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

List of usage examples for org.apache.commons.cli ParseException ParseException

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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:com.archivas.clienttools.arcmover.cli.ManagedCLIJob.java

private ManagedJobImpl getManagedJobImplFromCmdLine(CommandLine cmdLine, String whichCmd)
        throws ParseException, DatabaseException, JobException {
    JobId reRunJobID = null;//  w  ww.ja va2  s  .co m
    String jobName = cmdLine.getOptionValue(whichCmd);

    // If no option was provided get the last job run
    if (jobName == null) {
        // Get the last jobID
        try {
            reRunJobID = getLastJobID();
        } catch (NumberFormatException e) {
            throw new ParseException(
                    "Last job not found.  Either no jobs have been run or the job was deleted.");
        }

        if (reRunJobID == null) {
            throw new ParseException("Error determining the last job run.");
        }
    } else {
        List<ManagedJobSummary> jobList = arcMover.getAllManagedJobs();

        for (ManagedJobSummary job : jobList) {
            if (job.getJobName().equals(jobName)) {
                if (!job.getJobType().equals(getJobType())) {
                    throw new ParseException(
                            "Job name: " + jobName + " provided is not of type " + getJobType().getUiName());
                }
                reRunJobID = job.getJobId();
                break;
            }
        }
        if (reRunJobID == null) {
            throw new ParseException("Job name not found in job list.");
        }
    }
    return arcMover.loadManagedJob(reRunJobID, getJobType());
}

From source file:gov.nih.nci.ncicb.tcga.dcc.QCLiveTestDataGenerator.java

/**
 * Main entry point for the application. Configures the Spring context and calls the {@link QCLiveTestDataGenerator}
 * bean to load and generate test data for a specific archive name.
 * //from w w w .ja  v  a 2  s.  co m
 * @param args - list of arguments to be passed to the {@link QCLiveTestDataGenerator} bean
 */
public static void main(final String[] args) {

    // Display help if no arguments are provided, otherwise parse the arguments
    if (args.length == 0)
        displayHelp();
    else {
        try {
            // Parse the command line arguments 
            final CommandLine commandLine = new GnuParser().parse(CommandLineOptionType.getOptions(), args);

            // If the command line instance contains the -? (--help) option display help, otherwise call the QCLiveTestDataGenerator
            // to process the command line arguments
            if (commandLine.hasOption(CommandLineOptionType.HELP.name().toLowerCase())) {
                displayHelp();
            } else {
                final String archiveNameOption = CommandLineOptionType.ARCHIVE_NAME.getOptionValue().getOpt();
                final String sqlScriptFileOption = CommandLineOptionType.SQL_SCRIPT_FILE.getOptionValue()
                        .getOpt();
                final String schemaOption = CommandLineOptionType.SCHEMA.getOptionValue().getOpt();

                // Initialize the Spring context
                final ApplicationContext appCtx = new ClassPathXmlApplicationContext(APP_CONTEXT_FILE_NAME);

                // Retrieve the QCLiveTestDataGenerator from the Spring context
                final QCLiveTestDataGenerator qcLiveTestDataGenerator = (QCLiveTestDataGenerator) appCtx
                        .getBean("qcLiveTestDataGenerator");

                // Get the archive name from the command line argument(s) (if provided) and generate the test data
                if (commandLine.hasOption(archiveNameOption)) {
                    qcLiveTestDataGenerator.generateTestData(commandLine.getOptionValue(archiveNameOption));
                }

                // If the SQL script file and schema options are provided, execute the script
                if (commandLine.hasOption(sqlScriptFileOption)) {
                    if (commandLine.hasOption(schemaOption)) {
                        // Try to resolve the schema type from the provided schema name. If it cannot be resolved, throw an exception that
                        // indicates the supported schema types
                        final String schemaOptionValue = commandLine.getOptionValue(schemaOption);
                        SchemaType schemaTpye = null;
                        try {
                            schemaTpye = SchemaType.valueOf(schemaOptionValue.toUpperCase());
                        } catch (IllegalArgumentException iae) {
                            throw new ParseException("Could not resolve schema name '" + schemaOptionValue
                                    + "' to a supported schema type "
                                    + "when attempting to execute SQL script file '"
                                    + commandLine.getOptionValue(sqlScriptFileOption) + "'. "
                                    + "Supported types are '" + SchemaType.getSupportedSchemaTypes() + "'");
                        }

