Example usage for org.apache.commons.cli OptionBuilder isRequired

List of usage examples for org.apache.commons.cli OptionBuilder isRequired

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

Prototype

public static OptionBuilder isRequired()

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Document

The next Option created will be required.

Usage

From source file:org.schreibubi.JCombinationsTools.generateBinaryDiffValues.GenerateBinaryDiffValues.java

/**
 * This program takes the file with all possible combinations of variables and creates two set of variables for
 * relating the variable names to positions in the binary diff. Additionally a patch is created containing the
 * expected chunks from a binary diff.//w w w  .  j  a v a 2  s .  co  m
 * 
 * @param args
 */
@SuppressWarnings("static-access")
public static void main(String[] args) {
    String variablesInName = "";
    String outputDir = "";
    String seti = "";
    Options options = new Options();
    try {
        CommandLineParser CLparser = new PosixParser();

        // create the Options
        options.addOption(OptionBuilder.isRequired().withLongOpt("variablesIn")
                .withDescription("[in] file containing the variables").hasArg().withArgName("file")
                .create('i'));
        options.addOption(OptionBuilder.isRequired().withLongOpt("dir")
                .withDescription("[out] output directory").hasArg().withArgName("file").create('d'));
        options.addOption(OptionBuilder.withLongOpt("seti").withDescription("[in] enable seti-chain patching")
                .hasArg().withArgName("file").create('s'));
        options.addOption(OptionBuilder.withLongOpt("version").withDescription("version").create('v'));

        CommandLine line = CLparser.parse(options, args);

        if (line.hasOption("v")) {
            Info.printVersion("GenerateBinaryDiffValues");
            Runtime.getRuntime().exit(0);
        }
        if (line.hasOption("i")) {
            variablesInName = line.getOptionValue("i");
        }
        if (line.hasOption("s")) {
            seti = line.getOptionValue("s");
        }
        if (line.hasOption("d")) {
            outputDir = line.getOptionValue("d");
        }

        exec(variablesInName, outputDir, seti, "TEMPLATE");
    } catch (ParseException e) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(Info.getVersionString("GenerateBinaryDiffValues"), options);
    } catch (Exception e) {
        System.out.println("GenerateBinaryDiffValues error: " + e);
        e.printStackTrace();
    }

}

From source file:org.schreibubi.JCombinationsTools.generatePatchTemplate.GeneratePatchTemplate.java

/**
 * @param args/*from  w w w  .j  a v  a  2 s  . com*/
 *            binaryDiffResult allPossibleChunks difftemplate
 */
@SuppressWarnings("static-access")
public static void main(String[] args) {
    String diffResultFile = "";
    String diffTemplateFile = "";
    String possibleChunksFile = "";
    String possibleCombinationsIn = "";
    String possibleCombinationsOut = "";
    String seti = "";
    String templateNameFilter = "";
    Options options = new Options();
    try {
        CommandLineParser CLparser = new PosixParser();

        // create the Options
        options.addOption(OptionBuilder.isRequired().withLongOpt("diffResult")
                .withDescription("[in] file containing the result of the binary diff").hasArg()
                .withArgName("file").create('d'));
        options.addOption(OptionBuilder.isRequired().withLongOpt("possibleChunks")
                .withDescription("[in] file containing the possible chunks").hasArg().withArgName("file")
                .create('p'));
        options.addOption(OptionBuilder.isRequired().withLongOpt("possibleCombinationsIn")
                .withDescription("[in] list of all possible combinations").hasArg().withArgName("file")
                .create('i'));
        options.addOption(OptionBuilder.isRequired().withLongOpt("filter")
                .withDescription("filter only test which have this value in the TEMPLATE variable").hasArg()
                .withArgName("file").create('f'));
        options.addOption(OptionBuilder.isRequired().withLongOpt("possibleCombinationsOut")
                .withDescription("[out] list of all possible combinations").hasArg().withArgName("file")
                .create('o'));
        options.addOption(OptionBuilder.isRequired().withLongOpt("diffTemplate")
                .withDescription("[out] template for generating the patch chunks").hasArg().withArgName("file")
                .create('t'));
        options.addOption(OptionBuilder.withLongOpt("seti").withDescription("[in] enable seti-chain patching")
                .hasArg().withArgName("file").create('s'));
        options.addOption(OptionBuilder.withLongOpt("version").withDescription("version").create('v'));

