List of usage examples for java.lang Boolean parseBoolean
public static boolean parseBoolean(String s)
From source file:edu.usc.goffish.gopher.impl.client.DeploymentTool.java
public static void main(String[] args) throws IOException, ConfigurationException { if ("list".equals(args[0])) { if (args.length == 2) { new DeploymentTool().listDataNodes(args[1]); } else {//from w w w . j a v a2s. com System.out.println( "Invalid arguments - Expected args : " + "arg[0]=list arg[1]=gofsConfig file path"); } } else if ("setup".equals(args[0])) { if (args.length >= 4) { if (args.length == 4) { new DeploymentTool().setup(args[1], args[2], args[3], true); } else if (args.length == 5) { new DeploymentTool().setup(args[1], args[2], args[3], Boolean.parseBoolean(args[4])); } else { System.out.println("Invalid arguments - Expected args : " + "arg[0]=setup arg[1]=gofsConfig file path arg[2]=managerHost " + "arg[3]=coordinatorHost <Optional> arg[4]=true if needs to persist the floe graph"); } } else { System.out.println("Invalid arguments - Expected args : " + "arg[0]=setup arg[1]=gofsConfig file path arg[2]=managerHost " + "arg[3]=coordinatorHost <Optional> arg[4]=true if needs to persist the floe graph"); } } }
From source file:com.minoritycode.Application.java
public static void main(String[] args) { System.out.println("Trello Backup Application"); File configFile = new File(workingDir + "\\config.properties"); InputStream input = null;//ww w .ja v a2s .co m try { input = new FileInputStream(configFile); config.load(input); input.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } // String workingDir = System.getProperty("user.dir"); manualOperation = Boolean.parseBoolean(config.getProperty("manualOperation")); logger.startErrorLogger(); setBackupDir(); try { report.put("backupDate", backupDate); } catch (JSONException e) { e.printStackTrace(); logger.logLine(e.getMessage()); } lock = new ReentrantLock(); lockErrorRep = new ReentrantLock(); lockErrorLog = new ReentrantLock(); Application.key = config.getProperty("trellokey"); Application.token = config.getProperty("trellotoken"); boolean useProxy = Boolean.parseBoolean(config.getProperty("useProxy")); boolean proxySet = true; if (useProxy) { proxySet = setProxy(); } // GUI swingContainerDemo = new GUI(); // swingContainerDemo.showJPanelDemo(); if (proxySet) { Credentials credentials = new Credentials(); if (Application.key.isEmpty()) { Application.key = credentials.getKey(); } else { Application.key = config.getProperty("trellokey"); } if (token.isEmpty()) { Application.token = credentials.getToken(); } else { Application.token = config.getProperty("trellotoken"); } BoardDownloader downloader = new BoardDownloader(); downloader.downloadMyBoard(url); boards = downloader.downloadOrgBoard(url); if (boards != null) { try { report.put("boardNum", boards.size()); } catch (JSONException e) { e.printStackTrace(); logger.logLine(e.getMessage()); } Integer numberOfThreads = Integer.parseInt(config.getProperty("numberOfThreads")); if (numberOfThreads == null) { logger.logLine("error number of threads not set in config file"); if (manualOperation) { String message = "How many threads do you want to use (10) is average"; numberOfThreads = Integer.parseInt(Credentials.getInput(message)); Credentials.saveProperty("numberOfThreads", numberOfThreads.toString()); } else { if (Boolean.parseBoolean(config.getProperty("useMailer"))) { Mailer mailer = new Mailer(); mailer.SendMail(); } System.exit(-1); } } ArrayList<Thread> threadList = new ArrayList<Thread>(); for (int i = 0; i < numberOfThreads; i++) { Thread thread = new Thread(new Application(), "BoardDownloadThread"); threadList.add(thread); thread.start(); } } else { //create empty report try { report.put("boardsNotDownloaded", "99999"); report.put("boardNum", 0); report.put("boardNumSuccessful", 0); } catch (JSONException e) { e.printStackTrace(); logger.logLine(e.getMessage()); } if (Boolean.parseBoolean(config.getProperty("useMailer"))) { Mailer mailer = new Mailer(); mailer.SendMail(); } logger.logger(report); } } else { //create empty report try { report.put("boardsNotDownloaded", "99999"); report.put("boardNum", 0); report.put("boardNumSuccessful", 0); } catch (JSONException e) { e.printStackTrace(); logger.logLine(e.getMessage()); } if (Boolean.parseBoolean(config.getProperty("useMailer"))) { Mailer mailer = new Mailer(); mailer.SendMail(); } } }
From source file:com.hpe.nv.samples.basic.BasicAnalyzeNVTransactions.java
public static void main(String[] args) { try {//from w ww. j ava 2 s . c o m // program arguments Options options = new Options(); options.addOption("i", "server-ip", true, "[mandatory] NV Test Manager IP"); options.addOption("o", "server-port", true, "[mandatory] NV Test Manager port"); options.addOption("u", "username", true, "[mandatory] NV username"); options.addOption("w", "password", true, "[mandatory] NV password"); options.addOption("e", "ssl", true, "[optional] Pass true to use SSL. Default: false"); options.addOption("y", "proxy", true, "[optional] Proxy server host:port"); options.addOption("z", "zip-result-file-path", true, "[optional] File path to store the analysis results as a .zip file"); options.addOption("k", "analysis-ports", true, "[optional] A comma-separated list of ports for test analysis"); options.addOption("b", "browser", true, "[optional] The browser for which the Selenium WebDriver is built. Possible values: Chrome and Firefox. Default: Firefox"); options.addOption("d", "debug", true, "[optional] Pass true to view console debug messages during execution. Default: false"); options.addOption("h", "help", false, "[optional] Generates and prints help information"); // parse and validate the command line arguments CommandLineParser parser = new DefaultParser(); CommandLine line = parser.parse(options, args); if (line.hasOption("help")) { // print help if help argument is passed HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("BasicAnalyzeNVTransactions.java", options); return; } if (line.hasOption("server-ip")) { serverIp = line.getOptionValue("server-ip"); if (serverIp.equals("0.0.0.0")) { throw new Exception( "Please replace the server IP argument value (0.0.0.0) with your NV Test Manager IP"); } } else { throw new Exception("Missing argument -i/--server-ip <serverIp>"); } if (line.hasOption("server-port")) { serverPort = Integer.parseInt(line.getOptionValue("server-port")); } else { throw new Exception("Missing argument -o/--server-port <serverPort>"); } if (line.hasOption("username")) { username = line.getOptionValue("username"); } else { throw new Exception("Missing argument -u/--username <username>"); } if (line.hasOption("password")) { password = line.getOptionValue("password"); } else { throw new Exception("Missing argument -w/--password <password>"); } if (line.hasOption("ssl")) { ssl = Boolean.parseBoolean(line.getOptionValue("ssl")); } if (line.hasOption("zip-result-file-path")) { zipResultFilePath = line.getOptionValue("zip-result-file-path"); } if (line.hasOption("proxy")) { proxySetting = line.getOptionValue("proxy"); } if (line.hasOption("analysis-ports")) { String analysisPortsStr = line.getOptionValue("analysis-ports"); analysisPorts = analysisPortsStr.split(","); } else { analysisPorts = new String[] { "80", "8080" }; } if (line.hasOption("browser")) { browser = line.getOptionValue("browser"); } else { browser = "Firefox"; } if (line.hasOption("debug")) { debug = Boolean.parseBoolean(line.getOptionValue("debug")); } String