List of usage examples for java.lang Boolean valueOf
public static Boolean valueOf(String s)
From source file:net.ontopia.topicmaps.db2tm.Execute.java
public static void main(String[] argv) throws Exception { // Initialize logging CmdlineUtils.initializeLogging();//from w w w . java 2 s.c o m // Register logging options CmdlineOptions options = new CmdlineOptions("Execute", argv); CmdlineUtils.registerLoggingOptions(options); OptionsListener ohandler = new OptionsListener(); options.addLong(ohandler, "tm", 't', true); options.addLong(ohandler, "baseuri", 'b', true); options.addLong(ohandler, "out", 'o', true); options.addLong(ohandler, "relations", 'r', true); options.addLong(ohandler, "force-rescan", 'f', true); // Parse command line options try { options.parse(); } catch (CmdlineOptions.OptionsException e) { System.err.println("Error: " + e.getMessage()); System.exit(1); } // Get command line arguments String[] args = options.getArguments(); if (args.length < 2) { usage(); System.exit(3); } // Arguments String operation = args[0]; String cfgfile = args[1]; if (!"add".equals(operation) && !"sync".equals(operation) && !"remove".equals(operation)) { usage(); System.err.println("Operation '" + operation + "' not supported."); System.exit(3); } try { // Read mapping file log.debug("Reading relation mapping file {}", cfgfile); RelationMapping mapping = RelationMapping.read(new File(cfgfile)); // open topic map String tmurl = ohandler.tm; log.debug("Opening topic map {}", tmurl); TopicMapIF topicmap; if (tmurl == null || "tm:in-memory:new".equals(tmurl)) topicmap = new InMemoryTopicMapStore().getTopicMap(); else if ("tm:rdbms:new".equals(tmurl)) topicmap = new RDBMSTopicMapStore().getTopicMap(); else { TopicMapReaderIF reader = ImportExportUtils.getReader(tmurl); topicmap = reader.read(); } TopicMapStoreIF store = topicmap.getStore(); // base locator String outfile = ohandler.out; LocatorIF baseloc = (outfile == null ? store.getBaseAddress() : new URILocator(new File(outfile))); if (baseloc == null && tmurl != null) baseloc = (ohandler.baseuri == null ? new URILocator(tmurl) : new URILocator(ohandler.baseuri)); // figure out which relations to actually process Collection<String> relations = null; if (ohandler.relations != null) { String[] relnames = StringUtils.split(ohandler.relations, ","); if (relnames.length > 0) { relations = new HashSet<String>(relnames.length); relations.addAll(Arrays.asList(relnames)); } } try { // Process data sources in mapping if ("add".equals(operation)) Processor.addRelations(mapping, relations, topicmap, baseloc); else if ("sync".equals(operation)) { boolean rescan = ohandler.forceRescan != null && Boolean.valueOf(ohandler.forceRescan).booleanValue(); Processor.synchronizeRelations(mapping, relations, topicmap, baseloc, rescan); } else if ("remove".equals(operation)) Processor.removeRelations(mapping, relations, topicmap, baseloc); else throw new UnsupportedOperationException("Unsupported operation: " + operation); // export topicmap if (outfile != null) { log.debug("Exporting topic map to {}", outfile); TopicMapWriterIF writer = ImportExportUtils.getWriter(new File(outfile)); writer.write(topicmap); } // commit transaction store.commit(); log.debug("Transaction committed."); } catch (Exception t) { log.error("Error occurred while running operation '" + operation + "'", t); // abort transaction store.abort(); log.debug("Transaction aborted."); throw t; } finally { if (store.isOpen()) store.close(); } } catch (Exception e) { Throwable cause = e.getCause(); if (cause instanceof DB2TMException) System.err.println("Error: " + e.getMessage()); else throw e; } }
From source file:com.hp.test.framework.Reporting.Utlis.java
public static void main(String ar[]) throws IOException { ArrayList<String> runs_list = new ArrayList<String>(); String basepath = replacelogs(); String path = basepath + "ATU Reports\\Results"; File directory = new File(path); File[] subdirs = directory.listFiles((FileFilter) DirectoryFileFilter.DIRECTORY); String htmlReport = basepath + "HTML_Design_Files\\CSS\\HtmlReport.html"; for (File dir : subdirs) { runs_list.add(dir.getName());// ww w . ja v a 2s .co m } String Reports_path = basepath + "ATU Reports\\"; int LatestRun = Utlis.getLastRun(Reports_path); String Last_run_path = Reports_path + "Results\\Run_" + String.valueOf(LatestRun) + "\\"; HtmlParse.replaceMainTable(false, new File(Last_run_path + "/CurrentRun.html")); HtmlParse.replaceCountsinJSFile(new File("HTML_Design_Files/JS/3dChart.js"), Last_run_path); UpdateTestCaseDesciption.basepath = Last_run_path; UpdateTestCaseDesciption.getTestCaseHtmlPath(Last_run_path + "/CurrentRun.html"); UpdateTestCaseDesciption.replaceDetailsTable(Last_run_path + "/CurrentRun.html"); // GenerateFailReport.genarateFailureReport(new