        CommandLine line = CLparser.parse(options, args);

        if (line.hasOption("v")) {
            Info.printVersion("GeneratepatchTemplate");
            Runtime.getRuntime().exit(0);
        }
        if (line.hasOption("d")) {
            diffResultFile = line.getOptionValue("d");
        }
        if (line.hasOption("t")) {
            diffTemplateFile = line.getOptionValue("t");
        }
        if (line.hasOption("p")) {
            possibleChunksFile = line.getOptionValue("p");
        }
        if (line.hasOption("i")) {
            possibleCombinationsIn = line.getOptionValue("i");
        }
        if (line.hasOption("o")) {
            possibleCombinationsOut = line.getOptionValue("o");
        }
        if (line.hasOption("f")) {
            templateNameFilter = line.getOptionValue("f");
        }
        if (line.hasOption("s")) {
            seti = line.getOptionValue("s");
        }

        exec(diffResultFile, possibleChunksFile, diffTemplateFile, possibleCombinationsIn, templateNameFilter,
                possibleCombinationsOut, seti);

    } catch (ParseException e) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(Info.getVersionString("GeneratePatchTemplate"), options);
    } catch (Exception e) {
        System.out.println("GeneratePatchTemplate error: " + e);
        e.printStackTrace();
    }
}

From source file:org.schreibubi.JCombinationsTools.mergeResults.MergeResults.java

/**
 * @param args/*from   w  w  w.ja  v a  2s  .c  o m*/
 */
@SuppressWarnings("static-access")
public static void main(String[] args) {
    Options options = new Options();
    try {

        Properties defaultProperties = new Properties();
        Properties userProperties = new Properties(defaultProperties);

        defaultProperties.setProperty("triggerTrimColumn", "TRIM");
        defaultProperties.setProperty("triggerMeasureColumn", "MEASURE");
        defaultProperties.setProperty("trimColumns",
                "TRIM_TESTMODE,TRIM_TRIMMING,TRIM_RELATIVE,TRIM_ABS,TRIM_PATNAME,FORCE_VALUE");
        defaultProperties.setProperty("trimAbsColumn", "TRIM_ABS");
        defaultProperties.setProperty("trimRelativeColumn", "TRIM_RELATIVE");
        defaultProperties.setProperty("subtitleColumn", "COMMENT");
        defaultProperties.setProperty("dutSelection", "1-1024");
        defaultProperties.setProperty("dutOffset", "32");
        defaultProperties.setProperty("zip", "false");

        try {
            userProperties.loadFromXML(new FileInputStream("config.xml"));
        } catch (FileNotFoundException e) {
        }

        String dclogFile = "";
        ArrayList<String> dclogFiles = new ArrayList<String>();
        String outputFile = "";
        String combinationsFile = "";
        String triggerTrimColumn = userProperties.getProperty("triggerTrimColumn");
        String triggerMeasureColumn = userProperties.getProperty("triggerMeasureColumn");
        String trimColumnsString = userProperties.getProperty("trimColumns");
        String trimAbsColumn = userProperties.getProperty("trimAbsColumn");
        String trimRelativeColumn = userProperties.getProperty("trimRelativeColumn");
        String subtitleColumn = userProperties.getProperty("subtitleColumn");
        String dutSelectionString = userProperties.getProperty("dutSelection");
        String dutOffsetString = userProperties.getProperty("dutOffset");
        boolean zip = Boolean.parseBoolean(userProperties.getProperty("zip"));

        CommandLineParser CLparser = new PosixParser();

