List of usage examples for org.apache.commons.cli ParseException getMessage
public String getMessage()
From source file:net.douglasthrift.bigscreenbot.BigScreenBot.java
public static void main(String[] args) { Options options = new Options(); options.addOption("h", "help", false, "show this help message and exit"); options.addOption("v", "verbose", false, ""); CommandLine line = null;/* w w w . ja v a2 s .c o m*/ try { line = new GnuParser().parse(options, args); } catch (ParseException exception) { System.err.println("bigscreenbot: " + exception.getMessage()); } if (line.hasOption('h')) { new HelpFormatter().printHelp("bigscreenbot", options, true); return; } new BigScreenBot(line.hasOption('v')); }
From source file:com.archivas.clienttools.arcmover.cli.ArcProfileMgr.java
@SuppressWarnings({ "UseOfSystemOutOrSystemErr" })
public static void main(String args[]) {
ArcProfileMgr arcProfileMgr = null;/*w w w . j av a 2 s . c o m*/
ConfigurationHelper.validateLaunchOK();
try {
arcProfileMgr = new ArcProfileMgr(args);
arcProfileMgr.parseArgs();
if (arcProfileMgr.printHelp) {
System.out.println(arcProfileMgr.helpScreen());
} else {
arcProfileMgr.execute(new PrintWriter(System.out), new PrintWriter(System.err));
}
} catch (ParseException e) {
System.out.println("Error: " + e.getMessage());
System.out.println();
System.out.println(arcProfileMgr.helpScreen());
arcProfileMgr.setExitCode(EXIT_CODE_OPTION_PARSE_ERROR);
} catch (Exception e) {
LOG.log(Level.SEVERE, "Unexpected Exception.", e);
System.out.println();
System.out.println("Failed to create a new profile " + e.getMessage());
arcProfileMgr.setExitCode(EXIT_CODE_DM_ERROR);
} finally {
if (arcProfileMgr != null) {
arcProfileMgr.exit();
}
}
}
From source file:de.unisb.cs.st.javaslicer.slicing.Slicer.java
public static void main(String[] args) throws InterruptedException { Options options = createOptions();/*w w w.j av a2s . c om*/ CommandLineParser parser = new GnuParser(); CommandLine cmdLine; try { cmdLine = parser.parse(options, args, true); } catch (ParseException e) { System.err.println("Error parsing the command line arguments: " + e.getMessage()); return; } if (cmdLine.hasOption('h')) { printHelp(options, System.out); System.exit(0); } String[] additionalArgs = cmdLine.getArgs(); if (additionalArgs.length != 2) { printHelp(options, System.err); System.exit(-1); } // ?? 1. ? 2.? File traceFile = new File(additionalArgs[0]); String slicingCriterionString = additionalArgs[1]; Long threadId = null; if (cmdLine.hasOption('t')) { // the interesting thread id for slicing try { threadId = Long.parseLong(cmdLine.getOptionValue('t')); } catch (NumberFormatException e) { System.err.println("Illegal thread id: " + cmdLine.getOptionValue('t')); System.exit(-1); } } TraceResult trace; try { trace = TraceResult.readFrom(traceFile); } catch (IOException e) { System.err.format("Could not read the trace file \"%s\": %s%n", traceFile, e); System.exit(-1); return; } List<SlicingCriterion> sc = null; // a list contains the instruction's info corresponds to the slicing criterion //slicingCriterionString get from additionalArgs[1] try { sc = StaticSlicingCriterion.parseAll(slicingCriterionString, trace.getReadClasses()); } catch (IllegalArgumentException e) { System.err.println("Error parsing slicing criterion: " + e.getMessage()); System.exit(-1); return; } List<ThreadId> threads = trace.getThreads(); // the threads that generate the traces if (threads.size() == 0) { System.err.println("The trace file contains no tracing information."); System.exit(-1); } // threadID is used to mark the interesting thread ThreadId tracing = null; for (ThreadId t : threads) { if (threadId == null) { if ("main".equals(t.getThreadName()) && (tracing == null || t.getJavaThreadId() < tracing.getJavaThreadId())) tracing = t; } else if (t.getJavaThreadId() == threadId.longValue()) { tracing = t; } } if (tracing == null) { System.err.println(threadId == null ? "Couldn't find the main thread." : "The thread you specified was not found."); System.exit(-1); return; } long startTime = System.nanoTime(); Slicer slicer = new Slicer(trace); if (cmdLine.hasOption("progress")) // the parameter process indicates that we need to monitor the process of slicing slicer.addProgressMonitor(new ConsoleProgressMonitor()); boolean multithreaded; if (cmdLine.hasOption("multithreaded")) { String multithreadedStr = cmdLine.getOptionValue("multithreaded"); multithreaded = ("1".equals(multithreadedStr) || "true".equals(multithreadedStr)); } else { multithreaded = Runtime.getRuntime().availableProcessors() > 1; } boolean warnUntracedMethods = cmdLine.hasOption("warn-untraced"); // give some warns when encounters untraced functions //sliceInstructionCollector implements the interface slice visitor, which travel the dependence graph SliceInstructionsCollector collector = new SliceInstructionsCollector(); // the collector is used to collect the instructions in the dependence graph according to the slice criterion. slicer.addSliceVisitor(collector); // zhushi by yhb if (warnUntracedMethods) slicer.addUntracedCallVisitor(new PrintUniqueUntracedMethods()); // the user need the untraced function info, so add untraced call visitor slicer.process(tracing, sc, multithreaded); //----------------------the key process of slicing!!! Set<InstructionInstance> slice = collector.getDynamicSlice(); // return the slice result from the collector long endTime = System.nanoTime(); Instruction[] sliceArray = slice.toArray(new Instruction[slice.size()]); // convert the set to array Arrays.sort(sliceArray); // in order to ensure the sequence of dynamic execution // show the slicing result System.out.println("The dynamic slice for criterion " + sc + ":"); for (Instruction insn : sliceArray) { System.out.format((Locale) null, "%s.