File(htmlReport), Reports_path + "Results\\Run_" + String.valueOf(LatestRun)); genarateFailureReport(new File(htmlReport), Reports_path + "Results\\"); Map<String, List<String>> runCounts = GetCountsrunsWise(runs_list, path); int success = replaceCounts(runCounts, path); if (success == 0) { File SourceFile = new File(path + "\\lineChart_temp.js"); File RenameFile = new File(path + "\\lineChart.js"); renameOriginalFile(SourceFile, RenameFile); File SourceFile1 = new File(path + "\\barChart_temp.js"); File RenameFile1 = new File(path + "\\barChart.js"); renameOriginalFile(SourceFile1, RenameFile1); Utlis.getpaths(Reports_path + "\\Results\\Run_" + String.valueOf(LatestRun)); try { Utlis.replaceMainTable(false, new File(Reports_path + "index.html")); Utlis.replaceMainTable(true, new File(Reports_path + "results\\" + "ConsolidatedPage.html")); Utlis.replaceMainTable(true, new File(Reports_path + "Results\\Run_" + String.valueOf(LatestRun) + "CurrentRun.html")); fileList.add( new File(Reports_path + "\\Results\\Run_" + String.valueOf(LatestRun) + "CurrentRun.html")); for (File f : fileList) { Utlis.replaceMainTable(true, f); } } catch (Exception ex) { log.info("Error in updating Report format" + ex.getMessage()); } Last_run_path = Reports_path + "Results\\Run_" + String.valueOf(LatestRun) + "\\"; // HtmlParse.replaceMainTable(false, new File(Last_run_path + "/CurrentRun.html")); // HtmlParse.replaceCountsinJSFile(new File("../HTML_Design_Files/JS/3dChart.js"), Last_run_path); ArrayList<String> to_list = new ArrayList<String>(); ReportingProperties reportingproperties = new ReportingProperties(); String temp_eml = reportingproperties.getProperty("TOLIST"); String JenkinsURL = reportingproperties.getProperty("JENKINSURL"); String ScreenShotsDir = reportingproperties.getProperty("ScreenShotsDirectory"); Boolean cleanScreenshotsDir = Boolean.valueOf(reportingproperties.getProperty("CleanPreScreenShots")); Boolean generatescreenshots = Boolean.valueOf(reportingproperties.getProperty("GenerateScreenShots")); String HtmlreportFilePrefix = reportingproperties.getProperty("HtmlreportFilePrefix"); if (cleanScreenshotsDir) { if (!CleanFilesinDir(ScreenShotsDir)) { log.error("Not able to Clean the Previous Run Details in the paht" + ScreenShotsDir); } else { log.info("Cleaning Previous Run Details in the paht" + ScreenShotsDir + "Sucess"); } } List<String> scr_fileList; List<String> html_fileList; if (generatescreenshots) { scr_fileList = GetFileListinDir(ScreenShotsDir, "png"); int len = scr_fileList.size(); len = len + 1; screenshot.generatescreenshot(Last_run_path + "CurrentRun.html", ScreenShotsDir + "screenshot_" + len + ".png"); File source = new File(Reports_path + "Results\\HtmlReport.html"); File dest = new File(ScreenShotsDir + HtmlreportFilePrefix + "_HtmlReport.html"); // Files.copy(f.toPath(), (new File((ScreenShotsDir+HtmlreportFilePrefix+"_HtmlReport.html").toPath(),StandardCopyOption.REPLACE_EXISTING); FileUtils.copyFile(source, dest); scr_fileList.clear(); } scr_fileList = GetFileListinDir(ScreenShotsDir, "png"); html_fileList = GetFileListinDir(ScreenShotsDir, "html"); if (temp_eml.length() > 1) { String[] to_list_temp = temp_eml.split(","); if (to_list_temp.length > 0) { for (String to_list_temp1 : to_list_temp) { to_list.add(to_list_temp1); } } if (to_list.size() > 0) { screenshot.generatescreenshot(Last_run_path + "CurrentRun.html", Last_run_path + "screenshot.png"); // cleanTempDir.cleanandCreate(Reports_path, LatestRun); // ZipUtils.ZipFolder(Reports_path + "temp", Reports_path + "ISTF_Reports.zip"); if (generatescreenshots) { SendingEmail.sendmail(to_list, JenkinsURL, scr_fileList, html_fileList); } else { SendingEmail.sendmail(to_list, JenkinsURL, Reports_path + "/Results/HtmlReport.html", Last_run_path + "screenshot.png"); } // FileUtils.deleteQuietly(new File(Reports_path + "ISTF_Reports.zip")); // FileUtils.deleteDirectory(new File(Reports_path + "temp")); } } } }
From source file:com.alibaba.jstorm.daemon.supervisor.SandBoxMaker.java
public static void main(String[] args) { Map<Object, Object> conf = Utils.readStormConfig(); conf.put("java.sandbox.enable", Boolean.valueOf(true)); SandBoxMaker maker = new SandBoxMaker(conf); try {/* w ww. j ava 2 s .c o m*/ System.out.println("sandboxPolicy:" + maker.sandboxPolicy("simple", new HashMap<String, String>())); } catch (IOException e) { e.printStackTrace(); } }
From source file:com.sludev.mssqlapplylog.MSSQLApplyLogMain.java
