List of usage examples for java.io BufferedReader BufferedReader
public BufferedReader(Reader in)
From source file:com.gomoob.embedded.EmbeddedMongo.java
/** * Main entry of the program./*from w w w. j a v a2s .c o m*/ * * @param args arguments used to customize starting. * * @throws Exception If an error occured while executing the server. */ public static void main(String[] args) throws Exception { // Creates a default execution context, then the configuration of this context can be changed depending on the // command line parameters received. context = new Context(); // Parse the command line parseCommandLine(args); boolean terminated = false; System.out.println("MONGOD_HOST=" + context.getMongoContext().getNet().getServerAddress().getHostName()); System.out.println("MONGOD_PORT=" + context.getMongoContext().getNet().getPort()); System.out.println("SERVER_SOCKET_PORT=" + context.getSocketContext().getServerSocket().getLocalPort()); Socket socket = null; BufferedReader reader = null; Writer writer = null; while (!terminated) { socket = context.getSocketContext().getServerSocket().accept(); reader = new BufferedReader(new InputStreamReader(socket.getInputStream())); writer = new OutputStreamWriter(new DataOutputStream(socket.getOutputStream())); System.out.println("Waiting for command..."); String commandString = reader.readLine(); System.out.println(commandString); ICommand command = parseCommandString(commandString); IResponse response = command.run(context); writer.write(response.toJSON()); writer.close(); // If the current socket is opened close it if (!socket.isClosed()) { socket.close(); } // If stop is required terminated = response.isTerminationRequired(); } context.getSocketContext().getServerSocket().close(); }
From source file:gov.nih.nci.ncicb.tcga.dcc.dam.util.TempClinicalDataLoader.java
public static void main(String[] args) { // first get the db connection properties String url = urlSet.get(args[1]); String user = args[2];//from w ww . j a v a 2 s . co m String word = args[3]; // make sure we have the Oracle driver somewhere try { Class.forName("oracle.jdbc.OracleDriver"); Class.forName("org.postgresql.Driver"); } catch (Exception x) { System.out.println("Unable to load the driver class!"); System.exit(0); } // connect to the database try { dbConnection = DriverManager.getConnection(url, user, word); ClinicalBean.setDBConnection(dbConnection); } catch (SQLException x) { x.printStackTrace(); System.exit(1); } final String xmlList = args[0]; BufferedReader br = null; try { final Map<String, String> clinicalFiles = new HashMap<String, String>(); final Map<String, String> biospecimenFiles = new HashMap<String, String>(); final Map<String, String> fullFiles = new HashMap<String, String>(); //noinspection IOResourceOpenedButNotSafelyClosed br = new BufferedReader(new FileReader(xmlList)); // read the file list to get all the files to load while (br.ready()) { final String[] in = br.readLine().split("\\t"); String xmlfile = in[0]; String archive = in[1]; if (xmlfile.contains("_clinical")) { clinicalFiles.put(xmlfile, archive); } else if (xmlfile.contains("_biospecimen")) { biospecimenFiles.put(xmlfile, archive); } else { fullFiles.put(xmlfile, archive); } } Date dateAdded = Calendar.getInstance().getTime(); // NOTE!!! This deletes all data before the load starts, assuming we are re-loading everything. // a better way would be to figure out what has changed and load that, or to be able to load multiple versions of the data in the schema emptyClinicalTables(user); // load any "full" files first -- in case some archives aren't split yet for (final String file : fullFiles.keySet()) { String archive = fullFiles.get(file); System.out.println("Full file " + file + " in " + archive); // need to re-instantiate the disease-specific beans for each file createDiseaseSpecificBeans(xmlList); String disease = getDiseaseName(archive); processFullXmlFile(file, archive, disease, dateAdded); // memory leak or something... have to commit and close all connections and re-get connection // after each file to keep from using too much heap space. this troubles me, but I have never had // the time to figure out why it happens resetConnections(url, user, word); } // now process all clinical files, and insert patients and clinical data for (final String clinicalFile : clinicalFiles.keySet()) { createDiseaseSpecificBeans(xmlList); String archive = clinicalFiles.get(clinicalFile); System.out.println("Clinical file " + clinicalFile + " in " + archive); String disease = getDiseaseName(archive); processClinicalXmlFile(clinicalFile, archive, disease, dateAdded); resetConnections(url, user, word); } // now process biospecimen files for (final String biospecimenFile : biospecimenFiles.keySet()) { createDiseaseSpecificBeans(xmlList); String archive = biospecimenFiles.get(biospecimenFile); String disease = getDiseaseName(archive); System.out.println("Biospecimen file " + biospecimenFile); processBiospecimenXmlFile(biospecimenFile, archive, disease, dateAdded); resetConnections(url, user, word); } // this sets relationships between these clinical tables and data browser tables, since we delete // and reload every time setForeignKeys(); dbConnection.commit(); dbConnection.close(); } catch (Exception e) { e.printStackTrace(); System.exit(-1); } finally { IOUtils.closeQuietly(br); } }