%s:%d %s%n", insn.getMethod().getReadClass().getName(), insn.getMethod().getName(), insn.getLineNumber(), insn.toString()); } System.out.format((Locale) null, "%nSlice consists of %d bytecode instructions.%n", sliceArray.length); System.out.format((Locale) null, "Computation took %.2f seconds.%n", 1e-9 * (endTime - startTime)); }
From source file:net.antidot.semantic.rdf.rdb2rdf.main.Db2triples.java
public static void main(String[] args) { // Get all options Options options = new Options(); Options r2rmlOptions = new Options(); Options dmOptions = new Options(); options.addOption(modeOpt);//from ww w . j a va2 s .c o m options.addOption(userNameOpt); r2rmlOptions.addOption(userNameOpt); dmOptions.addOption(userNameOpt); options.addOption(passwordOpt); r2rmlOptions.addOption(passwordOpt); dmOptions.addOption(passwordOpt); options.addOption(URLOpt); r2rmlOptions.addOption(URLOpt); dmOptions.addOption(URLOpt); options.addOption(driverOpt); r2rmlOptions.addOption(driverOpt); dmOptions.addOption(driverOpt); options.addOption(dbOpt); r2rmlOptions.addOption(dbOpt); dmOptions.addOption(dbOpt); options.addOption(baseURIOpt); r2rmlOptions.addOption(baseURIOpt); dmOptions.addOption(baseURIOpt); options.addOption(forceOpt); r2rmlOptions.addOption(forceOpt); dmOptions.addOption(forceOpt); options.addOption(nativeOpt); r2rmlOptions.addOption(nativeOpt); dmOptions.addOption(nativeOpt); options.addOption(nativeStoreNameOpt); r2rmlOptions.addOption(nativeStoreNameOpt); dmOptions.addOption(nativeStoreNameOpt); options.addOption(outputOpt); r2rmlOptions.addOption(outputOpt); dmOptions.addOption(outputOpt); options.addOption(transformSPARQLFile); dmOptions.addOption(transformSPARQLFile); options.addOption(transformOutputFile); dmOptions.addOption(transformOutputFile); options.addOption(rdfFormat); r2rmlOptions.addOption(rdfFormat); dmOptions.addOption(rdfFormat); options.addOption(versionOpt); dmOptions.addOption(versionOpt); options.addOption(r2rmlFileOpt); r2rmlOptions.addOption(r2rmlFileOpt); // Init parameters String mode = null; String userName = null; String password = null; String url = null; DriverType driver = null; String dbName = null; String baseURI = null; boolean useNativeStore = false; boolean forceExistingRep = false; String nativeOutput = null; String output = null; String sparql = null; String sparqlOutput = null; String format = null; String r2rmlFile = null; int int_version = 1; // RDF Format output RDFFormat rdfFormat = RDFFormat.TURTLE; // Turtle by default // Norm version Version version = Version.WD_20120529; // Option parsing // Create the parser CommandLineParser parser = new GnuParser(); try { // parse the command line arguments CommandLine line = parser.parse(options, args); // Database settings // Mode if (!line.hasOption("mode")) { // automatically generate the help statement log.error("Mode is required. Use -m option to set it."); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(projectName, options); System.exit(-1); } else { mode = line.getOptionValue("mode"); if (!mode.equals("r2rml") && !mode.equals("dm")) { log.error("Unkonw mode. Please select 'r2rml' or 'dm' mode."); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(projectName, options); System.exit(-1); } } // user name if (!line.hasOption("user")) { // automatically generate the help statement log.error("User name is required. Use -u option to set it."); HelpFormatter formatter = new HelpFormatter(); if (mode.equals("r2rml")) { formatter.printHelp(projectNameR2RMLMode, r2rmlOptions); } else { formatter.printHelp(projectNameDirectMappingMode, dmOptions); } System.exit(-1); } else { userName = line.getOptionValue("user"); } // password if (!line.hasOption("pass")) { // automatically generate the help statement log.error("Password is required. Use -p option to set it."); HelpFormatter formatter = new HelpFormatter(); if (mode.equals("r2rml")) { formatter.printHelp(projectNameR2RMLMode, r2rmlOptions); } else { formatter.printHelp(projectNameDirectMappingMode, dmOptions); } System.exit(-1); } else { password = line.getOptionValue("pass"); } // Database URL url = line.getOptionValue("url", "jdbc:mysql://localhost/"); // driver driver = new DriverType(line.getOptionValue("driver", defaultDriver.getDriverName())); // Database name if (!line.hasOption("database")) { // automatically generate the help statement log.error("Database name is required. Use -b option to set it."); HelpFormatter formatter = new HelpFormatter(); if (mode.equals("r2rml")) { formatter.printHelp(projectNameR2RMLMode, r2rmlOptions); } else { formatter.printHelp(projectNameDirectMappingMode, dmOptions); } System.exit(-1); } else { dbName = line.getOptionValue("database"); } // Base URI baseURI = line.getOptionValue("base_uri", "http://foo.example/DB/"); // Use of native store ? useNativeStore = line.hasOption("n"); // Name of native store if (useNativeStore && !line.hasOption("native_output")) { // automatically generate the help statement log.error("Native triplestore path is required. Use -n option to set it."); HelpFormatter formatter = new HelpFormatter(); if (mode.equals("r2rml")) { formatter.printHelp(projectNameR2RMLMode, r2rmlOptions); } else { formatter.printHelp(projectNameDirectMappingMode, dmOptions); } System.exit(-1); } else { nativeOutput = line.getOptionValue("native_output"); } // Force loading of repository forceExistingRep = line.hasOption("f"); // Output output = line.getOptionValue("output", "output.ttl"); // SPARQL transformation if (line.hasOption("sparql")) { if (!mode.equals("dm")) { log.warn("sparql option is required only for 'dm' mode : it will be ignored..."); } else { sparql = line.getOptionValue("sparql"); sparqlOutput = line.getOptionValue("sparql_output", "output_sparql.ttl"); } } // RDF Format if (line.hasOption("format")) { format = line.getOptionValue("format"); if (format.equals("TURTLE")) rdfFormat = RDFFormat.TURTLE; else if (format.equals("RDFXML")) rdfFormat = RDFFormat.RDFXML; else if (format.equals("NTRIPLES")) rdfFormat = RDFFormat.NTRIPLES; else if (!format.equals("N3")) { log.error("Unknown RDF format. Please use RDFXML, TURTLE, N3 or NTRIPLES."); HelpFormatter formatter = new HelpFormatter(); if (mode.equals("r2rml")) { formatter.printHelp(projectNameR2RMLMode, r2rmlOptions); } else { formatter.printHelp(projectNameDirectMappingMode, dmOptions); } System.exit(-1); } } // Norm version if (line.hasOption("version")) { if (!mode.equals("dm")) { log.warn("version option is required only for 'dm' mode : it will be ignored..."); } switch (int_version) { case 1: version = Version.WD_20120529; break; case 2: version = Version.WD_20110324; // Check DB compatibilities if (!(driver.equals(DriverType.MysqlDriver) || driver.equals(DriverType.PostgreSQL))) { log.error( "Db2triples in Direct Mapping mode does'nt support this driver for the Working Draft" + " of 23 March 2011 (only MySQL and PostGreSQL for this time). " + "You can set the version option to select Working Draft of 20 September 2011."); System.exit(-1); } break; default: break; } } // r2rml instance if (mode.equals("r2rml")) { if (!line.hasOption("r2rml_file")) { log.error("R2RML config file is required. Use -r option to set it."); // automatically generate the help statement HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(projectNameR2RMLMode, r2rmlOptions); System.exit(-1); } else { r2rmlFile = line.getOptionValue("r2rml_file"); File r2rmlFileTest = new File(r2rmlFile); if (!r2rmlFileTest.exists()) { log.error("R2RML file does not exists."); System.exit(-1); } } } } catch (ParseException exp) { // oops, something went wrong log.error("Parsing failed. Reason : " + exp.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(projectName, options); System.exit(-1); } // Open test database Connection conn = null; try { // Connect database conn = SQLConnector.connect(userName, password, url + dbName, driver); // Generate RDF graph SesameDataSet g = null; // Check nature of storage (memory by default) if (useNativeStore) { File pathToNativeOutputDir = new File(nativeOutput); if (pathToNativeOutputDir.exists() && !forceExistingRep) { log.error("Directory " + pathToNativeOutputDir + " already exists. Use -f option to force loading of existing repository."); System.exit(-1); } // Extract database model according to convert mode if (mode.equals("r2rml")) { g = R2RMLProcessor.convertDatabase(conn, r2rmlFile, baseURI, nativeOutput, driver); } else { g = DirectMapper.generateDirectMapping(conn, version, driver, baseURI, null, nativeOutput); } } else { File outputFile = new File(output); if (outputFile.exists() && !forceExistingRep) { log.error("Output file " + outputFile.getAbsolutePath() + " already exists. Please remove it or modify ouput name option."); System.exit(-1); } // Extract database model if (mode.equals("r2rml")) { g = R2RMLProcessor.convertDatabase(conn, r2rmlFile, baseURI, driver); } else { g = DirectMapper.generateDirectMapping(conn, version, driver, baseURI, null, null); } // Dump graph log.info("Serialize RDF graph..."); g.dumpRDF(output, rdfFormat); log.info("RDF graph serialized into " + outputFile.getAbsolutePath()); } if (sparql != null && mode.equals("dm")) { log.info("Execute SPARQL transformation..."); Long start = System.currentTimeMillis(); String result = g.runSPARQLFromFile(sparql, rdfFormat); SesameDataSet gResult = new SesameDataSet(); gResult.addString(result, rdfFormat); gResult.dumpRDF(sparqlOutput, rdfFormat); Float stop = Float.valueOf(System.currentTimeMillis() - start) / 1000; log.info("Direct Mapping SPARQL query executed in " + stop + " seconds."); log.info("[DirectMapping:main] Number of triples after transformation : " + gResult.getSize()); } } catch (Exception e) { e.printStackTrace(); } finally { try { // Close db connection conn.close(); } catch (SQLException e) { e.printStackTrace(); } } }
From source file:ca.twoducks.vor.ossindex.report.Assistant.java
