List of usage examples for java.lang String isEmpty
public boolean isEmpty()
From source file:com.oltpbenchmark.DBWorkload.java
/** * @param args/*from ww w . j av a 2 s .c o m*/ * @throws Exception */ public static void main(String[] args) throws Exception { // Initialize log4j String log4jPath = System.getProperty("log4j.configuration"); if (log4jPath != null) { org.apache.log4j.PropertyConfigurator.configure(log4jPath); } else { throw new RuntimeException("Missing log4j.properties file"); } // create the command line parser CommandLineParser parser = new PosixParser(); XMLConfiguration pluginConfig = null; try { pluginConfig = new XMLConfiguration("config/plugin.xml"); } catch (ConfigurationException e1) { LOG.info("Plugin configuration file config/plugin.xml is missing"); e1.printStackTrace(); } pluginConfig.setExpressionEngine(new XPathExpressionEngine()); Options options = new Options(); options.addOption("b", "bench", true, "[required] Benchmark class. Currently supported: " + pluginConfig.getList("/plugin//@name")); options.addOption("c", "config", true, "[required] Workload configuration file"); options.addOption(null, "create", true, "Initialize the database for this benchmark"); options.addOption(null, "clear", true, "Clear all records in the database for this benchmark"); options.addOption(null, "load", true, "Load data using the benchmark's data loader"); options.addOption(null, "execute", true, "Execute the benchmark workload"); options.addOption(null, "runscript", true, "Run an SQL script"); options.addOption(null, "upload", true, "Upload the result"); options.addOption("v", "verbose", false, "Display Messages"); options.addOption("h", "help", false, "Print this help"); options.addOption("s", "sample", true, "Sampling window"); options.addOption("ss", false, "Verbose Sampling per Transaction"); options.addOption("o", "output", true, "Output file (default System.out)"); options.addOption("d", "directory", true, "Base directory for the result files, default is current directory"); options.addOption("t", "timestamp", false, "Each result file is prepended with a timestamp for the beginning of the experiment"); options.addOption(null, "histograms", false, "Print txn histograms"); options.addOption(null, "dialects-export", true, "Export benchmark SQL to a dialects file"); // parse the command line arguments CommandLine argsLine = parser.parse(options, args); if (argsLine.hasOption("h")) { printUsage(options); return; } else if (argsLine.hasOption("c") == false) { LOG.error("Missing Configuration file"); printUsage(options); return; } else if (argsLine.hasOption("b") == false) { LOG.fatal("Missing Benchmark Class to load"); printUsage(options); return; } // If an output directory is used, store the information String outputDirectory = ""; if (argsLine.hasOption("d")) { outputDirectory = argsLine.getOptionValue("d"); } String timestampValue = ""; if (argsLine.hasOption("t")) { timestampValue = String.valueOf(TimeUtil.getCurrentTime().getTime()) + "_"; } // ------------------------------------------------------------------- // GET PLUGIN LIST // ------------------------------------------------------------------- String plugins = argsLine.getOptionValue("b"); String[] pluginList = plugins.split(","); List<BenchmarkModule> benchList = new ArrayList<BenchmarkModule>(); // Use this list for filtering of the output List<TransactionType> activeTXTypes = new ArrayList<TransactionType>(); String configFile = argsLine.getOptionValue("c"); XMLConfiguration xmlConfig = new XMLConfiguration(configFile); xmlConfig.setExpressionEngine(new XPathExpressionEngine()); int lastTxnId = 0; for (String plugin : pluginList) { // ---------------------------------------------------------------- // WORKLOAD CONFIGURATION // ---------------------------------------------------------------- String pluginTest = ""; pluginTest = "[@bench='" + plugin + "']"; WorkloadConfiguration wrkld = new WorkloadConfiguration(); wrkld.setBenchmarkName(plugin); wrkld.setXmlConfig(xmlConfig); wrkld.setDBType(DatabaseType.get(xmlConfig.getString("dbtype"))); wrkld.setDBDriver(xmlConfig.getString("driver")); wrkld.setDBConnection(xmlConfig.getString("DBUrl")); wrkld.setDBName(xmlConfig.getString("DBName")); wrkld.setDBUsername(xmlConfig.getString("username")); wrkld.setDBPassword(xmlConfig.getString("password")); int terminals = xmlConfig.getInt("terminals[not(@bench)]", 0); terminals = xmlConfig.getInt("terminals" + pluginTest, terminals); wrkld.setTerminals(terminals); wrkld.setIsolationMode(xmlConfig.getString("isolation", "TRANSACTION_SERIALIZABLE")); wrkld.setScaleFactor(xmlConfig.getDouble("scalefactor", 1.0)); wrkld.setRecordAbortMessages(xmlConfig.getBoolean("recordabortmessages", false)); int size = xmlConfig.configurationsAt("/works/work").size(); for (int i = 1; i < size + 1; i++) { SubnodeConfiguration work = xmlConfig.configurationAt("works/work[" + i + "]"); List<String> weight_strings; // use a workaround if there multiple workloads or single // attributed workload if (pluginList.length > 1 || work.containsKey("weights[@bench]")) { weight_strings = get_weights(plugin, work); } else { weight_strings = work.getList("weights[not(@bench)]"); } int rate = 1; boolean rateLimited = true; boolean disabled = false; // can be "disabled", "unlimited" or a number String rate_string; rate_string = work.getString("rate[not(@bench)]", ""); rate_string = work.getString("rate" + pluginTest, rate_string); if (rate_string.equals(RATE_DISABLED)) { disabled = true; } else if (rate_string.equals(RATE_UNLIMITED)) { rateLimited = false; } else if (rate_string.isEmpty()) { LOG.fatal(String.format("Please specify the rate for phase %d and workload %s", i, plugin)); System.exit(-1); } else { try { rate = Integer.parseInt(rate_string); if (rate < 1) { LOG.fatal("Rate limit must be at least 1. Use unlimited or disabled values instead."); System.exit(-1); } } catch (NumberFormatException e) { LOG.fatal(String.format("Rate string must be '%s', '%s' or a number", RATE_DISABLED, RATE_UNLIMITED)); System.exit(-1); } } Phase.Arrival arrival = Phase.Arrival.REGULAR; String arrive = work.getString("@arrival", "regular"); if (arrive.toUpperCase().equals("POISSON")) arrival = Phase.Arrival.POISSON; int activeTerminals; activeTerminals = work.getInt("active_terminals[not(@bench)]", terminals); activeTerminals = work.getInt("active_terminals" + pluginTest, activeTerminals); if (activeTerminals > terminals) { System.out.println("Configuration error in work " + i + ": number of active terminals" + "" + "is bigger than the total number of terminals"); System.exit(-1); } wrkld.addWork(work.getInt("/time"), rate, weight_strings, rateLimited, disabled, activeTerminals, arrival); } // FOR int numTxnTypes = xmlConfig.configurationsAt("transactiontypes" + pluginTest + "/transactiontype") .size(); if (numTxnTypes == 0 && pluginList.length == 1) { //if it is a single workload run, <transactiontypes /> w/o attribute is used pluginTest = "[not(@bench)]"; numTxnTypes = xmlConfig.configurationsAt("transactiontypes" + pluginTest + "/transactiontype") .size(); } wrkld.setNumTxnTypes(numTxnTypes); // CHECKING INPUT PHASES int j = 0; for (Phase p : wrkld.getAllPhases()) { j++; if (p.getWeightCount() != wrkld.getNumTxnTypes()) { LOG.fatal(String.format( "Configuration files is inconsistent, phase %d contains %d weights but you defined %d transaction types", j, p.getWeightCount(), wrkld.getNumTxnTypes())); System.exit(-1); } } // FOR // Generate the dialect map wrkld.init(); assert (wrkld.getNumTxnTypes() >= 0); assert (xmlConfig != null); // ---------------------------------------------------------------- // BENCHMARK MODULE // ---------------------------------------------------------------- String classname = pluginConfig.getString("/plugin[@name='" + plugin + "']"); if (classname == null) { throw new ParseException("Plugin " + plugin + " is undefined in config/plugin.xml"); } BenchmarkModule bench = ClassUtil.newInstance(classname, new Object[] { wrkld }, new Class<?>[] { WorkloadConfiguration.class }); assert (benchList.get(0) != null); Map<String, Object> initDebug = new ListOrderedMap<String, Object>(); initDebug.put("Benchmark", String.format("%s {%s}", plugin.toUpperCase(), classname)); initDebug.put("Configuration", configFile); initDebug.put("Type", wrkld.getDBType()); initDebug.put("Driver", wrkld.getDBDriver()); initDebug.put("URL", wrkld.getDBConnection()); initDebug.put("Isolation", xmlConfig.getString("isolation", "TRANSACTION_SERIALIZABLE [DEFAULT]")); initDebug.put("Scale Factor", wrkld.getScaleFactor()); INIT_LOG.info(SINGLE_LINE + "\n\n" + StringUtil.formatMaps(initDebug)); INIT_LOG.info(SINGLE_LINE); // Load TransactionTypes List<TransactionType> ttypes = new ArrayList<TransactionType>(); // Always add an INVALID type for Carlo ttypes.add(TransactionType.INVALID); int txnIdOffset = lastTxnId; for (int i = 1; i < wrkld.getNumTxnTypes() + 1; i++) { String key = "transactiontypes" + pluginTest + "/transactiontype[" + i + "]"; String txnName = xmlConfig.getString(key + "/name"); int txnId = i + 1; if (xmlConfig.containsKey(key + "/id")) { txnId = xmlConfig.getInt(key + "/id"); } TransactionType tmpType = bench.initTransactionType(txnName, txnId + txnIdOffset); // Keep a reference for filtering activeTXTypes.add(tmpType); // Add a reference for the active TTypes in this benchmark ttypes.add(tmpType); lastTxnId = i; } // FOR TransactionTypes tt = new TransactionTypes(ttypes); wrkld.setTransTypes(tt); LOG.debug("Using the following transaction types: " + tt); benchList.add(bench); } // Export StatementDialects if (isBooleanOptionSet(argsLine, "dialects-export")) { BenchmarkModule bench = benchList.get(0); if (bench.getStatementDialects() != null) { LOG.info("Exporting StatementDialects for " + bench); String xml = bench.getStatementDialects().export(bench.getWorkloadConfiguration().getDBType(), bench.getProcedures().values()); System.out.println(xml); System.exit(0); } throw new RuntimeException("No StatementDialects is available for " + bench); } @Deprecated boolean verbose = argsLine.hasOption("v"); // Create the Benchmark's Database if (isBooleanOptionSet(argsLine, "create")) { for (BenchmarkModule benchmark : benchList) { CREATE_LOG.info("Creating new " + benchmark.getBenchmarkName().toUpperCase() + " database..."); runCreator(benchmark, verbose); CREATE_LOG.info("Finished!"); CREATE_LOG.info(SINGLE_LINE); } } else if (CREATE_LOG.isDebugEnabled()) { CREATE_LOG.debug("Skipping creating benchmark database tables"); CREATE_LOG.info(SINGLE_LINE); } // Clear the Benchmark's Database if (isBooleanOptionSet(argsLine, "clear")) { for (BenchmarkModule benchmark : benchList) { CREATE_LOG.info("Resetting " + benchmark.getBenchmarkName().toUpperCase() + " database..."); benchmark.clearDatabase(); CREATE_LOG.info("Finished!"); CREATE_LOG.info(SINGLE_LINE); } } else if (CREATE_LOG.isDebugEnabled()) { CREATE_LOG.debug("Skipping creating benchmark database tables"); CREATE_LOG.info(SINGLE_LINE); } // Execute Loader if (isBooleanOptionSet(argsLine, "load")) { for (BenchmarkModule benchmark : benchList) { LOAD_LOG.info("Loading data into " + benchmark.getBenchmarkName().toUpperCase() + " database..."); runLoader(benchmark, verbose); LOAD_LOG.info("Finished!"); LOAD_LOG.info(SINGLE_LINE); } } else if (LOAD_LOG.isDebugEnabled()) { LOAD_LOG.debug("Skipping loading benchmark database records"); LOAD_LOG.info(SINGLE_LINE); } // Execute a Script if (argsLine.hasOption("runscript")) { for (BenchmarkModule benchmark : benchList) { String script = argsLine.getOptionValue("runscript"); SCRIPT_LOG.info("Running a SQL script: " + script); runScript(benchmark, script); SCRIPT_LOG.info("Finished!"); SCRIPT_LOG.info(SINGLE_LINE); } } // Execute Workload if (isBooleanOptionSet(argsLine, "execute")) { // Bombs away! Results r = null; try { r = runWorkload(benchList, verbose); } catch (Throwable ex) { LOG.error("Unexpected error when running benchmarks.", ex); System.exit(1); } assert (r != null); PrintStream ps = System.out; PrintStream rs = System.out; ResultUploader ru = new ResultUploader(r, xmlConfig, argsLine); if (argsLine.hasOption("o")) { // Check if directory needs to be created if (outputDirectory.length() > 0) { FileUtil.makeDirIfNotExists(outputDirectory.split("/")); } // Build the complex path String baseFile = timestampValue + argsLine.getOptionValue("o"); // Increment the filename for new results String nextName = FileUtil.getNextFilename(FileUtil.joinPath(outputDirectory, baseFile + ".res")); ps = new PrintStream(new File(nextName)); EXEC_LOG.info("Output into file: " + nextName); nextName = FileUtil.getNextFilename(FileUtil.joinPath(outputDirectory, baseFile + ".raw")); rs = new PrintStream(new File(nextName)); EXEC_LOG.info("Output Raw data into file: " + nextName); nextName = FileUtil.getNextFilename(FileUtil.joinPath(outputDirectory, baseFile + ".summary")); PrintStream ss = new PrintStream(new File(nextName)); EXEC_LOG.info("Output summary data into file: " + nextName); ru.writeSummary(ss); ss.close(); nextName = FileUtil.getNextFilename(FileUtil.joinPath(outputDirectory, baseFile + ".db.cnf")); ss = new PrintStream(new File(nextName)); EXEC_LOG.info("Output db config into file: " + nextName); ru.writeDBParameters(ss); ss.close(); nextName = FileUtil.getNextFilename(FileUtil.joinPath(outputDirectory, baseFile + ".ben.cnf")); ss = new PrintStream(new File(nextName)); EXEC_LOG.info("Output benchmark config into file: " + nextName); ru.writeBenchmarkConf(ss); ss.close(); } else if (EXEC_LOG.isDebugEnabled()) { EXEC_LOG.debug("No output file specified"); } if (argsLine.hasOption("s")) { int windowSize = Integer.parseInt(argsLine.getOptionValue("s")); EXEC_LOG.info("Grouped into Buckets of " + windowSize + " seconds"); r.writeCSV(windowSize, ps); if (isBooleanOptionSet(argsLine, "upload")) { ru.uploadResult(); } // Allow more detailed reporting by transaction to make it easier to check if (argsLine.hasOption("ss")) { for (TransactionType t : activeTXTypes) { PrintStream ts = ps; if (ts != System.out) { // Get the actual filename for the output String baseFile = timestampValue + argsLine.getOptionValue("o") + "_" + t.getName(); String prepended = outputDirectory + timestampValue; String nextName = FileUtil .getNextFilename(FileUtil.joinPath(outputDirectory, baseFile + ".res")); ts = new PrintStream(new File(nextName)); r.writeCSV(windowSize, ts, t); ts.close(); } } } } else if (EXEC_LOG.isDebugEnabled()) { EXEC_LOG.warn("No bucket size specified"); } if (argsLine.hasOption("histograms")) { EXEC_LOG.info(SINGLE_LINE); EXEC_LOG.info("Completed Transactions:\n" + r.getTransactionSuccessHistogram() + "\n"); EXEC_LOG.info("Aborted Transactions:\n" + r.getTransactionAbortHistogram() + "\n"); EXEC_LOG.info("Rejected Transactions:\n" + r.getTransactionRetryHistogram()); EXEC_LOG.info("Unexpected Errors:\n" + r.getTransactionErrorHistogram()); if (r.getTransactionAbortMessageHistogram().isEmpty() == false) EXEC_LOG.info( "User Aborts:\n" + StringUtil.formatMaps(r.getTransactionAbortMessageHistogram())); } else if (EXEC_LOG.isDebugEnabled()) { EXEC_LOG.warn("No bucket size specified"); } r.writeAllCSVAbsoluteTiming(rs); ps.close(); rs.close(); } else { EXEC_LOG.info("Skipping benchmark workload execution"); } }
From source file:RoucairolCarvahloBasicVersion.java
public static void main(String[] args) throws FileNotFoundException, IOException, InterruptedException { //For parsing the file and storing the information String line; String configurationFile = "configuration.txt"; int lineCountInFile = 0; myProcessId = Integer.parseInt(args[0]); FileReader fileReader = new FileReader(configurationFile); BufferedReader bufferedReader = new BufferedReader(fileReader); while ((line = bufferedReader.readLine()) != null) { if ((!(line.startsWith("#"))) && (!(line.isEmpty()))) { lineCountInFile = lineCountInFile + 1; String[] splitLine = line.split(" "); switch (lineCountInFile) { case 1: numberOfProcesses = Integer.parseInt(splitLine[0]); interRequestDelay = Integer.parseInt(splitLine[1]); csExecutionTime = Integer.parseInt(splitLine[2]); maxNumberOfRequest = Integer.parseInt(splitLine[3]); machineNames = new String[Integer.parseInt(splitLine[0])]; portNumbers = new int[Integer.parseInt(splitLine[0])]; break; default: machineNames[lineCountInFile - 2] = splitLine[1]; portNumbers[lineCountInFile - 2] = Integer.parseInt(splitLine[2]); break; }// w ww . ja v a 2s. com } } //Initializing finish array finishFlagArray = new int[numberOfProcesses]; //Initializing vector class VectorClass.initialize(numberOfProcesses); //Fill the arrays with zero false value for (int o = 0; o < numberOfProcesses; o++) { finishFlagArray[o] = 0; } //Initializing key array and inserting values keyArray = new int[numberOfProcesses]; for (int q = 0; q < numberOfProcesses; q++) { if (q >= myProcessId) { keyArray[q] = 1; } } filename = filename + Integer.toString(myProcessId) + ".out"; file = new File(filename); file.createNewFile(); writer = new FileWriter(file); // Write clocks to file filenameClock = filenameClock + Integer.toString(myProcessId) + ".out"; fileClock = new File(filenameClock); fileClock.createNewFile(); //writerClock = new FileWriter(fileClock); fw = new FileWriter(fileClock); bw = new BufferedWriter(fw); // // Expo mean insert csExecutionExpoDelay = new ExponentialDistribution(csExecutionTime); interRequestExpoDelay = new ExponentialDistribution(interRequestDelay); // System.out.println("********************************************************"); System.out.println("My process id : " + myProcessId); System.out.println("Number of processes : " + numberOfProcesses); System.out.println("Inter-request delay : " + interRequestDelay); System.out.println("Critical section execution time : " + csExecutionTime); System.out.println("Maximum number of request : " + maxNumberOfRequest); System.out.println( "My process name : " + machineNames[myProcessId] + " My port number : " + portNumbers[myProcessId]); for (int i = 0; i < numberOfProcesses; i++) { System.out.println("Process name : " + machineNames[i] + " Port number : " + portNumbers[i]); } System.out.println("********************************************************"); for (int q = 0; q < numberOfProcesses; q++) { System.out.println("KeyArray" + q + " - " + keyArray[q]); } System.out.println("********************************************************"); //For hosting server localhost SctpServerChannel sctpServerChannel = SctpServerChannel.open(); InetSocketAddress serverAddr = new InetSocketAddress(portNumbers[myProcessId]); sctpServerChannel.bind(serverAddr); System.out.println("********************************************************"); System.out.println("Local server hosted"); System.out.println("********************************************************"); //For creating neighbor SCTP channels Thread.sleep(30000); socketAddress = new SocketAddress[numberOfProcesses]; sctpChannel = new SctpChannel[numberOfProcesses]; System.out.println("********************************************************"); System.out.println("Neighbor channels created"); System.out.println("********************************************************"); //Thread spanned for generating critical section request new Thread(new RoucairolCarvahloBasicVersion()).start(); while (true) { try (SctpChannel sctpChannelFromClient = sctpServerChannel.accept()) { mutex.acquire(); byteBufferFromNeighbor.clear(); String receiveMessage; MessageInfo messageInfoFromNeighbor = sctpChannelFromClient.receive(byteBufferFromNeighbor, null, null); //System.out.println("Raw Message : " + messageInfoFromNeighbor); receiveMessage = byteToString(byteBufferFromNeighbor, messageInfoFromNeighbor); System.out.println("Received Message : " + receiveMessage); if (receiveMessage.contains("Request")) { String[] parseMessage = receiveMessage.split("-"); lamportClock = Math.max(lamportClock, Integer.parseInt(parseMessage[3])) + 1; //vector clock update String[] stringNumericalTimestamp = parseMessage[4].split(","); int[] numericalTimestamp = new int[stringNumericalTimestamp.length]; for (int d = 0; d < stringNumericalTimestamp.length; d++) { numericalTimestamp[d] = Integer.parseInt(stringNumericalTimestamp[d]); } VectorClass.update(myProcessId, numericalTimestamp); // int requestMade = Integer.parseInt(parseMessage[3] + parseMessage[1]); if (outstandingRequest == 1) { if (requestMade < currentRequestBeingServed) { lamportClock++; //Newly inserted for vector timesatmp int[] vector = VectorClass.increment(myProcessId); String vectorClockConstruction = ""; for (int g = 0; g < vector.length; g++) { if (g == 0) { vectorClockConstruction = vectorClockConstruction + Integer.toString(vector[g]); } else { vectorClockConstruction = vectorClockConstruction + "," + Integer.toString(vector[g]); } } // keyArray[Integer.parseInt(parseMessage[1])] = 0; try { byteBufferToNeighbor.clear(); initializeChannels(); sctpChannel[Integer.parseInt(parseMessage[1])] .connect(socketAddress[Integer.parseInt(parseMessage[1])]); String sendMessage = "Key from Process-" + myProcessId + "-" + requestMade + "-" + lamportClock + "-" + vectorClockConstruction; System.out.println("Message sent is : " + sendMessage); MessageInfo messageInfoToNeighbor = MessageInfo.createOutgoing(null, 0); byteBufferToNeighbor.put(sendMessage.getBytes()); byteBufferToNeighbor.flip(); sctpChannel[Integer.parseInt(parseMessage[1])].send(byteBufferToNeighbor, messageInfoToNeighbor); totalMessageCount++; sctpChannel[Integer.parseInt(parseMessage[1])].close(); } catch (IOException ex) { Logger.getLogger(RoucairolCarvahloBasicVersion.class.getName()).log(Level.SEVERE, null, ex); } //Include block for reverse request lamportClock++; //Newly inserted for vector timesatmp int[] vector1 = VectorClass.increment(myProcessId); String vectorClockConstruction1 = ""; for (int g = 0; g < vector1.length; g++) { if (g == 0) { vectorClockConstruction1 = vectorClockConstruction1 + Integer.toString(vector1[g]); } else { vectorClockConstruction1 = vectorClockConstruction1 + "," + Integer.toString(vector1[g]); } } // try { byteBufferToNeighbor.clear(); initializeChannels(); sctpChannel[Integer.parseInt(parseMessage[1])] .connect(socketAddress[Integer.parseInt(parseMessage[1])]); String sendMessage = "ReverseSend from Process-" + myProcessId + "-" + currentRequestBeingServed + "-" + lamportClock + "-" + vectorClockConstruction1; System.out.println("Message sent is : " + sendMessage); MessageInfo messageInfoToNeighbor = MessageInfo.createOutgoing(null, 0); byteBufferToNeighbor.put(sendMessage.getBytes()); byteBufferToNeighbor.flip(); sctpChannel[Integer.parseInt(parseMessage[1])].send(byteBufferToNeighbor, messageInfoToNeighbor); totalMessageCount++; sctpChannel[Integer.parseInt(parseMessage[1])].close(); } catch (IOException ex) { Logger.getLogger(RoucairolCarvahloBasicVersion.class.getName()).log(Level.SEVERE, null, ex); } } else if (requestMade == currentRequestBeingServed) { if (Integer.parseInt(parseMessage[1]) < myProcessId) { lamportClock++; //Newly inserted for vector timesatmp int[] vector = VectorClass.increment(myProcessId); String vectorClockConstruction = ""; for (int g = 0; g < vector.length; g++) { if (g == 0) { vectorClockConstruction = vectorClockConstruction + Integer.toString(vector[g]); } else { vectorClockConstruction = vectorClockConstruction + "," + Integer.toString(vector[g]); } } // keyArray[Integer.parseInt(parseMessage[1])] = 0; try { byteBufferToNeighbor.clear(); initializeChannels(); sctpChannel[Integer.parseInt(parseMessage[1])] .connect(socketAddress[Integer.parseInt(parseMessage[1])]); String sendMessage = "Key from Process-" + myProcessId + "-" + requestMade + "-" + lamportClock + "-" + vectorClockConstruction; System.out.println("Message sent is : " + sendMessage); MessageInfo messageInfoToNeighbor = MessageInfo.createOutgoing(null, 0); byteBufferToNeighbor.put(sendMessage.getBytes()); byteBufferToNeighbor.flip(); sctpChannel[Integer.parseInt(parseMessage[1])].send(byteBufferToNeighbor, messageInfoToNeighbor); totalMessageCount++; sctpChannel[Integer.parseInt(parseMessage[1])].close(); } catch (IOException ex) { Logger.getLogger(RoucairolCarvahloBasicVersion.class.getName()) .log(Level.SEVERE, null, ex); } //Include block for reverse request lamportClock++; //Newly inserted for vector timesatmp int[] vector1 = VectorClass.increment(myProcessId); String vectorClockConstruction1 = ""; for (int g = 0; g < vector1.length; g++) { if (g == 0) { vectorClockConstruction1 = vectorClockConstruction1 + Integer.toString(vector1[g]); } else { vectorClockConstruction1 = vectorClockConstruction1 + "," + Integer.toString(vector1[g]); } } // try { byteBufferToNeighbor.clear(); initializeChannels(); sctpChannel[Integer.parseInt(parseMessage[1])] .connect(socketAddress[Integer.parseInt(parseMessage[1])]); String sendMessage = "ReverseSend from Process-" + myProcessId + "-" + currentRequestBeingServed + "-" + lamportClock + "-" + vectorClockConstruction1; System.out.println("Message sent is : " + sendMessage); MessageInfo messageInfoToNeighbor = MessageInfo.createOutgoing(null, 0); byteBufferToNeighbor.put(sendMessage.getBytes()); byteBufferToNeighbor.flip(); sctpChannel[Integer.parseInt(parseMessage[1])].send(byteBufferToNeighbor, messageInfoToNeighbor); totalMessageCount++; sctpChannel[Integer.parseInt(parseMessage[1])].close(); } catch (IOException ex) { Logger.getLogger(RoucairolCarvahloBasicVersion.class.getName()) .log(Level.SEVERE, null, ex); } } else if (myProcessId < Integer.parseInt(parseMessage[1])) { queue.add(requestMade); } } else if (requestMade > currentRequestBeingServed) { queue.add(requestMade); } } else if (outstandingRequest == 0) { lamportClock++; //Newly inserted for vector timesatmp int[] vector = VectorClass.increment(myProcessId); String vectorClockConstruction = ""; for (int g = 0; g < vector.length; g++) { if (g == 0) { vectorClockConstruction = vectorClockConstruction + Integer.toString(vector[g]); } else { vectorClockConstruction = vectorClockConstruction + "," + Integer.toString(vector[g]); } } // keyArray[Integer.parseInt(parseMessage[1])] = 0; try { byteBufferToNeighbor.clear(); initializeChannels(); sctpChannel[Integer.parseInt(parseMessage[1])] .connect(socketAddress[Integer.parseInt(parseMessage[1])]); String sendMessage = "Key from Process-" + myProcessId + "-" + requestMade + "-" + lamportClock + "-" + vectorClockConstruction; System.out.println("Message sent is : " + sendMessage); MessageInfo messageInfoToNeighbor = MessageInfo.createOutgoing(null, 0); byteBufferToNeighbor.put(sendMessage.getBytes()); byteBufferToNeighbor.flip(); sctpChannel[Integer.parseInt(parseMessage[1])].send(byteBufferToNeighbor, messageInfoToNeighbor); totalMessageCount++; sctpChannel[Integer.parseInt(parseMessage[1])].close(); } catch (IOException ex) { Logger.getLogger(RoucairolCarvahloBasicVersion.class.getName()).log(Level.SEVERE, null, ex); } } } else if (receiveMessage.contains("Key")) { //receive check condition execute critical section block String[] parseMessage = receiveMessage.split("-"); lamportClock = Math.max(lamportClock, Integer.parseInt(parseMessage[3])) + 1; //vector clock update String[] stringNumericalTimestamp = parseMessage[4].split(","); int[] numericalTimestamp = new int[stringNumericalTimestamp.length]; for (int d = 0; d < stringNumericalTimestamp.length; d++) { numericalTimestamp[d] = Integer.parseInt(stringNumericalTimestamp[d]); } VectorClass.update(myProcessId, numericalTimestamp); // keyArray[Integer.parseInt(parseMessage[1])] = 1; int countOnes = 0; for (int y = 0; y < numberOfProcesses; y++) { if (keyArray[y] == 1) { countOnes = countOnes + 1; } } if (countOnes == numberOfProcesses) { outstandingRequest = 0; currentRequestBeingServed = 0; enterCriticalSectionExecution(); timestamp2 = new Timestamp(System.currentTimeMillis()); csExit(); } } else if (receiveMessage.contains("ReverseSend")) { String[] parseMessage = receiveMessage.split("-"); lamportClock = Math.max(lamportClock, Integer.parseInt(parseMessage[3])) + 1; //vector clock update String[] stringNumericalTimestamp = parseMessage[4].split(","); int[] numericalTimestamp = new int[stringNumericalTimestamp.length]; for (int d = 0; d < stringNumericalTimestamp.length; d++) { numericalTimestamp[d] = Integer.parseInt(stringNumericalTimestamp[d]); } VectorClass.update(myProcessId, numericalTimestamp); // int requestMade = Integer.parseInt(parseMessage[2]); if (outstandingRequest == 1) { if (requestMade < currentRequestBeingServed) { lamportClock++; //Newly inserted for vector timesatmp int[] vector = VectorClass.increment(myProcessId); String vectorClockConstruction = ""; for (int g = 0; g < vector.length; g++) { if (g == 0) { vectorClockConstruction = vectorClockConstruction + Integer.toString(vector[g]); } else { vectorClockConstruction = vectorClockConstruction + "," + Integer.toString(vector[g]); } } // keyArray[Integer.parseInt(parseMessage[1])] = 0; try { byteBufferToNeighbor.clear(); initializeChannels(); sctpChannel[Integer.parseInt(parseMessage[1])] .connect(socketAddress[Integer.parseInt(parseMessage[1])]); String sendMessage = "Key from Process-" + myProcessId + "-" + requestMade + "-" + lamportClock + "-" + vectorClockConstruction; System.out.println("Message sent is : " + sendMessage); MessageInfo messageInfoToNeighbor = MessageInfo.createOutgoing(null, 0); byteBufferToNeighbor.put(sendMessage.getBytes()); byteBufferToNeighbor.flip(); sctpChannel[Integer.parseInt(parseMessage[1])].send(byteBufferToNeighbor, messageInfoToNeighbor); totalMessageCount++; sctpChannel[Integer.parseInt(parseMessage[1])].close(); } catch (IOException ex) { Logger.getLogger(RoucairolCarvahloBasicVersion.class.getName()).log(Level.SEVERE, null, ex); } //Include block for reverse request lamportClock++; //Newly inserted for vector timesatmp int[] vector1 = VectorClass.increment(myProcessId); String vectorClockConstruction1 = ""; for (int g = 0; g < vector1.length; g++) { if (g == 0) { vectorClockConstruction1 = vectorClockConstruction1 + Integer.toString(vector1[g]); } else { vectorClockConstruction1 = vectorClockConstruction1 + "," + Integer.toString(vector1[g]); } } // try { byteBufferToNeighbor.clear(); initializeChannels(); sctpChannel[Integer.parseInt(parseMessage[1])] .connect(socketAddress[Integer.parseInt(parseMessage[1])]); String sendMessage = "ReverseSend from Process-" + myProcessId + "-" + currentRequestBeingServed + "-" + lamportClock + "-" + vectorClockConstruction1; System.out.println("Message sent is : " + sendMessage); MessageInfo messageInfoToNeighbor = MessageInfo.createOutgoing(null, 0); byteBufferToNeighbor.put(sendMessage.getBytes()); byteBufferToNeighbor.flip(); sctpChannel[Integer.parseInt(parseMessage[1])].send(byteBufferToNeighbor, messageInfoToNeighbor); totalMessageCount++; sctpChannel[Integer.parseInt(parseMessage[1])].close(); } catch (IOException ex) { Logger.getLogger(RoucairolCarvahloBasicVersion.class.getName()).log(Level.SEVERE, null, ex); } } else