newLine = System.getProperty("line.separator"); String testDescription = "*** This sample demonstrates how to run transactions as part of an NV test. ***" + newLine + "*** ***" + newLine + "*** In this sample, the NV test starts with the \"3G Busy\" network scenario, running three transactions (see below). ***" + newLine + "*** After the sample stops and analyzes the NV test, it prints the analysis .zip file path to the console. ***" + newLine + "*** ***" + newLine + "*** This sample runs three NV transactions: ***" + newLine + "*** 1. \"Home Page\" transaction: Navigates to the home page in the HPE Network Virtualization website ***" + newLine + "*** 2. \"Get Started\" transaction: Navigates to the Get Started Now page in the HPE Network Virtualization website ***" + newLine + "*** 3. \"Overview\" transaction: Navigates back to the home page in the HPE Network Virtualization website ***" + newLine + "*** ***" + newLine + "*** You can view the actual steps of this sample in the BasicAnalyzeNVTransactions.java file. ***" + newLine; // print the sample's description System.out.println(testDescription); // start console spinner if (!debug) { spinner = new Thread(new Spinner()); spinner.start(); } // sample execution steps /***** Part 1 - Start the NV test with the "3G Busy" network scenario *****/ printPartDescription("\b------ Part 1 - Start the NV test with the \"3G Busy\" network scenario"); initTestManager(); startTest(); testRunning = true; printPartSeparator(); /***** Part 2 - Run three transactions - "Home Page", "Get Started" and "Overview" *****/ printPartDescription( "------ Part 2 - Run three transactions - \"Home Page\", \"Get Started\" and \"Overview\""); connectToTransactionManager(); startTransaction(1); transactionInProgress = true; buildSeleniumWebDriver(); seleniumNavigateToPage(); stopTransaction(1); transactionInProgress = false; startTransaction(2); transactionInProgress = true; seleniumGetStartedClick(); stopTransaction(2); transactionInProgress = false; startTransaction(3); transactionInProgress = true; seleniumOverviewClick(); stopTransaction(3); transactionInProgress = false; driverCloseAndQuit(); printPartSeparator(); /***** Part 3 - Stop the NV test, analyze it and print the results to the console *****/ printPartDescription( "------ Part 3 - Stop the NV test, analyze it and print the results to the console"); stopTestAndAnalyze(); testRunning = false; printPartSeparator(); doneCallback(); } catch (Exception e) { try { handleError(e.getMessage()); } catch (Exception e2) { System.out.println("Error occurred: " + e2.getMessage()); } } }
From source file:DIA_Umpire_Quant.DIA_Umpire_Quant.java
/** * @param args the command line arguments *//*from w w w .j a v a 2s. c o m*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire quantitation with targeted re-extraction analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, it should be like: java -jar -Xmx10G DIA_Umpire_Quant.jar diaumpire_quant.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_quant.log"); } catch (Exception e) { } try { Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; String UserMod = ""; String Combined_Prot = ""; String InternalLibID = ""; String ExternalLibPath = ""; String ExternalLibDecoyTag = "DECOY"; boolean DefaultProtFiltering = true; boolean DataSetLevelPepFDR = false; float ProbThreshold = 0.99f; float ExtProbThreshold = 0.99f; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; float MinFragMz = 200f; String FilterWeight = "GW"; float MinWeight = 0.9f; float RTWindow_Int = -1f; float RTWindow_Ext = -1f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean InternalLibSearch = false; boolean ExternalLibSearch = false; boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "TargetedExtraction": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "InternalLibSearch": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "ExternalLibSearch": { ExternalLibSearch = Boolean.parseBoolean(value); break; } case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "UserMod": { UserMod = value; break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } case "DataSetLevelPepFDR": { DataSetLevelPepFDR = Boolean.parseBoolean(value); break; } case "InternalLibID": { InternalLibID = value; break; } case "ExternalLibPath": { ExternalLibPath = value; break; } case "ExtProbThreshold": { ExtProbThreshold = Float.parseFloat(value); break; } case "RTWindow_Int": { RTWindow_Int = Float.parseFloat(value); break; } case "RTWindow_Ext": { RTWindow_Ext = Float.parseFloat(value); break; } case "ExternalLibDecoyTag": { ExternalLibDecoyTag = value; if (ExternalLibDecoyTag.endsWith("_")) { ExternalLibDecoyTag = ExternalLibDecoyTag.substring(0, ExternalLibDecoyTag.length() - 1); } break; } case "ProbThreshold": { ProbThreshold = Float.parseFloat(value); break; } case "ReSearchProb": { //ReSearchProb = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } case "MinFragMz": { MinFragMz = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); if (!UserMod.equals("")) { PTMManager.GetInstance().ImportUserMod(UserMod); } //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } } } LCMSID combinePepID = null; if (DataSetLevelPepFDR) { combinePepID = LCMSID.ReadLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); if (combinePepID == null) { FDR_DataSetLevel fdr = new FDR_DataSetLevel(); fdr.GeneratePepIonList(FileList, tandemPara, WorkFolder + "combinePepID.SerFS"); combinePepID = fdr.combineID; combinePepID.WriteLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); } } //process each DIA file for quantification based on untargeted identifications for (DIAPack DiaFile : FileList) { long time = System.currentTimeMillis(); Logger.getRootLogger().info("Loading identification results " + DiaFile.Filename + "...."); //If the LCMSID serialization is found if (!DiaFile.ReadSerializedLCMSID()) { DiaFile.ParsePepXML(tandemPara, combinePepID); DiaFile.BuildStructure(); if (!DiaFile.MS1FeatureMap.ReadPeakCluster()) { Logger.getRootLogger().info("Loading peak and structure failed, job is incomplete"); System.exit(1); } DiaFile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); //Generate mapping between index of precursor feature and pseudo MS/MS scan index DiaFile.GenerateClusterScanNomapping(); //Doing quantification DiaFile.AssignQuant(); DiaFile.ClearStructure(); } DiaFile.IDsummary.ReduceMemoryUsage(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(DiaFile.Filename + " 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)))); } //<editor-fold defaultstate="collapsed" desc="Targete re-extraction using internal library"> Logger.getRootLogger().info( "================================================================================================="); if (InternalLibSearch && FileList.size() > 1) { Logger.getRootLogger().info("Module C: Targeted extraction using internal library"); FragmentLibManager libManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, InternalLibID); if (libManager == null) { Logger.getRootLogger().info("Building internal spectral library"); libManager = new FragmentLibManager(InternalLibID); ArrayList<LCMSID> LCMSIDList = new ArrayList<>(); for (DIAPack dia : FileList) { LCMSIDList.add(dia.IDsummary); } libManager.ImportFragLibTopFrag(LCMSIDList, Freq, TopNFrag); libManager.WriteFragmentLibSerialization(WorkFolder); } libManager.ReduceMemoryUsage(); Logger.getRootLogger() .info("Building retention time prediction