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:kieker.tools.AbstractCommandLineTool.java
private CommandLine parseCommandLineArguments(final Options options, final String[] arguments) { final BasicParser parser = new BasicParser(); try {/*from ww w. ja v a 2 s . co m*/ return parser.parse(options, arguments); } catch (final ParseException ex) { // Note that we append ex.getMessage() to the log message on purpose to improve the // logging output on the console. LOG.error("An error occurred while parsing the command line arguments: " + ex.getMessage(), ex); LOG.info("Use the option `--" + CMD_OPT_NAME_HELP_LONG + "` for usage information"); return null; } }
From source file:fastacreator.ParseCLI.java
/** * Rutger Ozinga. ParseCLI Parses the commandline input and is able to * return the wanted option and value.//from www. ja v a2 s .c o m * * @param args are commandline arguments. * @throws org.apache.commons.cli.ParseException an exception */ public ParseCLI(final String[] args) throws org.apache.commons.cli.ParseException { HelpFormatter helpForm = new HelpFormatter(); Options cliOpt = new Options(); cliOpt.addOption("h", "help", false, "Displays help"); cliOpt.addOption("p", true, "Expects a path to a protein fasta file."); cliOpt.addOption("n", true, "Expects a path to place the new tab separated transcript file at."); cliOpt.addOption("i", true, "The index of the sequence"); if (args.length == 0) { helpForm.printHelp("Please enter all the " + "options below. ", cliOpt); System.exit(0); } else { BasicParser parser = new BasicParser(); CommandLine cliParser = parser.parse(cliOpt, args); if (cliParser.getOptions().length < 2) { System.out.println( "Error : " + "Please enter all options in" + " order for this program to work" + "!\n"); helpForm.printHelp("Please enter all of the " + "option ", cliOpt); System.exit(0); } else { if (cliParser.hasOption("h") && cliParser.hasOption("help")) { helpForm.printHelp("Command Line Help:\n", cliOpt); System.exit(0); } else { String snpFileString = cliParser.getOptionValue("p"); Path snpPath = Paths.get(snpFileString); if (Files.exists(snpPath)) { setCDSPath(snpPath); } else { System.out.println("The entered Path does" + " not exits"); helpForm.printHelp("Please enter -p followed by a valid" + " path ", cliOpt); System.exit(0); } String newFileString = cliParser.getOptionValue("n"); Matcher match2 = re.matcher(newFileString); String editedTranscriptFileString = match2.replaceAll(""); Path newFilePath = Paths.get(editedTranscriptFileString); if (Files.exists(newFilePath)) { setNewFilePath(newFileString); } else { System.out.println("The entered Path does" + " not exits"); helpForm.printHelp("Please enter -nt followed by a valid" + " path ", cliOpt); System.exit(0); } String indexString = cliParser.getOptionValue("i"); int index = Integer.parseInt(indexString); setIndex(index); } } } }
From source file:com.shmsoft.dmass.main.SHMcloudMain.java
/** * Process the command line arguments//from w w w.j a v a 2 s . c om * * @param args command line arguments */ private void processOptions(String[] args) { String customParameterFile; Project project = null; try { BasicParser parser = new BasicParser(); commandLine = parser.parse(options, args); // one-time actions if (commandLine.hasOption(CommandLineOption.HELP.getName()) || commandLine.getOptions().length == 0) { HelpFormatter f = new HelpFormatter(); f.printHelp("java -jar FreeEed.jar [options]\n\n" + "where options include:", options); } else if (commandLine.hasOption(CommandLineOption.VERSION.getName())) { System.out.println(Version.getVersionAndBuild()); } else if (commandLine.hasOption(CommandLineOption.GUI.getName())) { openGUI(); } else if (commandLine.hasOption(CommandLineOption.ENRON.getName())) { processEnronDataSet(); } else { if (commandLine.hasOption(CommandLineOption.PARAM_FILE.getName())) { // independent actions customParameterFile = commandLine.getOptionValue(CommandLineOption.PARAM_FILE.getName()); project = new Project().loadFromFile(new File(customParameterFile)); Project.setProject(project); SHMcloudLogging.init(false); } if (commandLine.hasOption(CommandLineOption.DRY.getName())) { System.out.println("Dry run - exiting now."); } else { if (project.isStage()) { stagePackageInput(); } String runWhere = project.getProcessWhere(); if (runWhere != null) { process(runWhere); } } } } catch (Exception e) { e.printStackTrace(System.out); } }
