir(hConf, tmpDir);
        HalvadeConf.setRefDirOnScratch(hConf, localRefDir);
        HalvadeConf.setRefOnHDFS(hConf, ref);
        if (STARGenome != null) {
            HalvadeConf.setStarDirOnHDFS(hConf, STARGenome);
        }
        HalvadeConf.setKnownSitesOnHDFS(hConf, hdfsSites);
        HalvadeConf.setIsPaired(hConf, paired);
        HalvadeConf.setIsRNA(hConf, rnaPipeline);
        if (bedFile != null) {
            HalvadeConf.setBed(hConf, bedFile);
        }
        if (filterBed != null) {
            HalvadeConf.setFilterBed(hConf, filterBed);
        }
        HalvadeConf.setInputIsBam(hConf, useBamInput);
        HalvadeConf.setFixQualEnc(hConf, fixQualEnc);
        HalvadeConf.setOutDir(hConf, out);
        HalvadeConf.setKeepFiles(hConf, keepFiles);
        HalvadeConf.setFilterDBSnp(hConf, filterDBSnp);
        HalvadeConf.clearTaskFiles(hConf);
        HalvadeConf.setUseElPrep(hConf, useElPrep);
        HalvadeConf.setUpdateReadGroup(hConf, updateRG);
        HalvadeConf.setUseUnifiedGenotyper(hConf, useGenotyper);
        HalvadeConf.setMergeBam(hConf, mergeBam);
        HalvadeConf.setKeepDups(hConf, keepDups);
        HalvadeConf.setRedistribute(hConf, redistribute);
        HalvadeConf.setReadGroup(hConf,
                "ID:" + RGID + " LB:" + RGLB + " PL:" + RGPL + " PU:" + RGPU + " SM:" + RGSM);
        HalvadeConf.setkeepChrSplitPairs(hConf, keepChrSplitPairs);
        if (STARGenome != null) {
            HalvadeConf.setStarDirPass2HDFS(hConf, out);
        }
        if (stargtf != null) {
            HalvadeConf.setStarGtf(hConf, stargtf);
        }

        if (chr != null) {
            HalvadeConf.setChrList(hConf, chr);
        }
        if (java != null) {
            HalvadeConf.setJava(hConf, java);
        }
        if (gff != null) {
            HalvadeConf.setGff(hConf, gff);
        }

        if (stand_call_conf > 0) {
            HalvadeConf.setSCC(hConf, stand_call_conf);
        }
        if (stand_emit_conf > 0) {
            HalvadeConf.setSEC(hConf, stand_emit_conf);
        }

    } catch (ParseException e) {
        Logger.DEBUG(e.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(80);
        formatter.printHelp(
                "hadoop jar HalvadeWithLibs.jar -I <input> -O <output> "
                        + "-R <ref> -D <dbsnp> -B <bin> -nodes <nodes> -mem <mem> -vcores <cores> [options]",
                options);
        return 1;
    }
    return 0;
}

From source file:eu.stratosphere.client.CliFrontend.java

/**
 * Prints the help for the client./*from  w w  w  .j  av  a  2s .co  m*/
 * 
 * @param options A map with options for actions. 
 */
private void printHelp() {
    System.out.println("./stratosphere <ACTION> [GENERAL_OPTIONS] [ARGUMENTS]");

    HelpFormatter formatter = new HelpFormatter();
    formatter.setWidth(80);
    formatter.setLeftPadding(5);
    formatter.setSyntaxPrefix("  general options:");
    formatter.printHelp(" ", GENRAL_OPTIONS);

    printHelpForRun();
    printHelpForInfo();
    printHelpForList();
    printHelpForCancel();
}

From source file:cycronix.udp2ct.UDP2CT.java

public UDP2CT(String[] arg) {

    int defaultPort = 4445;
    double defaultDT = 0.0;

    // For communicating with UDP server; we send a "keep alive" heartbeat message to this server
    // and will receive UDP packets from this server
    DatagramSocket clientSocket = null; // This socket will be shared by UDPread and UDPHeartbeatTask classes
    InetAddress udpserverIP = null;
    int udpserverPort = -1;
    int heartbeatPeriod_msec = -1;