                        qcLiveTestDataGenerator.executeSQLScriptFile(schemaTpye,
                                new FileSystemResource(commandLine.getOptionValue(sqlScriptFileOption)));
                    } else
                        throw new ParseException(
                                "Setting the -f (or -sql_script_file) option also requires the -s (or -schema) to be set.");
                }
            }
        } catch (ParseException pe) {
            System.err.println("\nParsing failed. Reason: " + pe.getMessage());
            displayHelp();
        } catch (IOException ioe) {
            logger.error(ioe.getMessage());
        } catch (SQLException sqle) {
            logger.error(sqle.getMessage());
        }
    }
}

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

protected void addCustomArguments(Configuration halvadeConf, String name, String property)
        throws ParseException {
    boolean found = false;
    int i = 0;/*from   w ww. java 2s  .  c  o  m*/
    while (!found && i < programNames.length) {
        if (name.equalsIgnoreCase(programNames[i])) {
            found = true;
        }
        i++;
    }
    if (found) {
        String[] split = name.split("_");
        String program = split[0];
        String tool = "";
        if (split.length > 1) {
            tool = split[1];
        }
        HalvadeConf.setCustomArgs(halvadeConf, program, tool, property);
        Logger.DEBUG("Custom arguments for " + name + ": \"" + property + "\"");
    } else {
        Logger.DEBUG("Unknown program: " + name + ", custom arguments [" + property + "] ignored");
        throw new ParseException("Program " + name + " not found, please use a valid name.");
    }
}

From source file:de.clusteval.serverclient.BackendClient.java

/**
 * This method is responsible for creating all the appender that are added
 * to the logger./* w  w  w  .ja  v  a2s . com*/
 * <p>
 * Three appenders are created:
 * <ul>
 * <li><b>ConsoleAppender</b>: Writes the logging output to the standard out
 * </li>
 * <li><b>FileAppender</b>: Writes the logging output as formatter text to
 * the file clustevalClient.log</li>
 * <li><b>FileAppender</b>: Writes the logging output in lilith binary
 * format to the file clustevalClient.lilith</li>
 * </ul>
 * 
 * @param cmd
 *            The command line parameters including possible options of
 *            logging
 * @throws ParseException
 */
private static void initLogging(CommandLine cmd) throws ParseException {
    Logger log = LoggerFactory.getLogger(BackendClient.class);

    Level logLevel;
    if (cmd.hasOption("logLevel")) {
        switch (Integer.parseInt(cmd.getOptionValue("logLevel"))) {
        case 0:
            logLevel = Level.ALL;
            break;
        case 1:
            logLevel = Level.TRACE;
            break;
        case 2:
            logLevel = Level.DEBUG;
            break;
        case 3:
            logLevel = Level.INFO;
            break;
        case 4:
            logLevel = Level.WARN;
            break;
        case 5:
            logLevel = Level.ERROR;
            break;
        case 6:
            logLevel = Level.OFF;
            break;
        default:
            throw new ParseException("The logLevel argument requires one of the value of [0,1,2,3,4,5,6]");
        }
    } else {
        logLevel = Level.INFO;
    }

    ch.qos.logback.classic.Logger logger = ((ch.qos.logback.classic.Logger) LoggerFactory
            .getLogger(Logger.ROOT_LOGGER_NAME));
    logger.setLevel(logLevel);

    // file appender for clustevalServer.log plaintext file
    FileAppender<ILoggingEvent> fileApp = new FileAppender<ILoggingEvent>();
    fileApp.setName("clientLogFile");
    String logFilePath = FileUtils.buildPath(System.getProperty("user.dir"), "clustevalClient.log");
    fileApp.setFile(logFilePath);

    fileApp.setAppend(true);
    fileApp.setContext((LoggerContext) LoggerFactory.getILoggerFactory());
    fileApp.setEncoder(new PatternLayoutEncoder());
    PatternLayout layout = new PatternLayout();
    layout.setPattern("%date{dd MMM yyyy HH:mm:ss.SSS} [%thread] %-5level %logger{35} - %msg%n");
    layout.setContext((LoggerContext) LoggerFactory.getILoggerFactory());
    layout.start();
    fileApp.setLayout(layout);
    fileApp.start();
    logger.addAppender(fileApp);