        // create the Options
        options.addOption(OptionBuilder.withLongOpt("dclog").withDescription("[in] dclog-files").hasArg()
                .withArgName("file").create('d'));
        options.addOption(OptionBuilder.isRequired().withLongOpt("combinations")
                .withDescription("[in] combinations file").hasArg().withArgName("file").create('c'));
        options.addOption(OptionBuilder.withLongOpt("output").withDescription("[out] output file").hasArg()
                .withArgName("file").create('o'));
        options.addOption(OptionBuilder.withLongOpt("trim")
                .withDescription("Column name of trim column, defaults to " + triggerTrimColumn).hasArg()
                .withArgName("column").create('t'));
        options.addOption(OptionBuilder.withLongOpt("measure")
                .withDescription("Column name of measure column, defaults to " + triggerMeasureColumn).hasArg()
                .withArgName("column").create('m'));
        options.addOption(OptionBuilder.withLongOpt("xvals")
                .withDescription("Column name containing the x-values, defaults to " + trimColumnsString)
                .hasArg().withArgName("column").create('x'));
        options.addOption(OptionBuilder.withLongOpt("relative")
                .withDescription(
                        "Column name containing the relative changes, defaults to " + trimRelativeColumn)
                .hasArg().withArgName("column").create('r'));
        options.addOption(OptionBuilder.withLongOpt("subtitle")
                .withDescription(
                        "Column name containing the subtitles for the shmoos, defaults to " + subtitleColumn)
                .hasArg().withArgName("column").create('s'));
        options.addOption(OptionBuilder.withLongOpt("zip").withDescription("zip output file").create('z'));
        options.addOption(
                OptionBuilder.withLongOpt("dut").withDescription("use only DUTs " + dutSelectionString).hasArg()
                        .withArgName("column").create('u'));
        options.addOption(OptionBuilder.withLongOpt("dutOffset")
                .withDescription("dut offset when merging multiple measurments " + dutOffsetString).hasArg()
                .withArgName("offset").create('f'));
        options.addOption(OptionBuilder.withLongOpt("version").withDescription("version").create('v'));

        CommandLine line = CLparser.parse(options, args);

        if (line.hasOption("v")) {
            Info.printVersion("MergeResults");
            Runtime.getRuntime().exit(0);
        }
        if (line.hasOption("c")) {
            combinationsFile = line.getOptionValue("c");
        }

        if (line.hasOption("d")) {
            dclogFile = line.getOptionValue("d");
            String[] dF = dclogFile.split(",");
            for (String s : dF) {
                dclogFiles.add(s);
            }
        } else {
            int dotPos = combinationsFile.lastIndexOf(".");
            if (dotPos > -1) {
                dclogFiles.add("dclog_af_b_source.csv_" + combinationsFile.substring(0, dotPos));
            } else {
                dclogFiles.add("dclog_af_b_source.csv_" + combinationsFile);
            }
        }

        if (line.hasOption("o")) {
            outputFile = line.getOptionValue("o");
        } else {
            int dotPos = combinationsFile.lastIndexOf(".");
            if (dotPos > -1) {
                outputFile = combinationsFile.substring(0, dotPos) + ".xml";
            } else {
                outputFile = combinationsFile + ".xml";
            }
        }

        if (line.hasOption("t")) {
            triggerTrimColumn = line.getOptionValue("t");
        }
        if (line.hasOption("m")) {
            triggerMeasureColumn = line.getOptionValue("m");
        }
        if (line.hasOption("x")) {
            trimColumnsString = line.getOptionValue("x");
        }
        if (line.hasOption("r")) {
            trimRelativeColumn = line.getOptionValue("r");
        }
        if (line.hasOption("s")) {
            subtitleColumn = line.getOptionValue("s");
        }
        if (line.hasOption("z")) {
            zip = true;
        }
        if (line.hasOption("u")) {
            dutSelectionString = line.getOptionValue("u");
        }
        if (line.hasOption("f")) {
            dutOffsetString = line.getOptionValue("f");
        }

        String[] tC = trimColumnsString.split(",");
        VArrayList<String> trimColumns = new VArrayList<String>();
        for (String s : tC) {
            trimColumns.add(s);
        }

        String[] dS = dutSelectionString.split("-");
        if (dS.length < 2)
            throw new Exception("dut specification is wrong, should be e.g. 1-16");
        int dutStart = Integer.parseInt(dS[0]);
        int dutStop = Integer.parseInt(dS[1]);

        int dutOffset = Integer.parseInt(dutOffsetString);
        merge(dclogFiles, combinationsFile, outputFile, zip, triggerTrimColumn, trimRelativeColumn,
                trimAbsColumn, trimColumns, triggerMeasureColumn, subtitleColumn, dutStart, dutStop, dutOffset);

    } catch (ParseException e) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(Info.getVersionString("MergeResults"), options);
    } catch (Exception e) {
        System.out.println("MergeResults error: " + e);
        e.printStackTrace();
    }

}

From source file:org.schreibubi.JCombinationsTools.templateEngine.TemplateEngine.java

/**
 * TemplateEngine/* ww  w .j  a v  a 2s.  c  o m*/
 * 
 * @param args
 *            assignments template
 */
@SuppressWarnings("static-access")
public static void main(String[] args) {
    Options options = new Options();
    try {
        CommandLineParser CLparser = new PosixParser();

