List of usage examples for java.util NoSuchElementException getMessage
public String getMessage()
From source file:com.continuent.tungsten.common.security.KeystoreManagerCtrl.java
/** * Password Manager entry point//from w ww. j a v a 2 s.co m * * @param argv * @throws Exception */ public static void main(String argv[]) throws Exception { keystoreManager = new KeystoreManagerCtrl(); // --- Options --- CommandLine line = null; try { CommandLineParser parser = new GnuParser(); // --- Parse the command line arguments --- // --- Help line = parser.parse(keystoreManager.helpOptions, argv, true); if (line.hasOption(_HELP)) { DisplayHelpAndExit(EXIT_CODE.EXIT_OK); } // --- Program command line options line = parser.parse(keystoreManager.options, argv); // --- Compulsory arguments : Get options --- if (line.hasOption(_KEYSTORE_LOCATION)) keystoreManager.keystoreLocation = line.getOptionValue(_KEYSTORE_LOCATION); if (line.hasOption(_KEY_ALIAS)) keystoreManager.keyAlias = line.getOptionValue(_KEY_ALIAS); if (line.hasOption(_KEY_TYPE)) { String keyType = line.getOptionValue(_KEY_TYPE); // This will throw an exception if the type is not recognised KEYSTORE_TYPE certificateTYpe = KEYSTORE_TYPE.fromString(keyType); keystoreManager.keyType = certificateTYpe; } if (line.hasOption(_KEYSTORE_PASSWORD)) keystoreManager.keystorePassword = line.getOptionValue(_KEYSTORE_PASSWORD); if (line.hasOption(_KEY_PASSWORD)) keystoreManager.keyPassword = line.getOptionValue(_KEY_PASSWORD); } catch (ParseException exp) { logger.error(exp.getMessage()); DisplayHelpAndExit(EXIT_CODE.EXIT_ERROR); } catch (Exception e) { // Workaround for Junit test if (e.toString().contains("CheckExitCalled")) { throw e; } else // Normal behaviour { logger.error(e.getMessage()); Exit(EXIT_CODE.EXIT_ERROR); } } // --- Perform commands --- // ######### Check password ########## if (line.hasOption(_CHECK)) { try { if (keystoreManager.keystorePassword == null || keystoreManager.keyPassword == null) { // --- Get passwords from stdin if not given on command line List<String> listPrompts = Arrays.asList("Keystore password:", MessageFormat.format("Password for key {0}:", keystoreManager.keyAlias)); List<String> listUserInput = keystoreManager.getUserInputFromStdin(listPrompts); if (listUserInput.size() == listPrompts.size()) { keystoreManager.keystorePassword = listUserInput.get(0); keystoreManager.keyPassword = listUserInput.get(1); } else { throw new NoSuchElementException(); } } try { // --- Check that all keys in keystore use the keystore // password logger.info(MessageFormat.format("Using keystore:{0}", keystoreManager.keystoreLocation)); SecurityHelper.checkKeyStorePasswords(keystoreManager.keystoreLocation, keystoreManager.keyType, keystoreManager.keystorePassword, keystoreManager.keyAlias, keystoreManager.keyPassword); logger.info(MessageFormat.format("OK : Identical password for Keystore and key={0}", keystoreManager.keyAlias)); } catch (UnrecoverableKeyException uke) { logger.error(MessageFormat.format("At least 1 key has a wrong password.{0}", uke.getMessage())); Exit(EXIT_CODE.EXIT_ERROR); } catch (Exception e) { logger.error(MessageFormat.format("{0}", e.getMessage())); Exit(EXIT_CODE.EXIT_ERROR); } } catch (NoSuchElementException nse) { logger.error(nse.getMessage()); Exit(EXIT_CODE.EXIT_ERROR); } catch (Exception e) { logger.error(MessageFormat.format("Error while running the program: {0}", e.getMessage())); Exit(EXIT_CODE.EXIT_ERROR); } } Exit(EXIT_CODE.EXIT_OK); }
From source file:com.act.lcms.v2.MZCollisionCounter.java