    // file appender for clustevalServer.lilith binary file
    // removed 30.01.2013
    // FileAppender fileAppLilith = new FileAppender();
    // fileAppLilith.setName("clientLogFileLilith");
    // logFilePath = FileUtils.buildPath(System.getProperty("user.dir"),
    // "clustevalClient.lilith");
    // fileAppLilith.setFile(logFilePath);
    //
    // fileAppLilith.setAppend(true);
    // fileAppLilith.setContext((LoggerContext) LoggerFactory
    // .getILoggerFactory());
    // ClassicLilithEncoder encoder = new ClassicLilithEncoder();
    // encoder.setIncludeCallerData(true);
    // fileAppLilith.setEncoder(encoder);
    //
    // fileAppLilith.start();
    // logger.addAppender(fileAppLilith);

    log.debug("Using log level " + logLevel);
}

From source file:com.symbian.driver.core.environment.TDConfig.java

/**
 * @param aKey/*from w w w .  ja v a2 s  .  c o m*/
 * @param aUri
 * @throws ParseException
 */
public void setPreferenceURI(final int aKey, URI aUri) throws ParseException {
    if (aKey != ENTRY_POINT_ADDRESS) {
        throw new ParseException("This preference " + aKey
                + " cannot use the setPreferenceURI() method. It must be of type " + URI.class);
    }

    setPreference(aKey, aUri.toString());
}

From source file:com.symbian.driver.core.environment.TDConfig.java

/**
 * @param aKey/* w  ww. j  a  v  a  2  s  .  c  o m*/
 * @return The preference as a URI.
 * @throws ParseException
 */
public URI getPreferenceURI(final int aKey) throws ParseException {
    if (aKey != ENTRY_POINT_ADDRESS) {
        throw new ParseException("This preference " + aKey
                + " cannot use the getPreferenceURI() method. It must be of type " + URI.class);
    }

    return URI.createURI(getPreference(aKey));
}

From source file:com.symbian.driver.core.environment.TDConfig.java

/**
 * @return The Test Execute (TEF) dependencies.
 * @throws ParseException//w  w w  .  j  av  a  2s .  co m
 */
public Map<String, String> getTEFOptionalDependencies() throws ParseException {

    Map<String, String> lOptionalDeps = new HashMap<String, String>();
    try {
        String[] lTefOptDepsList = TEF_DEPENDENCIES_OPT_EKA2.split(";");

        // optional dependencies is separated by ";" and each has
        // a [Filename]\t[Condition] format
        String lFileStr = null;
        String lConditionStr = null;
        for (String lTefOptDepStr : lTefOptDepsList) {
            lFileStr = lTefOptDepStr.split("\t")[0];
            lConditionStr = lTefOptDepStr.split("\t")[1];
            lOptionalDeps.put(lFileStr, lConditionStr);
        }
    } catch (Exception e) {
        throw new ParseException("Incorrect TEF optional dependencies describing format!");
    }
    return lOptionalDeps;
}

From source file:nl.knaw.huygens.timbuctoo.tools.other.SearchResultTool.java

private static Date getThreshold(String value) throws ParseException {
    Date threshold = null;//www  .ja va2 s .co  m
    if (!"all".equals(value)) {
        threshold = UTCUtils.stringToDate(value);
        if (threshold == null) {
            String message = String.format("Use ISO date format, e.g. '%s', or 'all'", UTCUtils.now());
            throw new ParseException(message);
        }
    }
    return threshold;
}

From source file:nl.systemsgenetics.cellTypeSpecificAlleleSpecificExpression.MainEntryPoint.java

public static void main(String... args) throws Exception {

    //Required Arguments
    String outputLocation = new String();

    //ASreads specific arguments
    String bamFile = new String();
    String couplingLocation = new String();
    String genotypeLocation = new String();
    String snpsLocation = new String();
    String regionLocation = new String();

    //BINOMTEST and BETABINOMTEST specific arguments
    String asFile = new String();

    //Cell type specific locations
    String phenoTypeLocation = new String();

    try {//from ww w  . jav a  2  s . com
        CommandLineParser parser = new PosixParser();
        final CommandLine commandLine = parser.parse(OPTIONS, args, true);

        try {
            //Read outputLocation

            if (commandLine.hasOption('O')) {
                outputLocation = commandLine.getOptionValue('O');
            } else {
                throw new ParseException("Required command line input: --output ");
            }