        // create the Options
        options.addOption(OptionBuilder.isRequired().withLongOpt("output-filename")
                .withDescription("[out] which variable is used for nameing the files").hasArg()
                .withArgName("variable name").create('o'));
        options.addOption(OptionBuilder.withLongOpt("multifile")
                .withDescription(
                        "output template to multiple files, -o contains variable name to use for filename")
                .create('m'));
        options.addOption(OptionBuilder.withLongOpt("multitemplate")
                .withDescription("use multiple templates, -t contains variable name to use for template")
                .create('u'));
        options.addOption(OptionBuilder.isRequired().withLongOpt("template")
                .withDescription("[in] the file containing the template to process").hasArg()
                .withArgName("file").create('t'));
        options.addOption(OptionBuilder.isRequired().withLongOpt("variables").withDescription(
                "[in] a file containing the values of the variables which should be replaced in the template")
                .hasArg().withArgName("file").create('v'));
        options.addOption(OptionBuilder.withLongOpt("outputDir")
                .withDescription("output directory to write the generated files to.").hasArg()
                .withArgName("file").create('d'));
        options.addOption(OptionBuilder.withLongOpt("header").withDescription("header to insert in each file")
                .hasArg().withArgName("file").create('h'));
        options.addOption(OptionBuilder.withLongOpt("footer").withDescription("footer to insert in each file")
                .hasArg().withArgName("file").create('f'));
        options.addOption(OptionBuilder.withLongOpt("version").withDescription("version").create('v'));

        CommandLine line = CLparser.parse(options, args);

        if (line.hasOption("v")) {
            Info.printVersion("TemplateEngine");
            Runtime.getRuntime().exit(0);
        }
        boolean generateSeparateFilesSwitch = false;
        if (line.hasOption("m")) {
            generateSeparateFilesSwitch = true;
        }
        boolean multiTemplateSwitch = false;
        if (line.hasOption("u")) {
            multiTemplateSwitch = true;
        }
        String outputFilenameOrVariable = "";
        if (line.hasOption("o")) {
            outputFilenameOrVariable = line.getOptionValue("o");
        }
        String templateFilenameOrVariable = "";
        if (line.hasOption("t")) {
            templateFilenameOrVariable = line.getOptionValue("t");
        }
        String variablesFilename = "";
        if (line.hasOption("v")) {
            variablesFilename = line.getOptionValue("v");
        }
        String outputDir = null;
        if (line.hasOption("d")) {
            outputDir = line.getOptionValue("d", null);
        }
        String header = null;
        if (line.hasOption("h")) {
            header = line.getOptionValue("h", null);
        }
        String footer = null;
        if (line.hasOption("f")) {
            outputDir = line.getOptionValue("f", null);
        }

        File variablesFile = new File(variablesFilename);
        File headerFile = new File(header);
        File footerFile = new File(footer);
        File inputDirFile = new File(".");
        File outputDirFile = new File(outputDir);

        exec(variablesFile, generateSeparateFilesSwitch, outputFilenameOrVariable, multiTemplateSwitch,
                templateFilenameOrVariable, inputDirFile, outputDirFile, headerFile, footerFile);
    } catch (ParseException e) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(Info.getVersionString("TemplateEngine"), options);
    } catch (Exception e) {
        System.out.println("TemplateEngine error: " + e.getMessage());
        e.printStackTrace();
        System.exit(1);
    }
}

From source file:sos.scheduler.cron.CronConverter.java

/**
 * @param args//w w w  . jav  a  2 s.  co m
 */
public static void main(final String[] args) {

    Logger logger = Logger.getLogger(CronConverter.class);
    @SuppressWarnings("unused")
    Log4JHelper objLogger = null;

    objLogger = new Log4JHelper(null);

    logger = Logger.getRootLogger();
    logger.info("SOS CronConverter - Main"); //$NON-NLS-1$