    // Concatenate all of the CTWriteMode types
    String possibleWriteModes = "";
    for (CTWriteMode wm : CTWriteMode.values()) {
        possibleWriteModes = possibleWriteModes + ", " + wm.name();
    }/*from w ww  . j  av  a 2s  .  c o m*/
    // Remove ", " from start of string
    possibleWriteModes = possibleWriteModes.substring(2);

    //
    // Argument processing using Apache Commons CLI
    //
    // 1. Setup command line options
    Options options = new Options();
    options.addOption("h", "help", false, "Print this message.");
    options.addOption(Option.builder("o").argName("base output dir").hasArg().desc(
            "Base output directory when writing data to local folder (i.e., CTdata location); default = \""
                    + outLoc + "\".")
            .build());
    options.addOption(Option.builder("session").argName("session name").hasArg()
            .desc("Optional session name; if specified, this name is prefixed to the source path.").build());
    options.addOption(Option.builder("source").argName("CT source name").hasArg().desc(
            "This field doubles as the CloudTurbine source name and the CT/Unity player ID; if not specified, defaults to the model color.")
            .build());
    options.addOption(Option.builder("m").argName("multicast address").hasArg()
            .desc("Multicast UDP address (224.0.0.1 to 239.255.255.255).").build());
    options.addOption(Option.builder("p").argName("UDP port").hasArg()
            .desc("Port number to listen for UDP packets on; default = " + Integer.toString(defaultPort) + ".")
            .build());
    options.addOption(Option.builder("d").argName("delta-Time").hasArg()
            .desc("Fixed delta-time (msec) between frames; specify 0 to use arrival-times; default = "
                    + Double.toString(defaultDT) + ".")
            .build());
    options.addOption(Option.builder("f").argName("autoFlush").hasArg().desc(
            "Flush interval (sec); amount of data per zipfile; default = " + Double.toString(autoFlush) + ".")
            .build());
    options.addOption(Option.builder("t").argName("trim-Time").hasArg().desc(
            "Trim (ring-buffer loop) time (sec); this is only used when writing data to local folder; specify 0 for indefinite; default = "
                    + Double.toString(trimTime) + ".")
            .build());
    options.addOption(Option.builder("udpserver").argName("IP,port,period_msec").hasArg().desc(
            "Talk to a UDP server; send a periodic keep-alive message to the given IP:port at the specified period and receive packets from this server; not to be used with the \"-p\" option.")
            .build());
    options.addOption(Option.builder("bps").argName("blocks per seg").hasArg()
            .desc("Number of blocks per segment; specify 0 for no segments; default = "
                    + Long.toString(blocksPerSegment) + ".")
            .build());
    options.addOption(Option.builder("mc").argName("model color").hasArg().desc(
            "Color of the Unity model; must be one of: Red, Blue, Green, Yellow; default = " + modelColor + ".")
            .build());
    options.addOption(Option.builder("mt").argName("model type").hasArg().desc(
            "Type of the Unity model; must be one of: Primplane, Ball, Biplane; default = " + modelType + ".")
            .build());
    options.addOption(
            Option.builder("w").argName("write mode").hasArg().desc("Type of CT write connection; one of "
                    + possibleWriteModes + "; default = " + writeMode.name() + ".").build());
    options.addOption(Option.builder("host").argName("host[:port]").hasArg()
            .desc("Host:port when writing to CT via FTP, HTTP, HTTPS.").build());
    options.addOption(Option.builder("u").argName("username,password").hasArg()
            .desc("Comma-delimited username and password when writing to CT via FTP or HTTPS.").build());
    options.addOption("xpack", false,
            "Don't pack blocks of data in the Sensors output source; the default (without this command line flag) is to pack this source.");
    options.addOption("xs", "no_sensors_out", false,
            "Don't save UDP packet details to the \"Sensors\" source.");
    options.addOption("xu", "udp_debug", false, "Enable UDP packet parsing debug output.");
    options.addOption("x", "debug", false, "Enable CloudTurbine debug output.");

    // 2. Parse command line options
    CommandLineParser parser = new DefaultParser();
    CommandLine line = null;
    try {
        line = parser.parse(options, arg);
    } catch (ParseException exp) { // oops, something went wrong
        System.err.println("Command line argument parsing failed: " + exp.getMessage());
        return;
    }