From source file:io.apiman.tools.jdbc.ApimanJdbcServer.java
public static void main(String[] args) { try {// w ww . ja va 2s. c om File dataDir = new File("target/h2"); String url = "jdbc:h2:tcp://localhost:9092/apiman"; if (dataDir.exists()) { FileUtils.deleteDirectory(dataDir); } dataDir.mkdirs(); Server.createTcpServer("-tcpPassword", "sa", "-baseDir", dataDir.getAbsolutePath(), "-tcpPort", "9092", "-tcpAllowOthers").start(); Class.forName("org.h2.Driver"); try (Connection connection = DriverManager.getConnection(url, "sa", "")) { System.out.println("Connection Established: " + connection.getMetaData().getDatabaseProductName() + "/" + connection.getCatalog()); executeUpdate(connection, "CREATE TABLE users ( username varchar(255) NOT NULL, password varchar(255) NOT NULL, PRIMARY KEY (username))"); executeUpdate(connection, "INSERT INTO users (username, password) VALUES ('bwayne', 'ae2efd698aefdf366736a4eda1bc5241f9fbfec7')"); executeUpdate(connection, "INSERT INTO users (username, password) VALUES ('ckent', 'ea59f7ca52a2087c99374caba0ff29be1b2dcdbf')"); executeUpdate(connection, "INSERT INTO users (username, password) VALUES ('ballen', 'ea59f7ca52a2087c99374caba0ff29be1b2dcdbf')"); executeUpdate(connection, "CREATE TABLE roles (rolename varchar(255) NOT NULL, username varchar(255) NOT NULL)"); executeUpdate(connection, "INSERT INTO roles (rolename, username) VALUES ('user', 'bwayne')"); executeUpdate(connection, "INSERT INTO roles (rolename, username) VALUES ('admin', 'bwayne')"); executeUpdate(connection, "INSERT INTO roles (rolename, username) VALUES ('ckent', 'user')"); executeUpdate(connection, "INSERT INTO roles (rolename, username) VALUES ('ballen', 'user')"); } System.out.println("======================================================"); System.out.println("JDBC (H2) server started successfully."); System.out.println(""); System.out.println(" Data: " + dataDir.getAbsolutePath()); System.out.println(" JDBC URL: " + url); System.out.println(" JDBC User: sa"); System.out.println(" JDBC Password: "); System.out.println( " Authentication Query: SELECT * FROM users u WHERE u.username = ? AND u.password = ?"); System.out.println(" Authorization Query: SELECT r.rolename FROM roles r WHERE r.username = ?"); System.out.println("======================================================"); System.out.println(""); System.out.println(""); System.out.println("Press Enter to stop the JDBC server."); new BufferedReader(new InputStreamReader(System.in)).readLine(); System.out.println("Shutting down the JDBC server..."); Server.shutdownTcpServer("tcp://localhost:9092", "", true, true); System.out.println("Done!"); } catch (Exception e) { e.printStackTrace(); } }
From source file:com.bitsofproof.example.Simple.java
public static void main(String[] args) { Security.addProvider(new BouncyCastleProvider()); final CommandLineParser parser = new GnuParser(); final Options gnuOptions = new Options(); gnuOptions.addOption("h", "help", false, "I can't help you yet"); gnuOptions.addOption("s", "server", true, "Server URL"); gnuOptions.addOption("u", "user", true, "User"); gnuOptions.addOption("p", "password", true, "Password"); System.out.println("BOP Bitcoin Server Simple Client 3.5.0 (c) 2013-2014 bits of proof zrt."); CommandLine cl = null;/*from w w w . jav a 2 s . c o m*/ String url = null; String user = null; String password = null; try { cl = parser.parse(gnuOptions, args); url = cl.getOptionValue('s'); user = cl.getOptionValue('u'); password = cl.getOptionValue('p'); } catch (org.apache.commons.cli.ParseException e) { e.printStackTrace(); System.exit(1); } if (url == null || user == null || password == null) { System.err.println("Need -s server -u user -p password"); System.exit(1); } BCSAPI api = getServer(url, user, password); try { BufferedReader input = new BufferedReader(new InputStreamReader(System.in)); long start = System.currentTimeMillis(); api.ping(start); System.out.println("Server round trip " + (System.currentTimeMillis() - start) + "ms"); api.addAlertListener(new AlertListener() { @Override public void alert(String s, int severity) { System.err.println("ALERT: " + s); } }); System.out.println("Talking to " + (api.isProduction() ? "PRODUCTION" : "test") + " server"); ConfirmationManager confirmationManager = new ConfirmationManager(); confirmationManager.init(api, 144); System.out.printf("Please enter wallet name: "); String wallet = input.readLine(); SimpleFileWallet w = new SimpleFileWallet(wallet + ".wallet"); TransactionFactory am = null; if (!w.exists()) { System.out.printf("Enter passphrase: "); String passphrase = input.readLine(); System.out.printf("Enter master (empty for new): "); String master = input.readLine(); if (master.equals("")) { w.init(passphrase); w.unlock(passphrase); System.out.printf("First account: "); String account = input.readLine(); am = w.createAccountManager(account); w.lock(); w.persist(); } else { StringTokenizer tokenizer = new StringTokenizer(master, "@"); String key = tokenizer.nextToken(); long since = 0; if (tokenizer.hasMoreElements()) { since = Long.parseLong(tokenizer.nextToken()) * 1000; } w.init(passphrase, ExtendedKey.parse(key), true, since); w.unlock(passphrase); System.out.printf("First account: "); String account = input.readLine(); am = w.createAccountManager(account); w.lock(); w.persist(); w.sync(api); } } else { w = SimpleFileWallet.read(wallet + ".wallet"); w.sync(api); List<String> names = w.getAccountNames(); System.out.println("Accounts:"); System.out.println("---------"); String first = null; for (String name : names) { System.out.println(name); if (first == null) { first = name; } } System.out.println("---------"); am = w.getAccountManager(first); System.out.println("Using account " + first); } confirmationManager.addAccount(am); api.registerTransactionListener(am); while (true) { printMenu(); String answer = input.readLine(); System.out.printf("\n"); if (answer.equals("1")) { System.out.printf("The balance is: " + printBit(am.getBalance()) + "\n"); System.out.printf(" confirmed: " + printBit(am.getConfirmed()) + "\n"); System.out.printf(" receiveing: " + printBit(am.getReceiving()) + "\n"); System.out.printf(" change: " + printBit(am.getChange()) + "\n"); System.out.printf("( sending: " + printBit(am.getSending()) + ")\n"); } else if (answer.equals("2")) { for (Address a : am.getAddresses()) { System.out.printf(a + "\n"); } } else if (answer.equals("3")) { ExtendedKeyAccountManager im = (ExtendedKeyAccountManager) am; System.out.printf( im.getMaster().serialize(api.isProduction()) + "@" + im.getCreated() / 1000 + "\n"); } else if (answer.equals("4")) { System.out.printf("Enter passphrase: "); String passphrase = input.readLine(); w.unlock(passphrase); ExtendedKeyAccountManager im = (ExtendedKeyAccountManager) am; System.out.printf( im.getMaster().serialize(api.isProduction()) + "@" + im.getCreated() / 1000 + "\n"); w.lock(); } else if (answer.equals("5")) { System.out.printf("Enter passphrase: "); String passphrase = input.readLine(); w.unlock(passphrase); System.out.printf("Number of recipients"); Integer nr = Integer.valueOf(input.readLine()); Transaction spend; if (nr.intValue() == 1) { System.out.printf("Receiver address: "); String address = input.readLine(); System.out.printf("amount (Bit): "); long amount = parseBit(input.readLine()); spend = am.pay(Address.fromSatoshiStyle(address), amount); System.out.println("About to send " + printBit(amount) + " to " + address); } else { List<Address> addresses = new ArrayList<>(); List<Long> amounts = new ArrayList<>(); long total = 0; for (int i = 0; i < nr; ++i) { System.out.printf("Receiver address: "); String address = input.readLine(); addresses.add(Address.fromSatoshiStyle(address)); System.out.printf("amount (Bit): "); long amount = parseBit(input.readLine()); amounts.add(amount); total += amount; } spend = am.pay(addresses, amounts); System.out.println("About to send " + printBit(total)); } System.out.println("inputs"); for (TransactionInput in : spend.getInputs()) { System.out.println(in.getSourceHash() + " " + in.getIx()); } System.out.println("outputs"); for (TransactionOutput out : spend.getOutputs()) { System.out.println(out.getOutputAddress() + " " + printBit(out.getValue())); } w.lock(); System.out.printf("Type yes to go: "); if (input.readLine().equals("yes")) { api.sendTransaction(spend); System.out.printf("Sent transaction: " + spend.getHash()); } else { System.out.printf("Nothing happened."); } } else if (answer.equals("6")) { System.out.printf("Address: "); Set<Address> match = new HashSet<Address>(); match.add(Address.fromSatoshiStyle(input.readLine())); api.scanTransactionsForAddresses(match, 0, new TransactionListener() { @Override public boolean process(Transaction t) { System.out.printf("Found transaction: " + t.getHash() + "\n"); return true; } }); } else if (answer.equals("7")) { System.out.printf("Public key: "); ExtendedKey ek = ExtendedKey.parse(input.readLine()); api.scanTransactions(ek, 0, 10, 0, new TransactionListener() { @Override public boolean process(Transaction t) { System.out.printf("Found transaction: " + t.getHash() + "\n"); return true; } }); } else if (answer.equals("a")) { System.out.printf("Enter account name: "); String account = input.readLine(); am = w.getAccountManager(account); api.registerTransactionListener(am); confirmationManager.addAccount(am); } else if (answer.equals("c")) { System.out.printf("Enter account name: "); String account = input.readLine(); System.out.printf("Enter passphrase: "); String passphrase = input.readLine(); w.unlock(passphrase); am = w.createAccountManager(account); System.out.println("using account: " + account); w.lock(); w.persist(); api.registerTransactionListener(am); confirmationManager.addAccount(am); } else