From source file:net.sf.clirr.cli.Clirr.java
private CommandLine parseCommandLine(String[] args, Options options) { BasicParser parser = new BasicParser(); CommandLine cmdline = null;/*from ww w . ja va 2 s .co m*/ try { cmdline = parser.parse(options, args); } catch (ParseException ex) { System.err.println("Invalid command line arguments."); printUsage(options, System.err); System.exit(-1); } return cmdline; }
From source file:cdscreator.ParseCLI.java
/** * Rutger Ozinga. ParseCLI Parses the commandline input and is able to * return the wanted option and value./* w w w.ja v a2 s . c o m*/ * * @param args are commandline arguments. * @throws org.apache.commons.cli.ParseException an exception */ public ParseCLI(final String[] args) throws org.apache.commons.cli.ParseException { HelpFormatter helpForm = new HelpFormatter(); Options cliOpt = new Options(); cliOpt.addOption("h", "help", false, "Displays help"); cliOpt.addOption("p", true, "Expects a path to a protein fasta file."); cliOpt.addOption("t", true, "Expects a path to a transcript fasta file."); cliOpt.addOption("nt", true, "Expects a path to place the new tab separated transcript file at."); cliOpt.addOption("o", true, "Expects a path to place the new tab separated protein file at"); if (args.length == 0) { helpForm.printHelp("Please enter all the " + "options below. ", cliOpt); System.exit(0); } else { BasicParser parser = new BasicParser(); CommandLine cliParser = parser.parse(cliOpt, args); if (cliParser.getOptions().length < 4) { System.out.println( "Error : " + "Please enter all options in" + " order for this program to work" + "!\n"); helpForm.printHelp("Please enter all of the " + "option ", cliOpt); System.exit(0); } else { if (cliParser.hasOption("h") && cliParser.hasOption("help")) { helpForm.printHelp("Command Line Help:\n", cliOpt); System.exit(0); } else { String snpFileString = cliParser.getOptionValue("p"); Path snpPath = Paths.get(snpFileString); if (Files.exists(snpPath)) { setProtPath(snpPath); } else { System.out.println("The entered Path does" + " not exits"); helpForm.printHelp("Please enter -p followed by a valid" + " path ", cliOpt); System.exit(0); } String transcriptFileString = cliParser.getOptionValue("t"); Path transcriptPath = Paths.get(transcriptFileString); if (Files.exists(transcriptPath)) { setTransPath(transcriptPath); } else { System.out.println("The entered Path does" + " not exits"); helpForm.printHelp("Please enter -t followed by a valid" + " path ", cliOpt); System.exit(0); } String newFileString = cliParser.getOptionValue("o"); Matcher match = re.matcher(newFileString); String editedFileString = match.replaceAll(""); Path newPath = Paths.get(editedFileString); if (Files.exists(newPath)) { setNewFilePath(newFileString); } else { System.out.println("The entered Path does" + " not exits"); helpForm.printHelp("Please enter -o followed by a valid" + " path ", cliOpt); System.exit(0); } String newTranscriptFileString = cliParser.getOptionValue("nt"); Matcher match2 = re.matcher(newTranscriptFileString); String editedTranscriptFileString = match2.replaceAll(""); Path newTranscriptPath = Paths.get(editedTranscriptFileString); if (Files.exists(newTranscriptPath)) { setNewTranscriptFilePath(newTranscriptFileString); } else { System.out.println("The entered Path does" + " not exits"); helpForm.printHelp("Please enter -nt followed by a valid" + " path ", cliOpt); System.exit(0); } } } } }
From source file:com.alcatel_lucent.nz.wnmsextract.WNMSTransform.java
