Example usage for org.apache.commons.cli ParseException ParseException

Introduction

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

Prototype

public ParseException(String message) 

Source Link

Document

Construct a new ParseException with the specified detail message.

Usage

From source file:lcmc.LCMC.java

/** Parse cluster options and create cluster button. */
private static void parseClusterOptions(final CommandLine cmd) throws ParseException {
    String clusterName = null;//w w  w  .ja  v a2  s .  co  m
    List<HostOptions> hostsOptions = null;
    final Map<String, List<HostOptions>> clusters = new LinkedHashMap<String, List<HostOptions>>();
    for (final Option option : cmd.getOptions()) {
        final String op = option.getLongOpt();
        if (CLUSTER_OP.equals(op)) {
            clusterName = option.getValue();
            if (clusterName == null) {
                throw new ParseException("could not parse " + CLUSTER_OP + " option");

            }
            clusters.put(clusterName, new ArrayList<HostOptions>());
        } else if (HOST_OP.equals(op)) {
            final String[] hostNames = option.getValues();
            if (clusterName == null) {
                clusterName = "default";
                clusters.put(clusterName, new ArrayList<HostOptions>());
            }
            if (hostNames == null) {
                throw new ParseException("could not parse " + HOST_OP + " option");
            }
            hostsOptions = new ArrayList<HostOptions>();
            for (final String hostNameEntered : hostNames) {
                String hostName;
                String port = null;
                if (hostNameEntered.indexOf(':') > 0) {
                    final String[] he = hostNameEntered.split(":");
                    hostName = he[0];
                    port = he[1];
                    if ("".equals(port) || !Tools.isNumber(port)) {
                        throw new ParseException("could not parse " + HOST_OP + " option");
                    }
                } else {
                    hostName = hostNameEntered;
                }
                final HostOptions ho = new HostOptions(hostName);
                if (port != null) {
                    ho.setPort(port);
                }
                hostsOptions.add(ho);
                clusters.get(clusterName).add(ho);
            }
        } else if (SUDO_OP.equals(op)) {
            if (hostsOptions == null) {
                throw new ParseException(SUDO_OP + " must be defined after " + HOST_OP);
            }
            for (final HostOptions ho : hostsOptions) {
                ho.setSudo(true);
            }
        } else if (USER_OP.equals(op)) {
            if (hostsOptions == null) {
                throw new ParseException(USER_OP + " must be defined after " + HOST_OP);
            }
            final String userName = option.getValue();
            if (userName == null) {
                throw new ParseException("could not parse " + USER_OP + " option");
            }
            for (final HostOptions ho : hostsOptions) {
                ho.setUser(userName);
            }
        } else if (PORT_OP.equals(op)) {
            if (hostsOptions == null) {
                throw new ParseException(PORT_OP + " must be defined after " + HOST_OP);
            }
            final String port = option.getValue();
            if (port == null) {
                throw new ParseException("could not parse " + PORT_OP + " option");
            }
            for (final HostOptions ho : hostsOptions) {
                ho.setPort(port);
            }
        }
    }
    for (final String cn : clusters.keySet()) {
        for (final HostOptions hostOptions : clusters.get(cn)) {
            if (hostsOptions.size() < 1
                    || (hostsOptions.size() == 1 && !Tools.getConfigData().isOneHostCluster())) {
                throw new ParseException("not enough hosts for cluster: " + cn);
            }
        }
    }
    final String failedHost = Tools.setUserConfigFromOptions(clusters);
    if (failedHost != null) {
        Tools.appWarning("could not resolve host \"" + failedHost + "\" skipping");
    }
}

---

From source file:bdsup2sub.cli.CommandLineParser.java

private void parsePaletteFileOption(CommandLine line) throws ParseException {
    if (line.hasOption(PALETTE_FILE)) { //TODO: only sub/idx
        String value = line.getOptionValue(PALETTE_FILE);
        paletteFile = new File(value);
        if (!paletteFile.exists()) {
            throw new ParseException("Palette file not found: " + value);
        } else {/* www . ja v  a  2 s. c  o  m*/
            if (!Arrays.equals("#COL".getBytes(), ToolBox.getFileID(value, 4))) {
                throw new ParseException("Invalid palette file: " + value);
            }
        }
    }
}