if (answer.equals("m")) { System.out.printf("Enter passphrase: "); String passphrase = input.readLine(); w.unlock(passphrase); System.out.println(w.getMaster().serialize(api.isProduction())); System.out.println(w.getMaster().getReadOnly().serialize(true)); w.lock(); } else if (answer.equals("s")) { System.out.printf("Enter private key: "); String key = input.readLine(); ECKeyPair k = ECKeyPair.parseWIF(key); KeyListAccountManager alm = new KeyListAccountManager(); alm.addKey(k); alm.syncHistory(api); Address a = am.getNextReceiverAddress(); Transaction t = alm.pay(a, alm.getBalance(), PaymentOptions.receiverPaysFee); System.out.println("About to sweep " + printBit(alm.getBalance()) + " to " + a); System.out.println("inputs"); for (TransactionInput in : t.getInputs()) { System.out.println(in.getSourceHash() + " " + in.getIx()); } System.out.println("outputs"); for (TransactionOutput out : t.getOutputs()) { System.out.println(out.getOutputAddress() + " " + printBit(out.getValue())); } System.out.printf("Type yes to go: "); if (input.readLine().equals("yes")) { api.sendTransaction(t); System.out.printf("Sent transaction: " + t.getHash()); } else { System.out.printf("Nothing happened."); } } else { System.exit(0); } } } catch (Exception e) { System.err.println("Something went wrong"); e.printStackTrace(); System.exit(1); } }
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(// w ww. ja v a 2 s . c om 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.yahoo.athenz.example.ztoken.HttpExampleClient.java
public static void main(String[] args) throws MalformedURLException, IOException { // parse our command line to retrieve required input CommandLine cmd = parseCommandLine(args); String domainName = cmd.getOptionValue("domain"); String serviceName = cmd.getOptionValue("service"); String privateKeyPath = cmd.getOptionValue("pkey"); String keyId = cmd.getOptionValue("keyid"); String url = cmd.getOptionValue("url"); String ztsUrl = cmd.getOptionValue("ztsurl"); String providerDomain = cmd.getOptionValue("provider-domain"); String providerRole = cmd.getOptionValue("provider-role"); // we need to generate our principal credentials (ntoken). In // addition to the domain and service names, we need the // the service's private key and the key identifier - the // service with the corresponding public key must already be // registered in ZMS PrivateKey privateKey = Crypto.loadPrivateKey(new File(privateKeyPath)); ServiceIdentityProvider identityProvider = new SimpleServiceIdentityProvider(domainName, serviceName, privateKey, keyId);/*from ww w . j a va2 s .c o m*/ // now we need to retrieve a role token (ztoken) for accessing // the provider Athenz enabled service RoleToken roleToken = null; try (ZTSClient ztsClient = new ZTSClient(ztsUrl, domainName, serviceName, identityProvider)) { roleToken = ztsClient.getRoleToken(providerDomain, providerRole); } if (roleToken == null) { System.out.println( "Unable to retrieve role token for: " + providerRole + " in domain: " + providerDomain); System.exit(1); } URL obj = new URL(url); HttpURLConnection con = (HttpURLConnection) obj.openConnection(); // set our Athenz credentials. The ZTSClient provides the header // name that we must use for authorization token while the role // token itself provides the token string (ztoken). System.out.println("Using RoleToken: " + roleToken.getToken()); con.setRequestProperty(ZTSClient.getHeader(), roleToken.getToken()); // now process our request int responseCode = con.getResponseCode(); switch (responseCode) { case HttpURLConnection.HTTP_FORBIDDEN: System.out.println("Request was forbidden - not authorized: " + con.getResponseMessage()); break; case HttpURLConnection.HTTP_OK: System.out.println("Successful response: "); try (BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()))) { String inputLine; while ((inputLine = in.readLine()) != null) { System.out.println(inputLine); } } break; default: System.out.println("Request failed - response status code: " + responseCode); } }
From source file:com.kappaware.logtrawler.Main.java
@SuppressWarnings("static-access") static public void main(String[] argv) throws Throwable { Config config;/*from w w w. ja v a 2 s . c o m*/ Options options = new Options(); options.addOption(OptionBuilder.hasArg().withArgName("configFile").withLongOpt("config-file") .withDescription("JSON configuration file").create("c")); options.addOption(OptionBuilder.hasArg().withArgName("folder").withLongOpt("folder") .withDescription("Folder to monitor").create("f")); options.addOption(OptionBuilder.hasArg().withArgName("exclusion").withLongOpt("exclusion") .withDescription("Exclusion regex").create("x")); options.addOption(OptionBuilder.hasArg().withArgName("adminEndpoint").withLongOpt("admin-endpoint") .withDescription("Endpoint for admin REST").create("e")); options.addOption(OptionBuilder.hasArg().withArgName("outputFlow").withLongOpt("output-flow") .withDescription("Target to post result