public static void main(String[] args) { CommandLineParser parser = new DefaultParser(); Options options = new Options(); // Most of the following defaults should be changed in // the --conf or "conf.properties" file String sqlURL = null;/*from w ww.j a va 2s .c o m*/ String sqlUser = null; String sqlPass = null; String sqlDb = null; String sqlHost = "127.0.0.1"; String backupDirStr = null; String laterThanStr = ""; String fullBackupPathStr = null; String fullBackupPatternStr = "(?:[\\w_-]+?)(\\d+)\\.bak"; String fullBackupDatePatternStr = "yyyyMMddHHmm"; String sqlProcessUser = null; String logBackupPatternStr = "(.*)\\.trn"; String logBackupDatePatternStr = "yyyyMMddHHmmss"; boolean doFullRestore = false; Boolean useLogFileLastMode = null; Boolean monitorLogBackupDir = null; options.addOption(Option.builder().longOpt("conf").desc("Configuration file.").hasArg().build()); options.addOption(Option.builder().longOpt("laterthan").desc("'Later Than' file filter.").hasArg().build()); options.addOption(Option.builder().longOpt("restore-full") .desc("Restore the full backup before continuing.").build()); options.addOption(Option.builder().longOpt("use-lastmod") .desc("Sort/filter the log backups using their File-System 'Last Modified' date.").build()); options.addOption(Option.builder().longOpt("monitor-backup-dir") .desc("Monitor the backup directory for new log backups, and apply them.").build()); CommandLine line = null; try { try { line = parser.parse(options, args); } catch (ParseException ex) { throw new MSSQLApplyLogException(String.format("Error parsing command line.'%s'", ex.getMessage()), ex); } String confFile = null; // Process the command line arguments Iterator cmdI = line.iterator(); while (cmdI.hasNext()) { Option currOpt = (Option) cmdI.next(); String currOptName = currOpt.getLongOpt(); switch (currOptName) { case "conf": // Parse the configuration file confFile = currOpt.getValue(); break; case "laterthan": // "Later Than" file date filter laterThanStr = currOpt.getValue(); break; case "restore-full": // Do a full backup restore before restoring logs doFullRestore = true; break; case "monitor-backup-dir": // Monitor the backup directory for new logs monitorLogBackupDir = true; break; case "use-lastmod": // Use the last-modified date on Log Backup files for sorting/filtering useLogFileLastMode = true; break; } } Properties confProperties = null; if (StringUtils.isBlank(confFile) || Files.isReadable(Paths.get(confFile)) == false) { throw new MSSQLApplyLogException( "Missing or unreadable configuration file. Please specify --conf"); } else { // Process the conf.properties file confProperties = new Properties(); try { confProperties.load(Files.newBufferedReader(Paths.get(confFile))); } catch (IOException ex) { throw new MSSQLApplyLogException("Error loading properties file", ex); } sqlURL = confProperties.getProperty("sqlURL", ""); sqlUser = confProperties.getProperty("sqlUser", ""); sqlPass = confProperties.getProperty("sqlPass", ""); sqlDb = confProperties.getProperty("sqlDb", ""); sqlHost = confProperties.getProperty("sqlHost", ""); backupDirStr = confProperties.getProperty("backupDir", ""); if (StringUtils.isBlank(laterThanStr)) { laterThanStr = confProperties.getProperty("laterThan", ""); } fullBackupPathStr = confProperties.getProperty("fullBackupPath", fullBackupPathStr); fullBackupPatternStr = confProperties.getProperty("fullBackupPattern", fullBackupPatternStr); fullBackupDatePatternStr = confProperties.getProperty("fullBackupDatePattern", fullBackupDatePatternStr); sqlProcessUser = confProperties.getProperty("sqlProcessUser", ""); logBackupPatternStr = confProperties.getProperty("logBackupPattern", logBackupPatternStr); logBackupDatePatternStr = confProperties.getProperty("logBackupDatePattern", logBackupDatePatternStr); if (useLogFileLastMode == null) { String useLogFileLastModeStr = confProperties.getProperty("useLogFileLastMode", "false"); useLogFileLastMode = Boolean .valueOf(StringUtils.lowerCase(StringUtils.trim(useLogFileLastModeStr))); } if (monitorLogBackupDir == null) { String monitorBackupDirStr = confProperties.getProperty("monitorBackupDir", "false"); monitorLogBackupDir = Boolean .valueOf(StringUtils.lowerCase(StringUtils.trim(monitorBackupDirStr))); } } } catch (MSSQLApplyLogException ex) { try (StringWriter sw = new StringWriter(); PrintWriter pw = new PrintWriter(sw)) { pw.append(String.format("Error : '%s'\n\n", ex.getMessage())); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(pw, 80, "\njava -jar mssqlapplylog.jar ", "\nThe MSSQLApplyLog application can be used in a variety of options and modes.