    /*try {
         test();
       } catch(Exception ex){
    ex.printStackTrace();
       }
    */
    try {
        //SOSArguments arguments = new SOSArguments(args);
        SOSLogger sosLogger;
        String sourceFile = "";
        String targetFile = "";
        String changeUser = "";
        File source = null;
        File target = null;
        int logLevel = 0;
        boolean sysTab = false;
        boolean useOldRunTime = false;
        String jobTimeout = "";
        /*
        try {
           sourceFile = arguments.as_string("-crontab=");
           if (sourceFile.equalsIgnoreCase("/etc/crontab")) sysTab = true;
           targetFile = arguments.as_string("-target=");
           logLevel = arguments.as_int("-v=",SOSStandardLogger.INFO);
           sysTab = arguments.as_bool("-system=",sysTab);
           useOldRunTime = arguments.as_bool("-oldRunTime=",false);
           changeUser = arguments.as_string("-change-user=", "su");
        } catch (Exception e1) {
           System.out.println(e1.getMessage());
           showUsage();
           System.exit(0);
        }*/
        Options options = new Options();
        OptionBuilder.withArgName("0|1");
        OptionBuilder.hasArg();
        OptionBuilder.withDescription("set to 1 if source is the system crontab (with user field)");

        Option optSysTab = OptionBuilder.create(conOptionsSYSTAB);

        OptionBuilder.withArgName("file");
        OptionBuilder.hasArgs();
        OptionBuilder.isRequired();
        OptionBuilder.withDescription("crontab file");

        Option optSourceFile = OptionBuilder.create(conOptionCRONTAB);
        OptionBuilder.withArgName("file");
        OptionBuilder.hasArgs();
        OptionBuilder.isRequired();
        OptionBuilder.withDescription("xml configuration file");

        Option optTargetFile = OptionBuilder.create(conOptionTARGET);
        OptionBuilder.withArgName("level");
        OptionBuilder.hasArg();
        OptionBuilder.withType(new Integer(0));
        OptionBuilder.withDescription("loglevel [0=info] [1=debug1]...[9=debug]");

        Option optLogLevel = OptionBuilder.create(conOptionVERBOSE);

        OptionBuilder.withArgName("command");
        OptionBuilder.hasArgs();
        OptionBuilder.withDescription(
                "change user command for -systab=1. 'su' or 'sudo' or define your own command using $SCHEDULER_CRONTAB_USER.");

        Option optChangeUser = OptionBuilder.create(conOptionCHANGEUSER);

        OptionBuilder.withArgName("seconds");
        OptionBuilder.hasArg();
        OptionBuilder.withDescription("job timeout (0 for unlimited");
        @SuppressWarnings("unused")
        Option optTimeOut = OptionBuilder.create(conOptionTIMEOUT);
        @SuppressWarnings("unused")
        Option optOldRunTime = new Option("oldRunTime", "");

        OptionBuilder.withArgName("true|false");
        OptionBuilder.hasArg();
        OptionBuilder.withDescription("set to true if script has to be mok'ed");
        Option optCreateMok = OptionBuilder.create(conOptionCREATE_MOCK);

        OptionBuilder.withArgName("true|false");
        OptionBuilder.hasArg();
        OptionBuilder.withDescription("set to true if you want to create jobChains and jobs");
        Option optCreateJobChains = OptionBuilder.create(conOptionCREATE_JobChains);

        options.addOption(optSysTab);
        options.addOption(optSourceFile);
        options.addOption(optTargetFile);
        options.addOption(optLogLevel);
        options.addOption(optChangeUser);
        options.addOption(optCreateMok);
        options.addOption(optCreateJobChains);

        CommandLineParser parser = new GnuParser();
        CommandLine line = null;
        try {
            line = parser.parse(options, args);
        } catch (Exception e) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("cronconverter", options, true);
            System.exit(0);
        }

        sourceFile = getWholeArgument(line.getOptionValues(conOptionCRONTAB));
        if (sourceFile.equalsIgnoreCase(conSystemCrontabName))
            sysTab = true;
        targetFile = getWholeArgument(line.getOptionValues(conOptionTARGET));

        String ll = line.getOptionValue(conOptionVERBOSE, "" + SOSStandardLogger.INFO);
        logLevel = Integer.parseInt(ll);
        if (line.hasOption(optSysTab.getOpt())) {
            sysTab = line.getOptionValue(optSysTab.getOpt()).trim().equals("1");
        }
        useOldRunTime = line.hasOption("oldRunTime");
        changeUser = "";
        if (line.hasOption(conOptionCHANGEUSER)) {
            changeUser = getWholeArgument(line.getOptionValues(conOptionCHANGEUSER));
        }

        jobTimeout = line.getOptionValue(conOptionTIMEOUT);
        if (logLevel == 0)
            logLevel = SOSLogger.INFO;
        sosLogger = new SOSStandardLogger(logLevel);

        target = new File(targetFile);
        source = new File(sourceFile);