on").create("o")); options.addOption(OptionBuilder.hasArg().withArgName("hostname").withLongOpt("hostname") .withDescription("This hostname").create("h")); options.addOption(OptionBuilder.withLongOpt("displayDot").withDescription("Display Dot").create("d")); options.addOption(OptionBuilder.hasArg().withArgName("mimeType").withLongOpt("mime-type") .withDescription("Valid MIME type").create("m")); options.addOption(OptionBuilder.hasArg().withArgName("allowedAdmin").withLongOpt("allowedAdmin") .withDescription("Allowed admin network").create("a")); options.addOption(OptionBuilder.hasArg().withArgName("configFile").withLongOpt("gen-config-file") .withDescription("Generate JSON configuration file").create("g")); options.addOption(OptionBuilder.hasArg().withArgName("maxBatchSize").withLongOpt("max-batch-size") .withDescription("Max JSON batch (array) size").create("b")); CommandLineParser clParser = new BasicParser(); CommandLine line; String configFile = null; try { // parse the command line argument line = clParser.parse(options, argv); if (line.hasOption("c")) { configFile = line.getOptionValue("c"); config = Json.fromJson(Config.class, new BufferedReader(new InputStreamReader(new FileInputStream(configFile)))); } else { config = new Config(); } if (line.hasOption("f")) { String[] fs = line.getOptionValues("f"); // Get the first agent (Create it if needed) if (config.getAgents() == null || config.getAgents().size() == 0) { Config.Agent agent = new Config.Agent("default"); config.addAgent(agent); } Config.Agent agent = config.getAgents().iterator().next(); for (String f : fs) { agent.addFolder(new Config.Agent.Folder(f, false)); } } if (line.hasOption("e")) { String e = line.getOptionValue("e"); config.setAdminEndpoint(e); } if (line.hasOption("o")) { String[] es = line.getOptionValues("o"); if (config.getAgents() != null) { for (Agent agent : config.getAgents()) { for (String s : es) { agent.addOuputFlow(s); } } } } if (line.hasOption("h")) { String e = line.getOptionValue("h"); config.setHostname(e); } if (line.hasOption("x")) { if (config.getAgents() != null) { for (Agent agent : config.getAgents()) { if (agent.getFolders() != null) { for (Folder folder : agent.getFolders()) { String[] exs = line.getOptionValues("x"); for (String ex : exs) { folder.addExcludedPath(ex); } } } } } } if (line.hasOption("m")) { if (config.getAgents() != null) { for (Agent agent : config.getAgents()) { String[] exs = line.getOptionValues("m"); for (String ex : exs) { agent.addLogMimeType(ex); } } } } if (line.hasOption("a")) { String[] exs = line.getOptionValues("a"); for (String ex : exs) { config.addAdminAllowedNetwork(ex); } } if (line.hasOption("d")) { config.setDisplayDot(true); } if (line.hasOption("b")) { Integer i = getIntegerParameter(line, "b"); if (config.getAgents() != null) { for (Agent agent : config.getAgents()) { agent.setOutputMaxBatchSize(i); } } } config.setDefault(); if (line.hasOption("g")) { String fileName = line.getOptionValue("g"); PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(fileName, false))); out.println(Json.toJson(config, true)); out.flush(); out.close(); System.exit(0); } } catch (ParseException exp) { // oops, something went wrong usage(options, exp.getMessage()); return; } try { // Check config if (config.getAgents() == null || config.getAgents().size() < 1) { throw new ConfigurationException("At least one folder to monitor must be provided!"); } Map<String, AgentHandler> agentHandlerByName = new HashMap<String, AgentHandler>(); for (Config.Agent agent : config.getAgents()) { agentHandlerByName.put(agent.getName(), new AgentHandler(agent)); } if (!Utils.isNullOrEmpty(config.getAdminEndpoint())) { new AdminServer(config, agentHandlerByName); } } catch (ConfigurationException e) { log.error(e.toString()); System.exit(1); } catch (Throwable t) { log.error("Error in main", t); System.exit(2); } }
From source file:ms1quant.MS1Quant.java
/** * @param args the command line arguments MS1Quant parameterfile *//*from ww w .j ava 2 s . c o m*/ public static void main(String[] args) throws Exception { BufferedReader reader = null; try { System.out.println( "================================================================================================="); System.out.println("Umpire MS1 quantification and feature detection analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length < 3 || !args[1].startsWith("-mode")) { System.out .println("command : java -jar -Xmx10G MS1Quant.jar ms1quant.params -mode[1 or 2] [Option]"); System.out.println("\n-mode"); System.out.println("\t1:Single file mode--> mzXML_file PepXML_file"); System.out.println("\t\tEx: -mode1 file1.mzXML file1.pep.xml"); System.out.println( "\t2:Folder mode--> mzXML_Folder PepXML_Folder, all generated csv tables will be merged into a single csv file"); System.out.println("\t\tEx: -mode2 /data/mzxml/ /data/pepxml/"); System.out.println("\nOptions"); System.out.println( "\t-C\tNo of concurrent files to be processed (only for folder mode), Ex. -C5, default:1"); System.out.println("\t-p\tMinimum