\n", options, 0, 2, " All Rights Reserved.", true); System.out.println(sw.toString()); } catch (IOException iex) { LOGGER.debug("Error processing usage", iex); } System.exit(1); } MSSQLApplyLogConfig config = MSSQLApplyLogConfig.from(backupDirStr, fullBackupPathStr, fullBackupDatePatternStr, laterThanStr, fullBackupPatternStr, logBackupPatternStr, logBackupDatePatternStr, sqlHost, sqlDb, sqlUser, sqlPass, sqlURL, sqlProcessUser, useLogFileLastMode, doFullRestore, monitorLogBackupDir); MSSQLApplyLog logProc = MSSQLApplyLog.from(config); BasicThreadFactory thFactory = new BasicThreadFactory.Builder().namingPattern("restoreThread-%d").build(); ExecutorService mainThreadExe = Executors.newSingleThreadExecutor(thFactory); Future<Integer> currRunTask = mainThreadExe.submit(logProc); mainThreadExe.shutdown(); Integer resp = 0; try { resp = currRunTask.get(); } catch (InterruptedException ex) { LOGGER.error("Application 'main' thread was interrupted", ex); } catch (ExecutionException ex) { LOGGER.error("Application 'main' thread execution error", ex); } finally { // If main leaves for any reason, shutdown all threads mainThreadExe.shutdownNow(); } System.exit(resp); }
From source file:benchmarkio.controlcenter.LaunchRocket.java
public static void main(final String[] args) throws Exception { // create the parser final CommandLineParser parser = new BasicParser(); // parse the command line arguments final CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("u")) { displayHelp();/*from w ww . j a va 2s .com*/ } final String host = cmd.getOptionValue("host"); final int port = Integer.parseInt(cmd.getOptionValue("port")); final BrokerType brokerType = BrokerType.valueOf(cmd.getOptionValue("broker-type")); final int numConsumers = Integer.parseInt(cmd.getOptionValue("num-consumers")); final int numProducers = Integer.parseInt(cmd.getOptionValue("num-producers")); final int totalNumberOfMessages = Integer.parseInt(cmd.getOptionValue("total-number-of-messages")); final double msgSizeInKB = Double.parseDouble(cmd.getOptionValue("msg-size-in-kb")); // Optional options final Optional<String> optionalBenchmarkType = Optional.fromNullable(cmd.getOptionValue("benchmark-type")); final Optional<String> optionalDurable = Optional.fromNullable(cmd.getOptionValue("durable")); // Kafka Specific final Optional<String> optionalZookeeper = Optional.fromNullable(cmd.getOptionValue("zookeeper")); Optional<String> optionalKafkaProducerType = Optional .fromNullable(cmd.getOptionValue("kafka-producer-type")); BenchmarkType benchmarkType; if (optionalBenchmarkType.isPresent()) { benchmarkType = BenchmarkType.valueOf(optionalBenchmarkType.get()); } else { log.info("Benchmark type was not specified, defaulting to: {}", BenchmarkType.PRODUCER_AND_CONSUMER); benchmarkType = BenchmarkType.PRODUCER_AND_CONSUMER; } boolean durable = false; if (optionalDurable.isPresent()) { durable = Boolean.valueOf(optionalDurable.get()); } else { log.info("Durable parameter was not specified, defaulting to: FALSE"); } if (brokerType == BrokerType.KAFKA) { if (!optionalZookeeper.isPresent()) { log.error("zookeeper is missing, it is a required property for KAFKA broker"); System.exit(0); } if (!optionalKafkaProducerType.isPresent()) { log.info("kafka-producer-type is not specified, defaulting to sync"); optionalKafkaProducerType = Optional.of("sync"); } else if (!optionalKafkaProducerType.get().equals("sync") && !optionalKafkaProducerType.get().equals("async")) { log.warn("kafka-producer-type is not one of the accepted sync | async values, defaulting to sync"); optionalKafkaProducerType = Optional.of("sync"); } } log.info("destination (topic or queue): {}", Consts.DESTINATION_NAME); log.info("host: {}", host); log.info("port: {}", port); log.info("broker-type: {}", brokerType); log.info("benchmark-type: {}", benchmarkType); log.info("durable: {}", durable); log.info("num-consumers: {}", numConsumers); log.info("num-producers: {}", numProducers); log.info("total-number-of-messages: {}", totalNumberOfMessages); log.info("msg-size-in-kb: {}", msgSizeInKB); if (brokerType == BrokerType.KAFKA) { log.info("zookeeper: {}", optionalZookeeper.get()); log.info("kafka-producer-type: {}", optionalKafkaProducerType.get()); } LaunchRocket.start(brokerType, benchmarkType, durable, host, port, numConsumers, numProducers, totalNumberOfMessages, msgSizeInKB, optionalZookeeper, optionalKafkaProducerType); System.exit(0); }
From source file:ms1quant.MS1Quant.java
/** * @param args the command line arguments MS1Quant parameterfile */// w ww . jav a 2 s.com public static void main(String[] args) throws Exception { BufferedReader reader = null; try { System.out.println( "================================================================================================="); System.out.println("Umpire MS1 quantification and feature detection analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length < 3 || !args[1].startsWith("-mode")) { System.out .println("command : java -jar -Xmx10G MS1Quant.jar ms1quant.params -mode[1 or 2] [Option]"); System.out.println("\n-mode"); System.out.println("\t1:Single file mode--> mzXML_file PepXML_file"); System.out.println("\t\tEx: -mode1 file1.mzXML