        CronConverter cc = new CronConverter(sosLogger);
        if (jobTimeout != null && jobTimeout.length() > 0) {
            cc.setTimeout(jobTimeout);
        }
        cc.setChangeUserCommand(changeUser);
        if (line.hasOption(conOptionCREATE_MOCK)) { // JITL-28
            cc.setCreateAMock(line.getOptionValue(conOptionCREATE_MOCK).equalsIgnoreCase(conTRUE));
        }
        if (line.hasOption(conOptionCREATE_JobChains)) { // JITL-28
            cc.setCreateJobChainJobs(line.getOptionValue(conOptionCREATE_JobChains).equalsIgnoreCase(conTRUE));
        }

        cc.setSystemCronTab(sysTab);
        cc.oldRunTime = useOldRunTime;
        cc.cronFile2SchedulerXMLFile(source, target);

    } catch (Exception e) {
        e.printStackTrace();
    }

}

From source file:sos.scheduler.cron.CrontabFileConverter.java

/**
 * @param args/*from  ww w  .  ja v a2  s. c o  m*/
 */
public static void main(final String[] args) {

    Logger logger = Logger.getLogger(CrontabFileConverter.class);
    @SuppressWarnings("unused")
    Log4JHelper objLogger = null;

    objLogger = new Log4JHelper(null);

    logger = Logger.getRootLogger();
    logger.info("SOS CronConverter - Main"); //$NON-NLS-1$

    /*try {
         test();
       } catch(Exception ex){
    ex.printStackTrace();
       }
    */
    try {
        //SOSArguments arguments = new SOSArguments(args);
        SOSLogger sosLogger;
        String sourceFile = "";
        String targetFile = "";
        String changeUser = "";
        File source = null;
        File target = null;
        int logLevel = 0;
        boolean sysTab = false;
        boolean useOldRunTime = false;
        String jobTimeout = "";
        /*
        try {
           sourceFile = arguments.as_string("-crontab=");
           if (sourceFile.equalsIgnoreCase("/etc/crontab")) sysTab = true;
           targetFile = arguments.as_string("-target=");
           logLevel = arguments.as_int("-v=",SOSStandardLogger.INFO);
           sysTab = arguments.as_bool("-system=",sysTab);
           useOldRunTime = arguments.as_bool("-oldRunTime=",false);
           changeUser = arguments.as_string("-change-user=", "su");
        } catch (Exception e1) {
           System.out.println(e1.getMessage());
           showUsage();
           System.exit(0);
        }*/
        Options options = new Options();
        OptionBuilder.withArgName("0|1");
        OptionBuilder.hasArg();
        OptionBuilder.withDescription("set to 1 if source is the system crontab (with user field)");

        Option optSysTab = OptionBuilder.create(conOptionsSYSTAB);

        OptionBuilder.withArgName("file");
        OptionBuilder.hasArgs();
        OptionBuilder.isRequired();
        OptionBuilder.withDescription("crontab file");

        Option optSourceFile = OptionBuilder.create(conOptionCRONTAB);
        OptionBuilder.withArgName("file");
        OptionBuilder.hasArgs();
        OptionBuilder.isRequired();
        OptionBuilder.withDescription("xml configuration file");

        Option optTargetFile = OptionBuilder.create(conOptionTARGET);
        OptionBuilder.withArgName("level");
        OptionBuilder.hasArg();
        OptionBuilder.withType(new Integer(0));
        OptionBuilder.withDescription("loglevel [0=info] [1=debug1]...[9=debug]");

        Option optLogLevel = OptionBuilder.create(conOptionVERBOSE);

        OptionBuilder.withArgName("command");
        OptionBuilder.hasArgs();
        OptionBuilder.withDescription(
                "change user command for -systab=1. 'su' or 'sudo' or define your own command using $SCHEDULER_CRONTAB_USER.");

        Option optChangeUser = OptionBuilder.create(conOptionCHANGEUSER);

        OptionBuilder.withArgName("seconds");
        OptionBuilder.hasArg();
        OptionBuilder.withDescription("job timeout (0 for unlimited");
        @SuppressWarnings("unused")
        Option optTimeOut = OptionBuilder.create(conOptionTIMEOUT);
        @SuppressWarnings("unused")
        Option optOldRunTime = new Option("oldRunTime", "");