model and generate candidate peptide list"); for (int i = 0; i < FileList.size(); i++) { FileList.get(i).IDsummary.ClearMappedPep(); } for (int i = 0; i < FileList.size(); i++) { for (int j = i + 1; j < FileList.size(); j++) { RTAlignedPepIonMapping alignment = new RTAlignedPepIonMapping(WorkFolder, FileList.get(i).GetParameter(), FileList.get(i).IDsummary, FileList.get(j).IDsummary); alignment.GenerateModel(); alignment.GenerateMappedPepIon(); } FileList.get(i).ExportID(); FileList.get(i).IDsummary = null; } Logger.getRootLogger().info("Targeted matching........"); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } if (!diafile.IDsummary.GetMappedPepIonList().isEmpty()) { diafile.UseMappedIon = true; diafile.FilterMappedIonByProb = false; diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); diafile.GenerateMassCalibrationRTMap(); diafile.TargetedExtractionQuant(false, libManager, 1.1f, RTWindow_Int); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); diafile.IDsummary.RemoveLowProbMappedIon(ProbThreshold); diafile.ExportID(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); diafile.ClearStructure(); } diafile.IDsummary = null; System.gc(); } Logger.getRootLogger().info( "================================================================================================="); } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library"> //External library search if (ExternalLibSearch) { Logger.getRootLogger().info("Module C: Targeted extraction using external library"); //Read exteranl library FragmentLibManager ExlibManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, FilenameUtils.getBaseName(ExternalLibPath)); if (ExlibManager == null) { ExlibManager = new FragmentLibManager(FilenameUtils.getBaseName(ExternalLibPath)); //Import traML file ExlibManager.ImportFragLibByTraML(ExternalLibPath, ExternalLibDecoyTag); //Check if there are decoy spectra ExlibManager.CheckDecoys(); //ExlibManager.ImportFragLibBySPTXT(ExternalLibPath); ExlibManager.WriteFragmentLibSerialization(WorkFolder); } Logger.getRootLogger() .info("No. of peptide ions in external lib:" + ExlibManager.PeptideFragmentLib.size()); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } //Generate RT mapping RTMappingExtLib RTmap = new RTMappingExtLib(diafile.IDsummary, ExlibManager, diafile.GetParameter()); RTmap.GenerateModel(); RTmap.GenerateMappedPepIon(); diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.GenerateMassCalibrationRTMap(); //Perform targeted re-extraction diafile.TargetedExtractionQuant(false, ExlibManager, ProbThreshold, RTWindow_Ext); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); //Remove target IDs below the defined probability threshold diafile.IDsummary.RemoveLowProbMappedIon(ExtProbThreshold); diafile.ExportID(); diafile.ClearStructure(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); } } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); diafile.IDsummary.ClearAssignPeakCluster(); //diafile.IDsummary.ClearPSMs(); } if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.MinFragMZ = MinFragMz; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:com.hpe.nv.samples.basic.BasicComparisonWithoutNV.java
public static void main(String[] args) throws Exception { try {//from w ww . j av a 2 s .c o m // program arguments Options options = new Options(); options.addOption("i", "server-ip", true, "[mandatory] NV Test Manager IP"); options.addOption("o", "server-port", true, "[mandatory] NV Test Manager port"); options.addOption("u", "username", true, "[mandatory] NV username"); options.addOption("w", "password", true, "[mandatory] NV password"); options.addOption("e", "ssl", true, "[optional] Pass true to use SSL. Default: false"); options.addOption("y", "proxy", true, "[optional] Proxy server host:port"); options.addOption("a", "active-adapter-ip", true, "[optional] Active adapter IP. Default: --server-ip argument"); options.addOption("t", "site-url", true, "[optional] Site under test URL. Default: HPE Network Virtualization site URL. If you change this value, make sure to change the --xpath argument too"); options.addOption("x", "xpath", true, "[optional] Parameter for ExpectedConditions.visibilityOfElementLocated(By.xpath(...)) method. Use an xpath expression of some element in the site. Default: //div[@id='content']"); options.addOption("k", "analysis-ports", true, "[optional] A comma-separated list of ports for test analysis"); options.addOption("b", "browser", true, "[optional] The browser for which the Selenium WebDriver is built. Possible values: Chrome, Firefox. Default: Firefox"); options.addOption("d", "debug", true, "[optional] Pass true to view console debug messages during execution. Default: false"); options.addOption("h", "help", false, "[optional] Generates and prints help information"); // parse and validate the command line arguments CommandLineParser parser = new DefaultParser(); CommandLine line = parser.parse(options, args); if (line.hasOption("help")) { // print help if help argument is passed HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("BasicComparisonWithoutNV.java", options); return; } if (line.hasOption("server-ip")) { serverIp = line.getOptionValue("server-ip"); if (serverIp.equals("0.0.0.0")) { throw new Exception( "Please replace the server IP argument value (0.0.0.0) with your NV Test Manager IP"); } } else { throw new Exception("Missing argument -i/--server-ip <serverIp>"); } if (line.hasOption("server-port")) { serverPort = Integer.parseInt(line.getOptionValue("server-port")); } else { throw new Exception("Missing argument -o/--server-port <serverPort>"); } if (line.hasOption("username")) { username = line.getOptionValue("username"); } else { throw new Exception("Missing argument -u/--username <username>"); } if (line.hasOption("password")) { password = line.getOptionValue("password"); } else { throw new Exception("Missing argument -w/--password <password>"); } if (line.hasOption("ssl")) { ssl = Boolean.parseBoolean(line.getOptionValue("ssl")); } if (line.hasOption("site-url")) { siteUrl = line.getOptionValue("site-url"); } else { siteUrl = "http://www8.hp.com/us/en/software-solutions/network-virtualization/index.html"; } if (line.hasOption("xpath")) { xpath = line.getOptionValue("xpath"); } else { xpath = "//div[@id='content']"; } if (line.hasOption("proxy")) { proxySetting = line.getOptionValue("proxy"); } if (line.hasOption("active-adapter-ip")) { activeAdapterIp = line.getOptionValue("active-adapter-ip"); } else { activeAdapterIp = serverIp; } if (line.hasOption("analysis-ports")) { String analysisPortsStr = line.getOptionValue("analysis-ports"); analysisPorts = analysisPortsStr.split(","); } else { analysisPorts = new String[] { "80", "8080" }; } if (line.hasOption("browser")) { browser = line.getOptionValue("browser"); } else { browser = "Firefox"; } if (line.hasOption("debug")) { debug = Boolean.parseBoolean(line.getOptionValue("debug")); } String newLine = System.getProperty("line.separator"); String testDescription = "*** This sample demonstrates how NV helps you test your application under various network conditions. ***" + newLine + "*** This test starts by navigating to the home page in the HPE Network Virtualization website using the Selenium WebDriver. ***" + newLine + "*** This initial step runs without NV emulation and provides a basis for comparison. ***" + newLine + "*** ***" + newLine + "*** Next, the sample starts an NV test configured with a \"3G Busy\" network