Example usage for org.apache.commons.cli Option setRequired

Introduction

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

Prototype

public void setRequired(boolean required) 

Source Link

Document

Sets whether this Option is mandatory.

Usage

From source file:nl.cyso.vcloud.client.config.ConfigMode.java

public void addRequiredOption(Option opt) {
    opt.setRequired(true);
    this.addOption(opt);
}

---

From source file:nl.imvertor.common.Configurator.java

@SuppressWarnings("static-access")
public void createOption(String stepName, String longKey, String description, String argKey, Boolean isRequired)
        throws Exception {
    if (longKey == null)
        throw new Exception("Missing option \"name\" in step " + stepName);
    if (description == null)
        throw new Exception("Missing option \"tip\" in step " + stepName);
    if (argKey == null)
        throw new Exception("Missing option \"arg\" in step " + stepName);
    if (isRequired == null)
        throw new Exception("Missing option \"required\" in step " + stepName);
    boolean hasArg = (argKey != null);
    Option option;
    option = OptionBuilder.withDescription(description).hasArg(hasArg).withArgName(argKey).create(longKey);
    // Options are not required for the cli processor; they are required in the chain.
    // So declare all parameters as optional and let every test check if the parameter is actually set
    // Note that this is because there is no way a parameter file can be read dynamically within the commonc CLI module. 
    // TODO check required parameters of replace commons CLI interface package
    option.setRequired(false);
    setOptionIsReady(longKey, !isRequired);
    options.addOption(option);/*from   w  w w .j av  a  2 s  .c  o  m*/

    // store the option to the configurator for final reporting
    writeCli(stepName, longKey, description, argKey, isRequired);

}

---

From source file:nl.nekoconeko.configmode.ConfigModes.java

public static ConfigMode getConsolidatedModes() {
    ConfigMode all = new ConfigMode();

    for (ConfigMode mode : ConfigModes.modeMap.values()) {
        for (Option opt : mode.getAllOptions()) {
            opt.setRequired(false);
            all.addOption(opt);/*from   w  w w  .  j ava  2s  .  co m*/
        }
    }

    return all;
}

---

From source file:nl.toolforge.karma.core.cmd.digester.OptionDescriptorCreationFactory.java

public Object createObject(Attributes attributes) throws Exception {

    String opt = attributes.getValue("opt");
    String description = attributes.getValue("description");
    String longOpt = attributes.getValue("longOpt");
    boolean hasArgs = ("true".equals(attributes.getValue("hasArgs")) ? true : false);

    Option option = new Option(opt, longOpt, hasArgs, description);

    boolean required = ("true".equals(attributes.getValue("required")) ? true : false);
    option.setRequired(required);

    return option;
}

---

From source file:no.uib.tools.AllShortestPaths.java

public static void main(String args[]) {

    // Define and parse command line options
    Conf.options = new Options();

    Option input = new Option("i", "input", true, "input file path");
    input.setRequired(true);
    options.addOption(input);/*from   ww w  . ja v a  2 s.c  o m*/

    Option output = new Option("o", "output", true, "output file path");
    output.setRequired(true);
    options.addOption(output);

    CommandLineParser parser = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine cmd;

    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {

        System.out.println(e.getMessage());
        formatter.printHelp("utility-name", options);

        System.exit(1);
        return;
    }

    //        GraphReactome G = new GraphReactome(cmd.getOptionValue("input").toString(), 45000);
    //        proteinSet = new TreeSet<>();
    //        
    //        proteinSet = getProteinList();
    //        
    //        G.shortestUnweightedPaths(proteinSet);
}

---

From source file:no.uib.tools.MODGet.java

public static void main(String args[]) {
    // Define and parse command line options
    Options options = new Options();
    CommandLineParser parser = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine cmd;/*w ww. j av a2 s  .c o  m*/

    Option modId = new Option("m", "mod", true,
            "The PSIMOD id for the Post Translational Modification that will be used to select the proteins that can have that modification.");
    modId.setRequired(true);
    options.addOption(modId);

    Option output = new Option("o", "output", true, "Output file path and name");
    output.setRequired(true);
    options.addOption(output);

    Option config = new Option("c", "confPath", true, "config.txt file path and name");
    config.setRequired(false);
    options.addOption(config);

    Option host = new Option("h", "host", true, "Url of the Neo4j database with Reactome");
    host.setRequired(false);
    options.addOption(host);

    Option username = new Option("u", "username", true, "Username to access the database with Reactome");
    username.setRequired(false);
    options.addOption(username);