---

From source file:edu.uci.ics.asterix.aoya.AsterixYARNClient.java

/**
 * Cursory sanity checks for argument sanity, without considering the mode of the client
 * // ww  w. ja va 2  s .c  om
 * @param args
 * @param cliParser
 *            The parsed arguments.
 * @throws ParseException
 */
private void checkConfSanity(String[] args, CommandLine cliParser) throws ParseException {
    String message = null;

    //Sanity check for no args 
    if (args.length == 0) {
        message = "No args specified for client to initialize";
    }
    //AM memory should be a sane value
    else if (amMemory < 0) {
        message = "Invalid memory specified for application master, exiting." + " Specified memory=" + amMemory;
    }
    //we're good!
    else {
        return;
    }
    //default:
    throw new ParseException(message);

}

---

From source file:edu.uci.ics.asterix.aoya.AsterixYARNClient.java

/**
 * Initialize the mode of the client from the arguments.
 * //from ww  w . j ava 2s .c om
 * @param args
 * @param cliParser
 * @throws ParseException
 */
private void initMode(String[] args, CommandLine cliParser) throws ParseException {
    @SuppressWarnings("unchecked")
    List<String> clientVerb = cliParser.getArgList();
    String message = null;
    //Now check if there is a mode
    if (clientVerb == null || clientVerb.size() < 1) {
        message = "You must specify an action.";
    }
    //But there can only be one mode...
    else if (clientVerb.size() > 1) {
        message = "Trailing arguments, or too many arguments. Only one action may be performed at a time.";
    }
    if (message != null) {
        throw new ParseException(message);
    }
    //Now we can initialize the mode and check it against parameters
    mode = Mode.fromAlias(clientVerb.get(0));
    if (mode == null) {
        mode = Mode.NOOP;
    }
}

---

From source file:com.bigdata.dastor.tools.DastorAdminCli.java

public static DastorAdminCli initCli(String[] args, ArrayList<String> cmdArgList)
        throws IOException, InterruptedException, ParseException {
    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;//from   w  w w  .ja va2 s  .co  m

    try {
        cmd = parser.parse(options, args);
    } catch (ParseException parseExcep) {
        System.err.println(parseExcep);
        printUsage();
        System.exit(1);
    }

    String host = cmd.getOptionValue(HOST_OPT_LONG);
    int port = defaultPort;

    String portNum = cmd.getOptionValue(PORT_OPT_LONG);
    if (portNum != null) {
        try {
            port = Integer.parseInt(portNum);
        } catch (NumberFormatException e) {
            throw new ParseException("Port must be a number");
        }
    }

    NodeProbe probe = null;
    try {
        probe = new NodeProbe(host, port);
    } catch (IOException ioe) {
        System.err.println("Error connecting to remote JMX agent!");
        ioe.printStackTrace();
        System.exit(3);
    }
    System.out.println("connected to " + host + ":" + port);

    for (String arg : cmd.getArgs()) {
        cmdArgList.add(arg);
    }

    return new DastorAdminCli(probe, host, port);
}

---

From source file:edu.upenn.ircs.lignos.morsel.MorphLearner.java

/**
 * Call the learner on the specified arguments. Exit using standard error codes
 * (sysexits.h) if an error is encountered.
 * @param args command line arguments//  w w  w . j  av  a  2s. c o  m
 */
public static void main(String[] args) {
    // create the command line parser
    CommandLineParser parser = new PosixParser();
    // Set up command line arguments
    Options options = new Options();
    options.addOption(new Option("h", "help", false, "dislay this help and exit"));
    Option encodingOption = new Option("e", "encoding", true,
            "input and output file encoding. Defaults to ISO8859_1.");
    encodingOption.setArgName("encoding");
    options.addOption(encodingOption);
    options.addOption(new Option("b", "base-inf", false,
            "output the examples of base inference. This does not change whether base inference"
                    + " is used; it simply outputs the examples that used it."));
    options.addOption(new Option("s", "conflation-sets", false, "output the learner's conflation sets"));
    options.addOption(new Option("c", "compounds", false,
            "output the learner's analsyis before final compounding is used"));
    HelpFormatter formatter = new HelpFormatter();
    String usage = "MorphLearner [options] wordlist outfile logfile paramfile";

    CommandLine line = null;
    String[] otherArgs = null;
    try {
        // Parse the command line arguments
        line = parser.parse(options, args);
        otherArgs = line.getArgs();