scenario. ***" + newLine + "*** The same step runs as before - navigating to the home page in the HPE Network Virtualization website - but this time, ***" + newLine + "*** it does so over an emulated \"3G Busy\" network as part of an NV transaction. ***" + newLine + "*** ***" + newLine + "*** When the sample finishes running, it prints a summary to the console. This summary displays a comparison of the time ***" + newLine + "*** it took to navigate to the site both with and without NV's network emulation. The results show that the slow \"3G Busy\" ***" + newLine + "*** network increases the time it takes to navigate to the site, as you would expect. ***" + newLine + "*** ***" + newLine + "*** You can view the actual steps of this sample in the BasicComparisonWithoutNV.java file. ***" + newLine; // print the sample's description System.out.println(testDescription); // start console spinner if (!debug) { spinner = new Thread(new Spinner()); spinner.start(); } // sample execution steps /***** Part 1 - Navigate to the site without using NV emulation *****/ printPartDescription("\b------ Part 1 - Navigate to the site without using NV emulation"); buildSeleniumWebDriver(); startNoNV = System.currentTimeMillis(); seleniumNavigateToPage(); stopNoNV = System.currentTimeMillis(); driverCloseAndQuit(); printPartSeparator(); /***** Part 2 - Navigate to the site using NV "3G Busy" network scenario emulation *****/ printPartDescription( "------ Part 2 - Navigate to the site using NV \"3G Busy\" network scenario emulation"); initTestManager(); setActiveAdapter(); startBusyTest(); testRunning = true; connectToTransactionManager(); startTransaction(); transactionInProgress = true; buildSeleniumWebDriver(); seleniumNavigateToPage(); stopTransaction(); transactionInProgress = false; driverCloseAndQuit(); stopTest(); testRunning = false; printPartSeparator(); /***** Part 3 - Analyze the NV test and print the results to the console *****/ printPartDescription("------ Part 3 - Analyze the NV test and print the results to the console"); analyzeTestJson(); printPartSeparator(); doneCallback(); } catch (Exception e) { try { handleError(e.getMessage()); } catch (Exception e2) { System.out.println("Error occurred: " + e2.getMessage()); } } }
From source file:com.hpe.nv.samples.advanced.AdvMultipleTestsSequential.java
public static void main(String[] args) throws Exception { try {//from w w w.j a va2 s . c o m // program arguments Options options = new Options(); options.addOption("i", "server-ip", true, "[mandatory] NV Test Manager IP"); options.addOption("o", "server-port", true, "[mandatory] NV Test Manager port"); options.addOption("u", "username", true, "[mandatory] NV username"); options.addOption("w", "password", true, "[mandatory] NV password"); options.addOption("e", "ssl", true, "[optional] Pass true to use SSL. Default: false"); options.addOption("y", "proxy", true, "[optional] Proxy server host:port"); options.addOption("t", "site-url", true, "[optional] Site under test URL. Default: HPE Network Virtualization site URL. If you change this value, make sure to change the --xpath argument too"); options.addOption("x", "xpath", true, "[optional] Parameter for ExpectedConditions.visibilityOfElementLocated(By.xpath(...)) method. Use an xpath expression of some element in the site. Default: //div[@id='content']"); options.addOption("a", "active-adapter-ip", true, "[optional] Active adapter IP. Default: --server-ip argument"); options.addOption("f", "first-zip-result-file-path", true, "[optional] File path to store the first test analysis results as a .zip file"); options.addOption("s", "second-zip-result-file-path", true, "[optional] File path to store the second test analysis results as a .zip file"); options.addOption("k", "analysis-ports", true, "[optional] A comma-separated list of ports for test analysis"); options.addOption("b", "browser", true, "[optional] The browser for which the Selenium WebDriver is built. Possible values: Chrome and Firefox. Default: Firefox"); options.addOption("d", "debug", true, "[optional] Pass true to view console debug messages during execution. Default: false"); options.addOption("h", "help", false, "[optional] Generates and prints help information"); // parse and validate the command line arguments CommandLineParser parser = new DefaultParser(); CommandLine line = parser.parse(options, args); if (line.hasOption("help")) { // print help if help argument is passed HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("AdvMultipleTestsSequential.java", options); return; } if (line.hasOption("server-ip")) { serverIp = line.getOptionValue("server-ip"); if (serverIp.equals("0.0.0.0")) { throw new Exception( "Please replace the server IP argument value (0.0.0.0) with your NV Test Manager IP"); } } else { throw new Exception("Missing argument -i/--server-ip <serverIp>"); } if (line.hasOption("server-port")) { serverPort = Integer.parseInt(line.getOptionValue("server-port")); } else { throw new Exception("Missing argument -o/--server-port <serverPort>"); } if (line.hasOption("username")) { username = line.getOptionValue("username"); } else { throw new Exception("Missing argument -u/--username <username>"); } if (line.hasOption("password")) { password = line.getOptionValue("password"); } else { throw new Exception("Missing argument -w/--password <password>"); } if (line.hasOption("ssl")) { ssl = Boolean.parseBoolean(line.getOptionValue("ssl")); } if (line.hasOption("site-url")) { siteUrl = line.getOptionValue("site-url"); } else { siteUrl = "http://www8.hp.com/us/en/software-solutions/network-virtualization/index.html"; } if (line.hasOption("xpath")) { xpath = line.getOptionValue("xpath"); } else { xpath = "//div[@id='content']"; } if (line.hasOption("first-zip-result-file-path")) { firstZipResultFilePath = line.getOptionValue("first-zip-result-file-path"); } if (line.hasOption("second-zip-result-file-path")) { secondZipResultFilePath = line.getOptionValue("second-zip-result-file-path"); } if (line.hasOption("proxy")) { proxySetting = line.getOptionValue("proxy"); } if (line.hasOption("active-adapter-ip")) { activeAdapterIp = line.getOptionValue("active-adapter-ip"); } else { activeAdapterIp = serverIp; } if (line.hasOption("analysis-ports")) { String analysisPortsStr = line.getOptionValue("analysis-ports"); analysisPorts = analysisPortsStr.split(","); } else { analysisPorts = new String[] { "80", "8080" }; } if (line.hasOption("browser")) { browser = line.getOptionValue("browser"); } else { browser = "Firefox"; } if (line.hasOption("debug")) { debug = Boolean.parseBoolean(line.getOptionValue("debug")); } String newLine = System.getProperty("line.separator"); String testDescription = "*** This sample shows how to run several tests sequentially with different network scenarios. ***" + newLine + "*** ***" + newLine + "*** You can view the actual steps of this sample in the AdvMultipleTestsSequential.java file. ***" + newLine; // print the sample's description System.out.println(testDescription); // start console spinner if (!debug) { spinner = new Thread(new Spinner()); spinner.start(); } // sample execution steps /***** Part 1 - Initialize the TestManager object and set the active adapter *****/ printPartDescription( "\b------ Part 1 - Initialize the TestManager object and set the active adapter"); initTestManager(); setActiveAdapter(); printPartSeparator(); /***** Part 2 - Start the first NV test with the "3G Busy" network scenario and