        OptionBuilder.withArgName("true|false");
        OptionBuilder.hasArg();
        OptionBuilder.withDescription("set to true if script has to be mok'ed");
        Option optCreateMok = OptionBuilder.create(conOptionCREATE_MOCK);

        OptionBuilder.withArgName("true|false");
        OptionBuilder.hasArg();
        OptionBuilder.withDescription("set to true if you want to create jobChains and jobs");
        Option optCreateJobChains = OptionBuilder.create(conOptionCREATE_JobChains);

        options.addOption(optSysTab);
        options.addOption(optSourceFile);
        options.addOption(optTargetFile);
        options.addOption(optLogLevel);
        options.addOption(optChangeUser);
        options.addOption(optCreateMok);
        options.addOption(optCreateJobChains);

        CommandLineParser parser = new GnuParser();
        CommandLine line = null;
        try {
            line = parser.parse(options, args);
        } catch (Exception e) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("cronconverter", options, true);
            System.exit(0);
        }

        sourceFile = getWholeArgument(line.getOptionValues(conOptionCRONTAB));
        if (sourceFile.equalsIgnoreCase(conSystemCrontabName))
            sysTab = true;
        targetFile = getWholeArgument(line.getOptionValues(conOptionTARGET));

        String ll = line.getOptionValue(conOptionVERBOSE, "" + SOSStandardLogger.INFO);
        logLevel = Integer.parseInt(ll);
        if (line.hasOption(optSysTab.getOpt())) {
            sysTab = line.getOptionValue(optSysTab.getOpt()).trim().equals("1");
        }
        useOldRunTime = line.hasOption("oldRunTime");
        changeUser = "";
        if (line.hasOption(conOptionCHANGEUSER)) {
            changeUser = getWholeArgument(line.getOptionValues(conOptionCHANGEUSER));
        }

        jobTimeout = line.getOptionValue(conOptionTIMEOUT);
        if (logLevel == 0)
            logLevel = SOSLogger.INFO;
        sosLogger = new SOSStandardLogger(logLevel);

        target = new File(targetFile);
        source = new File(sourceFile);

        CrontabFileConverter cc = new CrontabFileConverter(sosLogger);
        if (jobTimeout != null && jobTimeout.length() > 0) {
            cc.setTimeout(jobTimeout);
        }
        cc.setChangeUserCommand(changeUser);
        if (line.hasOption(conOptionCREATE_MOCK)) { // JITL-28
            cc.setCreateAMock(line.getOptionValue(conOptionCREATE_MOCK).equalsIgnoreCase(conTRUE));
        }
        if (line.hasOption(conOptionCREATE_JobChains)) { // JITL-28
            cc.setCreateJobChainJobs(line.getOptionValue(conOptionCREATE_JobChains).equalsIgnoreCase(conTRUE));
        }

        //         cc.setCreateAMock(line.getOptionValue(conOptionCREATE_MOCK).equalsIgnoreCase(conTRUE));
        //         cc.setCreateJobChainJobs(line.getOptionValue(conOptionCREATE_JobChains).equalsIgnoreCase(conTRUE));

        cc.setSystemCronTab(sysTab);
        cc.oldRunTime = useOldRunTime;
        cc.cronFile2SchedulerXMLFile(source, target);

    } catch (Exception e) {
        e.printStackTrace();
        System.exit(1);
    }

    System.exit(0);
}

From source file:ubc.pavlab.aspiredb.cli.DecipherPhenotypeUploadCLI.java

@Override
protected void buildOptions() {
    OptionBuilder.hasArg();/*from   w  ww .j a v a2  s . c  om*/
    OptionBuilder.withArgName("Directory");
    OptionBuilder.withDescription("Directory containing csv files");
    OptionBuilder.withLongOpt("directory");
    Option d = OptionBuilder.create('d');

    OptionBuilder.hasArg();
    OptionBuilder.withArgName("File name");
    OptionBuilder.withDescription("The file to parse");
    OptionBuilder.withLongOpt("filename");
    Option f = OptionBuilder.create('f');