probability, Ex. -p0.9, default:0.9"); System.out.println("\t-ID\tDetect identified feature only"); System.out.println("\t-O\toutput folder, Ex. -O/data/"); return; } ConsoleLogger consoleLogger = new ConsoleLogger(); consoleLogger.SetConsoleLogger(Level.DEBUG); consoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "ms1quant_debug.log"); Logger logger = Logger.getRootLogger(); logger.debug("Command: " + Arrays.toString(args)); logger.info("MS1Quant version: " + UmpireInfo.GetInstance().Version); String parameterfile = args[0]; logger.info("Parameter file: " + parameterfile); File paramfile = new File(parameterfile); if (!paramfile.exists()) { logger.error("Parameter file " + paramfile.getAbsolutePath() + " cannot be found. The program will exit."); } reader = new BufferedReader(new FileReader(paramfile.getAbsolutePath())); String line = ""; InstrumentParameter param = new InstrumentParameter(InstrumentParameter.InstrumentType.TOF5600); int NoCPUs = 2; int NoFile = 1; param.DetermineBGByID = false; param.EstimateBG = true; //<editor-fold defaultstate="collapsed" desc="Read parameter file"> while ((line = reader.readLine()) != null) { if (!"".equals(line) && !line.startsWith("#")) { logger.info(line); //System.out.println(line); if (line.split("=").length < 2) { continue; } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); if (type.startsWith("para.")) { type = type.replace("para.", "SE."); } String value = line.split("=")[1].trim(); switch (type) { case "Thread": { NoCPUs = Integer.parseInt(value); break; } //<editor-fold defaultstate="collapsed" desc="instrument parameters"> case "SE.MS1PPM": { param.MS1PPM = Float.parseFloat(value); break; } case "SE.MS2PPM": { param.MS2PPM = Float.parseFloat(value); break; } case "SE.SN": { param.SNThreshold = Float.parseFloat(value); break; } case "SE.MS2SN": { param.MS2SNThreshold = Float.parseFloat(value); break; } case "SE.MinMSIntensity": { param.MinMSIntensity = Float.parseFloat(value); break; } case "SE.MinMSMSIntensity": { param.MinMSMSIntensity = Float.parseFloat(value); break; } case "SE.MinRTRange": { param.MinRTRange = Float.parseFloat(value); break; } case "SE.MaxNoPeakCluster": { param.MaxNoPeakCluster = Integer.parseInt(value); param.MaxMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinNoPeakCluster": { param.MinNoPeakCluster = Integer.parseInt(value); param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinMS2NoPeakCluster": { param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MaxCurveRTRange": { param.MaxCurveRTRange = Float.parseFloat(value); break; } case "SE.Resolution": { param.Resolution = Integer.parseInt(value); break; } case "SE.RTtol": { param.RTtol = Float.parseFloat(value); break; } case "SE.NoPeakPerMin": { param.NoPeakPerMin = Integer.parseInt(value); break; } case "SE.StartCharge": { param.StartCharge = Integer.parseInt(value); break; } case "SE.EndCharge": { param.EndCharge = Integer.parseInt(value); break; } case "SE.MS2StartCharge": { param.MS2StartCharge = Integer.parseInt(value); break; } case "SE.MS2EndCharge": { param.MS2EndCharge = Integer.parseInt(value); break; } case "SE.NoMissedScan": { param.NoMissedScan = Integer.parseInt(value); break; } case "SE.Denoise": { param.Denoise = Boolean.valueOf(value); break; } case "SE.EstimateBG": { param.EstimateBG = Boolean.valueOf(value); break; } case "SE.RemoveGroupedPeaks": { param.RemoveGroupedPeaks = Boolean.valueOf(value); break; } case "SE.MinFrag": { param.MinFrag = Integer.parseInt(value); break; } case "SE.IsoPattern": { param.IsoPattern = Float.valueOf(value); break; } case "SE.StartRT": { param.startRT = Float.valueOf(value); } case "SE.EndRT": { param.endRT = Float.valueOf(value); } //</editor-fold> } } } //</editor-fold> int mode = 1; if (args[1].equals("-mode2")) { mode = 2; } else if (args[1].equals("-mode1")) { mode = 1; } else { logger.error("-mode number not recongized. The program will exit."); } String mzXML = ""; String pepXML = ""; String mzXMLPath = ""; String pepXMLPath = ""; File mzXMLfile = null; File pepXMLfile = null; File mzXMLfolder = null; File pepXMLfolder = null; int idx = 0; if (mode == 1) { mzXML = args[2]; logger.info("Mode1 mzXML file: " + mzXML); mzXMLfile = new File(mzXML); if (!mzXMLfile.exists()) { logger.error("Mode1 mzXML file " + mzXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } pepXML = args[3]; logger.info("Mode1 pepXML file: " + pepXML); pepXMLfile = new File(pepXML); if (!pepXMLfile.exists()) { logger.error("Mode1 pepXML file " + pepXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } idx = 4; } else if (mode == 2) { mzXMLPath = args[2]; logger.info("Mode2 mzXML folder: " + mzXMLPath); mzXMLfolder = new File(mzXMLPath); if (!mzXMLfolder.exists()) { logger.error("Mode2 mzXML folder " + mzXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } pepXMLPath = args[3]; logger.info("Mode2 pepXML folder: " + pepXMLPath); pepXMLfolder = new File(pepXMLPath); if (!pepXMLfolder.exists()) { logger.error("Mode2 pepXML folder " + pepXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } idx = 4; } String outputfolder = ""; float MinProb = 0f; for (int i = idx; i < args.length; i++) { if (args[i].startsWith("-")) { if (args[i].equals("-ID")) { param.TargetIDOnly = true; logger.info("Detect ID feature only: true"); } if (args[i].startsWith("-O")) { outputfolder = args[i].substring(2); logger.info("Output folder: " + outputfolder); File outputfile = new File(outputfolder); if (!outputfolder.endsWith("\\") | outputfolder.endsWith("/")) { outputfolder += "/"; } if (!outputfile.exists()) { outputfile.mkdir(); } } if (args[i].startsWith("-C")) { try { NoFile = Integer.parseInt(args[i].substring(2)); logger.info("No of concurrent files: " + NoFile); } catch (Exception ex) { logger.error(args[i] + " is not a correct integer format, will process only one file at a time."); } } if (args[i].startsWith("-p")) { try { MinProb = Float.parseFloat(args[i].substring(2)); logger.info("probability threshold: " + MinProb); } catch (Exception ex) { logger.error(args[i] + " is not a correct format, will use 0 as threshold instead."); } } } } reader.close(); TandemParam tandemparam = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); PTMManager.GetInstance(); if (param.TargetIDOnly) { param.EstimateBG = false; param.ApexDelta = 1.5f; param.NoMissedScan = 10; param.MiniOverlapP = 0.2f; param.RemoveGroupedPeaks = false; param.CheckMonoIsotopicApex = false; param.DetectByCWT = false; param.FillGapByBK = false; param.IsoCorrThreshold = -1f; param.SmoothFactor = 3; } if (mode == 1) { logger.info("Processing " + mzXMLfile.getAbsolutePath() + "...."); long time = System.currentTimeMillis(); LCMSPeakMS1 LCMS1 = new LCMSPeakMS1(mzXMLfile.getAbsolutePath(), NoCPUs); LCMS1.SetParameter(param); LCMS1.Resume = false; if (!param.TargetIDOnly) { LCMS1.CreatePeakFolder(); } LCMS1.ExportPeakClusterTable = true; if (pepXMLfile.exists()) { tandemparam.InteractPepXMLPath = pepXMLfile.getAbsolutePath(); LCMS1.ParsePepXML(tandemparam, MinProb); logger.info("No. of PSMs included: " + LCMS1.IDsummary.PSMList.size()); logger.info("No. of Peptide ions included: " + LCMS1.IDsummary.GetPepIonList().size()); } if (param.TargetIDOnly) { LCMS1.SaveSerializationFile = false; } if (param.TargetIDOnly || !LCMS1.ReadPeakCluster()) { LCMS1.PeakClusterDetection(); } if (pepXMLfile.exists()) { LCMS1.AssignQuant(false); LCMS1.IDsummary.ExportPepID(outputfolder); } time = System.currentTimeMillis() - time; logger.info(LCMS1.ParentmzXMLName + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); LCMS1.BaseClearAllPeaks(); LCMS1.SetSpectrumParser(null); LCMS1.IDsummary = null; LCMS1 = null; System.gc(); } else if (mode == 2) { LCMSID IDsummary = new LCMSID("", "", ""); logger.info("Parsing all pepXML files in " + pepXMLPath + "...."); for (File file : pepXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("pep.xml") || file.getName().toLowerCase().endsWith("pepxml")) { PepXMLParser pepXMLParser = new PepXMLParser(IDsummary, file.getAbsolutePath(), MinProb); } } HashMap<String, LCMSID> LCMSIDMap = IDsummary.GetLCMSIDFileMap(); ExecutorService executorPool = null; executorPool = Executors.newFixedThreadPool(NoFile); logger.info("Processing all mzXML files in " + mzXMLPath + "...."); for (File file : mzXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("mzxml")) { LCMSID id = LCMSIDMap.get(FilenameUtils.getBaseName(file.getName())); if (id == null || id.PSMList == null) { logger.warn("No IDs found in :" + FilenameUtils.getBaseName(file.getName()) + ". Quantification for this file is skipped"); continue; } if (!id.PSMList.isEmpty()) { MS1TargetQuantThread thread = new MS1TargetQuantThread(file, id, NoCPUs, outputfolder, param); executorPool.execute(thread); } } } LCMSIDMap.clear(); LCMSIDMap = null; IDsummary = null; executorPool.shutdown(); try { executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS); } catch (InterruptedException e) { logger.info("interrupted.."); } if (outputfolder == null | outputfolder.equals("")) { outputfolder = mzXMLPath; } logger.info("Merging PSM files.."); File output = new File(outputfolder); FileWriter writer = new FileWriter(output.getAbsolutePath() + "/PSM_merge.csv"); boolean header = false; for (File csvfile : output.listFiles()) { if (csvfile.getName().toLowerCase().endsWith("_psms.csv")) { BufferedReader outreader = new BufferedReader(new FileReader(csvfile)); String outline = outreader.readLine(); if (!header) { writer.write(outline + "\n"); header = true; } while ((outline = outreader.readLine()) != null) { writer.write(outline + "\n"); } outreader.close(); csvfile.delete(); } } writer.close(); } logger.info("MS1 quant module is complete."); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:com.dlmu.heipacker.crawler.client.ClientInteractiveAuthentication.java
