List of usage examples for org.apache.commons.cli BasicParser parse
public CommandLine parse(Options options, String[] arguments) throws ParseException
arguments based on the specifed Options . From source file:hivemall.utils.lang.CommandLineUtils.java
public static CommandLine parseOptions(final String[] args, final Options opts) { final BasicParser parser = new BasicParser(); final CommandLine cl; try {//from ww w .ja v a 2 s . c o m cl = parser.parse(opts, args); } catch (ParseException e) { throw new IllegalArgumentException(e); } return cl; }
From source file:gov.nih.nci.caintegrator.heatmap.invokeCBS2HeatMap.java
public static void ReadOptions(String[] args, HeatMapArgs hma) { try {// w w w. j av a 2 s .c om Options opt = new Options(); opt.addOption("h", false, "Print help for this application"); opt.addOption("big_bins", true, "name of big bin definition file"); opt.addOption("small_bins", true, "name of small bin definition file"); opt.addOption("seg", true, "name of file containing segmented copy number data"); opt.addOption("samples", true, "name of file specifying samples to include"); opt.addOption("genomeout", true, "name of genome matrix output file"); opt.addOption("geneout", true, "name of gene matrix output file"); opt.addOption("title", true, "title for output heatmap"); opt.addOption("genes", true, "name of RefSeq gene flat file"); opt.addOption("gender", true, "name of file mapping patients to gender"); opt.addOption("protocol", true, "matched or unmatched"); opt.addOption("scale", true, "comma-separated list of real positive numbers for interval upperbounds (default is '0.5,1.5,2.5,3.5,4.5')"); opt.addOption("minseg", true, "minimum segment length to consider (default = 500)"); opt.addOption("platform", true, "name of platform"); opt.addOption("submitter", true, "name of center that submitted the data"); opt.addOption("contact", true, "contact: name of NCI contact person for this heatmap"); opt.addOption("cnv_track", true, "name of file with cnv track info"); opt.addOption("project", true, "project: name of project"); opt.addOption("base", true, "assumed base (can be float) for log ratio values (defaults to 2)"); BasicParser parser = new BasicParser(); CommandLine cl = parser.parse(opt, args); if (cl.hasOption("h")) { HelpFormatter f = new HelpFormatter(); f.printHelp("OptionsTip", opt); System.exit(0); } else { if (cl.hasOption("small_bins")) { hma.setSmallBinFile(cl.getOptionValue("small_bins")); } if (cl.hasOption("big_bins")) { hma.setBigBinFile(cl.getOptionValue("big_bins")); } if (cl.hasOption("seg")) { hma.setSegmentFile(cl.getOptionValue("seg")); } if (cl.hasOption("samples")) { hma.setSampleFile(cl.getOptionValue("samples")); } if (cl.hasOption("genomeout")) { hma.setGenomeOutFile(cl.getOptionValue("genomeout")); } if (cl.hasOption("geneout")) { hma.setGeneOutFile(cl.getOptionValue("geneout")); } if (cl.hasOption("title")) { hma.setTitle(cl.getOptionValue("title")); } if (cl.hasOption("genes")) { hma.setRefGenesFile(cl.getOptionValue("genes")); } if (cl.hasOption("gender")) { hma.setGenderFile(cl.getOptionValue("gender")); } if (cl.hasOption("protocol")) { hma.setProtocol(cl.getOptionValue("protocol")); } if (cl.hasOption("scale")) { hma.setScale(cl.getOptionValue("scale")); } if (cl.hasOption("minseg")) { hma.setMinSegLength(Integer.parseInt(cl.getOptionValue("minseg"))); } if (cl.hasOption("platform")) { hma.setPlatform(cl.getOptionValue("platform")); } if (cl.hasOption("submitter")) { hma.setSubmitter(cl.getOptionValue("submitter")); } if (cl.hasOption("contact")) { hma.setContact(cl.getOptionValue("contact")); } if (cl.hasOption("cnv_track")) { hma.setCnvTrack(cl.getOptionValue("cnv_track")); } if (cl.hasOption("project")) { hma.setProject(cl.getOptionValue("project")); } if (cl.hasOption("base")) { hma.setBase(Integer.parseInt(cl.getOptionValue("base"))); } } } catch (ParseException e) { e.printStackTrace(); } }
From source file:com.cloudera.impala.testutil.ImpalaJdbcClient.java