run the "Home Page" transaction *****/ printPartDescription( "------ Part 2 - Start the first NV test with the \"3G Busy\" network scenario and run the \"Home Page\" transaction"); startTest("3G Busy"); testRunning = true; connectToTransactionManager(); startTransaction(); transactionInProgress = true; buildSeleniumWebDriver(); seleniumNavigateToPage(); stopTransaction(); transactionInProgress = false; driverCloseAndQuit(); printPartSeparator(); /***** Part 3 - Stop the first NV test, analyze it and print the results to the console *****/ printPartDescription( "------ Part 3 - Stop the first NV test, analyze it and print the results to the console"); stopTest(); testRunning = false; analyzeTest(); printPartSeparator(); /***** Part 4 - Start the second NV test with the "3G Good" network scenario and run the "Home Page" transaction *****/ printPartDescription( "------ Part 4 - Start the second NV test with the \"3G Good\" network scenario and run the \"Home Page\" transaction"); startTest("3G Good"); testRunning = true; connectToTransactionManager(); startTransaction(); transactionInProgress = true; buildSeleniumWebDriver(); seleniumNavigateToPage(); stopTransaction(); transactionInProgress = false; driverCloseAndQuit(); printPartSeparator(); /***** Part 5 - Stop the second NV test, analyze it and print the results to the console *****/ printPartDescription( "------ Part 3 - Stop the second NV test, analyze it and print the results to the console"); stopTest(); testRunning = false; analyzeTest(); printPartSeparator(); doneCallback(); } catch (Exception e) { try { handleError(e.getMessage()); } catch (Exception e2) { System.out.println("Error occurred: " + e2.getMessage()); } } }
From source file:com.hpe.nv.samples.advanced.AdvRealtimeUpdate.java
public static void main(String[] args) throws Exception { try {/*from w w w .j a va 2 s . c om*/ // program arguments Options options = new Options(); options.addOption("i", "server-ip", true, "[mandatory] NV Test Manager IP"); options.addOption("o", "server-port", true, "[mandatory] NV Test Manager port"); options.addOption("u", "username", true, "[mandatory] NV username"); options.addOption("w", "password", true, "[mandatory] NV password"); options.addOption("e", "ssl", true, "[optional] Pass true to use SSL. Default: false"); options.addOption("y", "proxy", true, "[optional] Proxy server host:port"); options.addOption("t", "site-url", true, "[optional] Site under test URL. Default: HPE Network Virtualization site URL. If you change this value, make sure to change the --xpath argument too"); options.addOption("x", "xpath", true, "[optional] Parameter for ExpectedConditions.visibilityOfElementLocated(By.xpath(...)) method. Use an xpath expression of some element in the site. Default: //div[@id='content']"); options.addOption("a", "active-adapter-ip", true, "[optional] Active adapter IP. Default: --server-ip argument"); options.addOption("n", "ntx-file-path", true, "[optional] File path (of an .ntx or .ntxx file) to update the test in ntx mode"); options.addOption("z", "zip-result-file-path", true, "[optional] File path to store the analysis results as a .zip file"); options.addOption("k", "analysis-ports", true, "[optional] A comma-separated list of ports for test analysis"); options.addOption("b", "browser", true, "[optional] The browser for which the Selenium WebDriver is built. Possible values: Chrome and Firefox. Default: Firefox"); options.addOption("d", "debug", true, "[optional] Pass true to view console debug messages during execution. Default: false"); options.addOption("h", "help", false, "[optional] Generates and prints help information"); // parse and validate the command line arguments CommandLineParser parser = new DefaultParser(); CommandLine line = parser.parse(options, args); if (line.hasOption("help")) { // print help if help argument is passed HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("AdvRealtimeUpdate.java", options); return; } if (line.hasOption("server-ip")) { serverIp = line.getOptionValue("server-ip"); if (serverIp.equals("0.0.0.0")) { throw new Exception( "Please replace the server IP argument value (0.0.0.0) with your NV Test Manager IP"); } } else { throw new Exception("Missing argument -i/--server-ip <serverIp>"); } if (line.hasOption("server-port")) { serverPort = Integer.parseInt(line.getOptionValue("server-port")); } else { throw new Exception("Missing argument -o/--server-port <serverPort>"); } if (line.hasOption("username")) { username = line.getOptionValue("username"); } else { throw new Exception("Missing argument -u/--username <username>"); } if (line.hasOption("password")) { password = line.getOptionValue("password"); } else { throw new Exception("Missing argument -w/--password <password>"); } if (line.hasOption("ssl")) { ssl = Boolean.parseBoolean(line.getOptionValue("ssl")); } if (line.hasOption("zip-result-file-path")) { zipResultFilePath = line.getOptionValue("zip-result-file-path"); } if (line.hasOption("site-url")) { siteUrl = line.getOptionValue("site-url"); } else { siteUrl = "http://www8.hp.com/us/en/software-solutions/network-virtualization/index.html"; } if (line.hasOption("xpath")) { xpath = line.getOptionValue("xpath"); } else { xpath = "//div[@id='content']"; } if (line.hasOption("proxy")) { proxySetting = line.getOptionValue("proxy"); } if (line.hasOption("active-adapter-ip")) { activeAdapterIp = line.getOptionValue("active-adapter-ip"); } else { activeAdapterIp = serverIp; } if (line.hasOption("analysis-ports")) { String analysisPortsStr = line.getOptionValue("analysis-ports"); analysisPorts = analysisPortsStr.split(","); } else { analysisPorts = new String[] { "80", "8080" }; } if (line.hasOption("ntx-file-path")) { ntxFilePath = line.getOptionValue("ntx-file-path"); } if (line.hasOption("browser")) { browser = line.getOptionValue("browser"); } else { browser = "Firefox"; } if (line.hasOption("debug")) { debug = Boolean.parseBoolean(line.getOptionValue("debug")); } String newLine = System.getProperty("line.separator"); String testDescription = "*** This sample demonstrates the real-time update API. You can use this API to update the test during runtime. ***" + newLine + "*** For example, you can update the network scenario to run several \"mini tests\" in a single test. ***" + newLine + "*** ***" + newLine + "*** This sample starts by running an NV test with a single transaction that uses the \"3G Busy\" network scenario. Then the ***" + newLine + "*** sample updates the network scenario to \"3G Good\" and reruns the transaction. You can update the test in real time ***" + newLine + "*** using either the NTX or Custom real-time update modes. ***" + newLine + "*** ***" + newLine + "*** You can view the actual steps of this sample in the AdvRealtimeUpdate.java file. ***" + newLine; // print the sample's description System.out.println(testDescription); // start console spinner if (!debug) { spinner = new Thread(new Spinner()); spinner.start(); } // sample execution steps /***** Part 1 - Navigate to the site with the NV "3G Busy" network scenario *****/ printPartDescription( "\b------ Part 1 - Navigate to the site with the NV \"3G Busy\" network scenario"); initTestManager(); setActiveAdapter(); startBusyTest(); testRunning = true; connectToTransactionManager(); startTransaction(); transactionInProgress = true; buildSeleniumWebDriver(); seleniumNavigateToPage(); stopTransaction(); transactionInProgress = false; driverCloseAndQuit(); printPartSeparator(); /***** Part 2 - Update the NV test in real-time---update the network scenario to "3G Good" *****/ printPartDescription( "------ Part 2 - Update the NV test in real time to the \"3G Good\" network scenario"); realTimeUpdateTest(); printPartSeparator(); /***** Part 3 - Navigate to the site with the NV \"3G Good\" network scenario *****/ printPartDescription( "------ Part 3 - Navigate to the site with the NV \"3G Good\" network scenario"); startTransactionAfterRTU(); transactionInProgress = true; buildSeleniumWebDriver(); seleniumNavigateToPage(); stopTransaction(); transactionInProgress = false; driverCloseAndQuit(); printPartSeparator(); /***** Part 4 - Stop the NV test, analyze it and print the results to the console *****/ printPartDescription( "------ Part 4 - Stop the NV test, analyze it and print the results to the console"); stopTest(); testRunning = false; analyzeTest(); printPartSeparator(); doneCallback(); } catch (Exception e) { try { handleError(e.getMessage()); } catch (Exception e2) { System.out.println("Error occurred: " + e2.getMessage()); } } }