        // Handle help
        if (line.hasOption("help")) {
            formatter.printHelp(usage, options);
            System.exit(0);
        }

        if (otherArgs.length != 4) {
            throw new ParseException("Incorrect number of required arguments specified");
        }
    } catch (ParseException exp) {
        System.out.println(exp.getMessage());
        formatter.printHelp(usage, options);
        System.exit(64);
    }

    // Get options
    String encoding = line.getOptionValue("encoding", "ISO8859_1");
    boolean outputBaseInf = line.hasOption("base-inf");
    boolean outputConflation = line.hasOption("conflation-sets");
    boolean outputCompounds = line.hasOption("compounds");

    // Setup timing
    long start;
    float elapsedSeconds;
    start = System.currentTimeMillis();

    // Initialize the learner
    MorphLearner learner = null;
    try {
        learner = new MorphLearner(otherArgs[0], otherArgs[1], otherArgs[2], otherArgs[3], encoding,
                outputBaseInf, outputConflation, outputCompounds);
    } catch (FileNotFoundException e) {
        System.err.println(e.getMessage());
        System.exit(66);
    } catch (UnsupportedEncodingException e) {
        System.err.println("Unsupported file encoding: " + encoding);
        System.exit(74);
    }

    // Output time stats
    elapsedSeconds = (System.currentTimeMillis() - start) / 1000F;
    System.out.println("Init time: " + elapsedSeconds + "s\n");

    // Time learning
    start = System.currentTimeMillis();

    learner.learn();
    learner.cleanUp();

    // Output time stats
    elapsedSeconds = (System.currentTimeMillis() - start) / 1000F;
    System.out.println("\nLearning time: " + elapsedSeconds + "s");
}

---

From source file:edu.uci.ics.asterix.aoya.AsterixYARNClient.java

/**
 * Determine if the command line arguments are sufficient for the requested client mode.
 * /*from w  ww . j a  va2  s . c om*/
 * @param args
 *            The command line arguments.
 * @param cliParser
 *            Parsed command line arguments.
 * @throws ParseException
 */

private void checkModeSanity(String[] args, CommandLine cliParser) throws ParseException {

    String message = null;
    //The only time you can use the client without specifiying an instance, is to list all of the instances it sees.
    if (!cliParser.hasOption("name") && mode != Mode.DESCRIBE) {
        message = "You must give a name for the instance to be acted upon";
    } else if (mode == Mode.INSTALL && !cliParser.hasOption("asterixConf")) {
        message = "No Configuration XML given. Please specify a config for cluster installation";
    } else if (mode != Mode.START && cliParser.hasOption("refresh")) {
        message = "Cannot specify refresh in any mode besides start, mode is: " + mode;
    } else if (cliParser.hasOption("snapshot") && !(mode == Mode.RESTORE || mode == Mode.RMBACKUP)) {
        message = "Cannot specify a snapshot to restore in any mode besides restore or rmbackup, mode is: "
                + mode;
    } else if ((mode == Mode.ALTER || mode == Mode.INSTALL) && baseConfig == null
            && !(new File(DEFAULT_PARAMETERS_PATH).exists())) {
        message = "Default asterix parameters file is not in the default location, and no custom location is specified";
    }
    //nothing is wrong, so exit
    else {
        return;
    }
    //otherwise, something is bad.
    throw new ParseException(message);

}

---

From source file:com.archivas.clienttools.arcmover.cli.ManagedCLIJob.java

protected boolean handleRerunAndResume(CommandLine cmdLine, LoadSchedule schedule) throws ParseException {
    boolean result = false;

    String whichCmd = null;//from  w  w w .j a  va  2 s .c  om
    if (cmdLine.hasOption(RERUN) && cmdLine.hasOption(RESUME)) {
        throw new ParseException(
                "Cannot use both --resume and --rerun.  Please use just one.  Consult your manual if you have questions.");
    } else if (cmdLine.hasOption(RERUN)) {
        whichCmd = RERUN;
    } else if (cmdLine.hasOption(RESUME)) {
        whichCmd = RESUME;
    }

    if (whichCmd != null) {
        try {
            managedJobImpl = getManagedJobImplFromCmdLine(cmdLine, whichCmd);