            // Optional arguments that are not passed to the Entry constructors
            // But are saved in the GlobalVariables class.

            if (commandLine.hasOption("minimum_hets")) {
                GlobalVariables.minHets = Integer.parseInt(commandLine.getOptionValue("minimum_hets"));
                //Check if this is bigger than 0, otherwise exit 
                if (GlobalVariables.minHets <= 0) {
                    throw new IllegalDataException(
                            "Minimum Number of hets cannot be smaller than one for AS testing\n" + "Exitting");
                }

            }

            if (commandLine.hasOption("minimum_reads")) {
                GlobalVariables.minReads = Integer.parseInt(commandLine.getOptionValue("minimum_reads"));
                //Check if this is bigger than 0, otherwise exit
                if (GlobalVariables.minReads <= 0) {
                    throw new IllegalDataException(
                            "Minimum Number of reads cannot be smaller than one for AS testing\n" + "Exitting");
                }
            }

            if (commandLine.hasOption('A')) {
                String programAction = commandLine.getOptionValue('A').toUpperCase();

                if (programAction.equals("ASREADS") || programAction.equals("1")) {

                    //Do the AS determination part of the program

                    //read genotype from options 
                    if (commandLine.hasOption('G')) {
                        genotypeLocation = commandLine.getOptionValue('G');
                    } else {
                        throw new ParseException(
                                "Required command line input --genotype_location when --action is ASreads");
                    }

                    //Read binomTest arguments
                    if (commandLine.hasOption('C')) {
                        couplingLocation = commandLine.getOptionValue('C');
                    } else {
                        throw new ParseException(
                                "Required command line input --coupling_file when --action is ASreads");
                    }

                    if (commandLine.hasOption('B')) {
                        bamFile = commandLine.getOptionValue('B');
                    } else {
                        throw new ParseException(
                                "Required command line input --bam_file when --action is ASreads");
                    }
                    if (commandLine.hasOption("snp_list")) {
                        snpsLocation = commandLine.getOptionValue("snp_list");
                    } else {
                        snpsLocation = "";

                    }

                    /*
                    START reading for AS reads.
                    */
                    readGenoAndAsFromIndividual(bamFile, genotypeLocation, couplingLocation, outputLocation,
                            snpsLocation);

                } else if (programAction.equals("ASEPERSNP") || programAction.equals("2")) {

                    if (commandLine.hasOption('L')) {
                        asFile = commandLine.getOptionValue('L');
                    } else {
                        throw new ParseException(
                                "Required command line input --as_location when --action is ASEperSNP");
                    }
                    if (commandLine.hasOption('P')) {
                        phenoTypeLocation = commandLine.getOptionValue('P');
                    } else {
                        phenoTypeLocation = null;
                    }

                    /*
                    START BINOMIAL CELL TYPE SPECIFIC TEST
                    */

                    NonPhasedEntry a = new NonPhasedEntry(asFile, phenoTypeLocation, outputLocation);

                } else if (programAction.equals("ASEPERREGION") || programAction.equals("3")) {

                    if (commandLine.hasOption('L')) {
                        asFile = commandLine.getOptionValue('L');
                    } else {
                        throw new ParseException(
                                "Required command line input --as_location when --action is ASEperRegion");
                    }
                    if (commandLine.hasOption('C')) {
                        couplingLocation = commandLine.getOptionValue('C');
                    } else {
                        throw new ParseException(
                                "Required command line input --coupling_file when --action is ASEperRegion");
                    }
                    if (commandLine.hasOption('P')) {
                        phenoTypeLocation = commandLine.getOptionValue('P');
                    } else {
                        phenoTypeLocation = null;
                    }
                    if (commandLine.hasOption('G')) {
                        genotypeLocation = commandLine.getOptionValue('G');
                    } else {
                        throw new ParseException(
                                "Required command line input --genotype_Location when --action is ASEperRegion");
                    }

                    if (commandLine.hasOption('R')) {
                        regionLocation = commandLine.getOptionValue('R');
                    } else {
                        throw new ParseException(
                                "Required command line input --region_file when --action is ASEperRegion");
                    }