From source file:com.hpe.nv.samples.basic.BasicAnalyze2Scenarios.java
public static void main(String[] args) { try {/* ww w . ja v a 2s.c o m*/ // program arguments Options options = new Options(); options.addOption("i", "server-ip", true, "[mandatory] NV Test Manager IP"); options.addOption("o", "server-port", true, "[mandatory] NV Test Manager port"); options.addOption("u", "username", true, "[mandatory] NV username"); options.addOption("w", "password", true, "[mandatory] NV password"); options.addOption("e", "ssl", true, "[optional] Pass true to use SSL. Default: false"); options.addOption("y", "proxy", true, "[optional] Proxy server host:port"); options.addOption("a", "active-adapter-ip", true, "[optional] Active adapter IP. Default: --server-ip argument"); options.addOption("z", "zip-result-file-path", true, "[optional] File path to store the analysis results as a .zip file"); options.addOption("k", "analysis-ports", true, "[optional] A comma-separated list of ports for test analysis"); options.addOption("b", "browser", true, "[optional] The browser for which the Selenium WebDriver is built. Possible values: Chrome and Firefox. Default: Firefox"); options.addOption("d", "debug", true, "[optional] Pass true to view console debug messages during execution. Default: false"); options.addOption("h", "help", false, "[optional] Generates and prints help information"); // parse and validate the command line arguments CommandLineParser parser = new DefaultParser(); CommandLine line = parser.parse(options, args); if (line.hasOption("help")) { // print help if help argument is passed HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("BasicAnalyze2Scenarios.java", options); return; } if (line.hasOption("server-ip")) { serverIp = line.getOptionValue("server-ip"); if (serverIp.equals("0.0.0.0")) { throw new Exception( "Please replace the server IP argument value (0.0.0.0) with your NV Test Manager IP"); } } else { throw new Exception("Missing argument -i/--server-ip <serverIp>"); } if (line.hasOption("server-port")) { serverPort = Integer.parseInt(line.getOptionValue("server-port")); } else { throw new Exception("Missing argument -o/--server-port <serverPort>"); } if (line.hasOption("username")) { username = line.getOptionValue("username"); } else { throw new Exception("Missing argument -u/--username <username>"); } if (line.hasOption("password")) { password = line.getOptionValue("password"); } else { throw new Exception("Missing argument -w/--password <password>"); } if (line.hasOption("ssl")) { ssl = Boolean.parseBoolean(line.getOptionValue("ssl")); } if (line.hasOption("zip-result-file-path")) { zipResultFilePath = line.getOptionValue("zip-result-file-path"); } if (line.hasOption("proxy")) { proxySetting = line.getOptionValue("proxy"); } if (line.hasOption("active-adapter-ip")) { activeAdapterIp = line.getOptionValue("active-adapter-ip"); } else { activeAdapterIp = serverIp; } if (line.hasOption("analysis-ports")) { String analysisPortsStr = line.getOptionValue("analysis-ports"); analysisPorts = analysisPortsStr.split(","); } else { analysisPorts = new String[] { "80", "8080" }; } if (line.hasOption("browser")) { browser = line.getOptionValue("browser"); } else { browser = "Firefox"; } if (line.hasOption("debug")) { debug = Boolean.parseBoolean(line.getOptionValue("debug")); } String newLine = System.getProperty("line.separator"); String testDescription = "*** This sample demonstrates a comparison between two network scenarios - \"WiFi\" and \"3G Busy\". ***" + newLine + "*** ***" + newLine + "*** In this sample, the NV test starts with the \"WiFi\" network scenario, running three transactions (see below). ***" + newLine + "*** Then, the sample updates the NV test's network scenario to \"3G Busy\" using the real-time update API and runs the same ***" + newLine + "*** transactions again. ***" + newLine + "*** ***" + newLine + "*** After the sample analyzes the NV test and extracts the transaction times from the analysis results, it prints a ***" + newLine + "*** summary to the console. The summary displays the comparative network times for each transaction in both ***" + newLine + "*** network scenarios. ***" + newLine + "*** ***" + newLine + "*** This sample runs three identical NV transactions before and after the real-time update: ***" + newLine + "*** 1. \"Home Page\" transaction: Navigates to the home page in the HPE Network Virtualization website ***" + newLine + "*** 2. \"Get Started\" transaction: Navigates to the Get Started Now page in the HPE Network Virtualization website ***" + newLine + "*** 3. \"Overview\" transaction: Navigates back to the home page in the HPE Network Virtualization website ***" + newLine + "*** ***" + newLine + "*** You can view the actual steps of this sample in the BasicAnalyze2Scenarios.java file. ***" + newLine; // print the sample's description System.out.println(testDescription); // start console spinner if (!debug) { spinner = new Thread(new Spinner()); spinner.start(); } // sample execution steps /***** Part 1 - Start the NV test with the "WiFi" network scenario *****/ printPartDescription("\b------ Part 1 - Start the NV test with the \"WiFi\" network scenario"); initTestManager(); setActiveAdapter(); startTest(); testRunning = true; printPartSeparator(); /***** Part 2 - Run three transactions - "Home Page", "Get Started" and "Overview" *****/ printPartDescription( "------ Part 2 - Run three transactions - \"Home Page\", \"Get Started\" and \"Overview\""); connectToTransactionManager(); startTransaction(1); transactionInProgress = true; buildSeleniumWebDriver(); seleniumNavigateToPage(); stopTransaction(1); transactionInProgress = false; startTransaction(2); transactionInProgress = true; seleniumGetStartedClick(); stopTransaction(2); transactionInProgress = false; startTransaction(3); transactionInProgress = true; seleniumOverviewClick(); stopTransaction(3); transactionInProgress = false; driverCloseAndQuit(); printPartSeparator(); /***** Part 3 - Update the NV test in real time to the "3G Busy" network scenario *****/ printPartDescription( "------ Part 3 - Update the NV test in real time to the \"3G Busy\" network scenario"); realTimeUpdateTest(); printPartSeparator(); /***** Part 4 - Rerun the transactions *****/ printPartDescription("------ Part 4 - Rerun the transactions"); startTransactionAfterRTU(1); transactionInProgress = true; buildSeleniumWebDriver(); seleniumNavigateToPage(); stopTransaction(1); transactionInProgress = false; startTransactionAfterRTU(2); transactionInProgress = true; seleniumGetStartedClick(); stopTransaction(2); transactionInProgress = false; startTransactionAfterRTU(3); transactionInProgress = true; seleniumOverviewClick(); stopTransaction(3); transactionInProgress = false; driverCloseAndQuit(); printPartSeparator(); /***** Part 5 - Stop the NV test, analyze it and print the results to the console *****/ printPartDescription( "------ Part 5 - Stop the NV test, analyze it and print the results to the console"); stopTest(); testRunning = false; analyzeTestZip(); analyzeTestJson(); printPartSeparator(); doneCallback(); } catch (Exception e) { try { handleError(e.getMessage()); } catch (Exception e2) { System.out.println("Error occurred: " + e2.getMessage()); } } }