public static void main(String[] args) throws Exception { CLIUtil cliUtil = new CLIUtil(MassChargeCalculator.class, HELP_MESSAGE, OPTION_BUILDERS); CommandLine cl = cliUtil.parseCommandLine(args); File inputFile = new File(cl.getOptionValue(OPTION_INPUT_INCHI_LIST)); if (!inputFile.exists()) { cliUtil.failWithMessage("Input file at does not exist at %s", inputFile.getAbsolutePath()); }/* w w w . jav a2s. c om*/ List<MassChargeCalculator.MZSource> sources = new ArrayList<>(); try (BufferedReader reader = new BufferedReader(new FileReader(inputFile))) { String line; while ((line = reader.readLine()) != null) { line = line.trim(); sources.add(new MassChargeCalculator.MZSource(line)); if (sources.size() % 1000 == 0) { LOGGER.info("Loaded %d sources from input file", sources.size()); } } } Set<String> considerIons = Collections.emptySet(); if (cl.hasOption(OPTION_ONLY_CONSIDER_IONS)) { List<String> ions = Arrays.asList(cl.getOptionValues(OPTION_ONLY_CONSIDER_IONS)); LOGGER.info("Only considering ions for m/z calculation: %s", StringUtils.join(ions, ", ")); considerIons = new HashSet<>(ions); } TSVWriter<String, Long> tsvWriter = new TSVWriter<>(Arrays.asList("collisions", "count")); tsvWriter.open(new File(cl.getOptionValue(OPTION_OUTPUT_FILE))); try { LOGGER.info("Loaded %d sources in total from input file", sources.size()); MassChargeCalculator.MassChargeMap mzMap = MassChargeCalculator.makeMassChargeMap(sources, considerIons); if (!cl.hasOption(OPTION_COUNT_WINDOW_INTERSECTIONS)) { // Do an exact analysis of the m/z collisions if windowing is not specified. LOGGER.info("Computing precise collision histogram."); Iterable<Double> mzs = mzMap.ionMZIter(); Map<Integer, Long> collisionHistogram = histogram( StreamSupport.stream(mzs.spliterator(), false).map(mz -> { // See comment about Iterable below. try { return mzMap.ionMZToMZSources(mz).size(); } catch (NoSuchElementException e) { LOGGER.error("Caught no such element exception for mz %f: %s", mz, e.getMessage()); throw e; } })); List<Integer> sortedCollisions = new ArrayList<>(collisionHistogram.keySet()); Collections.sort(sortedCollisions); for (Integer collision : sortedCollisions) { tsvWriter.append(new HashMap<String, Long>() { { put("collisions", collision.longValue()); put("count", collisionHistogram.get(collision)); } }); } } else { /* After some deliberation (thanks Gil!), the windowed variant of this calculation counts the number of * structures whose 0.01 Da m/z windows (for some set of ions) overlap with each other. * * For example, let's assume we have five total input structures, and are only searching for one ion. Let's * also assume that three of those structures have m/z A and the remaining two have m/z B. The windows might * look like this in the m/z domain: * |----A----| * |----B----| * Because A represents three structures and overlaps with B, which represents two, we assign A a count of 5-- * this is the number of structures we believe could fall into the range of A given our current peak calling * approach. Similarly, B is assigned a count of 5, as the possibility for collision/confusion is symmetric. * * Note that this is an over-approximation of collisions, as we could more precisely only consider intersections * when the exact m/z of B falls within the window around A and vice versa. However, because we have observed * cases where the MS sensor doesn't report structures at exactly the m/z we predict, we employ this weaker * definition of intersection to give a slightly pessimistic view of what confusions might be possible. */ // Compute windows for every m/z. We don't care about the original mz values since we just want the count. List<Double> mzs = mzMap.ionMZsSorted(); final Double windowHalfWidth; if (cl.hasOption(OPTION_WINDOW_HALFWIDTH)) { // Don't use get with default for this option, as we want the exact FP value of the default tolerance. windowHalfWidth = Double.valueOf(cl.getOptionValue(OPTION_WINDOW_HALFWIDTH)); } else { windowHalfWidth = DEFAULT_WINDOW_TOLERANCE; } /* Window = (lower bound, upper bound), counter of represented m/z's that collide with this window, and number * of representative structures (which will be used in counting collisions). */ LinkedList<CollisionWindow> allWindows = new LinkedList<CollisionWindow>() { { for (Double mz : mzs) { // CPU for memory trade-off: don't re-compute the window bounds over and over and over and over and over. try { add(new CollisionWindow(mz, windowHalfWidth, mzMap.ionMZToMZSources(mz).size())); } catch (NoSuchElementException e) { LOGGER.error("Caught no such element exception for mz %f: %s", mz, e.getMessage()); throw e; } } } }; // Sweep line time! The window ranges are the interesting points. We just accumulate