Examples with CommandLineParser org.apache.commons.cli.CommandLineParser used on opensource projects

Example 86 with CommandLineParser

use of org.apache.commons.cli.CommandLineParser in project goci by EBISPOT.

the class GOCIDataReleaseQCDriver method parseArguments.

private int parseArguments(String[] args) {
    CommandLineParser parser = new GnuParser();
    HelpFormatter help = new HelpFormatter();
    Options options = bindOptions();
    int parseArgs = 0;
    try {
        CommandLine cl = parser.parse(options, args, true);
        // check for mode help option
        if (cl.hasOption("")) {
            // print out mode help
            help.printHelp("qc", options, true);
            parseArgs += 1;
        } else {
            // find -o option (for asserted output file)
            if (cl.hasOption("a")) {
                this.opMode = OperationMode.ALL;
            } else if (cl.hasOption("k")) {
                this.opMode = OperationMode.KNOWLEDGE_BASE;
            } else if (cl.hasOption("e")) {
                this.opMode = OperationMode.SUMMARY_EMAIL;
            } else if (cl.hasOption("d")) {
                this.opMode = OperationMode.DIAGRAM;
            } else if (cl.hasOption("s")) {
                this.opMode = OperationMode.SOLR_INDEX;
            } else {
                System.err.println("-o (ontology output file) argument is required");
                help.printHelp("publish", options, true);
                parseArgs += 2;
            }
        }
    } catch (ParseException e) {
        System.err.println("Failed to read supplied arguments");
        help.printHelp("publish", options, true);
        parseArgs += 4;
    }
    return parseArgs;
}

Example 87 with CommandLineParser

use of org.apache.commons.cli.CommandLineParser in project goci by EBISPOT.

the class KBMetricsDriver method parseArguments.

private static int parseArguments(String[] args) {
    CommandLineParser parser = new GnuParser();
    HelpFormatter help = new HelpFormatter();
    Options options = bindOptions();
    int parseArgs = 0;
    try {
        CommandLine cl = parser.parse(options, args, true);
        // check for mode help option
        if (cl.hasOption("")) {
            // print out mode help
            help.printHelp("evaluate", options, true);
            parseArgs += 1;
        } else {
            System.out.println("Metrics will be calculated with the following options...");
            for (Option opt : cl.getOptions()) {
                System.out.println("\t" + opt.getLongOpt() + ": " + opt.getValue() + " (" + opt.getArgName() + ")");
            }
            if (cl.hasOption("efo")) {
                _efoLocation = new URL(cl.getOptionValue("efo"));
                System.out.println(_efoLocation);
            } else {
                System.err.println("-efo (EFO location) argument is required");
                help.printHelp("evaluate", options, true);
                parseArgs += 2;
            }
            if (cl.hasOption("gwas")) {
                _gwasSchemaLocation = new File(cl.getOptionValue("gwas")).toURI().toURL();
                System.out.println(_gwasSchemaLocation);
            } else {
                System.err.println("-gwas (GWAS Schema File) argument is required");
                help.printHelp("evaluate", options, true);
                parseArgs += 2;
            }
            if (cl.hasOption("kb")) {
                _kbLocation = new File(cl.getOptionValue("kb")).toURI().toURL();
                System.out.println(_kbLocation);
            } else {
                System.err.println("-kb (Knowledgebase File) argument is required");
                help.printHelp("evaluate", options, true);
                parseArgs += 2;
            }
            if (cl.hasOption("w")) {
                _watershedCutoff = Integer.parseInt(cl.getOptionValue("w"));
            //                    System.setProperty("watershed.cutoff", String.valueOf(_watershedCutoff));
            } else {
                System.err.println("-w (Watershed cutoff) argument is required");
                help.printHelp("evaluate", options, true);
                parseArgs += 2;
            }
            if (cl.hasOption("out")) {
                String outOpt = cl.getOptionValue("out");
                _out = new BufferedOutputStream(new FileOutputStream(new File(outOpt)));
            } else {
                System.out.println("No output file specified, report will be written to standard out");
                _out = System.out;
            }
        }
    } catch (ParseException e) {
        System.err.println("Failed to read supplied arguments (" + e.getMessage() + ")");
        help.printHelp("evaluate", options, true);
        parseArgs += 4;
    } catch (FileNotFoundException e) {
        System.err.println("Failed to read supplied arguments - file not found (" + e.getMessage() + ")");
        help.printHelp("evaluate", options, true);
        parseArgs += 5;
    } catch (MalformedURLException e) {
        System.err.println("Failed to read supplied arguments - a supplied argument was not a valid URL " + "(" + e.getMessage() + ")");
        help.printHelp("evaluate", options, true);
        parseArgs += 6;
    }
    return parseArgs;
}