file1.pep.xml"); System.out.println( "\t2:Folder mode--> mzXML_Folder PepXML_Folder, all generated csv tables will be merged into a single csv file"); System.out.println("\t\tEx: -mode2 /data/mzxml/ /data/pepxml/"); System.out.println("\nOptions"); System.out.println( "\t-C\tNo of concurrent files to be processed (only for folder mode), Ex. -C5, default:1"); System.out.println("\t-p\tMinimum probability, Ex. -p0.9, default:0.9"); System.out.println("\t-ID\tDetect identified feature only"); System.out.println("\t-O\toutput folder, Ex. -O/data/"); return; } ConsoleLogger consoleLogger = new ConsoleLogger(); consoleLogger.SetConsoleLogger(Level.DEBUG); consoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "ms1quant_debug.log"); Logger logger = Logger.getRootLogger(); logger.debug("Command: " + Arrays.toString(args)); logger.info("MS1Quant version: " + UmpireInfo.GetInstance().Version); String parameterfile = args[0]; logger.info("Parameter file: " + parameterfile); File paramfile = new File(parameterfile); if (!paramfile.exists()) { logger.error("Parameter file " + paramfile.getAbsolutePath() + " cannot be found. The program will exit."); } reader = new BufferedReader(new FileReader(paramfile.getAbsolutePath())); String line = ""; InstrumentParameter param = new InstrumentParameter(InstrumentParameter.InstrumentType.TOF5600); int NoCPUs = 2; int NoFile = 1; param.DetermineBGByID = false; param.EstimateBG = true; //<editor-fold defaultstate="collapsed" desc="Read parameter file"> while ((line = reader.readLine()) != null) { if (!"".equals(line) && !line.startsWith("#")) { logger.info(line); //System.out.println(line); if (line.split("=").length < 2) { continue; } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); if (type.startsWith("para.")) { type = type.replace("para.", "SE."); } String value = line.split("=")[1].trim(); switch (type) { case "Thread": { NoCPUs = Integer.parseInt(value); break; } //<editor-fold defaultstate="collapsed" desc="instrument parameters"> case "SE.MS1PPM": { param.MS1PPM = Float.parseFloat(value); break; } case "SE.MS2PPM": { param.MS2PPM = Float.parseFloat(value); break; } case "SE.SN": { param.SNThreshold = Float.parseFloat(value); break; } case "SE.MS2SN": { param.MS2SNThreshold = Float.parseFloat(value); break; } case "SE.MinMSIntensity": { param.MinMSIntensity = Float.parseFloat(value); break; } case "SE.MinMSMSIntensity": { param.MinMSMSIntensity = Float.parseFloat(value); break; } case "SE.MinRTRange": { param.MinRTRange = Float.parseFloat(value); break; } case "SE.MaxNoPeakCluster": { param.MaxNoPeakCluster = Integer.parseInt(value); param.MaxMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinNoPeakCluster": { param.MinNoPeakCluster = Integer.parseInt(value); param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinMS2NoPeakCluster": { param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MaxCurveRTRange": { param.MaxCurveRTRange = Float.parseFloat(value); break; } case "SE.Resolution": { param.Resolution = Integer.parseInt(value); break; } case "SE.RTtol": { param.RTtol = Float.parseFloat(value); break; } case "SE.NoPeakPerMin": { param.NoPeakPerMin = Integer.parseInt(value); break; } case "SE.StartCharge": { param.StartCharge = Integer.parseInt(value); break; } case "SE.EndCharge": { param.EndCharge = Integer.parseInt(value); break; } case "SE.MS2StartCharge": { param.MS2StartCharge = Integer.parseInt(value); break; } case "SE.MS2EndCharge": { param.MS2EndCharge = Integer.parseInt(value); break; } case "SE.NoMissedScan": { param.NoMissedScan = Integer.parseInt(value); break; } case "SE.Denoise": { param.Denoise = Boolean.valueOf(value); break; } case "SE.EstimateBG": { param.EstimateBG = Boolean.valueOf(value); break; } case "SE.RemoveGroupedPeaks": { param.RemoveGroupedPeaks = Boolean.valueOf(value); break; } case "SE.MinFrag": { param.MinFrag = Integer.parseInt(value); break; } case "SE.IsoPattern": { param.IsoPattern = Float.valueOf(value); break; } case "SE.StartRT": { param.startRT = Float.valueOf(value); } case "SE.EndRT": { param.endRT = Float.valueOf(value); } //</editor-fold> } } } //</editor-fold> int mode = 1; if (args[1].equals("-mode2")) { mode = 2; } else if (args[1].equals("-mode1")) { mode = 1; } else { logger.error("-mode number not recongized. The program will exit."); } String mzXML = ""; String pepXML = ""; String mzXMLPath = ""; String pepXMLPath = ""; File mzXMLfile = null; File pepXMLfile = null; File mzXMLfolder = null; File pepXMLfolder = null; int idx = 0; if (mode == 1) { mzXML = args[2]; logger.info("Mode1 mzXML file: " + mzXML); mzXMLfile = new File(mzXML); if (!mzXMLfile.exists()) { logger.error("Mode1 mzXML file " + mzXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } pepXML = args[3]; logger.info("Mode1 pepXML