public static void main(String[] args) throws Exception { DefaultHttpClient httpclient = new DefaultHttpClient(); try {/*from w ww . j a va 2s . co m*/ // Create local execution context HttpContext localContext = new BasicHttpContext(); HttpGet httpget = new HttpGet("http://localhost/test"); boolean trying = true; while (trying) { System.out.println("executing request " + httpget.getRequestLine()); HttpResponse response = httpclient.execute(httpget, localContext); System.out.println("----------------------------------------"); System.out.println(response.getStatusLine()); // Consume response content HttpEntity entity = response.getEntity(); EntityUtils.consume(entity); int sc = response.getStatusLine().getStatusCode(); AuthState authState = null; HttpHost authhost = null; if (sc == HttpStatus.SC_UNAUTHORIZED) { // Target host authentication required authState = (AuthState) localContext.getAttribute(ClientContext.TARGET_AUTH_STATE); authhost = (HttpHost) localContext.getAttribute(ExecutionContext.HTTP_TARGET_HOST); } if (sc == HttpStatus.SC_PROXY_AUTHENTICATION_REQUIRED) { // Proxy authentication required authState = (AuthState) localContext.getAttribute(ClientContext.PROXY_AUTH_STATE); authhost = (HttpHost) localContext.getAttribute(ExecutionContext.HTTP_PROXY_HOST); } if (authState != null) { System.out.println("----------------------------------------"); AuthScheme authscheme = authState.getAuthScheme(); System.out.println("Please provide credentials for " + authscheme.getRealm() + "@" + authhost.toHostString()); BufferedReader console = new BufferedReader(new InputStreamReader(System.in)); System.out.print("Enter username: "); String user = console.readLine(); System.out.print("Enter password: "); String password = console.readLine(); if (user != null && user.length() > 0) { Credentials creds = new UsernamePasswordCredentials(user, password); httpclient.getCredentialsProvider().setCredentials(new AuthScope(authhost), creds); trying = true; } else { trying = false; } } else { trying = false; } } } finally { // When HttpClient instance is no longer needed, // shut down the connection manager to ensure // immediate deallocation of all system resources httpclient.getConnectionManager().shutdown(); } }
From source file:SequentialPersonalizedPageRank.java
@SuppressWarnings({ "static-access" })
public static void main(String[] args) throws IOException {
Options options = new Options();
options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
options.addOption(/* w w w . j av a 2 s. co m*/
OptionBuilder.withArgName("val").hasArg().withDescription("random jump factor").create(JUMP));
options.addOption(OptionBuilder.withArgName("node").hasArg()
.withDescription("source node (i.e., destination of the random jump)").create(SOURCE));
CommandLine cmdline = null;
CommandLineParser parser = new GnuParser();
try {
cmdline = parser.parse(options, args);
} catch (ParseException exp) {
System.err.println("Error parsing command line: " + exp.getMessage());
System.exit(-1);
}
if (!cmdline.hasOption(INPUT) || !cmdline.hasOption(SOURCE)) {
System.out.println("args: " + Arrays.toString(args));
HelpFormatter formatter = new HelpFormatter();
formatter.setWidth(120);
formatter.printHelp(SequentialPersonalizedPageRank.class.getName(), options);
ToolRunner.printGenericCommandUsage(System.out);
System.exit(-1);
}
String infile = cmdline.getOptionValue(INPUT);
final String source = cmdline.getOptionValue(SOURCE);
float alpha = cmdline.hasOption(JUMP) ? Float.parseFloat(cmdline.getOptionValue(JUMP)) : 0.15f;
int edgeCnt = 0;
DirectedSparseGraph<String, Integer> graph = new DirectedSparseGraph<String, Integer>();
BufferedReader data = new BufferedReader(new InputStreamReader(new FileInputStream(infile)));
String line;
while ((line = data.readLine()) != null) {
line.trim();
String[] arr = line.split("\\t");
for (int i = 1; i < arr.length; i++) {
graph.addEdge(new Integer(edgeCnt++), arr[0], arr[i]);
}
}
data.close();
if (!graph.containsVertex(source)) {
System.err.println("Error: source node not found in the graph!");
System.exit(-1);
}
WeakComponentClusterer<String, Integer> clusterer = new WeakComponentClusterer<String, Integer>();
Set<Set<String>> components = clusterer.transform(graph);
int numComponents = components.size();
System.out.println("Number of components: " + numComponents);
System.out.println("Number of edges: " + graph.getEdgeCount());
System.out.println("Number of nodes: " + graph.getVertexCount());
System.out.println("Random jump factor: " + alpha);
// Compute personalized PageRank.
PageRankWithPriors<String, Integer> ranker = new PageRankWithPriors<String, Integer>(graph,
new Transformer<String, Double>() {
@Override
public Double transform(String vertex) {
return vertex.equals(source) ? 1.0 : 0;
}
}, alpha);
ranker.evaluate();
// Use priority queue to sort vertices by PageRank values.
PriorityQueue<Ranking<String>> q = new PriorityQueue<Ranking<String>>();
int i = 0;
for (String pmid : graph.getVertices()) {
q.add(new Ranking<String>(i++, ranker.getVertexScore(pmid), pmid));
}
// Print PageRank values.
System.out.println("\nPageRank of nodes, in descending order:");
Ranking<String> r = null;
while ((r = q.poll()) != null) {
System.out.println(r.rankScore + "\t" + r.getRanked());
}
}