Example 88 with CommandLineParser

use of org.apache.commons.cli.CommandLineParser in project GNS by MobilityFirst.

the class ThroughputAsynchMultiClientTest method initializeOptions.

private static CommandLine initializeOptions(String[] args) throws ParseException {
    Option helpOption = new Option("help", "Prints Usage");
    Option aliasOption = OptionBuilder.withArgName("alias").hasArg().withDescription("the alias (HRN) to use").create("alias");
    Option operationOption = OptionBuilder.withArgName("op").hasArg().withDescription("the operation to perform (read or update - default is read)").create("op");
    Option rateOption = OptionBuilder.withArgName("rate").hasArg().withDescription("the rate in ops per second").create("rate");
    Option incOption = OptionBuilder.withArgName("inc").hasArg().withDescription("the increment used with rate").create("inc");
    Option clientsOption = OptionBuilder.withArgName("clients").hasArg().withDescription("number of clients used to send (default 10)").create("clients");
    Option requestsPerClientOption = OptionBuilder.withArgName("requests").hasArg().withDescription("number of requests sent by each client each time").create("requests");
    Option guidsPerRequestOption = OptionBuilder.withArgName("guids").hasArg().withDescription("number of guids for each request").create("guids");
    Option useExistingGuidsOption = new Option("useExistingGuids", "use guids in account Guid instead of creating new ones");
    Option updateAliasOption = new Option("updateAlias", true, "Alias of guid to update/read");
    Option updateFieldOption = new Option("updateField", true, "Field to read/update");
    Option updateValueOption = new Option("updateValue", true, "Value to use in read/update");
    commandLineOptions = new Options();
    commandLineOptions.addOption(aliasOption);
    commandLineOptions.addOption(operationOption);
    commandLineOptions.addOption(rateOption);
    commandLineOptions.addOption(incOption);
    commandLineOptions.addOption(clientsOption);
    commandLineOptions.addOption(requestsPerClientOption);
    commandLineOptions.addOption(guidsPerRequestOption);
    commandLineOptions.addOption(helpOption);
    commandLineOptions.addOption(updateAliasOption);
    commandLineOptions.addOption(updateFieldOption);
    commandLineOptions.addOption(updateValueOption);
    commandLineOptions.addOption(useExistingGuidsOption);
    CommandLineParser parser = new GnuParser();
    return parser.parse(commandLineOptions, args);
}

Example 89 with CommandLineParser

use of org.apache.commons.cli.CommandLineParser in project GNS by MobilityFirst.

the class ReplicaLatencyTest method initializeOptions.

private static CommandLine initializeOptions(String[] args) throws ParseException {
    Option help = new Option("help", "Prints Usage");
    Option alias = OptionBuilder.withArgName("alias").hasArg().withDescription("the alias (HRN) to use for the account").create("alias");
    Option host = OptionBuilder.withArgName("host").hasArg().withDescription("the GNS host").create("host");
    Option port = OptionBuilder.withArgName("port").hasArg().withDescription("the GNS port").create("port");
    Option debug = new Option("debug", "show output");
    Option closeActiveReplica = OptionBuilder.withArgName("closeAR").hasArg().withDescription("the active replica close to you").create("closeAR");
    commandLineOptions = new Options();
    commandLineOptions.addOption(alias);
    commandLineOptions.addOption(host);
    commandLineOptions.addOption(port);
    commandLineOptions.addOption(debug);
    commandLineOptions.addOption(closeActiveReplica);
    commandLineOptions.addOption(help);
    CommandLineParser parser = new GnuParser();
    return parser.parse(commandLineOptions, args);
}

Example 90 with CommandLineParser

use of org.apache.commons.cli.CommandLineParser in project GNS by MobilityFirst.

the class CommandLineInterface method initializeOptions.

private static CommandLine initializeOptions(String[] args) throws ParseException {
    Option help = new Option("help", "Prints Usage");
    Option silent = new Option("silent", "Disables output");
    Option noDefaults = new Option("noDefaults", "Don't use server and guid defaults");
    commandLineOptions = new Options();
    commandLineOptions.addOption(help);
    commandLineOptions.addOption(silent);
    commandLineOptions.addOption(noDefaults);
    CommandLineParser parser = new GnuParser();
    return parser.parse(commandLineOptions, args, false);
}