file: " + pepXML); pepXMLfile = new File(pepXML); if (!pepXMLfile.exists()) { logger.error("Mode1 pepXML file " + pepXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } idx = 4; } else if (mode == 2) { mzXMLPath = args[2]; logger.info("Mode2 mzXML folder: " + mzXMLPath); mzXMLfolder = new File(mzXMLPath); if (!mzXMLfolder.exists()) { logger.error("Mode2 mzXML folder " + mzXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } pepXMLPath = args[3]; logger.info("Mode2 pepXML folder: " + pepXMLPath); pepXMLfolder = new File(pepXMLPath); if (!pepXMLfolder.exists()) { logger.error("Mode2 pepXML folder " + pepXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } idx = 4; } String outputfolder = ""; float MinProb = 0f; for (int i = idx; i < args.length; i++) { if (args[i].startsWith("-")) { if (args[i].equals("-ID")) { param.TargetIDOnly = true; logger.info("Detect ID feature only: true"); } if (args[i].startsWith("-O")) { outputfolder = args[i].substring(2); logger.info("Output folder: " + outputfolder); File outputfile = new File(outputfolder); if (!outputfolder.endsWith("\\") | outputfolder.endsWith("/")) { outputfolder += "/"; } if (!outputfile.exists()) { outputfile.mkdir(); } } if (args[i].startsWith("-C")) { try { NoFile = Integer.parseInt(args[i].substring(2)); logger.info("No of concurrent files: " + NoFile); } catch (Exception ex) { logger.error(args[i] + " is not a correct integer format, will process only one file at a time."); } } if (args[i].startsWith("-p")) { try { MinProb = Float.parseFloat(args[i].substring(2)); logger.info("probability threshold: " + MinProb); } catch (Exception ex) { logger.error(args[i] + " is not a correct format, will use 0 as threshold instead."); } } } } reader.close(); TandemParam tandemparam = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); PTMManager.GetInstance(); if (param.TargetIDOnly) { param.EstimateBG = false; param.ApexDelta = 1.5f; param.NoMissedScan = 10; param.MiniOverlapP = 0.2f; param.RemoveGroupedPeaks = false; param.CheckMonoIsotopicApex = false; param.DetectByCWT = false; param.FillGapByBK = false; param.IsoCorrThreshold = -1f; param.SmoothFactor = 3; } if (mode == 1) { logger.info("Processing " + mzXMLfile.getAbsolutePath() + "...."); long time = System.currentTimeMillis(); LCMSPeakMS1 LCMS1 = new LCMSPeakMS1(mzXMLfile.getAbsolutePath(), NoCPUs); LCMS1.SetParameter(param); LCMS1.Resume = false; if (!param.TargetIDOnly) { LCMS1.CreatePeakFolder(); } LCMS1.ExportPeakClusterTable = true; if (pepXMLfile.exists()) { tandemparam.InteractPepXMLPath = pepXMLfile.getAbsolutePath(); LCMS1.ParsePepXML(tandemparam, MinProb); logger.info("No. of PSMs included: " + LCMS1.IDsummary.PSMList.size()); logger.info("No. of Peptide ions included: " + LCMS1.IDsummary.GetPepIonList().size()); } if (param.TargetIDOnly) { LCMS1.SaveSerializationFile = false; } if (param.TargetIDOnly || !LCMS1.ReadPeakCluster()) { LCMS1.PeakClusterDetection(); } if (pepXMLfile.exists()) { LCMS1.AssignQuant(false); LCMS1.IDsummary.ExportPepID(outputfolder); } time = System.currentTimeMillis() - time; logger.info(LCMS1.ParentmzXMLName + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); LCMS1.BaseClearAllPeaks(); LCMS1.SetSpectrumParser(null); LCMS1.IDsummary = null; LCMS1 = null; System.gc(); } else if (mode == 2) { LCMSID IDsummary = new LCMSID("", "", ""); logger.info("Parsing all pepXML files in " + pepXMLPath + "...."); for (File file : pepXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("pep.xml") || file.getName().toLowerCase().endsWith("pepxml")) { PepXMLParser pepXMLParser = new PepXMLParser(IDsummary, file.getAbsolutePath(), MinProb); } } HashMap<String, LCMSID> LCMSIDMap = IDsummary.GetLCMSIDFileMap(); ExecutorService executorPool = null; executorPool = Executors.newFixedThreadPool(NoFile); logger.info("Processing all mzXML files in " + mzXMLPath + "...."); for (File file : mzXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("mzxml")) { LCMSID id = LCMSIDMap.get(FilenameUtils.getBaseName(file.getName())); if (id == null || id.PSMList == null) { logger.warn("No IDs found in :" + FilenameUtils.getBaseName(file.getName()) + ". Quantification for this file is skipped"); continue; } if (!id.PSMList.isEmpty()) { MS1TargetQuantThread thread = new MS1TargetQuantThread(file, id, NoCPUs, outputfolder, param); executorPool.execute(thread); } } } LCMSIDMap.clear(); LCMSIDMap = null; IDsummary = null; executorPool.shutdown(); try { executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS); } catch (InterruptedException e) { logger.info("interrupted.."); } if (outputfolder == null | outputfolder.equals("")) { outputfolder = mzXMLPath; } logger.info("Merging PSM files.."); File output = new File(outputfolder); FileWriter writer = new FileWriter(output.getAbsolutePath() + "/PSM_merge.csv"); boolean header = false; for (File csvfile : output.listFiles()) { if (csvfile.getName().toLowerCase().endsWith("_psms.csv")) { BufferedReader outreader = new BufferedReader(new FileReader(csvfile)); String outline = outreader.readLine(); if (!header) { writer.write(outline + "\n"); header = true; } while ((outline = outreader.readLine()) != null) { writer.write(outline + "\n"); } outreader.close(); csvfile.delete(); } } writer.close(); } logger.info("MS1 quant module is complete."); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:net.bican.wordpress.Main.java