if (requestMade == currentRequestBeingServed) { if (Integer.parseInt(parseMessage[1]) < myProcessId) { lamportClock++; //Newly inserted for vector timesatmp int[] vector = VectorClass.increment(myProcessId); String vectorClockConstruction = ""; for (int g = 0; g < vector.length; g++) { if (g == 0) { vectorClockConstruction = vectorClockConstruction + Integer.toString(vector[g]); } else { vectorClockConstruction = vectorClockConstruction + "," + Integer.toString(vector[g]); } } // keyArray[Integer.parseInt(parseMessage[1])] = 0; try { byteBufferToNeighbor.clear(); initializeChannels(); sctpChannel[Integer.parseInt(parseMessage[1])] .connect(socketAddress[Integer.parseInt(parseMessage[1])]); String sendMessage = "Key from Process-" + myProcessId + "-" + requestMade + "-" + lamportClock + "-" + vectorClockConstruction; System.out.println("Message sent is : " + sendMessage); MessageInfo messageInfoToNeighbor = MessageInfo.createOutgoing(null, 0); byteBufferToNeighbor.put(sendMessage.getBytes()); byteBufferToNeighbor.flip(); sctpChannel[Integer.parseInt(parseMessage[1])].send(byteBufferToNeighbor, messageInfoToNeighbor); totalMessageCount++; sctpChannel[Integer.parseInt(parseMessage[1])].close(); } catch (IOException ex) { Logger.getLogger(RoucairolCarvahloBasicVersion.class.getName()) .log(Level.SEVERE, null, ex); } //Include block for reverse request lamportClock++; //Newly inserted for vector timesatmp int[] vector1 = VectorClass.increment(myProcessId); String vectorClockConstruction1 = ""; for (int g = 0; g < vector1.length; g++) { if (g == 0) { vectorClockConstruction1 = vectorClockConstruction1 + Integer.toString(vector1[g]); } else { vectorClockConstruction1 = vectorClockConstruction1 + "," + Integer.toString(vector1[g]); } } // try { byteBufferToNeighbor.clear(); initializeChannels(); sctpChannel[Integer.parseInt(parseMessage[1])] .connect(socketAddress[Integer.parseInt(parseMessage[1])]); String sendMessage = "ReverseSend from Process-" + myProcessId + "-" + currentRequestBeingServed + "-" + lamportClock + "-" + vectorClockConstruction1; System.out.println("Message sent is : " + sendMessage); MessageInfo messageInfoToNeighbor = MessageInfo.createOutgoing(null, 0); byteBufferToNeighbor.put(sendMessage.getBytes()); byteBufferToNeighbor.flip(); sctpChannel[Integer.parseInt(parseMessage[1])].send(byteBufferToNeighbor, messageInfoToNeighbor); totalMessageCount++; sctpChannel[Integer.parseInt(parseMessage[1])].close(); } catch (IOException ex) { Logger.getLogger(RoucairolCarvahloBasicVersion.class.getName()) .log(Level.SEVERE, null, ex); } } else if (myProcessId < Integer.parseInt(parseMessage[1])) { queue.add(requestMade); } } else if (requestMade > currentRequestBeingServed) { queue.add(requestMade); } } else if (outstandingRequest == 0) { lamportClock++; //Newly inserted for vector timesatmp int[] vector = VectorClass.increment(myProcessId); String vectorClockConstruction = ""; for (int g = 0; g < vector.length; g++) { if (g == 0) { vectorClockConstruction = vectorClockConstruction + Integer.toString(vector[g]); } else { vectorClockConstruction = vectorClockConstruction + "," + Integer.toString(vector[g]); } } // keyArray[Integer.parseInt(parseMessage[1])] = 0; try { byteBufferToNeighbor.clear(); initializeChannels(); sctpChannel[Integer.parseInt(parseMessage[1])] .connect(socketAddress[Integer.parseInt(parseMessage[1])]); String sendMessage = "Key from Process-" + myProcessId + "-" + requestMade + "-" + lamportClock + "-" + vectorClockConstruction; System.out.println("Message sent is : " + sendMessage); MessageInfo messageInfoToNeighbor = MessageInfo.createOutgoing(null, 0); byteBufferToNeighbor.put(sendMessage.getBytes()); byteBufferToNeighbor.flip(); sctpChannel[Integer.parseInt(parseMessage[1])].send(byteBufferToNeighbor, messageInfoToNeighbor); totalMessageCount++; sctpChannel[Integer.parseInt(parseMessage[1])].close(); } catch (IOException ex) { Logger.getLogger(RoucairolCarvahloBasicVersion.class.getName()).log(Level.SEVERE, null, ex); } } } else if (receiveMessage.contains("Finish")) { String[] parseMessage = receiveMessage.split("-"); lamportClock = Math.max(lamportClock, Integer.parseInt(parseMessage[3])) + 1; //vector clock update String[] stringNumericalTimestamp = parseMessage[4].split(","); int[] numericalTimestamp = new int[stringNumericalTimestamp.length]; for (int d = 0; d < stringNumericalTimestamp.length; d++) { numericalTimestamp[d] = Integer.parseInt(stringNumericalTimestamp[d]); } VectorClass.update(myProcessId, numericalTimestamp); // finishFlagArray[Integer.parseInt(parseMessage[1])] = 1; int count = 0; for (int v = 0; v < numberOfProcesses; v++) { if (finishFlagArray[v] == 1) { count = count + 1; } } if (count == numberOfProcesses) { break; } } } mutex.release(); } }
From source file:herddb.cli.HerdDBCLI.java
public static void main(String... args) throws IOException { try {//ww w. j a v a2s . c o m DefaultParser parser = new DefaultParser(); Options options = new Options(); options.addOption("x", "url", true, "JDBC URL"); options.addOption("u", "username", true, "JDBC Username"); options.addOption("pwd", "password", true, "JDBC Password"); options.addOption("q", "query", true, "Execute inline query"); options.addOption("v", "verbose", false, "Verbose output"); options.addOption("a", "async", false, "Use (experimental) executeBatchAsync for sending DML"); options.addOption("s", "schema", true, "Default tablespace (SQL schema)"); options.addOption("fi", "filter", true, "SQL filter mode: all|ddl|dml"); options.addOption("f", "file", true, "SQL Script to execute (statement separated by 'GO' lines)"); options.addOption("at", "autotransaction", false, "Execute scripts in autocommit=false mode and commit automatically"); options.addOption("atbs", "autotransactionbatchsize", true, "Batch size for 'autotransaction' mode"); options.addOption("g", "script", true, "Groovy Script to execute"); options.addOption("i", "ignoreerrors", false, "Ignore SQL Errors during file execution"); options.addOption("sc", "sqlconsole", false, "Execute SQL console in interactive mode"); options.addOption("fmd", "mysql", false, "Intruct the parser that the script is coming from a MySQL Dump"); options.addOption("rwst", "rewritestatements", false, "Rewrite all statements to use JDBC parameters"); options.addOption("b", "backup", false, "Backup one or more tablespaces (selected with --schema)"); options.addOption("r", "restore", false, "Restore tablespace"); options.addOption("nl", "newleader", true, "Leader for new restored tablespace"); options.addOption("ns", "newschema", true, "Name for new restored tablespace"); options.addOption("tsm", "tablespacemapper", true, "Path to groovy script with a custom functin to map table names to tablespaces"); options.addOption("dfs", "dumpfetchsize", true, "Fetch size for dump operations. Defaults to chunks of 100000 records"); options.addOption("n", "nodeid", true, "Node id"); options.addOption("t", "table", true, "Table name"); options.addOption("p", "param", true, "Parameter name"); options.addOption("val", "values", true, "Parameter values"); options.addOption("lts", "list-tablespaces", false, "List available tablespaces"); options.addOption("ln", "list-nodes", false, "List available nodes"); options.addOption("sts", "show-tablespace", false, "Show full informations about a tablespace (needs -s option)"); options.addOption("lt", "list-tables", false, "List tablespace tables (needs -s option)"); options.addOption("st", "show-table", false, "Show full informations about a table (needs -s and -t options)"); options.addOption("ar", "add-replica", false, "Add a replica to the tablespace (needs -s and -r options)"); options.addOption("rr", "remove-replica", false, "Remove a replica from the tablespace (needs -s and -r options)"); options.addOption("adt", "create-tablespace", false, "Create a tablespace (needs -ns and -nl options)"); options.addOption("at", "alter-tablespace", false, "Alter a tablespace (needs -s, -param and --values options)"); options.addOption("d", "describe", false, "Checks and describes a raw file"); options.addOption("ft", "filetype", true, "Checks and describes a raw file (valid options are txlog, datapage, tablecheckpoint, indexcheckpoint, tablesmetadata"); options.addOption("mdf", "metadatafile", true, "Tables metadata file, required for 'datapage' filetype"); options.addOption("tsui", "tablespaceuuid", true, "Tablespace UUID, used for describing raw files"); org.apache.commons.cli.CommandLine commandLine; try { commandLine = parser.parse(options, args); } catch (ParseException error) { println("Syntax error: " + error); failAndPrintHelp(options); return; } if (args.length == 0) { failAndPrintHelp(options); return; } String schema = commandLine.getOptionValue("schema", TableSpace.DEFAULT); String tablespaceuuid = commandLine.getOptionValue("tablespaceuuid", ""); final boolean verbose = commandLine.hasOption("verbose"); final boolean async = commandLine.hasOption("async"); final String filter = commandLine.getOptionValue("filter", "all"); if (!verbose) { LogManager.getLogManager().reset(); } String file = commandLine.getOptionValue("file", ""); String tablesmetadatafile = commandLine.getOptionValue("metadatafile", ""); String table = commandLine.getOptionValue("table", ""); boolean describe = commandLine.hasOption("describe"); String filetype = commandLine.getOptionValue("filetype", ""); if (describe) { try { if (file.isEmpty()) { throw new IllegalArgumentException("file option is required"); } describeRawFile(tablespaceuuid, table, tablesmetadatafile, file, filetype); } catch (Exception error) { if (verbose) { error.printStackTrace(); } else { println("error:" + error); } exitCode = 1; } return; } String url = commandLine.getOptionValue("url", "jdbc:herddb:server:localhost:7000"); String username = commandLine.getOptionValue("username", ClientConfiguration.PROPERTY_CLIENT_USERNAME_DEFAULT); String password = commandLine.getOptionValue("password", ClientConfiguration.PROPERTY_CLIENT_PASSWORD_DEFAULT); String query = commandLine.getOptionValue("query", ""); boolean backup = commandLine.hasOption("backup"); boolean restore = commandLine.hasOption("restore"); String newschema = commandLine.getOptionValue("newschema", ""); String leader = commandLine.getOptionValue("newleader", ""); String script = commandLine.getOptionValue("script", ""); String tablespacemapperfile = commandLine.getOptionValue("tablespacemapper", ""); int dumpfetchsize = Integer.parseInt(commandLine.getOptionValue("dumpfetchsize", 100000 + "")); final boolean ignoreerrors = commandLine.hasOption("ignoreerrors"); boolean sqlconsole = commandLine.hasOption("sqlconsole"); final boolean frommysqldump = commandLine.hasOption("mysql"); final boolean rewritestatements = commandLine.hasOption("rewritestatements") || !tablespacemapperfile.isEmpty() || frommysqldump; boolean autotransaction = commandLine.hasOption("autotransaction") || frommysqldump; int autotransactionbatchsize = Integer .parseInt(commandLine.getOptionValue("autotransactionbatchsize", 100000 + "")); if (!autotransaction) { autotransactionbatchsize = 0; } String nodeId = commandLine.getOptionValue("nodeid", ""); String param = commandLine.getOptionValue("param", ""); String values = commandLine.getOptionValue("values", ""); boolean listTablespaces = commandLine.hasOption("list-tablespaces"); boolean listNodes = commandLine.hasOption("list-nodes"); boolean showTablespace = commandLine.hasOption("show-tablespace"); boolean listTables = commandLine.hasOption("list-tables"); boolean showTable = commandLine.hasOption("show-table"); if (showTable) { if (table.equals("")) { println("Specify the table (-t <table>)"); exitCode = 1; System.exit(exitCode); } } boolean createTablespace = commandLine.hasOption("create-tablespace"); if (createTablespace) { if (newschema.equals("")) { println("Specify the tablespace name (--newschema <schema>)"); exitCode = 1; System.exit(exitCode); } if (leader.equals("")) { println("Specify the leader node (--newleader <nodeid>)"); exitCode = 1; System.exit(exitCode); } } boolean alterTablespace = commandLine.hasOption("alter-tablespace"); if (alterTablespace) { if (commandLine.getOptionValue("schema", null) == null) { println("Cowardly refusing to assume the default schema in an alter command. Explicitly use \"-s " + TableSpace.DEFAULT + "\" instead"); exitCode = 1; System.exit(exitCode); } if (param.equals("")) { println("Specify the parameter (--param <par>)"); exitCode = 1; System.exit(exitCode); } if (values.equals("")) { println("Specify values (--values <vals>)"); exitCode = 1; System.exit(exitCode); } } boolean addReplica = commandLine.hasOption("add-replica"); if (addReplica) { if (commandLine.getOptionValue("schema", null) == null) { println("Cowardly refusing to assume the default schema in an alter command. Explicitly use \"-s " + TableSpace.DEFAULT + "\" instead"); exitCode = 1; System.exit(exitCode); } if (nodeId.equals("")) { println("Specify the node (-n <nodeid>)"); exitCode = 1; System.exit(exitCode); } } boolean removeReplica = commandLine.hasOption("remove-replica"); if (removeReplica) { if (commandLine.getOptionValue("schema", null) == null) { println("Cowardly refusing to assume the default schema in an alter command. Explicitly use \"-s " + TableSpace.DEFAULT + "\" instead"); exitCode = 1; System.exit(exitCode); } if (nodeId.equals("")) { println("Specify the node (-n <nodeid>)"); exitCode = 1; System.exit(exitCode); } } TableSpaceMapper tableSpaceMapper = buildTableSpaceMapper(tablespacemapperfile); try (HerdDBDataSource datasource = new HerdDBDataSource()) { datasource.setUrl(url); datasource.setUsername(username); datasource.setPassword(password); try (Connection connection = datasource.getConnection(); Statement statement = connection.createStatement()) { connection.setSchema(schema); if (sqlconsole) { runSqlConsole(connection, statement, PRETTY_PRINT); } else if (backup) { performBackup(statement, schema, file, options, connection, dumpfetchsize); } else if (restore) { performRestore(file, leader, newschema, options, statement, connection); } else if (!query.isEmpty()) { executeStatement(verbose, ignoreerrors, false, false, query, statement, tableSpaceMapper, false, PRETTY_PRINT); } else if (!file.isEmpty()) { executeSqlFile(autotransactionbatchsize, connection, file, verbose, async, ignoreerrors, frommysqldump, rewritestatements, statement, tableSpaceMapper, PRETTY_PRINT, filter, datasource); } else if (!script.isEmpty()) { executeScript(connection, datasource, statement, script); } else if (listTablespaces) { printTableSpaces(verbose, ignoreerrors, statement, tableSpaceMapper); } else if (listNodes) { printNodes(verbose, ignoreerrors, statement, tableSpaceMapper); } else if (showTablespace) { printTableSpaceInfos(verbose, ignoreerrors, statement, tableSpaceMapper, schema); } else if (listTables) { listTables(verbose, ignoreerrors, statement, tableSpaceMapper, schema); } else if (showTable) { printTableInfos(verbose, ignoreerrors, statement, tableSpaceMapper, schema, table); } else if (addReplica) { changeReplica(verbose, ignoreerrors, statement, tableSpaceMapper, schema, nodeId, ChangeReplicaAction.ADD); } else if (removeReplica) { changeReplica(verbose, ignoreerrors, statement, tableSpaceMapper, schema, nodeId, ChangeReplicaAction.REMOVE); } else if (createTablespace) { createTablespace(verbose, ignoreerrors, statement, tableSpaceMapper, newschema, leader); } else if (alterTablespace) { alterTablespace(verbose, ignoreerrors, statement, tableSpaceMapper, schema, param, values); } else { failAndPrintHelp(options); return; } } exitCode = 0; } catch (Exception error) { if (verbose) { error.printStackTrace(); } else { println("error:" + error); } exitCode = 1; } } finally { System.exit(exitCode); } }
From source file:edu.cmu.lti.oaqa.apps.Client.java
public static void main(String args[]) { BufferedReader inp = new BufferedReader(new InputStreamReader(System.in)); Options opt = new Options(); Option o = new Option(PORT_SHORT_PARAM, PORT_LONG_PARAM, true, PORT_DESC); o.setRequired(true);/*from w w w . ja v a2 s. co m*/ opt.addOption(o); o = new Option(HOST_SHORT_PARAM, HOST_LONG_PARAM, true, HOST_DESC); o.setRequired(true); opt.addOption(o); opt.addOption(K_SHORT_PARAM, K_LONG_PARAM, true, K_DESC); opt.addOption(R_SHORT_PARAM, R_LONG_PARAM, true, R_DESC); opt.addOption(QUERY_TIME_SHORT_PARAM, QUERY_TIME_LONG_PARAM, true, QUERY_TIME_DESC); opt.addOption(RET_OBJ_SHORT_PARAM, RET_OBJ_LONG_PARAM, false, RET_OBJ_DESC); opt.addOption(RET_EXTERN_ID_SHORT_PARAM, RET_EXTERN_ID_LONG_PARAM, false, RET_EXTERN_ID_DESC); CommandLineParser parser = new org.apache.commons.cli.GnuParser(); try { CommandLine cmd = parser.parse(opt, args); String host = cmd.getOptionValue(HOST_SHORT_PARAM); String tmp = null; tmp = cmd.getOptionValue(PORT_SHORT_PARAM); int port = -1; try { port = Integer.parseInt(tmp); } catch (NumberFormatException e) { Usage("Port should be integer!"); } boolean retObj = cmd.hasOption(RET_OBJ_SHORT_PARAM); boolean retExternId = cmd.hasOption(RET_EXTERN_ID_SHORT_PARAM); String queryTimeParams = cmd.getOptionValue(QUERY_TIME_SHORT_PARAM); if (null == queryTimeParams) queryTimeParams = ""; SearchType searchType = SearchType.kKNNSearch; int k = 0; double r = 0; if (cmd.hasOption(K_SHORT_PARAM)) { if (cmd.hasOption(R_SHORT_PARAM)) { Usage("Range search is not allowed if the KNN search is specified!"); } tmp = cmd.getOptionValue(K_SHORT_PARAM); try { k = Integer.parseInt(tmp); } catch (NumberFormatException e) { Usage("K should be integer!"); } searchType = SearchType.kKNNSearch; } else if (cmd.hasOption(R_SHORT_PARAM)) { if (cmd.hasOption(K_SHORT_PARAM)) { Usage("KNN search is not allowed if the range search is specified!"); } searchType = SearchType.kRangeSearch; tmp = cmd.getOptionValue(R_SHORT_PARAM); try { r = Double.parseDouble(tmp); } catch (NumberFormatException e) { Usage("The range value should be numeric!"); } } else { Usage("One has to specify either range or KNN-search parameter"); } String separator = System.getProperty("line.separator"); StringBuffer sb = new StringBuffer(); String s; while ((s = inp.readLine()) != null) { sb.append(s); sb.append(separator); } String queryObj = sb.toString(); try { TTransport transport = new TSocket(host, port); transport.open(); TProtocol protocol = new TBinaryProtocol(transport); QueryService.Client client = new QueryService.Client(protocol); if (!queryTimeParams.isEmpty()) client.setQueryTimeParams(queryTimeParams); List<ReplyEntry> res = null; long t1 = System.nanoTime(); if (searchType == SearchType.kKNNSearch) { System.out.println(String.format("Running a %d-NN search", k)); res = client.knnQuery(k, queryObj, retExternId, retObj); } else { System.out.println(String.format("Running a range search (r=%g)", r)); res = client.rangeQuery(r, queryObj, retExternId, retObj); } long t2 = System.nanoTime(); System.out.println(String.format("Finished in %g ms", (t2 - t1) / 1e6)); for (ReplyEntry e : res) { System.out.println(String.format("id=%d dist=%g %s", e.getId(), e.getDist(), retExternId ? "externId=" + e.getExternId() : "")); if (retObj) System.out.println(e.getObj()); } transport.close(); // Close transport/socket ! } catch (TException te) { System.err.println("Apache Thrift exception: " + te); te.printStackTrace(); } } catch (ParseException e) { Usage("Cannot parse arguments"); } catch (Exception e) { e.printStackTrace(); System.exit(1); } }
From source file:IMAPService.java