/** * Parses command line options//from www.ja v a2s. co m */ private static ClientExecOptions parseOptions(String[] args) throws ParseException { Options options = new Options(); options.addOption("i", true, "host:port of target machine impalad is listening on"); options.addOption("c", true, "Full connection string to use. Overrides host/port value"); options.addOption("t", true, "SASL/NOSASL, whether to use SASL transport or not"); options.addOption("q", true, "Query String"); options.addOption("help", false, "Help"); BasicParser optionParser = new BasicParser(); CommandLine cmdArgs = optionParser.parse(options, args); String transportOption = cmdArgs.getOptionValue("t"); if (transportOption == null) { LOG.error("Must specify '-t' option, whether to use SASL transport or not."); LOG.error("Using the wrong type of transport will cause the program to hang."); LOG.error("Usage: " + options.toString()); System.exit(1); } if (!transportOption.equalsIgnoreCase("SASL") && !transportOption.equalsIgnoreCase("NOSASL")) { LOG.error("Invalid argument " + transportOption + " to '-t' option."); LOG.error("Usage: " + options.toString()); System.exit(1); } boolean useSasl = transportOption.equalsIgnoreCase("SASL"); String connStr = cmdArgs.getOptionValue("c", null); // If the user didn't specify a custom connection string, build a connection // string using HiveServer 2 JDBC driver and no security. if (connStr == null) { String hostPort = cmdArgs.getOptionValue("i", "localhost:21050"); connStr = "jdbc:hive2://" + hostPort + "/"; } // Append appropriate auth option to connection string. if (useSasl) { connStr = connStr + ";auth=none"; } else { // As of Hive 0.11 'noSasl' is case sensitive. See HIVE-4232 for more details. connStr = connStr + ";auth=noSasl"; } String query = cmdArgs.getOptionValue("q"); if (query == null) { LOG.error("Must specify a query to execute."); LOG.error("Usage: " + options.toString()); System.exit(1); } return new ClientExecOptions(connStr, query); }
From source file:com.cloudera.impala.util.ImpalaJdbcClient.java
/** * Parses command line options//from ww w. j a v a 2 s . c o m */ private static ClientExecOptions parseOptions(String[] args) throws ParseException { Options options = new Options(); options.addOption("i", true, "host:port of target machine impalad is listening on"); options.addOption("c", true, "Full connection string to use. Overrides host/port value"); options.addOption("t", true, "SASL/NOSASL, whether to use SASL transport or not"); options.addOption("q", true, "Query String"); options.addOption("help", false, "Help"); BasicParser optionParser = new BasicParser(); CommandLine cmdArgs = optionParser.parse(options, args); String transportOption = cmdArgs.getOptionValue("t"); if (transportOption == null) { LOG.error("Must specify '-t' option, whether to use SASL transport or not."); LOG.error("Using the wrong type of transport will cause the program to hang."); LOG.error("Usage: " + options.toString()); System.exit(1); } if (!transportOption.equalsIgnoreCase("SASL") && !transportOption.equalsIgnoreCase("NOSASL")) { LOG.error("Invalid argument " + transportOption + " to '-t' option."); LOG.error("Usage: " + options.toString()); System.exit(1); } boolean useSasl = transportOption.equalsIgnoreCase("SASL"); String connStr = cmdArgs.getOptionValue("c", null); // If the user didn't specify a custom connection string, build a connection // string using HiveServer 2 JDBC driver and no security. if (connStr == null) { String hostPort = cmdArgs.getOptionValue("i", "localhost:21050"); connStr = "jdbc:hive2://" + hostPort + "/"; } // Append appropriate auth option to connection string. if (useSasl) { connStr = connStr + SASL_AUTH_SPEC; } else { connStr = connStr + NOSASL_AUTH_SPEC; } String query = cmdArgs.getOptionValue("q"); if (query == null) { LOG.error("Must specify a query to execute."); LOG.error("Usage: " + options.toString()); System.exit(1); } return new ClientExecOptions(connStr, query); }
From source file:jettyClient.simpleClient.Parameters.java