/** Main method. Very simple, does not perform sanity checks on input. * /*w ww . ja va 2s . com*/ * @param args * @throws IOException */ public static void main(String[] args) throws IOException { CommandLineParser parser = new BasicParser(); try { // parse the command line arguments CommandLine line = parser.parse(getOptions(), args); if (line.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("assistant", getOptions()); return; } // Instantiate assistant Assistant assistant = new Assistant(); // Add default plugins assistant.addScanPlugin(ChecksumPlugin.class); assistant.addScanPlugin(HtmlDependencyPlugin.class); assistant.addScanPlugin(NodeDependencyPlugin.class); assistant.addScanPlugin(MavenDependencyPlugin.class); assistant.addScanPlugin(GemfileDependencyPlugin.class); if (line.hasOption(NO_DEPENDENCIES_OPTION)) { assistant.setExportDependencies(false); } else { assistant.setExportDependencies(true); } assistant.setIncludeImages(!line.hasOption(NO_IMAGES_OPTION)); assistant.setIncludeArtifacts(!line.hasOption(NO_ARTIFACTS_OPTION)); // Determine operation type boolean doScan = line.hasOption("scan"); boolean doMerge = line.hasOption("merge"); boolean doImport = line.hasOption("import"); int count = 0; if (doScan) count++; if (doMerge) count++; if (doImport) count++; if (count > 1) { System.err.println("Only one of 'scan', 'merge', or import may be selected"); return; } if (doScan) { // Get the output directory if (!line.hasOption("D")) { System.err.println("An output directory must be specified"); return; } File outputDir = new File(line.getOptionValue("D")); if (!outputDir.exists()) outputDir.mkdir(); if (!outputDir.isDirectory()) { System.err.println("Output option is not a directory: " + outputDir); return; } doScan(assistant, line.getOptionValue("scan"), outputDir, line.hasOption(VERBOSE_OUTPUT_OPTION)); return; } if (doMerge) { // Get the output directory if (!line.hasOption("D")) { System.err.println("An output directory must be specified"); return; } File outputDir = new File(line.getOptionValue("D")); if (!outputDir.exists()) outputDir.mkdir(); if (!outputDir.isDirectory()) { System.err.println("Output option is not a directory: " + outputDir); return; } doMerge(assistant, line.getOptionValues("merge"), outputDir); return; } if (doImport) { // Get the output directory if (!line.hasOption("D")) { System.err.println("An output directory must be specified"); return; } File outputDir = new File(line.getOptionValue("D")); if (!outputDir.exists()) outputDir.mkdir(); if (!outputDir.isDirectory()) { System.err.println("Output option is not a directory: " + outputDir); return; } doImport(assistant, line.getOptionValue("import"), outputDir); return; } } catch (ParseException exp) { System.err.println("Parsing failed. Reason: " + exp.getMessage()); } HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("assistant", getOptions()); return; }
From source file:com.netscape.cms.servlet.test.CATest.java
public static void main(String args[]) { String host = null;// ww w .ja v a2 s. c o m String port = null; String token_pwd = null; String db_dir = "./"; String protocol = "http"; // parse command line arguments Options options = new Options(); options.addOption("h", true, "Hostname of the CA"); options.addOption("p", true, "Port of the CA"); options.addOption("s", true, "Attempt Optional Secure SSL connection"); options.addOption("w", true, "Token password"); options.addOption("d", true, "Directory for tokendb"); options.addOption("c", true, "Optional SSL Client cert Nickname"); try { CommandLineParser parser = new PosixParser(); CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("h")) { host = cmd.getOptionValue("h"); } else { System.err.println("Error: no hostname provided."); usage(options); } if (cmd.hasOption("p")) { port = cmd.getOptionValue("p"); } else { System.err.println("Error: no port provided"); usage(options); } if (cmd.hasOption("w")) { token_pwd = cmd.getOptionValue("w"); } else { log("Notice: no token password provided"); } if (cmd.hasOption("d")) { db_dir = cmd.getOptionValue("d"); } if (cmd.hasOption("s")) { if (cmd.getOptionValue("s") != null && cmd.getOptionValue("s").equals("true")) { protocol = "https"; } } if (cmd.hasOption("c")) { String nick = cmd.getOptionValue("c"); if (nick != null && protocol.equals("https")) { clientCertNickname = nick; } } } catch (ParseException e) { System.err.println("Error in parsing command line options: " + e.getMessage()); usage(options); } CryptoManager manager = null; CryptoToken token = null; // Initialize token try { CryptoManager.initialize(db_dir); } catch (AlreadyInitializedException e) { // it is ok if it is already initialized } catch (Exception e) { log("INITIALIZATION ERROR: " + e.toString()); System.exit(1); } // log into token try { manager = CryptoManager.getInstance(); token = manager.getInternalKeyStorageToken(); Password password = new Password(token_pwd.toCharArray()); try { token.login(password); } catch (Exception e) { log("login Exception: " + e.toString()); if (!token.isLoggedIn()) { token.initPassword(password, password); } } } catch (Exception e) { log("Exception in logging into token:" + e.toString()); } CAClient client; CACertClient certClient; ProfileClient profileClient; try { ClientConfig config = new ClientConfig(); config.setServerURL(protocol + "://" + host + ":" + port); config.setCertNickname(clientCertNickname); client = new CAClient(new PKIClient(config, null)); certClient = (CACertClient) client.getClient("cert"); profileClient = (ProfileClient) client.getClient("profile"); } catch (Exception e) { e.printStackTrace(); return; } Collection<CertRequestInfo> list = null; try { list = certClient.listRequests("complete", null, null, null, null, null).getEntries(); } catch (Exception e) { e.printStackTrace(); } printRequests(list); //Get a CertInfo int certIdToPrint = 1; CertId id = new CertId(certIdToPrint); CertData certData = null; try { certData = certClient.getCert(id); } catch (CertNotFoundException e) { e.printStackTrace(); log("Cert: " + certIdToPrint + " not found. \n" + e.toString()); } printCertificate(certData); //Try an invalid Cert to print out //Get a CertInfo int certIdBadToPrint = 9999999; CertId certIdBad = new CertId(certIdBadToPrint); CertData certDataBad = null; try { certDataBad = certClient.getCert(certIdBad); } catch (CertNotFoundException e) { e.printStackTrace(); log("Cert: " + certIdBadToPrint + " not found. \n" + e.toString()); } printCertificate(certDataBad); //Get a CertInfoList CertDataInfos infos = null; try { infos = certClient.listCerts("VALID", null, null, null, null); } catch (Exception e) { e.printStackTrace(); } printCertInfos(infos, "no search filter:"); //Initiate a Certificate Enrollment CertEnrollmentRequest data = createUserCertEnrollment(); enrollAndApproveCertRequest(certClient, data); // submit a RA authenticated user cert request CertEnrollmentRequest rdata = createRAUserCertEnrollment(); enrollCertRequest(certClient, rdata); // now try a manually approved server cert CertEnrollmentRequest serverData = createServerCertEnrollment(); enrollAndApproveCertRequest(certClient, serverData); // submit using an agent approval profile serverData.setProfileId("caAgentServerCert"); enrollCertRequest(certClient, serverData); //Perform a sample certificate search with advanced search terms CertSearchRequest searchData = new CertSearchRequest(); searchData.setSerialNumberRangeInUse(true); searchData.setSerialFrom("9999"); searchData.setSerialTo("99990"); infos = certClient.findCerts(searchData, 100, 10); printCertInfos(infos, new FilterBuilder(searchData).buildFilter()); // Try to get a non existing request RequestId idBad = new RequestId("999999"); CertRequestInfo infoBad = null; try { infoBad = certClient.getRequest(idBad); } catch (RequestNotFoundException e) { e.printStackTrace(); log("Exception getting request #: " + idBad.toString() + "\n" + e.toString()); } printRequestInfo(infoBad); //Perform another sample certificate search with advanced search terms searchData = new CertSearchRequest(); searchData.setSubjectInUse(true); searchData.setEmail("jmagne@redhat.com"); searchData.setMatchExactly(true); infos = certClient.findCerts(searchData, 100, 10); printCertInfos(infos, new FilterBuilder(searchData).buildFilter()); //Get a list of Profiles ProfileDataInfos pInfos = profileClient.listProfiles(null, null); printProfileInfos(pInfos); // Get a specific profile String pId = "caUserCert"; ProfileData pData = profileClient.retrieveProfile(pId); printProfileData(pData); }
From source file:com.archivas.clienttools.arcmover.cli.ManagedCLIJob.java
@SuppressWarnings({ "UseOfSystemOutOrSystemErr" })
public static void main(String args[]) {
if (LOG.isLoggable(Level.FINE)) {
StringBuffer sb = new StringBuffer();
sb.append("Program Arguments").append(NEWLINE);
for (int i = 0; i < args.length; i++) {
sb.append(" ").append(i).append(": ").append(args[i]);
sb.append(NEWLINE);//from w ww.j a v a 2 s . co m
}
LOG.log(Level.FINE, sb.toString());
}
ConfigurationHelper.validateLaunchOK();
ManagedCLIJob arcCmd = null;
try {
if (args[0].equals("copy")) {
arcCmd = new ArcCopy(args, 2);
} else if (args[0].equals("delete")) {
arcCmd = new ArcDelete(args, 2);
} else if (args[0].equals("metadata")) {
arcCmd = new ArcMetadata(args, 2);
} else {
throw new RuntimeException("Unsupported operation: " + args[0]);
}
arcCmd.parseArgs();
if (arcCmd.shouldPrintHelp()) {
System.out.println(arcCmd.helpScreen());
} else {
arcCmd.execute(new PrintWriter(System.out), new PrintWriter(System.err));
}
} catch (ParseException e) {
System.out.println("Error: " + e.getMessage());
System.out.println();
System.out.println(arcCmd.helpScreen());
arcCmd.setExitCode(EXIT_CODE_OPTION_PARSE_ERROR);
} catch (Exception e) {
LOG.log(Level.SEVERE, e.getMessage(), e);
System.out.println();
System.err.println("Job failed. " + e.getMessage());
if (arcCmd != null) {
arcCmd.setExitCode(EXIT_CODE_DM_ERROR);
}
} finally {
if (arcCmd != null) {
arcCmd.exit();
}
}
}
From source file:erigo.filepump.FilePump.java