            // Error Handling
            // Rerun only works on not completed jobs
            // Resume only works on completed jobs that have no failed objects
            if (whichCmd.equals(RERUN)) {
                if (managedJobImpl.getStatus() != JobStatus.COMPLETED) {
                    throw new ParseException(
                            "The job with this job name: \"" + managedJobImpl.getJob().getJobName()
                                    + "\" has not completed.  Please run this job using --resume.");
                }

                if (managedJobImpl.getFailedObjectCount() == 0) {
                    throw new ParseException(
                            "The job with this job name: \"" + managedJobImpl.getJob().getJobName()
                                    + "\" has already run to completion and has no failed files.");
                }
            } else if (whichCmd.equals(RESUME)) {
                if (managedJobImpl.getStatus() == JobStatus.COMPLETED) {
                    throw new ParseException("The job with this job name: \""
                            + managedJobImpl.getJob().getJobName()
                            + "\" has already run to completion.  Please run that job with --rerun if there were failed files.");
                }
            }

            managedJob = managedJobImpl.getJob();
            if (cmdLine.hasOption(RERUN) || cmdLine.hasOption(RESUME)) {
                LoadSchedule RerunResumeSchedule = managedJob.getLoadSchedule();
                getLoadSchedule(cmdLine, RerunResumeSchedule);
                managedJob.setLoadSchedule(RerunResumeSchedule);
            } else {
                managedJob.setLoadSchedule(schedule);
            }

            // Flush the stats
            arcMover.getManagedJobDetails(managedJobImpl, true);

            result = true;
        } catch (JobNotFoundException e) {
            throw new ParseException(
                    "JobNotFoundException which trying to " + whichCmd + " a job.  Msg: " + e.getMessage());
        } catch (DatabaseException e) {
            throw new ParseException(
                    "DatabaseException trying to get job to " + whichCmd + " a job.  Msg: " + e.getMessage());
        } catch (JobException e) {
            throw new ParseException(
                    "JobException trying to initialize job to " + whichCmd + " .  Msg: " + e.getMessage());
        }
    }
    return result;
}

---

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

protected boolean parseArguments(String[] args, Configuration halvadeConf) throws ParseException {
    createOptions();//from   ww w  .  ja  v a  2 s . c  o m
    CommandLineParser parser = new GnuParser();
    CommandLine line = parser.parse(options, args);

    in = line.getOptionValue("I");
    out = line.getOptionValue("O");
    if (!out.endsWith("/"))
        out += "/";
    ref = line.getOptionValue("R");
    sites = line.getOptionValue("D");
    halvadeBinaries = line.getOptionValue("B");
    hdfsSites = sites.split(",");
    if (line.hasOption("bam")) {
        useBamInput = true;
    }
    if (line.hasOption("rna")) {
        rnaPipeline = true;
        if (line.hasOption("star"))
            STARGenome = line.getOptionValue("star");
        if (!useBamInput && STARGenome == null) {
            throw new ParseException(
                    "the '-rna' option requires --star pointing to the location of the STAR reference directory if alignment with STAR aligner is required (fastq).");
        }
    }