    OptionBuilder.isRequired();
    OptionBuilder.hasArg();
    OptionBuilder.withArgName("Project name");
    OptionBuilder.withDescription(
            "The project where this data will reside. Project will be created if does not exist,"
                    + "If the project does exist use the existingproject option to add to an existing project");
    Option project = OptionBuilder.create("project");

    addOption("existingproject", false, "You must use this option if you are adding to an existing project");

    addOption(d);
    addOption(f);
    addOption(project);
}

From source file:ubc.pavlab.aspiredb.cli.DecipherVariantUploadCLI.java

@Override
protected void buildOptions() {
    OptionBuilder.isRequired();
    OptionBuilder.hasArg();/*  www .j ava 2 s. c o  m*/
    OptionBuilder.withArgName("Directory");
    OptionBuilder.withDescription("Directory containing csv files");
    OptionBuilder.withLongOpt("directory");
    Option d = OptionBuilder.create('d');

    OptionBuilder.isRequired();
    OptionBuilder.hasArg();
    OptionBuilder.withArgName("File name");
    OptionBuilder.withDescription("The file to parse");
    OptionBuilder.withLongOpt("filename");
    Option f = OptionBuilder.create('f');

    OptionBuilder.isRequired();
    OptionBuilder.hasArg();
    OptionBuilder.withArgName("Project name");
    OptionBuilder.withDescription(
            "The project where this data will reside. Project will be deleted if existingproject option is not specified,"
                    + "Acceptable values = 'DECIPHER");
    // Decipher will reside in a 'Special project' and are all CNVs
    Option project = OptionBuilder.create("project");

    addOption("existingproject", false, "You must use this option if you are adding to an existing project");

    addOption("dryrun", false, "Use this option to validate your data before uploading");

    addOption(d);
    addOption(f);

    addOption(project);

}

From source file:ubc.pavlab.aspiredb.cli.DGVVariantUploadCLI.java

@Override
protected void buildOptions() {
    OptionBuilder.isRequired();
    OptionBuilder.hasArg();//from  w w  w .  j av a  2 s.co  m
    OptionBuilder.withArgName("Directory");
    OptionBuilder.withDescription("Directory containing csv files");
    OptionBuilder.withLongOpt("directory");
    Option d = OptionBuilder.create('d');

    OptionBuilder.isRequired();
    OptionBuilder.hasArg();
    OptionBuilder.withArgName("File name");
    OptionBuilder.withDescription("The file to parse");
    OptionBuilder.withLongOpt("filename");
    Option f = OptionBuilder.create('f');

    OptionBuilder.isRequired();
    OptionBuilder.hasArg();
    OptionBuilder.withArgName("Project name");
    OptionBuilder.withDescription(
            "The project where this data will reside. Project will be deleted if existingproject option is not specified,"
                    + "Acceptable values = 'DGV");
    // DGV will reside in a 'Special project' and are all CNVs
    /*
     * Option variantType = OptionBuilder.isRequired().hasArg().withArgName( "Variant Type" ) .withDescription(
     * "The type of variant in this file, one of: CNV, Indel, SNV, Inversion" ) .create( "variant" );
     */
    Option project = OptionBuilder.create("project");

    addOption("existingproject", false, "You must use this option if you are adding to an existing project");

    addOption("dryrun", false, "Use this option to validate your data before uploading");

    addOption(d);
    addOption(f);

    addOption(project);

}

From source file:ubc.pavlab.aspiredb.cli.ProjectManagerCLI.java

@Override
protected void buildOptions() {

    OptionBuilder.hasArg();/*from ww  w .  j a v  a  2  s .  co  m*/
    OptionBuilder.withArgName("group name");
    OptionBuilder.withDescription("The group to give permissions to");
    Option groupname = OptionBuilder.create("groupname");

    OptionBuilder.isRequired();
    OptionBuilder.hasArg();
    OptionBuilder.withArgName("Project name");
    OptionBuilder.withDescription("The project that will be affected by these operations");
    Option project = OptionBuilder.create("project");

    OptionBuilder.hasArg();
    OptionBuilder.withArgName("Overlap Project name");
    OptionBuilder
            .withDescription("The project that the other project will have its overlaps calculated against");
    Option projectOverlap = OptionBuilder.create("overlapProject");

    addOption("delete", false, "Using this option will delete the project");
    addOption("grant", false, "Using this option will grant the group read permissions on the project");
    addOption("restrict", false, "Using this option will remove the group's read permissions on the project");

    addOption("populateOverlap", false,
            "Using this option will populate the overlap between project and overlapProject");

    addOption(groupname);
    addOption(project);

    addOption(projectOverlap);
}