public static void main(String[] args) { // Arguments// w w w. j ava 2 s . co m String server = ""; int port = -1; String login = ""; String password = ""; boolean deleteAfterDownload = false; boolean downloadAll = false; String[] foldersToDownload = null; // Set up apache cli Options options = new Options(); Option S = new Option("S", true, "Server Name"); S.setRequired(true); options.addOption(S); Option P = new Option("P", true, "Port Number"); P.setRequired(true); options.addOption(P); Option l = new Option("l", true, "Login"); l.setRequired(true); options.addOption(l); Option p = new Option("p", true, "Password if not on stdin"); options.addOption(p); Option d = new Option("d", false, "Delete after downloading"); d.setRequired(false); options.addOption(d); Option a = new Option("a", false, "Download from all folders"); a.setRequired(false); options.addOption(a); Option f = new Option("f", true, "Download messages from specified folder"); options.addOption(f); CommandLineParser clp = new DefaultParser(); try { CommandLine cl = clp.parse(options, args); if (cl.hasOption("S")) server = cl.getOptionValue("S"); if (cl.hasOption("P")) port = Integer.parseInt(cl.getOptionValue("P")); if (cl.hasOption("l")) login = cl.getOptionValue("l"); if (cl.hasOption("p")) password = cl.getOptionValue("p"); if (cl.hasOption("d")) deleteAfterDownload = true; if (cl.hasOption("a")) downloadAll = true; else if (cl.hasOption("f")) foldersToDownload = cl.getOptionValues("f"); else { showArgMenu(options); return; } } catch (Exception e) { showArgMenu(options); return; } if (password.isEmpty()) { // Grab p/w of stdin if it's there Scanner sc = new Scanner(System.in); password = sc.nextLine(); sc.close(); } if (!server.isEmpty() && port != -1 && !login.isEmpty() && !password.isEmpty() && (downloadAll || foldersToDownload != null)) { //IMAPService imapService = new IMAPService("imap.gmail.com", 993); IMAPService imapService = new IMAPService(server, port); //imapService.login("kinglibingli@gmail.com", "kingli1bingli"); imapService.login(login, password); imapService.buildMailbox(); // Check if service should delete emails if (deleteAfterDownload) imapService.deleteEmailsAfterDownload(); // Proceed with downloads if (downloadAll) imapService.downloadAllFolders(); else { for (String folderNames : foldersToDownload) { imapService.downloadFoldersEmails(folderNames); } } imapService.logout(); } }
From source file:ca.uqac.info.monitor.BeepBeepMonitor.java
public static void main(String[] args) { int verbosity = 1, slowdown = 0, tcp_port = 0; boolean show_stats = false, to_stdout = false; String trace_filename = "", pipe_filename = "", event_name = "message"; final MonitorFactory mf = new MonitorFactory(); // In case we open a socket ServerSocket m_serverSocket = null; Socket m_connection = null;/*from w ww . ja va 2s. co m*/ // Parse command line arguments Options options = setupOptions(); CommandLine c_line = setupCommandLine(args, options); assert c_line != null; if (c_line.hasOption("verbosity")) { verbosity = Integer.parseInt(c_line.getOptionValue("verbosity")); } if (verbosity > 0) { showHeader(); } if (c_line.hasOption("version")) { System.err.println("(C) 2008-2013 Sylvain Hall et al., Universit du Qubec Chicoutimi"); System.err.println("This program comes with ABSOLUTELY NO WARRANTY."); System.err.println("This is a free software, and you are welcome to redistribute it"); System.err.println("under certain conditions. See the file COPYING for details.\n"); System.exit(ERR_OK); } if (c_line.hasOption("h")) { showUsage(options); System.exit(ERR_OK); } if (c_line.hasOption("version")) { System.exit(ERR_OK); } if (c_line.hasOption("slowdown")) { slowdown = Integer.parseInt(c_line.getOptionValue("slowdown")); if (verbosity > 0) System.err.println("Slowdown factor: " + slowdown + " ms"); } if (c_line.hasOption("stats")) { show_stats = true; } if (c_line.hasOption("csv")) { // Will output data in CSV format to stdout to_stdout = true; } if (c_line.hasOption("eventname")) { // Set event name event_name = c_line.getOptionValue("eventname"); } if (c_line.hasOption("t")) { // Read events from a trace trace_filename = c_line.getOptionValue("t"); } if (c_line.hasOption("p")) { // Read events from a pipe pipe_filename = c_line.getOptionValue("p"); } if (c_line.hasOption("k")) { // Read events from a TCP port tcp_port = Integer.parseInt(c_line.getOptionValue("k")); } if (!trace_filename.isEmpty() && !pipe_filename.isEmpty()) { System.err.println("ERROR: you must specify at most one of trace file or named pipe"); showUsage(options); System.exit(ERR_ARGUMENTS); } @SuppressWarnings("unchecked") List<String> remaining_args = c_line.getArgList(); if (remaining_args.isEmpty()) { System.err.println("ERROR: no input formula specified"); showUsage(options); System.exit(ERR_ARGUMENTS); } // Instantiate the event notifier boolean notify = (verbosity > 0); EventNotifier en = new EventNotifier(notify); en.m_slowdown = slowdown; en.m_csvToStdout = to_stdout; // Create one monitor for each input file and add it to the notifier for (String formula_filename : remaining_args) { try { String formula_contents = FileReadWrite.readFile(formula_filename); Operator op = Operator.parseFromString(formula_contents); op.accept(mf); Monitor mon = mf.getMonitor(); Map<String, String> metadata = getMetadata(formula_contents); metadata.put("Filename", formula_filename); en.addMonitor(mon, metadata); } catch (IOException e) { e.printStackTrace(); System.exit(ERR_IO); } catch (Operator.ParseException e) { System.err.println("Error parsing input formula"); System.exit(ERR_PARSE); } } // Read trace and iterate // Opens file PipeReader pr = null; try { if (!pipe_filename.isEmpty()) { // We tell the pipe reader we read a pipe File f = new File(pipe_filename); if (verbosity > 0) System.err.println("Reading from pipe named " + f.getName()); pr = new PipeReader(new FileInputStream(f), en, false); } else if (!trace_filename.isEmpty()) { // We tell the pipe reader we read a regular file File f = new File(trace_filename); if (verbosity > 0) System.err.println("Reading from file " + f.getName()); pr = new PipeReader(new FileInputStream(f), en, true); } else if (tcp_port > 0) { // We tell the pipe reader we read from a socket if (verbosity > 0) System.err.println("Reading from TCP port " + tcp_port); m_serverSocket = new ServerSocket(tcp_port); m_connection = m_serverSocket.accept(); pr = new PipeReader(m_connection.getInputStream(), en, false); } else { // We tell the pipe reader we read from standard input if (verbosity > 0) System.err.println("Reading from standard input"); pr = new PipeReader(System.in, en, false); } } catch (FileNotFoundException ex) { // We print both trace and pipe since one of them must be empty System.err.println("ERROR: file not found " + trace_filename + pipe_filename); System.exit(ERR_IO); } catch (IOException e) { // Caused by socket error e.printStackTrace(); System.exit(ERR_IO); } pr.setSeparator("<" + event_name + ">", "</" + event_name + ">"); // Check parameters for the event notifier if (c_line.hasOption("no-trigger")) { en.m_notifyOnVerdict = false; } else { en.m_notifyOnVerdict = true; } if (c_line.hasOption("mirror")) { en.m_mirrorEventsOnStdout = true; } // Start event notifier en.reset(); Thread th = new Thread(pr); long clock_start = System.nanoTime(); th.start(); try { th.join(); // Wait for thread to finish } catch (InterruptedException e1) { // Thread is finished } if (tcp_port > 0 && m_serverSocket != null) { // We opened a socket; now we close it try { m_serverSocket.close(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } long clock_end = System.nanoTime(); int ret_code = pr.getReturnCode(); switch (ret_code) { case PipeReader.ERR_EOF: if (verbosity > 0) System.err.println("\nEnd of file reached"); break; case PipeReader.ERR_EOT: if (verbosity > 0) System.err.println("\nEOT received on pipe: closing"); break; case PipeReader.ERR_OK: // Do nothing break; default: // An error System.err.println("Runtime error"); System.exit(ERR_RUNTIME); break; } if (show_stats) { if (verbosity > 0) { System.out.println("Messages: " + en.m_numEvents); System.out.println("Time: " + (int) (en.m_totalTime / 1000000f) + " ms"); System.out.println("Clock time: " + (int) ((clock_end - clock_start) / 1000000f) + " ms"); System.out.println("Max heap: " + (int) (en.heapSize / 1048576f) + " MB"); } else { // If stats are asked but verbosity = 0, only show time value // (both monitor and wall clock) System.out.print((int) (en.m_totalTime / 1000000f)); System.out.print(","); System.out.print((int) ((clock_end - clock_start) / 1000000f)); } } System.exit(ERR_OK); }
From source file:main.DOORS_Service.java
/** * Login to the DWA server and perform some OSLC actions * @param args/*w w w . j a va 2 s . com*/ * @throws ParseException */ public static void main(String[] args) throws ParseException { Options options = new Options(); options.addOption("url", true, "url"); options.addOption("user", true, "user ID"); options.addOption("password", true, "password"); options.addOption("project", true, "project area"); CommandLineParser cliParser = new GnuParser(); //Parse the command line CommandLine cmd = cliParser.parse(options, args); if (!validateOptions(cmd)) { logger.severe( "Syntax: java <class_name> -url https://<server>:port/<context>/ -user <user> -password <password> -project \"<project_area>\""); logger.severe( "Example: java DoorsOauthSample -url https://exmple.com:9443/dwa -user ADMIN -password ADMIN -project \"JKE Banking (Requirements Management)\""); return; } String webContextUrl = cmd.getOptionValue("url"); String user = cmd.getOptionValue("user"); String passwd = cmd.getOptionValue("password"); String projectArea = cmd.getOptionValue("project"); try { //STEP 1: Initialize a Jazz rootservices helper and indicate we're looking for the RequirementManagement catalog // The root services for DOORs is found at /public level JazzRootServicesHelper helper = new JazzRootServicesHelper(webContextUrl + "/public", OSLCConstants.OSLC_RM); //STEP 2: Create a new OSLC OAuth capable client OslcOAuthClient client = helper.initOAuthClient("JIRA", "JIRA"); if (client != null) { //STEP 3: Try to access the context URL to trigger the OAuth dance and login try { client.getResource(webContextUrl, OSLCConstants.CT_RDF); } catch (OAuthRedirectException oauthE) { validateTokens(client, oauthE.getRedirectURL() + "?oauth_token=" + oauthE.getAccessor().requestToken, user, passwd, webContextUrl + "/j_acegi_security_check"); // Try to access again ClientResponse response = client.getResource(webContextUrl, OSLCConstants.CT_RDF); response.getEntity(InputStream.class).close(); } //STEP 4: Get our requirements collection that we want //TODO: Replace with option from startup String serviceProviderUrl = "http://usnx47:8080/dwa/rm/urn:rational::1-4d2b67b464226e12-M-0000048a"; ClientResponse response = client.getResource(serviceProviderUrl, "application/x-oslc-rm-requirement-collection-1.0+xml"); //build the rdf Model rdfModel = ModelFactory.createDefaultModel(); rdfModel.read(response.getEntity(InputStream.class), serviceProviderUrl); response.consumeContent(); //get the statements List<Statement> reqs = rdfModel.getResource(serviceProviderUrl).listProperties().toList(); HashMap<String, String> requirements = new HashMap<String, String>(); for (Statement s : reqs) { String reqURI = s.getObject().toString(); if (reqURI.contains("http")) { response = client.getResource(reqURI, "application/x-oslc-rm-requirement-1.0+xml"); if (response.getStatusCode() == 200) { InputStream in = response.getEntity(InputStream.class); Model model = ModelFactory.createDefaultModel(); try { model.read(in, reqURI); } catch (Exception sa) { System.out.println(reqURI); } //Properties to traverse on Property attrDef = model .createProperty("http://jazz.net/doors/xmlns/prod/jazz/doors/1.0/attrDef"); Property name = model .createProperty("http://jazz.net/doors/xmlns/prod/jazz/doors/1.0/name"); //Flags we use for parsing int count = 0; boolean isText = false; boolean isID = false; boolean done = false; //Text of the DOORS Object and its ID are what we are going to extract String text = ""; String id = ""; //Look through all of the possible fields StmtIterator statementIter = model.listStatements(); while (statementIter.hasNext() && done != true) { Statement field = statementIter.next(); //Get the attrDef property to find out what kind of value we have StmtIterator props = field.getSubject().listProperties(attrDef); while (props.hasNext() && done != true) { Statement kind = props.next(); RDFNode propertyNode = kind.getObject(); StmtIterator propIt = propertyNode.asResource().listProperties(name); //Check all of the properties for our desired fields while (propIt.hasNext()) { Statement node = propIt.next(); if (node.getObject().isLiteral()) { if (node.getObject().toString().contains("Object+Text") && field.getObject().isLiteral()) { text = field.getLiteral().toString(); text = text.substring(0, text.indexOf("^")); count++; } if (node.getObject().toString().contains("Absolute+Number") && field.getObject().isLiteral()) { id = field.getLiteral().toString(); id = id.substring(0, id.indexOf("^")); count++; } } } if (count == 2) { if (!text.isEmpty()) { //System.out.println( "Req: " + id ); //System.out.println( text ); requirements.put(id, text); count = 0; done = true; break; } } } } } } response.consumeContent(); } //check if already in JIRA //post to jira for (Entry<String, String> e : requirements.entrySet()) { } } } catch (Exception e) { logger.log(Level.SEVERE, e.getMessage(), e); } }
From source file:com.mijecu25.sqlplus.SQLPlus.java
public static void main(String[] args) throws IOException { // Create and load the properties from the application properties file Properties properties = new Properties(); properties.load(SQLPlus.class.getClassLoader().getResourceAsStream(SQLPlus.APPLICATION_PROPERTIES_FILE)); SQLPlus.logger.info("Initializing " + SQLPlus.PROGRAM_NAME + " version " + properties.getProperty(SQLPlus.APPLICATION_PROPERTIES_FILE_VERSION)); // Check if the user is using a valid console (i.e. not from Eclipse) if (System.console() == null) { // The Console object for the JVM could not be found. Alert the user SQLPlus.logger.fatal(Messages.FATAL + "A JVM Console object was not found. Try running " + SQLPlus.PROGRAM_NAME + "from the command line"); System.out.println(//from w w w .ja va2 s .c o m Messages.FATAL + SQLPlus.PROGRAM_NAME + " was not able to find your JVM's Console object. " + "Try running " + SQLPlus.PROGRAM_NAME + " from the command line."); SQLPlus.exitSQLPlus(); SQLPlus.logger.fatal(Messages.FATAL + Messages.QUIT_PROGRAM_ERROR(PROGRAM_NAME)); return; } // UI intro System.out.println("Welcome to " + SQLPlus.PROGRAM_NAME + "! This program has a DSL to add alerts to various SQL DML events."); System.out.println("Be sure to use " + SQLPlus.PROGRAM_NAME + " from the command line."); System.out.println(); // Get the version System.out.println("Version: " + properties.getProperty(SQLPlus.APPLICATION_PROPERTIES_FILE_VERSION)); System.out.println(); // Read the license file BufferedReader bufferedReader; bufferedReader = new BufferedReader(new FileReader(SQLPlus.LICENSE_FILE)); // Read a line String line = bufferedReader.readLine(); // While the line is not null while (line != null) { System.out.println(line); // Read a new lines line = bufferedReader.readLine(); } // Close the buffer bufferedReader.close(); System.out.println(); // Create the jline console that allows us to remember commands, use arrow keys, and catch interruptions // from the user SQLPlus.console = new ConsoleReader(); SQLPlus.console.setHandleUserInterrupt(true); try { // Get credentials from the user SQLPlus.logger.info("Create SQLPlusConnection"); SQLPlus.createSQLPlusConnection(); } catch (NullPointerException | SQLException | IllegalArgumentException e) { // NPE: This exception can occur if the user is running the program where the JVM Console // object cannot be found. // SQLE: TODO should I add here the error code? // This exception can occur when trying to establish a connection // IAE: This exception can occur when trying to establish a connection SQLPlus.logger .fatal(Messages.FATAL + Messages.FATAL_EXIT(SQLPlus.PROGRAM_NAME, e.getClass().getName())); System.out.println(Messages.FATAL + Messages.FATAL_EXCEPTION_ACTION(e.getClass().getSimpleName()) + " " + Messages.CHECK_LOG_FILES); SQLPlus.exitSQLPlus(); SQLPlus.logger.fatal(Messages.FATAL + Messages.QUIT_PROGRAM_ERROR(SQLPlus.PROGRAM_NAME)); return; } catch (UserInterruptException uie) { SQLPlus.logger.warn(Messages.WARNING + "The user typed an interrupt instruction."); SQLPlus.exitSQLPlus(); return; } System.out.println("Connection established! Commands end with " + SQLPlus.END_OF_COMMAND); System.out.println("Type " + SQLPlus.EXIT + " or " + SQLPlus.QUIT + " to exit the application "); try { // Execute the input scanner while (true) { // Get a line from the user until the hit enter (carriage return, line feed/ new line). System.out.print(SQLPlus.PROMPT); try { line = SQLPlus.console.readLine().trim(); } catch (NullPointerException npe) { // TODO test this behavior // If this exception is catch, it is very likely that the user entered the end of line command. // This means that the program should quit. SQLPlus.logger.warn(Messages.WARNING + "The input from the user is null. It is very likely that" + "the user entered the end of line command and they want to quit."); SQLPlus.exitSQLPlus(); return; } // If the user did not enter anything if (line.isEmpty()) { // Continue to the next iteration continue; } if (line.equals(".")) { line = "use courses;"; } if (line.equals("-")) { line = "select created_at from classes;"; } if (line.equals("--")) { line = "select name, year from classes;"; } if (line.equals("*")) { line = "select * from classes;"; } if (line.equals("x")) { line = "select name from classes, classes;"; } if (line.equals("e")) { line = "select * feom classes;"; } // Logic to quit if (line.equals(SQLPlus.QUIT) || line.equals(SQLPlus.EXIT)) { SQLPlus.logger.info("The user wants to quit " + SQLPlus.PROGRAM_NAME); SQLPlus.exitSQLPlus(); break; } // Use a StringBuilder since jline works weird when it has read a line. The issue we were having was with the // end of command logic. jline does not keep the input from the user in the variable that was stored in. Each // time jline reads a new line, the variable is empty StringBuilder query = new StringBuilder(); query.append(line); // While the user does not finish the command with the SQLPlus.END_OF_COMMAND while (query.charAt(query.length() - 1) != SQLPlus.END_OF_COMMAND) { // Print the wait for command prompt and get the next line for the user System.out.print(SQLPlus.WAIT_FOR_END_OF_COMMAND); query.append(" "); line = StringUtils.stripEnd(SQLPlus.console.readLine(), null); query.append(line); } SQLPlus.logger.info("Raw input from the user: " + query); try { Statement statement; try { // Execute the antlr code to parse the user input SQLPlus.logger.info("Will parse the user input to determine what to execute"); ANTLRStringStream input = new ANTLRStringStream(query.toString()); SQLPlusLex lexer = new SQLPlusLex(input); CommonTokenStream tokens = new CommonTokenStream(lexer); SQLPlusParser parser = new SQLPlusParser(tokens); statement = parser.sqlplus(); } catch (RecognitionException re) { // TODO move this to somehwere else // String message = Messages.WARNING + "You have an error in your SQL syntax. Check the manual" // + " that corresponds to your " + SQLPlus.sqlPlusConnection.getCurrentDatabase() // + " server or " + SQLPlus.PROGRAM_NAME + " for the correct syntax"; // SQLPlus.logger.warn(message); // System.out.println(message); statement = new StatementDefault(); } statement.setStatement(query.toString()); SQLPlus.sqlPlusConnection.execute(statement); } catch (UnsupportedOperationException uoe) { // This exception can occur when the user entered a command allowed by the parsers, but not currently // supported by SQLPlus. This can occur because the parser is written in such a way that supports // the addition of features. SQLPlus.logger.warn(Messages.WARNING + uoe); System.out.println( Messages.WARNING + Messages.FATAL_EXCEPTION_ACTION(uoe.getClass().getSimpleName()) + " " + Messages.CHECK_LOG_FILES); SQLPlus.logger.warn(Messages.WARNING + "The previous command is not currently supported."); } } } catch (IllegalArgumentException iae) { // This exception can occur when a command is executed but it had illegal arguments. Most likely // it is a programmer's error and should be addressed by the developer. SQLPlus.logger .fatal(Messages.FATAL + Messages.FATAL_EXIT(SQLPlus.PROGRAM_NAME, iae.getClass().getName())); SQLPlus.exitSQLPlus(); SQLPlus.logger.fatal(Messages.FATAL + Messages.QUIT_PROGRAM_ERROR(SQLPlus.PROGRAM_NAME)); } catch (UserInterruptException uie) { SQLPlus.logger.warn(Messages.WARNING + "The user typed an interrupt instruction."); SQLPlus.exitSQLPlus(); } }
From source file:com.github.codingtogenomic.CodingToGenomic.java