    // 3. Retrieve the command line values
    if (line.hasOption("help")) { // Display help message and quit
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp("UDP2CT", options);
        return;
    }

    outLoc = line.getOptionValue("o", outLoc);
    if (!outLoc.endsWith("\\") && !outLoc.endsWith("/")) {
        outLoc = outLoc + File.separator;
    }
    // Make sure the base output folder location ends in "CTdata"
    if (!outLoc.endsWith("CTdata\\") && !outLoc.endsWith("CTdata/")) {
        outLoc = outLoc + "CTdata" + File.separator;
    }

    sessionName = line.getOptionValue("session", sessionName);
    if (!sessionName.isEmpty()) {
        if (!sessionName.endsWith("\\") && !sessionName.endsWith("/")) {
            sessionName = sessionName + File.separator;
        }
    }

    multiCast = line.getOptionValue("m", multiCast);

    String portStr = line.getOptionValue("p", Integer.toString(defaultPort));
    int portNum = Integer.parseInt(portStr);

    String sdt = line.getOptionValue("d", Double.toString(defaultDT));
    double dt = Double.parseDouble(sdt);

    autoFlush = Double.parseDouble(line.getOptionValue("f", "" + autoFlush));

    trimTime = Double.parseDouble(line.getOptionValue("t", Double.toString(trimTime)));

    blocksPerSegment = Long.parseLong(line.getOptionValue("bps", Long.toString(blocksPerSegment)));

    packMode = !line.hasOption("xpack");

    bSavePacketDataToCT = !line.hasOption("no_sensors_out");

    udp_debug = line.hasOption("udp_debug");

    debug = line.hasOption("debug");

    // Type of output connection
    String writeModeStr = line.getOptionValue("w", writeMode.name());
    boolean bMatch = false;
    for (CTWriteMode wm : CTWriteMode.values()) {
        if (wm.name().toLowerCase().equals(writeModeStr.toLowerCase())) {
            writeMode = wm;
            bMatch = true;
        }
    }
    if (!bMatch) {
        System.err.println("Unrecognized write mode, \"" + writeModeStr + "\"; write mode must be one of "
                + possibleWriteModes);
        System.exit(0);
    }

    if (writeMode != CTWriteMode.LOCAL) {
        // User must have specified the host
        // If FTP or HTTPS, they may also specify username/password
        serverHost = line.getOptionValue("host", serverHost);
        if (serverHost.isEmpty()) {
            System.err.println(
                    "When using write mode \"" + writeModeStr + "\", you must specify the server host.");
            System.exit(0);
        }
        if ((writeMode == CTWriteMode.FTP) || (writeMode == CTWriteMode.HTTPS)) {
            String userpassStr = line.getOptionValue("u", "");
            if (!userpassStr.isEmpty()) {
                // This string should be comma-delimited username and password
                String[] userpassCSV = userpassStr.split(",");
                if (userpassCSV.length != 2) {
                    System.err.println("When specifying a username and password for write mode \""
                            + writeModeStr + "\", separate the username and password by a comma.");
                    System.exit(0);
                }
                serverUser = userpassCSV[0];
                serverPassword = userpassCSV[1];
            }
        }
    }

    // Parameters when talking to a UDP server
    // Can't specify both "-p" and "-udpserver"
    if (line.hasOption("p") && line.hasOption("udpserver")) {
        System.err.println(
                "Specify either \"-p\" (to listen on the given port(s)) or \"-udpserver\" (to talk to UDP server), not both.");
        System.exit(0);
    }
    if (line.hasOption("udpserver")) {
        String udpserverStr = line.getOptionValue("udpserver");
        // Parse the server,port,period_msec from this string
        String[] udpserverConfigCSV = udpserverStr.split(",");
        if (udpserverConfigCSV.length != 3) {
            System.err.println(
                    "Error: the \"-udpserver\" argument must contain 3 parameters: IP,port,period_msec");
            System.exit(0);
        }
        try {
            udpserverIP = InetAddress.getByName(udpserverConfigCSV[0]);
        } catch (UnknownHostException e) {
            System.err.println("Error processing the \"-udpserver\" server name:\n" + e);
            System.exit(0);
        }
        try {
            udpserverPort = Integer.parseInt(udpserverConfigCSV[1]);
            if (udpserverPort <= 0) {
                throw new Exception("Invalid port number");
            }
        } catch (Exception e) {
            System.err.println("Error: the \"-udpserver\" port must be an integer greater than 0.");
            System.exit(0);
        }
        try {
            heartbeatPeriod_msec = Integer.parseInt(udpserverConfigCSV[2]);
            if (heartbeatPeriod_msec <= 0) {
                throw new Exception("Invalid period");
            }
        } catch (Exception e) {
            System.err.println("Error: the \"-udpserver\" period_msec must be an integer greater than 0.");
            System.exit(0);
        }
        // Initialize communication with the UDP server
        try {
            // This DatagramSocket will be shared by UDPread and UDPHeartbeatTask classes
            clientSocket = new DatagramSocket();
        } catch (SocketException e) {
            System.err.println("Error creating DatagramSocket:\n" + e);
            System.exit(0);
        }
        Timer time = new Timer();
        UDPHeartbeatTask heartbeatTask = new UDPHeartbeatTask(clientSocket, udpserverIP, udpserverPort);
        time.schedule(heartbeatTask, 0, heartbeatPeriod_msec);
    }