public static void main(String[] argsI) { boolean local_bShowGUI = true; String initial_outputFolder = "."; double initial_filesPerSec = 1.0; int initial_totNumFiles = 1000; String initial_mode_str = "local"; String initial_ftpHost;/*from w ww . ja v a 2 s . c om*/ String initial_ftpUser; String initial_ftpPassword; // // Parse command line arguments // // We use the Apche Commons CLI library to handle command line // arguments. See https://commons.apache.org/proper/commons-cli/usage.html // for examples, although note that we use the more up-to-date form // (Option.builder) to create Option objects. // // 1. Setup command line options // Options options = new Options(); // Example of a Boolean option (i.e., only the flag, no argument goes with it) options.addOption("h", "help", false, "Print this message."); // The following example is for: -outputfolder <folder> Location of output files Option outputFolderOption = Option.builder("outputfolder").argName("folder").hasArg() .desc("Location of output files; this folder must exist (it will not be created); default = \"" + initial_outputFolder + "\".") .build(); options.addOption(outputFolderOption); Option filesPerSecOption = Option.builder("fps").argName("filespersec").hasArg() .desc("Desired file rate, files/sec; default = " + initial_filesPerSec + ".").build(); options.addOption(filesPerSecOption); Option totNumFilesOption = Option.builder("totnum").argName("num").hasArg().desc( "Total number of output files; use -1 for unlimited number; default = " + initial_totNumFiles + ".") .build(); options.addOption(totNumFilesOption); Option outputModeOption = Option.builder("mode").argName("mode").hasArg() .desc("Specifies output interface, one of <local|ftp|sftp>; default = " + initial_mode_str + ".") .build(); options.addOption(outputModeOption); Option ftpHostOption = Option.builder("ftphost").argName("host").hasArg() .desc("Host name, for FTP or SFTP.").build(); options.addOption(ftpHostOption); Option ftpUsernameOption = Option.builder("ftpuser").argName("user").hasArg() .desc("Username, for FTP or SFTP.").build(); options.addOption(ftpUsernameOption); Option ftpPasswordOption = Option.builder("ftppass").argName("password").hasArg() .desc("Password, for FTP or SFTP.").build(); options.addOption(ftpPasswordOption); Option autoRunOption = new Option("x", "Automatically run at startup."); options.addOption(autoRunOption); // // 2. Parse command line options // CommandLineParser parser = new DefaultParser(); CommandLine line = null; try { line = parser.parse(options, argsI); } catch (ParseException exp) { // oops, something went wrong System.err.println("Command line argument parsing failed: " + exp.getMessage()); return; } // // 3. Retrieve the command line values // if (line.hasOption("help")) { // Display help message and quit HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("FilePump", options); return; } if (line.hasOption("x")) { local_bShowGUI = false; } // Where to write the files to initial_outputFolder = line.getOptionValue("outputfolder", initial_outputFolder); // How many files per second the pump should output try { initial_filesPerSec = Double.parseDouble(line.getOptionValue("fps", "" + initial_filesPerSec)); } catch (NumberFormatException nfe) { System.err.println("\nError parsing \"fps\" (it should be a floating point value):\n" + nfe); return; } // Total number of files to write out; -1 indicates unlimited try { initial_totNumFiles = Integer.parseInt(line.getOptionValue("totnum", "" + initial_totNumFiles)); } catch (NumberFormatException nfe) { System.err.println("\nError parsing \"totnum\" (it should be an integer):\n" + nfe); return; } // Specifies how files will be written out initial_mode_str = line.getOptionValue("mode", initial_mode_str); if (!initial_mode_str.equals("local") && !initial_mode_str.equals("ftp") && !initial_mode_str.equals("sftp")) { System.err.println(new String("\nUnrecognized mode, \"" + initial_mode_str + "\"")); return; } // FTP hostname initial_ftpHost = line.getOptionValue("ftphost", ""); // FTP username initial_ftpUser = line.getOptionValue("ftpuser", ""); // FTP password initial_ftpPassword = line.getOptionValue("ftppass", ""); // Create the FilePump object new FilePump(local_bShowGUI, initial_outputFolder, initial_filesPerSec, initial_totNumFiles, initial_mode_str, initial_ftpHost, initial_ftpUser, initial_ftpPassword); }
From source file:com.act.lcms.db.analysis.StandardIonAnalysis.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());/* w ww.j a v a 2 s . co m*/ } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s\n", e.getMessage()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } File lcmsDir = new File(cl.getOptionValue(OPTION_DIRECTORY)); if (!lcmsDir.isDirectory()) { System.err.format("File at %s is not a directory\n", lcmsDir.getAbsolutePath()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } try (DB db = DB.openDBFromCLI(cl)) { ScanFile.insertOrUpdateScanFilesInDirectory(db, lcmsDir); StandardIonAnalysis analysis = new StandardIonAnalysis(); HashMap<Integer, Plate> plateCache = new HashMap<>(); String plateBarcode = cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE); String inputChemicals = cl.getOptionValue(OPTION_STANDARD_CHEMICAL); String medium = cl.getOptionValue(OPTION_MEDIUM); // If standard chemical is specified, do standard LCMS ion selection analysis if (inputChemicals != null && !inputChemicals.equals("")) { String[] chemicals; if (!inputChemicals.contains(",")) { chemicals = new String[1]; chemicals[0] = inputChemicals; } else { chemicals = inputChemicals.split(","); } String outAnalysis = cl.getOptionValue(OPTION_OUTPUT_PREFIX) + "." + CSV_FORMAT; String plottingDirectory = cl.getOptionValue(OPTION_PLOTTING_DIR); String[] headerStrings = { "Molecule", "Plate Bar Code", "LCMS Detection Results" }; CSVPrinter printer = new CSVPrinter(new FileWriter(outAnalysis), CSVFormat.DEFAULT.withHeader(headerStrings)); for (String inputChemical : chemicals) { List<StandardWell> standardWells; Plate queryPlate = Plate.getPlateByBarcode(db, cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE)); if (plateBarcode != null && medium != null) { standardWells = analysis.getStandardWellsForChemicalInSpecificPlateAndMedium(db, inputChemical, queryPlate.getId(), medium); } else if (plateBarcode != null) { standardWells = analysis.getStandardWellsForChemicalInSpecificPlate(db, inputChemical, queryPlate.getId()); } else { standardWells = analysis.getStandardWellsForChemical(db, inputChemical); } if (standardWells.size() == 0) { throw new RuntimeException("Found no LCMS wells for " + inputChemical); } // Sort in descending order of media where MeOH and Water related media are promoted to the top and // anything derived from yeast media are demoted. Collections.sort(standardWells, new Comparator<StandardWell>() { @Override public int compare(StandardWell o1, StandardWell o2) { if (StandardWell.doesMediaContainYeastExtract(o1.getMedia()) && !StandardWell.doesMediaContainYeastExtract(o2.getMedia())) { return 1; } else { return 0; } } }); Map<StandardWell, StandardIonResult> wellToIonRanking = StandardIonAnalysis .getBestMetlinIonsForChemical(inputChemical, lcmsDir, db, standardWells, plottingDirectory); if (wellToIonRanking.size() != standardWells.size() && !cl.hasOption(OPTION_OVERRIDE_NO_SCAN_FILE_FOUND)) { throw new Exception("Could not find a scan file associated with one of the standard wells"); } for (StandardWell well : wellToIonRanking.keySet()) { LinkedHashMap<String, XZ> snrResults = wellToIonRanking.get(well).getAnalysisResults(); String snrRankingResults = ""; int numResultsToShow = 0; Plate plateForWellToAnalyze = Plate.getPlateById(db, well.getPlateId()); for (Map.Entry<String, XZ> ionToSnrAndTime : snrResults.entrySet()) { if (numResultsToShow > 3) { break; } String ion = ionToSnrAndTime.getKey(); XZ snrAndTime = ionToSnrAndTime.getValue(); snrRankingResults += String.format(ion + " (%.2f SNR at %.2fs); ", snrAndTime.getIntensity(), snrAndTime.getTime()); numResultsToShow++; } String[] resultSet = { inputChemical, plateForWellToAnalyze.getBarcode() + " " + well.getCoordinatesString() + " " + well.getMedia() + " " + well.getConcentration(), snrRankingResults }; printer.printRecord(resultSet); } } try { printer.flush(); printer.close(); } catch (IOException e) { System.err.println("Error while flushing/closing csv writer."); e.printStackTrace(); } } else { // Get the set of chemicals that includes the construct and all it's intermediates Pair<ConstructEntry, List<ChemicalAssociatedWithPathway>> constructAndPathwayChems = analysis .getChemicalsForConstruct(db, cl.getOptionValue(OPTION_CONSTRUCT)); System.out.format("Construct: %s\n", constructAndPathwayChems.getLeft().getCompositionId()); for (ChemicalAssociatedWithPathway pathwayChem : constructAndPathwayChems.getRight()) { System.out.format(" Pathway chem %s\n", pathwayChem.getChemical()); // Get all the standard wells for the pathway chemicals. These wells contain only the // the chemical added with controlled solutions (ie no organism or other chemicals in the // solution) List<StandardWell> standardWells; if (plateBarcode != null) { Plate queryPlate = Plate.getPlateByBarcode(db, cl.getOptionValue(OPTION_STANDARD_PLATE_BARCODE)); standardWells = analysis.getStandardWellsForChemicalInSpecificPlate(db, pathwayChem.getChemical(), queryPlate.getId()); } else { standardWells = analysis.getStandardWellsForChemical(db, pathwayChem.getChemical()); } for (StandardWell wellToAnalyze : standardWells) { List<StandardWell> negativeControls = analysis.getViableNegativeControlsForStandardWell(db, wellToAnalyze); Map<StandardWell, List<ScanFile>> allViableScanFiles = analysis .getViableScanFilesForStandardWells(db, wellToAnalyze, negativeControls); List<String> primaryStandardScanFileNames = new ArrayList<>(); for (ScanFile scanFile : allViableScanFiles.get(wellToAnalyze)) { primaryStandardScanFileNames.add(scanFile.getFilename()); } Plate plate = plateCache.get(wellToAnalyze.getPlateId()); if (plate == null) { plate = Plate.getPlateById(db, wellToAnalyze.getPlateId()); plateCache.put(plate.getId(), plate); } System.out.format(" Standard well: %s @ %s, '%s'%s%s\n", plate.getBarcode(), wellToAnalyze.getCoordinatesString(), wellToAnalyze.getChemical(), wellToAnalyze.getMedia() == null ? "" : String.format(" in %s", wellToAnalyze.getMedia()), wellToAnalyze.getConcentration() == null ? "" : String.format(" @ %s", wellToAnalyze.getConcentration())); System.out.format(" Scan files: %s\n", StringUtils.join(primaryStandardScanFileNames, ", ")); for (StandardWell negCtrlWell : negativeControls) { plate = plateCache.get(negCtrlWell.getPlateId()); if (plate == null) { plate = Plate.getPlateById(db, negCtrlWell.getPlateId()); plateCache.put(plate.getId(), plate); } List<String> negativeControlScanFileNames = new ArrayList<>(); for (ScanFile scanFile : allViableScanFiles.get(negCtrlWell)) { negativeControlScanFileNames.add(scanFile.getFilename()); } System.out.format(" Viable negative: %s @ %s, '%s'%s%s\n", plate.getBarcode(), negCtrlWell.getCoordinatesString(), negCtrlWell.getChemical(), negCtrlWell.getMedia() == null ? "" : String.format(" in %s", negCtrlWell.getMedia()), negCtrlWell.getConcentration() == null ? "" : String.format(" @ %s", negCtrlWell.getConcentration())); System.out.format(" Scan files: %s\n", StringUtils.join(negativeControlScanFileNames, ", ")); // TODO: do something useful with the standard wells and their scan files, and then stop all the printing. } } } } } }