    Option password = new Option("p", "password", true,
            "Password related to the username provided to access the database with Reactome");
    password.setRequired(false);
    options.addOption(password);

    //Verify command line options
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        System.out.println(e.getMessage());
        formatter.printHelp("utility-name", options);

        System.exit(1);
        return;
    }

    //        System.out.println("modId: " + cmd.getOptionValue("mod"));
    //        System.out.println("output: " + cmd.getOptionValue("output"));
    Conf.setEmptyMaps();
    Conf.setDefaultNeo4jValues();
    if (cmd.hasOption("confPath")) {
        Conf.readConf();
    }
    if (cmd.hasOption("host")) {
        Conf.setValue("host", cmd.getOptionValue("host"));
    }
    if (cmd.hasOption("username")) {
        Conf.setValue("username", cmd.getOptionValue("username"));
    }
    if (cmd.hasOption("password")) {
        Conf.setValue("password", cmd.getOptionValue("password"));
    }

    ConnectionNeo4j.driver = GraphDatabase.driver(Conf.strMap.get(StrVars.host),
            AuthTokens.basic(Conf.strMap.get(StrVars.username), Conf.strMap.get(StrVars.password)));

    try {
        FileWriter resultFW = new FileWriter(cmd.getOptionValue("output"));

        // Access EBI fot the onthology to get the mod descendants
        List<String> modList = OnthologyHttpClient.getTermDescendants("mod", cmd.getOptionValue("mod"),
                "descendants");
        modList.add(cmd.getOptionValue("mod"));
        //            List<String> modList = Arrays.asList("00818",  "00173",  "00170",  "00171",  "00172",  "00167",  "00168",  "00169",  "00491",  "00895",  "00152",  "00153",  "00154",  "01146",  "00226",  "01182",  "01668",  "00896",  "01164",  "00354",  "00355",  "00225",  "01611",  "00356",  "00357",  "00358",  "01804",  "00301",  "00302",  "01847",  "00151",  "00159",  "01475",  "01474",  "00176",  "00583",  "01362",  "01361",  "01363",  "00639",  "01308",  "01307",  "01309",  "00635",  "01588",  "01587",  "00640",  "01973",  "01972",  "00696",  "00043",  "01456",  "00890",  "00045",  "00044",  "01931",  "00227",  "01455",  "00046",  "01452",  "01451",  "00047",  "00048",  "00042",  "01606",  "00311",  "00797",  "00787",  "00788");
        //            System.out.println("The list of related mods is:");
        //            for (String mod : modList) {
        //                System.out.println(mod);
        //            }

        // Get list of proteins from Reactome
        List<String> proteinList = ReactomeAccess.getProteinListByMods(modList);

        // Write list to file
        for (String protein : proteinList) {
            resultFW.write(protein + "\n");
        }

        resultFW.close();
    } catch (IOException ex) {
        System.out.println("Could not create the output file in the specified path.");
        //Logger.getLogger(MODGet.class.getName()).log(Level.SEVERE, null, ex);
    }
}

---

From source file:org.akvo.flow.InstanceConfigurator.java

private static Options getOptions() {

    Options options = new Options();

    Option orgName = new Option("on", "Organzation name");
    orgName.setLongOpt("orgName");
    orgName.setArgs(1);//from  ww  w .j a  va 2 s  .  c  o  m
    orgName.setRequired(true);

    Option awsId = new Option("ak", "AWS Access Key");
    awsId.setLongOpt("awsKey");
    awsId.setArgs(1);
    awsId.setRequired(true);

    Option awsSecret = new Option("as", "AWS Access Secret");
    awsSecret.setLongOpt("awsSecret");
    awsSecret.setArgs(1);
    awsSecret.setRequired(true);

    Option bucketName = new Option("bn", "AWS S3 bucket name");
    bucketName.setLongOpt("bucketName");
    bucketName.setArgs(1);
    bucketName.setRequired(true);

    Option gaeServer = new Option("gae", "GAE instance id - The `x` in https://x.appspot.com");
    gaeServer.setLongOpt("gaeId");
    gaeServer.setArgs(1);
    gaeServer.setRequired(true);

    Option emailFrom = new Option("ef", "Sender email - NOTE: Must be developer in GAE instance");
    emailFrom.setLongOpt("emailFrom");
    emailFrom.setArgs(1);
    emailFrom.setRequired(false);