/** * Stores the given command line arguments for the client to use. * //from w w w.j av a 2s .c o m * @param args * Command line arguments. * @return Options for the client to use. */ public static ClientOptions setOptions(String[] args) { CommandLine line = null; Options options = defineOptions(); BasicParser parser = new BasicParser(); if (args.length > 0) { // Parse the given options try { line = parser.parse(options, args); } catch (ParseException e) { if (e instanceof MissingArgumentException) { System.out.println("Error: " + e.getMessage()); logger.debug("MissingArgumentException: " + e.getMessage()); } else { System.out.println("Error: " + e.getMessage()); logger.debug("ParseException:" + e.getMessage()); } showHelp(options); } // Print help if (line.hasOption(help)) { showHelp(options); } // Set the options read from the command line. ClientOptions clientOptions = setOptions(line); return clientOptions; } else { showHelp(options); } // Unreachable. return null; }
From source file:io.github.agentsoz.abmjadex.super_central.ABMSimStarter.java
private static void parsingArguments(String[] args, Options options) { //flags//from w ww.ja va2 s.co m boolean isRunningCO = true; boolean isForced = false; //Overwrite any existing CO xml file boolean isRunningSC = true; boolean isLogToConsole = false; Level logLevel = Level.INFO; Properties prop = null; CommandLine line = null; BasicParser parser = new BasicParser(); ArrayList<String> argsList = new ArrayList<String>(); //Initialize argsList with args for (int i = 0; i < args.length; i++) { argsList.add(args[i]); } //Update 04/17/2013 String[] specificArgs = packageOptionSpecific(args); try { // parse the command line arguments //line = parser.parse(options, args ); //Update 04/17/2013 line = parser.parse(options, specificArgs); //Commandline required -prop argument to be filled with valid properties file location if (line.hasOption(HELP)) { //Remove app specific arguments from total arguments int helpIndex = argsList.indexOf("-" + HELP); if (helpIndex == -1) helpIndex = argsList.indexOf("-" + HELP_LONG); argsList.remove(helpIndex); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Jadex-ABMS", options); } if (line.hasOption(PROP)) { //Remove app specific arguments from total arguments int propIndex = argsList.indexOf("-" + PROP); if (propIndex == -1) propIndex = argsList.indexOf("-" + PROP_LONG); argsList.remove(propIndex + 1); argsList.remove(propIndex); String propertiesLoc = line.getOptionValue(PROP).replace("\\", "/").replace("\\\\", "/"); prop = new Properties(); try { prop.load(new FileInputStream(propertiesLoc)); //Parsing options value into local flags------------------------ if (line.hasOption(MODE)) { String mode = line.getOptionValue(MODE); if (mode.equalsIgnoreCase(CO_ONLY)) { isRunningSC = false; } else if (mode.equalsIgnoreCase(SC_CO)) { //Default value is to run an SC and a CO } else if (mode.equalsIgnoreCase(SC_ONLY)) { isRunningCO = false; } else { throw new ParseException("Wrong argument for -mode."); } //Remove app specific arguments from total arguments int modeIndex = argsList.indexOf("-" + MODE); argsList.remove(modeIndex + 1); argsList.remove(modeIndex); } if (line.hasOption(FORCED)) { isForced = true; //Remove app specific arguments from total arguments int modeIndex = argsList.indexOf("-" + FORCED); if (modeIndex == -1) modeIndex = argsList.indexOf("-" + FORCED_LONG); argsList.remove(modeIndex); } if (line.hasOption(GUI)) { String guiMode = line.getOptionValue(GUI); if (!guiMode.equalsIgnoreCase("true") && !guiMode.equalsIgnoreCase("false")) throw new ParseException("Wrong argument for -gui."); } else { argsList.add("-" + GUI); int guiIndex = argsList.indexOf("-" + GUI); argsList.add(guiIndex + 1, "false"); } if (line.hasOption(LOG_CONSOLE)) { isLogToConsole = true; //Remove app specific arguments from total arguments int logCIndex = argsList.indexOf("-" + LOG_CONSOLE); argsList.remove(logCIndex); } if (line.hasOption(LOG_LVL)) { String level = line.getOptionValue(LOG_LVL); if (level.equalsIgnoreCase("INFO")) { logLevel = Level.INFO; } else if (level.equalsIgnoreCase("ALL")) { logLevel = Level.ALL; } else if (level.equalsIgnoreCase("CONFIG")) { logLevel = Level.CONFIG; } else if (level.equalsIgnoreCase("FINE")) { logLevel = Level.FINE; } else if (level.equalsIgnoreCase("FINER")) { logLevel = Level.FINER; } else if (level.equalsIgnoreCase("FINEST")) { logLevel = Level.FINEST; } else if (level.equalsIgnoreCase("OFF")) { logLevel = Level.OFF; } else if (level.equalsIgnoreCase("SEVERE")) { logLevel = Level.SEVERE; } else if (level.equalsIgnoreCase("WARNING")) { logLevel = Level.WARNING; } else { throw new ParseException("argument for loglvl unknown"); } //Remove app specific arguments from total arguments int logLvlIndex = argsList.indexOf("-" + LOG_LVL); argsList.remove(logLvlIndex + 1); argsList.remove(logLvlIndex); } //Setup logger try { ABMBDILoggerSetter.initialized(prop, isLogToConsole, logLevel); ABMBDILoggerSetter.setup(LOGGER); } catch (IOException e) { e.printStackTrace(); LOGGER.severe(e.getMessage()); throw new RuntimeException("Problems with creating logfile"); } //Translate argsList into array------------------------------ String[] newargs = new String[argsList.size()]; for (int i = 0; i < argsList.size(); i++) { newargs[i] = argsList.get(i); } //Running the system---------------------------------------- if (isRunningSC == true) { runSC(prop); } if (isRunningCO == true) { runCO(prop, newargs, isForced); } } catch (IOException e) { e.printStackTrace(); LOGGER.severe(e.getMessage()); } } else { throw new ParseException("-prop <properties_location> is a required option"); } } catch (ParseException exp) { LOGGER.severe("Unexpected exception:" + exp.getMessage()); //If its not working print out help info HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Jadex-ABMS", options); } }
From source file:com.medvision360.medrecord.tools.dumpadl.CommandLineReader.java
/** * Parse the command line options./* www . jav a 2s . c o m*/ * * @param args The command line arguments. */ public void parse(final String[] args) throws ParseException { final BasicParser parser = new BasicParser(); m_commandLine = parser.parse(m_options, args); }
From source file:com.twitter.distributedlog.service.MonitorServiceApp.java
private void run() { try {/*from w w w . j a va2 s. c o m*/ logger.info("Running monitor service."); BasicParser parser = new BasicParser(); CommandLine cmdline = parser.parse(options, args); runCmd(cmdline); } catch (ParseException pe) { printUsage(); Runtime.getRuntime().exit(-1); } catch (IOException ie) { logger.error("Failed to start monitor service : ", ie); Runtime.getRuntime().exit(-1); } }
From source file:com.twitter.distributedlog.benchmark.stream.StreamBenchmark.java
protected void parseCommandLine(String[] args) throws Exception { BasicParser parser = new BasicParser(); CommandLine cmdline = parser.parse(options, args); if (cmdline.hasOption("h")) { printUsage();/*from www . ja va 2s. c o m*/ System.exit(0); } if (cmdline.hasOption("u")) { this.uri = URI.create(cmdline.getOptionValue("u")); } else { printUsage(); System.exit(0); } this.conf = new DistributedLogConfiguration(); if (cmdline.hasOption("c")) { String configFile = cmdline.getOptionValue("c"); this.conf.loadConf(new File(configFile).toURI().toURL()); } if (cmdline.hasOption("p")) { statsProvider = ReflectionUtils.newInstance(cmdline.getOptionValue("p"), StatsProvider.class); } else { statsProvider = new NullStatsProvider(); } if (cmdline.hasOption("s")) { this.streamName = cmdline.getOptionValue("s"); } else { printUsage(); System.exit(0); } parseCommandLine(cmdline); }
From source file:com.twitter.distributedlog.service.DistributedLogServerApp.java
private void run() { try {/* w ww .ja v a 2 s .com*/ logger.info("Running distributedlog server : args = {}", Arrays.toString(args)); BasicParser parser = new BasicParser(); CommandLine cmdline = parser.parse(options, args); runCmd(cmdline); } catch (ParseException pe) { logger.error("Argument error : {}", pe.getMessage()); printUsage(); Runtime.getRuntime().exit(-1); } catch (IllegalArgumentException iae) { logger.error("Argument error : {}", iae.getMessage()); printUsage(); Runtime.getRuntime().exit(-1); } catch (ConfigurationException ce) { logger.error("Configuration error : {}", ce.getMessage()); printUsage(); Runtime.getRuntime().exit(-1); } catch (IOException ie) { logger.error("Failed to start distributedlog server : ", ie); Runtime.getRuntime().exit(-1); } }