                    PhasedEntry a = new PhasedEntry(asFile, couplingLocation, outputLocation, phenoTypeLocation,
                            genotypeLocation, regionLocation);

                } else {
                    throw new ParseException(
                            "Unable to determine what to do. Please specify a correct value to --Action");
                }
            }

        } catch (ParseException ex) {
            LOGGER.fatal("Invalid command line arguments");
            LOGGER.fatal(ex.getMessage());
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp(" ", OPTIONS);

        }

    } catch (ParseException ex) {
        LOGGER.fatal("Invalid command line arguments: ");
        LOGGER.fatal(ex.getMessage());
        System.err.println();
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(" ", OPTIONS);
    }
}

From source file:org.apache.accumulo.core.util.shell.commands.FateCommand.java

@Override
public int execute(final String fullCommand, final CommandLine cl, final Shell shellState)
        throws ParseException, KeeperException, InterruptedException, IOException {
    Instance instance = shellState.getInstance();
    String[] args = cl.getArgs();
    if (args.length <= 0) {
        throw new ParseException("Must provide a command to execute");
    }// www  . ja  va  2s .com
    String cmd = args[0];
    boolean failedCommand = false;

    AdminUtil<FateCommand> admin = new AdminUtil<FateCommand>(false);

    String path = ZooUtil.getRoot(instance) + Constants.ZFATE;
    String masterPath = ZooUtil.getRoot(instance) + Constants.ZMASTER_LOCK;
    IZooReaderWriter zk = getZooReaderWriter(shellState.getInstance(),
            cl.getOptionValue(secretOption.getOpt()));
    ZooStore<FateCommand> zs = new ZooStore<FateCommand>(path, zk);

    if ("fail".equals(cmd)) {
        if (args.length <= 1) {
            throw new ParseException("Must provide transaction ID");
        }
        for (int i = 1; i < args.length; i++) {
            if (!admin.prepFail(zs, zk, masterPath, args[i])) {
                System.out.printf("Could not fail transaction: %s%n", args[i]);
                failedCommand = true;
            }
        }
    } else if ("delete".equals(cmd)) {
        if (args.length <= 1) {
            throw new ParseException("Must provide transaction ID");
        }
        for (int i = 1; i < args.length; i++) {
            if (admin.prepDelete(zs, zk, masterPath, args[i])) {
                admin.deleteLocks(zs, zk, ZooUtil.getRoot(instance) + Constants.ZTABLE_LOCKS, args[i]);
            } else {
                System.out.printf("Could not delete transaction: %s%n", args[i]);
                failedCommand = true;
            }
        }
    } else if ("list".equals(cmd) || "print".equals(cmd)) {
        // Parse transaction ID filters for print display
        Set<Long> filterTxid = null;
        if (args.length >= 2) {
            filterTxid = new HashSet<Long>(args.length);
            for (int i = 1; i < args.length; i++) {
                try {
                    Long val = Long.parseLong(args[i], 16);
                    filterTxid.add(val);
                } catch (NumberFormatException nfe) {
                    // Failed to parse, will exit instead of displaying everything since the intention was to potentially filter some data
                    System.out.printf("Invalid transaction ID format: %s%n", args[i]);
                    return 1;
                }
            }
        }

        // Parse TStatus filters for print display
        EnumSet<TStatus> filterStatus = null;
        if (cl.hasOption(statusOption.getOpt())) {
            filterStatus = EnumSet.noneOf(TStatus.class);
            String[] tstat = cl.getOptionValues(statusOption.getOpt());
            for (int i = 0; i < tstat.length; i++) {
                try {
                    filterStatus.add(TStatus.valueOf(tstat[i]));
                } catch (IllegalArgumentException iae) {
                    System.out.printf("Invalid transaction status name: %s%n", tstat[i]);
                    return 1;
                }
            }
        }

        StringBuilder buf = new StringBuilder(8096);
        Formatter fmt = new Formatter(buf);
        admin.print(zs, zk, ZooUtil.getRoot(instance) + Constants.ZTABLE_LOCKS, fmt, filterTxid, filterStatus);
        shellState.printLines(Collections.singletonList(buf.toString()).iterator(), true);
    } else {
        throw new ParseException("Invalid command option");
    }

    return failedCommand ? 1 : 0;
}