/** * Called if the Transformer class is called as a main. Useful for one off XML parse jobs * @param args// w w w . j av a 2s . c o m */ public void processcli(String[] args) { String xf = null, sf = null, of = null; try { Options opt = new Options(); opt.addOption("h", "help", false, "Print help for this application"); opt.addOption("x", "xml", true, "The XCM file to load"); opt.addOption("s", "xsl", true, "The stylesheet to apply"); opt.addOption("o", true, "The output CSV to generate"); BasicParser bp = new BasicParser(); CommandLine cl = bp.parse(opt, args); ALUParser p = new ALUParserFactory("WIPS").getInstance(); if (cl.hasOption('h')) { HelpFormatter f = new HelpFormatter(); f.printHelp("OptionsTip", opt); } else { //XCM snapshot if (cl.hasOption('x')) { xf = cl.getOptionValue("x"); } else { System.err.println("XML File not Specified"); System.exit(1); } //stylesheet if (cl.hasOption('s')) { sf = cl.getOptionValue("s"); } else { System.err.println("XSL File not Specified"); System.exit(1); } //output if (cl.hasOption('o')) { of = cl.getOptionValue("o"); } else { String sfn = sf.substring(sf.lastIndexOf("\\") + 1, sf.length() - 4); of = xf.substring(0, xf.length() - 4) + "." + sfn + ".csv"; } System.out.println(xf + " + " + sf + " -> " + of); p.setParseFile(xf); p.setTransformFile(sf); p.setResultFile(of); //how is this ever supposed to work if you never call transform?!? } } catch (ParseException e) { e.printStackTrace(); } }
From source file:com.amazonaws.mturk.cmd.AbstractCmd.java
public void run(String[] args) { try {//ww w . ja va 2s. c o m BasicParser parser = new BasicParser(); CommandLine cmdLine = parser.parse(opt, args); if (cmdLine.hasOption(ARG_HELP) || cmdLine.hasOption(ARG_HELP_SHORT)) { printHelp(); System.exit(-1); } if (cmdLine.hasOption(ARG_SANDBOX) && !ClientConfig.SANDBOX_SERVICE_URL.equalsIgnoreCase(config.getServiceURL())) { log.info("Sandbox override"); setSandBoxMode(); } else { initService(); } log.debug(String.format("Running command against %s", config.getServiceURL())); runCommand(cmdLine); } catch (Exception e) { log.error("An error occurred: " + e.getLocalizedMessage(), e); System.exit(-1); } }
From source file:createconversioncdsfile.ParseCLI.java
/** * Rutger Ozinga. ParseCLI Parses the commandline input and is able to * return the wanted option and value.// w w w . ja v a2s. c o m * * @param args are commandline arguments. * @throws org.apache.commons.cli.ParseException an exception */ public ParseCLI(final String[] args) throws org.apache.commons.cli.ParseException { HelpFormatter helpForm = new HelpFormatter(); Options cliOpt = new Options(); cliOpt.addOption("h", "help", false, "Displays help"); cliOpt.addOption("p", true, "Expects a path to a protein fasta file."); cliOpt.addOption("t", true, "Expects a path to a transcript fasta file."); cliOpt.addOption("c", true, "Expects a path to a conversion file at."); cliOpt.addOption("cds", true, "Expects a path to a cds file at."); cliOpt.addOption("o", true, "Expects a path to place the new tab separated protein file at"); if (args.length == 0) { helpForm.printHelp("Please enter all the " + "options below. ", cliOpt); System.exit(0); } else { BasicParser parser = new BasicParser(); CommandLine cliParser = parser.parse(cliOpt, args); if (cliParser.getOptions().length < 4) { System.out.println( "Error : " + "Please enter all options in" + " order for this program to work" + "!