/** * @param args execute with "-?" for an explanation of args * @throws ParseException When the command line options cannot be parsed *//*from w w w . j av a 2s. c o m*/ public static void main(String[] args) throws ParseException { try { Options options = new Options(); options.addOption("?", "help", false, "Print usage information"); options.addOption("h", "url", true, "Specify the url to xmlrpc.php"); options.addOption("u", "user", true, "User name"); options.addOption("p", "pass", true, "Password"); options.addOption("a", "authors", false, "Get author list"); options.addOption("s", "slug", true, "Slug for categories"); options.addOption("pi", "parentid", true, "Parent id for categories"); options.addOption("oi", "postid", true, "Post id for pages and posts"); options.addOption("c", "categories", false, "Get category list"); options.addOption("cn", "newcategory", true, "New category (uses --slug and --parentid)"); options.addOption("pg", "pages", false, "Get page list (full)"); options.addOption("pl", "pagelist", false, "Get page list"); options.addOption("ps", "page", true, "Get page"); options.addOption("pn", "newpage", true, "New page from file <arg> (needs --publish)"); options.addOption("pe", "editpage", true, "Edit page (needs --postid and --publish"); options.addOption("pd", "deletepage", true, "Delete page (needs --publish)"); options.addOption("l", "publish", true, "Publish status for \"new\" options"); options.addOption("us", "userinfo", false, "Get user information"); options.addOption("or", "recentposts", true, "Get recent posts"); options.addOption("os", "getpost", true, "Get post"); options.addOption("on", "newpost", true, "New post from file <arg> (needs --publish)"); options.addOption("oe", "editpost", true, "Edit post (needs --postid and --publish"); options.addOption("od", "deletepost", true, "Delete post (needs --publish)"); options.addOption("sm", "supportedmethods", false, "List supported methods"); options.addOption("st", "supportedfilters", false, "List supported text filters"); options.addOption("mn", "newmedia", true, "New media file (uses --overwrite)"); options.addOption("ov", "overwrite", false, "Allow overwrite in uploading new media"); options.addOption("so", "supportedstatus", false, "Print supported page and post status values"); options.addOption("cs", "commentstatus", false, "Print comment status names for the blog"); options.addOption("cc", "commentcount", true, "Get comment count for a post (-1 for all posts)"); options.addOption("ca", "newcomment", true, "New comment from file"); options.addOption("cd", "deletecomment", true, "Delete comment"); options.addOption("ce", "editcomment", true, "Edit comment from file"); options.addOption("cg", "getcomment", true, "Get comment"); options.addOption("ct", "getcomments", true, "Get comments for the post"); options.addOption("cs", "commentstatus", true, "Comment status (for --getcomments)"); options.addOption("co", "commentoffset", true, "Comment offset # (for --getcomments)"); options.addOption("cm", "commentnumber", true, "Comment # (for --getcomments)"); try { WpCliConfiguration config = new WpCliConfiguration(args, options, Main.class); if (config.hasOption("help")) { showHelp(options); } else if ((!config.hasOption("url")) || (!config.hasOption("user")) || (!config.hasOption("pass"))) { System.err.println("Specify --user, --pass and --url"); } else { try { Wordpress wp = new Wordpress(config.getOptionValue("user"), config.getOptionValue("pass"), config.getOptionValue("url")); if (config.hasOption("authors")) { printList(wp.getAuthors(), Author.class, true); } else if (config.hasOption("categories")) { printList(wp.getCategories(), Category.class, true); } else if (config.hasOption("newcategory")) { String slug = config.getOptionValue("slug"); Integer parentId = getInteger("parentid", config); if (slug == null) slug = ""; if (parentId == null) parentId = 0; System.out .println(wp.newCategory(config.getOptionValue("newcategory"), slug, parentId)); } else if (config.hasOption("pages")) { printList(wp.getPages(), Page.class, false); } else if (config.hasOption("pagelist")) { printList(wp.getPageList(), PageDefinition.class, false); } else