From source file:io.s4.util.LoadGenerator.java
public static void main(String args[]) { Options options = new Options(); boolean warmUp = false; options.addOption(//from ww w. j a v a 2s .c om OptionBuilder.withArgName("rate").hasArg().withDescription("Rate (events per second)").create("r")); options.addOption(OptionBuilder.withArgName("display_rate").hasArg() .withDescription("Display Rate at specified second boundary").create("d")); options.addOption(OptionBuilder.withArgName("start_boundary").hasArg() .withDescription("Start boundary in seconds").create("b")); options.addOption(OptionBuilder.withArgName("run_for").hasArg() .withDescription("Run for a specified number of seconds").create("x")); options.addOption(OptionBuilder.withArgName("cluster_manager").hasArg().withDescription("Cluster manager") .create("z")); options.addOption(OptionBuilder.withArgName("sender_application_name").hasArg() .withDescription("Sender application name").create("a")); options.addOption(OptionBuilder.withArgName("listener_application_name").hasArg() .withDescription("Listener application name").create("g")); options.addOption( OptionBuilder.withArgName("sleep_overhead").hasArg().withDescription("Sleep overhead").create("o")); options.addOption(new Option("w", "Warm-up")); CommandLineParser parser = new GnuParser(); CommandLine line = null; try { // parse the command line arguments line = parser.parse(options, args); } catch (ParseException exp) { // oops, something went wrong System.err.println("Parsing failed. Reason: " + exp.getMessage()); System.exit(1); } int expectedRate = 250; if (line.hasOption("r")) { try { expectedRate = Integer.parseInt(line.getOptionValue("r")); } catch (Exception e) { System.err.println("Bad expected rate specified " + line.getOptionValue("r")); System.exit(1); } } int displayRateIntervalSeconds = 20; if (line.hasOption("d")) { try { displayRateIntervalSeconds = Integer.parseInt(line.getOptionValue("d")); } catch (Exception e) { System.err.println("Bad display rate value specified " + line.getOptionValue("d")); System.exit(1); } } int startBoundary = 2; if (line.hasOption("b")) { try { startBoundary = Integer.parseInt(line.getOptionValue("b")); } catch (Exception e) { System.err.println("Bad start boundary value specified " + line.getOptionValue("b")); System.exit(1); } } int updateFrequency = 0; if (line.hasOption("f")) { try { updateFrequency = Integer.parseInt(line.getOptionValue("f")); } catch (Exception e) { System.err.println("Bad query udpdate frequency specified " + line.getOptionValue("f")); System.exit(1); } System.out.printf("Update frequency is %d\n", updateFrequency); } int runForTime = 0; if (line.hasOption("x")) { try { runForTime = Integer.parseInt(line.getOptionValue("x")); } catch (Exception e) { System.err.println("Bad run for time specified " + line.getOptionValue("x")); System.exit(1); } System.out.printf("Run for time is %d\n", runForTime); } String clusterManagerAddress = null; if (line.hasOption("z")) { clusterManagerAddress = line.getOptionValue("z"); } String senderApplicationName = null; if (line.hasOption("a")) { senderApplicationName = line.getOptionValue("a"); } String listenerApplicationName = null; if (line.hasOption("a")) { listenerApplicationName = line.getOptionValue("g"); } if (listenerApplicationName == null) { listenerApplicationName = senderApplicationName; } long sleepOverheadMicros = -1; if (line.hasOption("o")) { try { sleepOverheadMicros = Long.parseLong(line.getOptionValue("o")); } catch (NumberFormatException e) { System.err.println("Bad sleep overhead specified " + line.getOptionValue("o")); System.exit(1); } System.out.printf("Specified sleep overhead is %d\n", sleepOverheadMicros); } if (line.hasOption("w")) { warmUp = true; } List loArgs = line.getArgList(); if (loArgs.size() < 1) { System.err.println("No input file specified"); System.exit(1); } String inputFilename = (String) loArgs.get(0); EventEmitter emitter = null; SerializerDeserializer serDeser = new KryoSerDeser(); CommLayerEmitter clEmitter = new CommLayerEmitter(); clEmitter.setAppName(senderApplicationName); clEmitter.setListenerAppName(listenerApplicationName); clEmitter.setClusterManagerAddress(clusterManagerAddress); clEmitter.setSenderId(String.valueOf(System.currentTimeMillis() / 1000)); clEmitter.setSerDeser(serDeser); clEmitter.init(); emitter = clEmitter; long endTime = 0; if (runForTime > 0) { endTime = System.currentTimeMillis() + (runForTime * 1000); } LoadGenerator loadGenerator = new LoadGenerator(); loadGenerator.setInputFilename(inputFilename); loadGenerator.setEventEmitter(clEmitter); loadGenerator.setDisplayRateInterval(displayRateIntervalSeconds); loadGenerator.setExpectedRate(expectedRate); loadGenerator.run(); System.exit(0); }