    if (line.hasOption("tmp")) {
        tmpDir = line.getOptionValue("tmp");
    }
    if (line.hasOption("stargtf")) {
        stargtf = line.getOptionValue("stargtf");
    }
    if (line.hasOption("refdir")) {
        localRefDir = line.getOptionValue("refdir");
        if (!localRefDir.endsWith("/"))
            localRefDir += "/";
    }
    if (line.hasOption("nodes")) {
        nodes = Integer.parseInt(line.getOptionValue("nodes"));
    }
    if (line.hasOption("vcores")) {
        vcores = Integer.parseInt(line.getOptionValue("vcores"));
    }
    if (line.hasOption("smt")) {
        smtEnabled = true;
    }
    if (line.hasOption("remove_dups")) {
        keepDups = false;
    }
    if (line.hasOption("mem")) {
        mem = Double.parseDouble(line.getOptionValue("mem"));
    }
    if (line.hasOption("rpr")) {
        readCountsPerRegionFile = line.getOptionValue("rpr");
    }
    if (line.hasOption("mpn")) {
        setMapContainers = false;
        mapContainersPerNode = Integer.parseInt(line.getOptionValue("mpn"));
    }
    if (line.hasOption("rpn")) {
        setReduceContainers = false;
        reducerContainersPerNode = Integer.parseInt(line.getOptionValue("rpn"));
    }
    if (line.hasOption("mapmem")) {
        overrideMapMem = (int) (Double.parseDouble(line.getOptionValue("mapmem")) * 1024);
    }
    if (line.hasOption("redmem")) {
        overrideRedMem = (int) (Double.parseDouble(line.getOptionValue("redmem")) * 1024);
    }
    if (line.hasOption("scc")) {
        stand_call_conf = Integer.parseInt(line.getOptionValue("scc"));
    }
    if (line.hasOption("sec")) {
        stand_emit_conf = Integer.parseInt(line.getOptionValue("sec"));
    }
    if (line.hasOption("count")) {
        countOnly = true;
    }
    if (line.hasOption("report_all")) {
        reportAll = true;
    }
    if (line.hasOption("illumina")) {
        fixQualEnc = true;
    }
    if (line.hasOption("keep")) {
        keepFiles = true;
    }
    if (line.hasOption("update_rg")) {
        updateRG = true;
    }
    if (line.hasOption("redistribute")) {
        redistribute = true;
    }
    if (line.hasOption("single")) {
        paired = false;
    }
    if (line.hasOption("justalign")) {
        justAlign = true;
        combineVcf = false;
    }
    if (line.hasOption("aln")) {
        aln = Integer.parseInt(line.getOptionValue("aln"));
        if (aln < 0 || aln > 3)
            aln = 0; // default value
    }
    if (line.hasOption("J")) {
        java = line.getOptionValue("J");
    }
    if (line.hasOption("gff")) {
        gff = line.getOptionValue("gff");
    }
    if (line.hasOption("dryrun")) {
        dryRun = true;
        combineVcf = false;
    }
    if (line.hasOption("drop")) {
        keepChrSplitPairs = false;
    }
    //        if (line.hasOption("cov")) {
    //            coverage = Double.parseDouble(line.getOptionValue("cov"));
    //        }
    if (line.hasOption("merge_bam")) {
        mergeBam = true;
    }
    if (line.hasOption("c")) {
        justCombine = true;
        combineVcf = true;
    }
    if (line.hasOption("filter_dbsnp")) {
        filterDBSnp = true;
    }
    if (line.hasOption("reorder_regions")) {
        reorderRegions = true;
    }
    if (line.hasOption("haplotypecaller")) {
        useGenotyper = false;
    }
    if (line.hasOption("elprep")) {
        useElPrep = true;
    }
    if (line.hasOption("id")) {
        RGID = line.getOptionValue("id");
    }
    if (line.hasOption("lb")) {
        RGLB = line.getOptionValue("lb");
    }
    if (line.hasOption("pl")) {
        RGPL = line.getOptionValue("pl");
    }
    if (line.hasOption("pu")) {
        RGPU = line.getOptionValue("pu");
    }
    if (line.hasOption("sm")) {
        RGSM = line.getOptionValue("sm");
    }
    if (line.hasOption("bed")) {
        bedFile = line.getOptionValue("bed");
    }
    if (line.hasOption("fbed")) {
        filterBed = line.getOptionValue("fbed");
    }
    if (line.hasOption("v")) {
        Logger.SETLEVEL(Integer.parseInt(line.getOptionValue("v")));
    }

    if (line.hasOption("CA")) {
        Properties props = line.getOptionProperties("CA");
        Enumeration names = props.propertyNames();
        while (names.hasMoreElements()) {
            String name = (String) names.nextElement();
            addCustomArguments(halvadeConf, name, props.getProperty(name));
        }
    }
    return true;
}

---

From source file:com.archivas.clienttools.arcmover.cli.ArcCopy.java

private String validateTargetPath(CommandLine cmdLine) throws ParseException {
    if (!cmdLine.hasOption(DESTINATION_PATH_OPTION)) {
        throw new ParseException("Missing Option: " + DESTINATION_PATH_OPTION);
    }/*w w  w.j a v a  2 s  .  co m*/

    String value = cmdLine.getOptionValue(DESTINATION_PATH_OPTION);
    String retval = null;

    if (value != null) {
        retval = value;
    }
    if (retval == null) {
        throw new ParseException("Invalid " + DESTINATION_PATH_OPTION + " : " + value);
    }
    return retval;
}

---

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