From source file:com.cloud.test.stress.TestClientWithAPI.java
public static void main(String[] args) { String host = "http://localhost"; String port = "8092"; String devPort = "8080"; String apiUrl = "/client/api"; try {/*from www . ja v a 2s . c om*/ // Parameters List<String> argsList = Arrays.asList(args); Iterator<String> iter = argsList.iterator(); while (iter.hasNext()) { String arg = iter.next(); // host if (arg.equals("-h")) { host = "http://" + iter.next(); } if (arg.equals("-p")) { port = iter.next(); } if (arg.equals("-dp")) { devPort = iter.next(); } if (arg.equals("-t")) { numThreads = Integer.parseInt(iter.next()); } if (arg.equals("-s")) { sleepTime = Long.parseLong(iter.next()); } if (arg.equals("-a")) { accountName = iter.next(); } if (arg.equals("-c")) { cleanUp = Boolean.parseBoolean(iter.next()); if (!cleanUp) sleepTime = 0L; // no need to wait if we don't ever // cleanup } if (arg.equals("-r")) { repeat = Boolean.parseBoolean(iter.next()); } if (arg.equals("-u")) { numOfUsers = Integer.parseInt(iter.next()); } if (arg.equals("-i")) { internet = Boolean.parseBoolean(iter.next()); } if (arg.equals("-w")) { wait = Integer.parseInt(iter.next()); } if (arg.equals("-z")) { zoneId = iter.next(); } if (arg.equals("-snapshot")) { snapshot_test = "yes"; } if (arg.equals("-so")) { serviceOfferingId = iter.next(); } if (arg.equals("-do")) { diskOfferingId = iter.next(); } if (arg.equals("-no")) { networkOfferingId = iter.next(); } if (arg.equals("-pass")) { vmPassword = iter.next(); } if (arg.equals("-url")) { downloadUrl = iter.next(); } } final String server = host + ":" + port + "/"; final String developerServer = host + ":" + devPort + apiUrl; s_logger.info("Starting test against server: " + server + " with " + numThreads + " thread(s)"); if (cleanUp) s_logger.info("Clean up is enabled, each test will wait " + sleepTime + " ms before cleaning up"); if (numOfUsers > 0) { s_logger.info("Pre-generating users for test of size : " + numOfUsers); users = new String[numOfUsers]; Random ran = new Random(); for (int i = 0; i < numOfUsers; i++) { users[i] = Math.abs(ran.nextInt()) + "-user"; } } for (int i = 0; i < numThreads; i++) { new Thread(new Runnable() { @Override public void run() { do { String username = null; try { long now = System.currentTimeMillis(); Random ran = new Random(); if (users != null) { username = users[Math.abs(ran.nextInt()) % numOfUsers]; } else { username = Math.abs(ran.nextInt()) + "-user"; } NDC.push(username); s_logger.info("Starting test for the user " + username); int response = executeDeployment(server, developerServer, username, snapshot_test); boolean success = false; String reason = null; if (response == 200) { success = true; if (internet) { s_logger.info("Deploy successful...waiting 5 minute before SSH tests"); Thread.sleep(300000L); // Wait 60 // seconds so // the windows VM // can boot up and do a sys prep. if (accountName == null) { s_logger.info("Begin Linux SSH test for account " + _account.get()); reason = sshTest(_linuxIP.get(), _linuxPassword.get(), snapshot_test); } if (reason == null) { s_logger.info( "Linux SSH test successful for account " + _account.get()); s_logger.info("Begin WindowsSSH test for account " + _account.get()); reason = sshTest(_linuxIP.get(), _linuxPassword.get(), snapshot_test); // reason = sshWinTest(_windowsIP.get()); } // release the linux IP now... _linuxIP.set(null); // release the Windows IP now _windowsIP.set(null); } // sleep for 3 min before getting the latest network stat // s_logger.info("Sleeping for 5 min before getting the lates network stat for the account"); // Thread.sleep(300000); // verify that network stat is correct for the user; if it's not - stop all the resources // for the user // if ((reason == null) && (getNetworkStat(server) == false) ) { // s_logger.error("Stopping all the resources for the account " + _account.get() + // " as network stat is incorrect"); // int stopResponseCode = executeStop( // server, developerServer, // username, false); // s_logger // .info("stop command finished with response code: " // + stopResponseCode); // success = false; // since the SSH test // // } else if (reason == null) { if (internet) { s_logger.info( "Windows SSH test successful for account " + _account.get()); } else { s_logger.info("deploy test successful....now cleaning up"); if (cleanUp) { s_logger.info( "Waiting " + sleepTime + " ms before cleaning up vms"); Thread.sleep(sleepTime); } else { success = true; } } if (usageIterator >= numThreads) { int eventsAndBillingResponseCode = executeEventsAndBilling(server, developerServer); s_logger.info( "events and usage records command finished with response code: " + eventsAndBillingResponseCode); usageIterator = 1; } else { s_logger.info( "Skipping events and usage records for this user: usageIterator " + usageIterator + " and number of Threads " + numThreads); usageIterator++; } if ((users == null) && (accountName == null)) { s_logger.info("Sending cleanup command"); int cleanupResponseCode = executeCleanup(server, developerServer, username); s_logger.info("cleanup command finished with response code: " + cleanupResponseCode); success = (cleanupResponseCode == 200); } else { s_logger.info("Sending stop DomR / destroy VM command"); int stopResponseCode = executeStop(server, developerServer, username, true); s_logger.info("stop(destroy) command finished with response code: " + stopResponseCode); success = (stopResponseCode == 200); } } else { // Just stop but don't destroy the // VMs/Routers s_logger.info("SSH test failed for account " + _account.get() + "with reason '" + reason + "', stopping VMs"); int stopResponseCode = executeStop(server, developerServer, username, false); s_logger.info( "stop command finished with response code: " + stopResponseCode); success = false; // since the SSH test // failed, mark the // whole test as // failure } } else { // Just stop but don't destroy the // VMs/Routers s_logger.info("Deploy test failed with reason '" + reason + "', stopping VMs"); int stopResponseCode = executeStop(server, developerServer, username, true); s_logger.info("stop command finished with response code: " + stopResponseCode); success = false; // since the deploy test // failed, mark the // whole test as failure } if (success) { s_logger.info("***** Completed test for user : " + username + " in " + ((System.currentTimeMillis() - now) / 1000L) + " seconds"); } else { s_logger.info("##### FAILED test for user : " + username + " in " + ((System.currentTimeMillis() - now) / 1000L) + " seconds with reason : " + reason); } s_logger.info("Sleeping for " + wait + " seconds before starting next iteration"); Thread.sleep(wait); } catch (Exception e) { s_logger.warn("Error in thread", e); try { int stopResponseCode = executeStop(server, developerServer, username, true); s_logger.info("stop response code: " + stopResponseCode); } catch (Exception e1) { } } finally { NDC.clear(); } } while (repeat); } }).start(); } } catch (Exception e) { s_logger.error(e); } }