if (config.hasOption("page")) { printItem(wp.getPage(getInteger("page", config)), Page.class); } else if (config.hasOption("userinfo")) { printItem(wp.getUserInfo(), User.class); } else if (config.hasOption("recentposts")) { printList(wp.getRecentPosts(getInteger("recentposts", config)), Page.class, false); } else if (config.hasOption("getpost")) { printItem(wp.getPost(getInteger("getpost", config)), Page.class); } else if (config.hasOption("supportedmethods")) { printList(wp.supportedMethods(), String.class, false); } else if (config.hasOption("supportedfilters")) { printList(wp.supportedTextFilters(), String.class, false); } else if (config.hasOption("newpage")) { if (!config.hasOption("publish")) { showHelp(options); } else { System.out.println( wp.newPage(Page.fromFile(new File(config.getOptionValue("newpage"))), config.getOptionValue("publish"))); } } else if (config.hasOption("editpage")) { edit(options, config, wp, "editpage", true); } else if (config.hasOption("editpost")) { edit(options, config, wp, "editpost", false); } else if (config.hasOption("deletepage")) { delete(options, config, wp, "deletepage", true); } else if (config.hasOption("deletepost")) { delete(options, config, wp, "deletepost", false); } else if (config.hasOption("newpost")) { if (!config.hasOption("publish")) { showHelp(options); } else { System.out.println( wp.newPost(Page.fromFile(new File(config.getOptionValue("newpost"))), Boolean.valueOf(config.getOptionValue("publish")))); } } else if (config.hasOption("newmedia")) { String fileName = config.getOptionValue("newmedia"); File file = new File(fileName); String mimeType = new MimetypesFileTypeMap().getContentType(file); Boolean overwrite = Boolean.FALSE; if (config.hasOption("overwrite")) overwrite = Boolean.TRUE; MediaObject result = wp.newMediaObject(mimeType, file, overwrite); if (result != null) { System.out.println(result); } } else if (config.hasOption("supportedstatus")) { System.out.println("Recognized status values for posts:"); printList(wp.getPostStatusList(), PostAndPageStatus.class, true); System.out.println("\nRecognized status values for pages:"); printList(wp.getPageStatusList(), PostAndPageStatus.class, true); } else if (config.hasOption("commentstatus")) { showCommentStatus(wp); } else if (config.hasOption("commentcount")) { showCommentCount(config, wp); } else if (config.hasOption("newcomment")) { editComment(wp, config.getOptionValue("newcomment"), "newcomment"); } else if (config.hasOption("editcomment")) { editComment(wp, config.getOptionValue("editcomment"), "editcomment"); } else if (config.hasOption("deletecomment")) { System.err.println(Integer.valueOf(config.getOptionValue("deletecomment"))); deleteComment(wp, Integer.valueOf(config.getOptionValue("deletecomment"))); } else if (config.hasOption("getcomment")) { printComment(wp, Integer.valueOf(config.getOptionValue("getcomment"))); } else if (config.hasOption("getcomments")) { Integer postID = Integer.valueOf(config.getOptionValue("getcomments")); String commentStatus = config.getOptionValue("commentstatus"); Integer commentOffset; try { commentOffset = Integer.valueOf(config.getOptionValue("commentoffset")); } catch (NumberFormatException e) { commentOffset = null; } Integer commentNumber; try { commentNumber = Integer.valueOf(config.getOptionValue("commentnumber")); } catch (Exception e) { commentNumber = null; } printComments(wp, postID, commentStatus, commentOffset, commentNumber); } else { showHelp(options); } } catch (MalformedURLException e) { System.err.println("URL \"" + config.getOptionValue("url") + "\" is invalid, reason is: " + e.getLocalizedMessage()); } catch (IOException e) { System.err.println("Can't read from file, reason is: " + e.getLocalizedMessage()); } catch (InvalidPostFormatException e) { System.err.println("Input format is invalid."); } } } catch (ParseException e) { System.err.println("Can't process command line arguments, reason is: " + e.getLocalizedMessage()); } } catch (XmlRpcFault e) { String reason = e.getLocalizedMessage(); System.err.println("Operation failed, reason is: " + reason); } }
From source file:Main.java
public static final boolean objectToBoolean(Object o) { return o != null ? Boolean.valueOf(o.toString()).booleanValue() : false; }
From source file:Main.java
private static boolean transformToBoolean(String v) { return Boolean.valueOf(v); }
From source file:Main.java
public static boolean getBooleanValue(Object o, boolean defaultVal) { if (o == null) return Boolean.valueOf(defaultVal); if (o.toString().trim().length() == 0) return Boolean.valueOf(defaultVal); if (o instanceof Boolean) return (Boolean) o; if (o instanceof String) return Boolean.parseBoolean((String) o); return Boolean.valueOf(defaultVal); }