public static void main(String[] args) throws Exception { //parse commandline Options options = new Options(); CommandLineParser parser = new PosixParser(); String gene = new String(); String transcript = new String(); String species = "human"; boolean mapCdna = false; String coordinate = new String(); StringBuilder errorMsg = new StringBuilder(); try {//w ww . ja v a 2s.c o m options = getOptions(args); } catch (org.apache.commons.cli.ParseException ex) { System.err.println("Parsing failed. Reason: " + ex.getMessage()); System.exit(1); } CommandLine line = parser.parse(options, args); if (line.hasOption("help")) { showHelp(options); } if (line.hasOption("gene")) { gene = line.getOptionValue("gene"); } else { if (!line.hasOption("transcript")) { errorMsg.append("Either --gene or --transcript argument is required\n"); } } if (line.hasOption("transcript")) { if (line.hasOption("gene")) { errorMsg.append("Please specify only one of " + "--gene or --transcript arguments, not both\n"); } else { transcript = line.getOptionValue("transcript"); if (line.hasOption("species")) { System.out.println("Ignoring --species option when using --transcript argument"); } } } if (line.hasOption("coordinate")) { coordinate = line.getOptionValue("coordinate"); } else { errorMsg.append("--coordinate argument is required\n"); } if (line.hasOption("species")) { species = line.getOptionValue("species").replaceAll("\\s+", "_"); } if (line.hasOption("b37")) { if (species.equalsIgnoreCase("human") || species.equalsIgnoreCase("homo sapiens")) { SERVER = GRCh37Server; } else { System.out.println("--b37 argument will be ignored - it can only be " + "used when human is the species of interest. Current species" + " is " + species + ".\n"); } } if (line.hasOption("noncoding")) { mapCdna = true; } if (errorMsg.length() > 0) { showHelp(options, errorMsg.toString(), 2); } int c = 0; boolean threePrimeUtr = false; String prefix = "c."; if (mapCdna) { prefix = "n."; try { c = Integer.parseInt(coordinate); } catch (NumberFormatException ex) { showHelp(options, "--coordinate argument '" + coordinate + "' could not " + "be parsed as an integer", 2); } } else if (coordinate.startsWith("*")) { threePrimeUtr = true; prefix = "c.*"; String coord = coordinate.replaceFirst("\\*", ""); try { c = Integer.parseInt(coord); } catch (NumberFormatException ex) { showHelp(options, "--coordinate argument '" + coordinate + "' could not " + "be parsed as an integer or UTR coordinate", 2); } } else { try { c = Integer.parseInt(coordinate); } catch (NumberFormatException ex) { showHelp(options, "--coordinate argument '" + coordinate + "' could not " + "be parsed as an integer", 2); } } //got arguments String result; String header = "Input\tSymbol\tEnsemblGene\tEnsemblTranscript\tGenomicCoordinate"; if (!gene.isEmpty()) { IdParser idParser = new IdParser(gene); System.out.println("Interpretting " + gene + " as of type " + idParser.getIdentifierType()); if (idParser.isEnsemblId()) { if (line.hasOption("species")) { System.out.println("Ignoring --species option when searching Ensembl ID."); } if (idParser.isTranscript()) { result = codingToGenomicTranscript(gene, c, threePrimeUtr, mapCdna); } else if (idParser.isEnsp()) { result = codingToGenomicEnsp(gene, c, threePrimeUtr, mapCdna); } else { result = codingToGenomicId(gene, c, threePrimeUtr, mapCdna); } } else { if (idParser.isTranscript()) { //append user input to beginning result = codingToGenomicXrefTranscript(species, gene, c, threePrimeUtr, mapCdna); } else { result = codingToGenomicXref(species, gene, c, threePrimeUtr, mapCdna); } } if (idParser.isTranscript() || idParser.isEnsp()) { result = gene + ":" + prefix + c + "\t" + result; } else { result = convertGeneResult(result, gene, c, prefix); } } else { System.out.println("Searching for " + transcript + " as Ensembl transcript ID"); result = codingToGenomicTranscript(transcript, c, threePrimeUtr, mapCdna); //append user input to beginning result = transcript + ":" + prefix + c + "\t" + result; } System.out.println(header); System.out.println(result); }
From source file:at.illecker.hama.hybrid.examples.onlinecf.OnlineCFTrainHybridBSP.java
public static void main(String[] args) throws Exception { // Defaults//from w ww. j a v a 2s . co m int numBspTask = 1; // CPU + GPU tasks int numGpuBspTask = 1; // GPU tasks int blockSize = BLOCK_SIZE; int gridSize = GRID_SIZE; int maxIteration = 3; // 150; int matrixRank = 3; int skipCount = 1; double alpha = ALPHA; int userCount = 0; int itemCount = 0; int percentNonZeroValues = 0; int GPUPercentage = 20; boolean useTestExampleInput = true; boolean isDebugging = true; String inputFile = ""; String separator = "\\t"; Configuration conf = new HamaConfiguration(); FileSystem fs = FileSystem.get(conf); // Set numBspTask to maxTasks // BSPJobClient jobClient = new BSPJobClient(conf); // ClusterStatus cluster = jobClient.getClusterStatus(true); // numBspTask = cluster.getMaxTasks(); if (args.length > 0) { if (args.length >= 14) { numBspTask = Integer.parseInt(args[0]); numGpuBspTask = Integer.parseInt(args[1]); blockSize = Integer.parseInt(args[2]); gridSize = Integer.parseInt(args[3]); maxIteration = Integer.parseInt(args[4]); matrixRank = Integer.parseInt(args[5]); skipCount = Integer.parseInt(args[6]); alpha = Double.parseDouble(args[7]); userCount = Integer.parseInt(args[8]); itemCount = Integer.parseInt(args[9]); percentNonZeroValues = Integer.parseInt(args[10]); GPUPercentage = Integer.parseInt(args[11]); useTestExampleInput = Boolean.parseBoolean(args[12]); isDebugging = Boolean.parseBoolean(args[13]); // optional parameters if (args.length > 14) { inputFile = args[14]; } if (args.length > 15) { separator = args[15]; } } else { System.out.println("Wrong argument size!"); System.out.println(" Argument1=numBspTask"); System.out.println(" Argument2=numGpuBspTask"); System.out.println(" Argument3=blockSize"); System.out.println(" Argument4=gridSize"); System.out.println( " Argument5=maxIterations | Number of maximal iterations (" + maxIteration + ")"); System.out.println(" Argument6=matrixRank | matrixRank (" + matrixRank + ")"); System.out.println(" Argument7=skipCount | skipCount (" + skipCount + ")"); System.out.println(" Argument8=alpha | alpha (" + alpha + ")"); System.out.println(" Argument9=userCount | userCount (" + userCount + ")"); System.out.println(" Argument10=itemCount | itemCount (" + itemCount + ")"); System.out.println(" Argument11=percentNonZeroValues | percentNonZeroValues (" + percentNonZeroValues + ")"); System.out.println(" Argument12=GPUPercentage (percentage of input)"); System.out.println(" Argument13=testExample | Use testExample input (true|false=default)"); System.out.println(" Argument14=debug | Enable debugging (true|false=default)"); System.out.println(" Argument15=inputFile (optional) | MovieLens inputFile"); System.out.println(" Argument16=separator (optional) | default '" + separator + "' "); return; } } // Check if inputFile exists if ((!inputFile.isEmpty()) && (!new File(inputFile).exists())) { System.out.println("Error: inputFile: " + inputFile + " does not exist!"); return; } // Check parameters if ((inputFile.isEmpty()) && (!useTestExampleInput) && (userCount <= 0) && (itemCount <= 0) && (percentNonZeroValues <= 0)) { System.out.println("Invalid parameter: userCount: " + userCount + " itemCount: " + itemCount + " percentNonZeroValues: " + percentNonZeroValues); return; } // Check if blockSize < matrixRank when using GPU if ((numGpuBspTask > 0) && (blockSize < matrixRank)) { System.out.println("Error: BlockSize < matrixRank"); return; } // Check GPUPercentage if ((GPUPercentage < 0) && (GPUPercentage > 100)) { System.out.println("Error: GPUPercentage must be between 0 and 100 percent"); return; } // Set config variables conf.setBoolean(CONF_DEBUG, isDebugging); conf.setBoolean("hama.pipes.logging", isDebugging); // Set CPU tasks conf.setInt("bsp.peers.num", numBspTask); // Set GPU tasks conf.setInt("bsp.peers.gpu.num", numGpuBspTask); // Set GPU blockSize and gridSize conf.set(CONF_BLOCKSIZE, "" + blockSize); conf.set(CONF_GRIDSIZE, "" + gridSize); conf.setInt(OnlineCF.CONF_ITERATION_COUNT, maxIteration); conf.setInt(OnlineCF.CONF_MATRIX_RANK, matrixRank); conf.setInt(OnlineCF.CONF_SKIP_COUNT, skipCount); // Debug output LOG.info("NumBspTask: " + conf.getInt("bsp.peers.num", 0)); LOG.info("NumGpuBspTask: " + conf.getInt("bsp.peers.gpu.num", 0)); LOG.info("bsp.tasks.maximum: " + conf.get("bsp.tasks.maximum")); LOG.info("BlockSize: " + conf.get(CONF_BLOCKSIZE)); LOG.info("GridSize: " + conf.get(CONF_GRIDSIZE)); LOG.info("GPUPercentage: " + GPUPercentage); LOG.info("isDebugging: " + isDebugging); LOG.info("useTestExampleInput: " + useTestExampleInput); LOG.info("inputPath: " + CONF_INPUT_DIR); LOG.info("outputPath: " + CONF_OUTPUT_DIR); LOG.info("maxIteration: " + maxIteration); LOG.info("matrixRank: " + matrixRank); LOG.info("skipCount: " + skipCount); LOG.info("alpha: " + alpha); LOG.info("userCount: " + userCount); LOG.info("itemCount: " + itemCount); LOG.info("percentNonZeroValues: " + percentNonZeroValues); if (!inputFile.isEmpty()) { LOG.info("inputFile: " + inputFile); LOG.info("separator: " + separator); } // prepare Input int maxTestPrefs = 10; Path preferencesIn = new Path(CONF_INPUT_DIR, "preferences_in.seq"); List<Preference<Long, Long>> testPrefs = null; if (useTestExampleInput) { testPrefs = prepareTestInputData(conf, fs, CONF_INPUT_DIR, preferencesIn); } else if (inputFile.isEmpty()) { testPrefs = generateRandomInputData(conf, fs, CONF_INPUT_DIR, numBspTask, numGpuBspTask, userCount, itemCount, percentNonZeroValues, GPUPercentage, maxTestPrefs); } else if (!inputFile.isEmpty()) { // parse inputFile and return first entries for testing testPrefs = convertInputData(conf, fs, CONF_INPUT_DIR, preferencesIn, inputFile, separator, maxTestPrefs); } // Generate Job config BSPJob job = createOnlineCFTrainHybridBSPConf(conf, CONF_INPUT_DIR, CONF_OUTPUT_DIR); // Execute Job long startTime = System.currentTimeMillis(); if (job.waitForCompletion(true)) { LOG.info("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds"); // Load Job results for testing OnlineCF recommender = new OnlineCF(); recommender.load(CONF_OUTPUT_DIR.toString(), false); // Test results int error = 0; double totalError = 0; for (Preference<Long, Long> test : testPrefs) { double expected = test.getValue().get(); double estimated = recommender.estimatePreference(test.getUserId(), test.getItemId()); if (testPrefs.size() <= 20) { LOG.info("(" + test.getUserId() + ", " + test.getItemId() + ", " + expected + "): " + estimated + " error: " + Math.abs(expected - estimated)); } totalError += Math.abs(expected - estimated); error += (Math.abs(expected - estimated) < 0.5) ? 1 : 0; } LOG.info("totalError: " + totalError); LOG.info("assertEquals(expected: " + (testPrefs.size() * 0.75) + " == " + error + " actual) with delta: 1"); if (isDebugging) { printOutput(conf, fs, ".log", new IntWritable(), new PipesVectorWritable()); } } }