\n"); helpForm.printHelp("Please enter all of the " + "option ", cliOpt); System.exit(0); } else { if (cliParser.hasOption("h") && cliParser.hasOption("help")) { helpForm.printHelp("Command Line Help:\n", cliOpt); System.exit(0); } else { String snpFileString = cliParser.getOptionValue("p"); Path snpPath = Paths.get(snpFileString); if (Files.exists(snpPath)) { setProtPath(snpPath); } else { System.out.println("The entered Path does" + " not exits"); helpForm.printHelp("Please enter -p followed by a valid" + " path ", cliOpt); System.exit(0); } String conversionFileString = cliParser.getOptionValue("c"); Path conversionPath = Paths.get(conversionFileString); if (Files.exists(conversionPath)) { setConversionFilePath(conversionPath); } else { System.out.println("The entered Path does" + " not exits"); helpForm.printHelp("Please enter -c followed by a valid" + " path ", cliOpt); System.exit(0); } String cdsFileString = cliParser.getOptionValue("cds"); Path cdsPath = Paths.get(cdsFileString); if (Files.exists(cdsPath)) { setCdsPath(cdsPath); } else { System.out.println("The entered Path does" + " not exits"); helpForm.printHelp("Please enter -cds followed by a valid" + " path ", cliOpt); System.exit(0); } String transcriptFileString = cliParser.getOptionValue("t"); Path transcriptPath = Paths.get(transcriptFileString); if (Files.exists(transcriptPath)) { setTransPath(transcriptPath); } else { System.out.println("The entered Path does" + " not exits"); helpForm.printHelp("Please enter -t followed by a valid" + " path ", cliOpt); System.exit(0); } String newFileString = cliParser.getOptionValue("o"); Matcher match = re.matcher(newFileString); String editedFileString = match.replaceAll(""); Path newPath = Paths.get(editedFileString); if (Files.exists(newPath)) { setNewFilePath(newFileString); } else { System.out.println("The entered Path does" + " not exits"); helpForm.printHelp("Please enter -o followed by a valid" + " path ", cliOpt); System.exit(0); } } } } }
From source file:com.twitter.distributedlog.benchmark.Benchmarker.java
void run() throws Exception { logger.info("Running benchmark."); BasicParser parser = new BasicParser(); CommandLine cmdline = parser.parse(options, args); if (cmdline.hasOption("h")) { printUsage();//from www. ja va 2 s .c o m System.exit(0); } if (cmdline.hasOption("s")) { String serversetPathStr = cmdline.getOptionValue("s"); serversetPaths = Arrays.asList(StringUtils.split(serversetPathStr, ',')); } if (cmdline.hasOption("fn")) { String finagleNameStr = cmdline.getOptionValue("fn"); finagleNames = Arrays.asList(StringUtils.split(finagleNameStr, ',')); } if (cmdline.hasOption("i")) { shardId = Integer.parseInt(cmdline.getOptionValue("i")); } if (cmdline.hasOption("d")) { durationMins = Integer.parseInt(cmdline.getOptionValue("d")); } if (cmdline.hasOption("sp")) { streamPrefix = cmdline.getOptionValue("sp"); } if (cmdline.hasOption("sc")) { numStreams = Integer.parseInt(cmdline.getOptionValue("sc")); } if (cmdline.hasOption("ms")) { msgSize = Integer.parseInt(cmdline.getOptionValue("ms")); } if (cmdline.hasOption("r")) { rate = Integer.parseInt(cmdline.getOptionValue("r")); } if (cmdline.hasOption("mr")) { maxRate = Integer.parseInt(cmdline.getOptionValue("mr")); } if (cmdline.hasOption("cr")) { changeRate = Integer.parseInt(cmdline.getOptionValue("cr")); } if (cmdline.hasOption("ci")) { changeRateSeconds = Integer.parseInt(cmdline.getOptionValue("ci")); } if (cmdline.hasOption("t")) { concurrency = Integer.parseInt(cmdline.getOptionValue("t")); } if (cmdline.hasOption("m")) { mode = cmdline.getOptionValue("m"); } if (cmdline.hasOption("u")) { dlUri = URI.create(cmdline.getOptionValue("u")); } if (cmdline.hasOption("bs")) { batchSize = Integer.parseInt(cmdline.getOptionValue("bs")); Preconditions.checkArgument("write" != mode, "batchSize supported only for mode=write"); } if (cmdline.hasOption("c")) { String configFile = cmdline.getOptionValue("c"); conf.loadConf(new File(configFile).toURI().toURL()); } if (cmdline.hasOption("rps")) { readersPerStream = Integer.parseInt(cmdline.getOptionValue("rps")); } if (cmdline.hasOption("msid")) { maxStreamId = Integer.parseInt(cmdline.getOptionValue("msid")); } if (cmdline.hasOption("ti")) { truncationInterval = Integer.parseInt(cmdline.getOptionValue("ti")); } if (cmdline.hasOption("ssid")) { startStreamId = Integer.parseInt(cmdline.getOptionValue("ssid")); } if (cmdline.hasOption("esid")) { endStreamId = Integer.parseInt(cmdline.getOptionValue("esid")); } if (cmdline.hasOption("hccs")) { hostConnectionCoreSize = Integer.parseInt(cmdline.getOptionValue("hccs")); } if (cmdline.hasOption("hcl")) { hostConnectionLimit = Integer.parseInt(cmdline.getOptionValue("hcl")); } if (cmdline.hasOption("sb")) { sendBufferSize = Integer.parseInt(cmdline.getOptionValue("sb")); } if (cmdline.hasOption("rb")) { recvBufferSize = Integer.parseInt(cmdline.getOptionValue("rb")); } thriftmux = cmdline.hasOption("mx"); handshakeWithClientInfo = cmdline.hasOption("hsci"); readFromHead = cmdline.hasOption("rfh"); enableBatching = cmdline.hasOption("bt"); Preconditions.checkArgument(shardId >= 0, "shardId must be >= 0"); Preconditions.checkArgument(numStreams > 0, "numStreams must be > 0"); Preconditions.checkArgument(durationMins > 0, "durationMins must be > 0"); Preconditions.checkArgument(streamPrefix != null, "streamPrefix must be defined"); Preconditions.checkArgument(hostConnectionCoreSize > 0, "host connection core size must be > 0"); Preconditions.checkArgument(hostConnectionLimit > 0, "host connection limit must be > 0"); if (cmdline.hasOption("p")) { statsProvider = ReflectionUtils.newInstance(cmdline.getOptionValue("p"), StatsProvider.class); } else { statsProvider = new NullStatsProvider(); } logger.info("Starting stats provider : {}.", statsProvider.getClass()); statsProvider.start(conf); Worker w = null; if (mode.startsWith("read")) { w = runReader(); } else if (mode.startsWith("write")) { w = runWriter(); } else if (mode.startsWith("dlwrite")) { w = runDLWriter(); } else if (mode.startsWith("dlread")) { w = runDLReader(); } if (w == null) { throw new IOException("Unknown mode " + mode + " to run the benchmark."); } Thread workerThread = new Thread(w, mode + "-benchmark-thread"); workerThread.start(); TimeUnit.MINUTES.sleep(durationMins); logger.info("{} minutes passed, exiting...", durationMins); w.close(); if (null != statsProvider) { statsProvider.stop(); } Runtime.getRuntime().exit(0); }
From source file:de.rrze.idmone.utils.jidgen.cli.IdGenOptions.java
/** * Fill the internal variable data by parsing a given * array of command line options./*from ww w. ja v a 2 s. c om*/ * * @param args * the String array containing all command line options * @return the data collection * @throws ParseException */ public HashMap<String, String> parse(String[] args) throws ParseException { // get a list of all stored option objects to be processed // excluding all dummy options Collection<IdGenOption> options = new HashSet<IdGenOption>(); options.addAll(this.getOptions()); options.removeAll(this.dummyOptions.values()); Iterator<IdGenOption> iter = options.iterator(); // init the parser BasicParser parser = new BasicParser(); CommandLine commandLine = parser.parse(this, args); // iterate over all possible options while (iter.hasNext()) { IdGenOption currentOption = iter.next(); //logger.trace("Processing option \"" + currentOption.getShortOpt() + "\""); if (commandLine.hasOption(currentOption.getShortOpt())) { // option was specified String value = commandLine.getOptionValue(currentOption.getShortOpt()); if (value != null) { // option has a specified value this.data.put(currentOption.getShortOpt(), value); logger.info(currentOption.getShortOpt() + " = " + value); } else if (currentOption.hasArg()) { // option does NOT have a specified value logger.error(currentOption.getShortOpt() + " " + Messages.getString("IdGenOptions.MISSING_ARGUMENT")); System.out.println(this.getHelp(false)); System.exit(170); } else { // at least put an entry with an empty string in the data array // to mark that the option was specified this.data.put(currentOption.getShortOpt(), ""); } } else { // option was NOT specified, so use default if available if (currentOption.hasDefaultValue()) { // has default logger.info(currentOption.getShortOpt() + " " + Messages.getString("IdGenOptions.USING_DEFAULT") + " " + currentOption.getDefaultValue()); this.data.put(currentOption.getShortOpt(), currentOption.getDefaultValue()); } } } return this.data; }