From source file:com.seanmadden.fast.ldap.main.Main.java
/** * The Main Event./*from ww w . ja v a2s . com*/ * * @param args */ @SuppressWarnings("static-access") public static void main(String[] args) { BasicConfigurator.configure(); log.debug("System initializing"); try { Logger.getRootLogger().addAppender( new FileAppender(new PatternLayout(PatternLayout.TTCC_CONVERSION_PATTERN), "log.log")); } catch (IOException e1) { log.error("Unable to open the log file..?"); } /* * Initialize the configuration engine. */ XMLConfiguration config = new XMLConfiguration(); config.setListDelimiter('|'); /* * Initialize the Command-Line parsing engine. */ CommandLineParser parser = new PosixParser(); Options opts = new Options(); opts.addOption(OptionBuilder.withLongOpt("config-file").hasArg() .withDescription("The configuration file to load").withArgName("config.xml").create("c")); opts.addOption(OptionBuilder.withLongOpt("profile").hasArg().withDescription("The profile to use") .withArgName("Default").create("p")); opts.addOption(OptionBuilder.withLongOpt("password").hasArg().withDescription("Password to connect with") .withArgName("password").create("P")); opts.addOption(OptionBuilder.withLongOpt("debug").hasArg(false).create('d')); opts.addOption(OptionBuilder.withLongOpt("verbose").hasArg(false).create('v')); File configurationFile = new File("config.xml"); try { // Parse the command-line options CommandLine cmds = parser.parse(opts, args); if (!cmds.hasOption('p')) { Logger.getRootLogger().addAppender(new GuiErrorAlerter(Level.ERROR)); } Logger.getRootLogger().setLevel(Level.ERROR); if (cmds.hasOption('v')) { Logger.getRootLogger().setLevel(Level.INFO); } if (cmds.hasOption('d')) { Logger.getRootLogger().setLevel(Level.DEBUG); } log.debug("Enabling configuration file parsing"); // The user has given us a file to parse. if (cmds.hasOption("c")) { configurationFile = new File(cmds.getOptionValue("c")); } log.debug("Config file: " + configurationFile); // Load the configuration file if (configurationFile.exists()) { config.load(configurationFile); } else { log.error("Cannot find config file"); } /* * Convert the profiles into memory */ Vector<ConnectionProfile> profs = new Vector<ConnectionProfile>(); List<?> profList = config.configurationAt("Profiles").configurationsAt("Profile"); for (Object p : profList) { SubnodeConfiguration profile = (SubnodeConfiguration) p; String name = profile.getString("[@name]"); String auth = profile.getString("LdapAuthString"); String server = profile.getString("LdapServerString"); String group = profile.getString("LdapGroupsLocation"); ConnectionProfile prof = new ConnectionProfile(name, server, auth, group); profs.add(prof); } ConnectionProfile prof = null; if (!cmds.hasOption('p')) { /* * Deploy the profile selector, to select a profile */ ProfileSelector profSel = new ProfileSelector(profs); prof = profSel.getSelection(); if (prof == null) { return; } /* * Empty the profiles and load a clean copy - then save it back * to the file */ config.clearTree("Profiles"); for (ConnectionProfile p : profSel.getProfiles()) { config.addProperty("Profiles.Profile(-1)[@name]", p.getName()); config.addProperty("Profiles.Profile.LdapAuthString", p.getLdapAuthString()); config.addProperty("Profiles.Profile.LdapServerString", p.getLdapServerString()); config.addProperty("Profiles.Profile.LdapGroupsLocation", p.getLdapGroupsString()); } config.save(configurationFile); } else { for (ConnectionProfile p : profs) { if (p.getName().equals(cmds.getOptionValue('p'))) { prof = p; break; } } } log.info("User selected " + prof); String password = ""; if (cmds.hasOption('P')) { password = cmds.getOptionValue('P'); } else { password = PasswordPrompter.promptForPassword("Password?"); } if (password.equals("")) { return; } LdapInterface ldap = new LdapInterface(prof.getLdapServerString(), prof.getLdapAuthString(), prof.getLdapGroupsString(), password); /* * Gather options information from the configuration engine for the * specified report. */ Hashtable<String, Hashtable<String, ReportOption>> reportDataStructure = new Hashtable<String, Hashtable<String, ReportOption>>(); List<?> repConfig = config.configurationAt("Reports").configurationsAt("Report"); for (Object p : repConfig) { SubnodeConfiguration repNode = (SubnodeConfiguration) p; // TODO Do something with the report profile. // Allowing the user to deploy "profiles" is a nice feature // String profile = repNode.getString("[@profile]"); String reportName = repNode.getString("[@report]"); Hashtable<String, ReportOption> reportOptions = new Hashtable<String, ReportOption>(); reportDataStructure.put(reportName, reportOptions); // Loop through the options and add each to the table. for (Object o : repNode.configurationsAt("option")) { SubnodeConfiguration option = (SubnodeConfiguration) o; String name = option.getString("[@name]"); String type = option.getString("[@type]"); String value = option.getString("[@value]"); ReportOption ro = new ReportOption(); ro.setName(name); if (type.toLowerCase().equals("boolean")) { ro.setBoolValue(Boolean.parseBoolean(value)); } else if (type.toLowerCase().equals("integer")) { ro.setIntValue(Integer.valueOf(value)); } else { // Assume a string type here then. ro.setStrValue(value); } reportOptions.put(name, ro); log.debug(ro); } } System.out.println(reportDataStructure); /* * At this point, we now need to deploy the reports window to have * the user pick a report and select some happy options to allow * that report to work. Let's go. */ /* * Deploy the Reports selector, to select a report */ Reports.getInstance().setLdapConnection(ldap); ReportsWindow reports = new ReportsWindow(Reports.getInstance().getAllReports(), reportDataStructure); Report report = reports.getSelection(); if (report == null) { return; } /* * Empty the profiles and load a clean copy - then save it back to * the file */ config.clearTree("Reports"); for (Report r : Reports.getInstance().getAllReports()) { config.addProperty("Reports.Report(-1)[@report]", r.getClass().getCanonicalName()); config.addProperty("Reports.Report[@name]", "Standard"); for (ReportOption ro : r.getOptions().values()) { config.addProperty("Reports.Report.option(-1)[@name]", ro.getName()); config.addProperty("Reports.Report.option[@type]", ro.getType()); config.addProperty("Reports.Report.option[@value]", ro.getStrValue()); } } config.save(configurationFile); ProgressBar bar = new ProgressBar(); bar.start(); report.execute(); ASCIIFormatter format = new ASCIIFormatter(); ReportResult res = report.getResult(); format.format(res, new File(res.getForName() + "_" + res.getReportName() + ".txt")); bar.stop(); JOptionPane.showMessageDialog(null, "The report is at " + res.getForName() + "_" + res.getReportName() + ".txt", "Success", JOptionPane.INFORMATION_MESSAGE); } catch (ParseException e) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("FAST Ldap Searcher", opts); } catch (ConfigurationException e) { e.printStackTrace(); log.fatal("OH EM GEES! Configuration errors."); } catch (Exception e) { e.printStackTrace(); } }