    Option emailTo = new Option("et", "Recipient email of error notifications");
    emailTo.setLongOpt("emailTo");
    emailTo.setArgs(1);
    emailTo.setRequired(true);

    Option flowServices = new Option("fs", "FLOW Services url, e.g. http://services.akvoflow.org");
    flowServices.setLongOpt("flowServices");
    flowServices.setArgs(1);
    flowServices.setRequired(true);

    Option outputFolder = new Option("o", "Output folder for configuration files");
    outputFolder.setLongOpt("outFolder");
    outputFolder.setArgs(1);
    outputFolder.setRequired(true);

    Option alias = new Option("a", "Instance alias, e.g. instance.akvoflow.org");
    alias.setLongOpt("alias");
    alias.setArgs(1);
    alias.setRequired(true);

    Option signingKey = new Option("sk", "Signing Key");
    signingKey.setLongOpt("signingKey");
    signingKey.setArgs(1);
    signingKey.setRequired(true);

    options.addOption(orgName);
    options.addOption(awsId);
    options.addOption(awsSecret);
    options.addOption(bucketName);
    options.addOption(gaeServer);
    options.addOption(emailFrom);
    options.addOption(emailTo);
    options.addOption(outputFolder);
    options.addOption(flowServices);
    options.addOption(alias);
    options.addOption(signingKey);

    return options;
}

---

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

public static Option tableOpt(final String description) {
    final Option tableOpt = new Option(Shell.tableOption, "table", true, description);
    tableOpt.setArgName("table");
    tableOpt.setRequired(false);
    return tableOpt;
}

---

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

public static Option namespaceOpt(final String description) {
    final Option namespaceOpt = new Option(Shell.namespaceOption, "namespace", true, description);
    namespaceOpt.setArgName("namespace");
    namespaceOpt.setRequired(false);
    return namespaceOpt;
}

---

From source file:org.apache.accumulo.server.util.VerifyTabletAssignments.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();

    Option zooKeeperInstance = new Option("z", "zooKeeperInstance", true,
            "use a zookeeper instance with the given instance name and list of zoo hosts");
    zooKeeperInstance.setArgName("name hosts");
    zooKeeperInstance.setArgs(2);//ww  w .  j  av a 2s .c o  m
    opts.addOption(zooKeeperInstance);

    Option usernameOption = new Option("u", "user", true, "username (required)");
    usernameOption.setArgName("user");
    usernameOption.setRequired(true);
    opts.addOption(usernameOption);

    Option passwOption = new Option("p", "password", true,
            "password (prompt for password if this option is missing)");
    passwOption.setArgName("pass");
    opts.addOption(passwOption);

    Option verboseOption = new Option("v", "verbose", false, "verbose mode (prints locations of tablets)");
    opts.addOption(verboseOption);

    CommandLine cl = null;
    String user = null;
    String passw = null;
    Instance instance = null;
    ConsoleReader reader = new ConsoleReader();
    try {
        cl = new BasicParser().parse(opts, args);

        if (cl.hasOption(zooKeeperInstance.getOpt())
                && cl.getOptionValues(zooKeeperInstance.getOpt()).length != 2)
            throw new MissingArgumentException(zooKeeperInstance);

        user = cl.getOptionValue(usernameOption.getOpt());
        passw = cl.getOptionValue(passwOption.getOpt());

        if (cl.hasOption(zooKeeperInstance.getOpt())) {
            String[] zkOpts = cl.getOptionValues(zooKeeperInstance.getOpt());
            instance = new ZooKeeperInstance(zkOpts[0], zkOpts[1]);
        } else {
            instance = HdfsZooInstance.getInstance();
        }

        if (passw == null)
            passw = reader.readLine(
                    "Enter current password for '" + user + "'@'" + instance.getInstanceName() + "': ", '*');
        if (passw == null) {
            reader.printNewline();
            return;
        } // user canceled

        if (cl.getArgs().length != 0)
            throw new ParseException("Unrecognized arguments: " + cl.getArgList());

    } catch (ParseException e) {
        PrintWriter pw = new PrintWriter(System.err);
        new HelpFormatter().printHelp(pw, Integer.MAX_VALUE,
                "accumulo " + VerifyTabletAssignments.class.getName(), null, opts, 2, 5, null, true);
        pw.flush();
        System.exit(1);
    }

    Connector conn = instance.getConnector(user, passw.getBytes());

    for (String table : conn.tableOperations().list())
        checkTable(user, passw, table, null, cl.hasOption(verboseOption.getOpt()));

}

---

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