    // CT/Unity model parameters
    String modelColorRequest = line.getOptionValue("mc", modelColor);
    modelColor = "";
    for (ModelColor mc : ModelColor.values()) {
        if (mc.name().toLowerCase().equals(modelColorRequest.toLowerCase())) {
            modelColor = mc.name();
        }
    }
    if (modelColor.isEmpty()) {
        System.err.println(
                "Unrecognized model color, \"" + modelColorRequest + "\"; model color must be one of:");
        for (ModelColor mc : ModelColor.values()) {
            System.err.println("\t" + mc.name());
        }
        System.exit(0);
    }
    String modelTypeRequest = line.getOptionValue("mt", modelType);
    modelType = "";
    for (ModelType mt : ModelType.values()) {
        if (mt.name().toLowerCase().equals(modelTypeRequest.toLowerCase())) {
            modelType = mt.name();
        }
    }
    if (modelType.isEmpty()) {
        System.err.println("Unrecognized model type, \"" + modelTypeRequest + "\"; model type must be one of:");
        for (ModelType mt : ModelType.values()) {
            System.err.println("\t" + mt.name());
        }
        System.exit(0);
    }

    // Set playerName (source name)
    // Need to set this after setting model color, becasue if the user hasn't
    // set the source name then we default to what they specified for modelColor.
    playerName = line.getOptionValue("source", modelColor);

    //
    // setup 2 instances of CTwriter:
    // 1. ctgamew:   this source will only contain the "CTstates.json" output channel, used by
    //               the CT/Unity game; since this source is a text channel, we don't want this source to be packed
    // 2. ctsensorw: output source for data unpacked from the captured UDP packetes; it is up to the parser class
    //               being employed as to what channels are written to this source
    //
    autoFlushMillis = (long) (autoFlush * 1000.);
    System.err.println("Model: " + modelType);
    // If sessionName isn't blank, it will end in a file separator
    String srcName = sessionName + "GamePlay" + File.separator + playerName;
    System.err.println("Game source: " + srcName);
    // NB, 2018-09-27: force bPack false for the GamePlay source;
    //                 this source will only contain a String channel,
    //                 and as of right now CT *will* pack String
    //                 channels (but we don't want this channel packed)
    ctgamew = createCTwriter(srcName, false);
    if (!bSavePacketDataToCT) {
        System.err.println("Sensor data will not be written out");
    } else {
        // If sessionName isn't blank, it will end in a file separator
        srcName = sessionName + "Sensors" + File.separator + playerName;
        System.err.println("Sensor data source: " + srcName);
        ctsensorw = createCTwriter(srcName, packMode);
    }

    //
    // Start UDPread
    //
    if (clientSocket != null) {
        System.err.println("Talk to UDP server at " + udpserverIP + ":" + udpserverPort);
        new UDPread(this, clientSocket, dt).start();
    } else {
        System.err.println("Capture UDP packets on port: " + portNum);
        new UDPread(this, portNum, dt).start();
    }
}

From source file:eu.stratosphere.client.CliFrontend.java

private void printHelpForInfo() {
    HelpFormatter formatter = new HelpFormatter();
    formatter.setLeftPadding(5);//w  w  w  . ja  v  a 2 s.  c  o  m
    formatter.setWidth(80);

    System.out.println("\nAction \"info\" displays information about a program.");
    formatter.setSyntaxPrefix("  \"info\" action arguments:");
    formatter.printHelp(" ", getInfoOptionsWithoutDeprecatedOptions(new Options()));
}