overlap counts as we go. LinkedList<CollisionWindow> workingSet = new LinkedList<>(); List<CollisionWindow> finished = new LinkedList<>(); while (allWindows.size() > 0) { CollisionWindow thisWindow = allWindows.pop(); // Remove any windows from the working set that don't overlap with the next window. while (workingSet.size() > 0 && workingSet.peekFirst().getMaxMZ() < thisWindow.getMinMZ()) { finished.add(workingSet.pop()); } for (CollisionWindow w : workingSet) { /* Add the size of the new overlapping window's structure count to each of the windows in the working set, * which represents the number of possible confused structures that fall within the overlapping region. * We exclude the window itself as it should already have counted the colliding structures it represents. */ w.getAccumulator().add(thisWindow.getStructureCount()); /* Reciprocally, add the structure counts of all windows with which the current window overlaps to it. */ thisWindow.getAccumulator().add(w.getStructureCount()); } // Now that accumulation is complete, we can safely add the current window. workingSet.add(thisWindow); } // All the interesting events are done, so drop the remaining windows into the finished set. finished.addAll(workingSet); Map<Long, Long> collisionHistogram = histogram( finished.stream().map(w -> w.getAccumulator().longValue())); List<Long> sortedCollisions = new ArrayList<>(collisionHistogram.keySet()); Collections.sort(sortedCollisions); for (Long collision : sortedCollisions) { tsvWriter.append(new HashMap<String, Long>() { { put("collisions", collision); put("count", collisionHistogram.get(collision)); } }); } } } finally { if (tsvWriter != null) { tsvWriter.close(); } } }
From source file:fr.cls.atoll.motu.library.misc.utils.PropertiesUtilities.java
/** * Replace in the properties values the name of the system variable that follows the scheme * <tt>${var}<tt> with their corresponding values. * // w w w. java2s.c om * @param props properties to substitute. */ static public void replaceSystemVariable(Properties props) { Iterator it; Map.Entry entry; String value; for (it = props.entrySet().iterator(); it.hasNext();) { entry = (Map.Entry) it.next(); try { value = replaceSystemVariable((String) entry.getValue()); } catch (NoSuchElementException ex) { throw new NoSuchElementException( ex.getMessage() + " subsitution for property " + (String) entry.getKey()); } entry.setValue(value); } }
From source file:com.act.lcms.v2.MZCollisionCounter.java
public static <T> Map<T, Long> histogram(Stream<T> stream) { Map<T, Long> hist = new HashMap<>(); // This could be done with reduce (fold) or collector cleverness, but this invocation makes the intention clear. //stream.forEach(x -> hist.merge(x, 1l, (acc, one) -> one + acc)); stream.forEach(x -> {/*ww w . j av a 2s . c o m*/ try { hist.put(x, hist.getOrDefault(x, 0l) + 1); } catch (NoSuchElementException e) { LOGGER.error("Caught no such element exception for %s: %s", x.toString(), e.getMessage()); throw e; } }); return hist; }
From source file:nl.minvenj.pef.stream.LiveCapture.java
private static boolean checkConfiguration(final XMLConfiguration config) { final long MAX_FILE_SIZE = 1000; //Test if all fields are available. For now it exits per field. try {/*from w w w. j ava 2s . c om*/ //First all normal fields. The library field is optional, default to metal. final boolean live = config.getBoolean("live"); final String inputFile = config.getString("input"); if (!live) { if (inputFile == null) { throw new NoSuchElementException( "For offline use, the parameter 'input' file needs to be specified"); } File testInput = new File(inputFile); if (!testInput.exists()) { logger.severe("The specified input file " + testInput.toPath().toAbsolutePath().toString() + " does not exist."); return false; } if (!testInput.canRead()) { logger.severe("The user is not allowed to read the file"); } } // Will throw an error if conversion fails. config.getBoolean("remove_failing_packets"); config.getBoolean("remove_unknown_protocols"); config.getBoolean("checksum_reset"); config.getBoolean("timer", false); final String outputDir = config.getString("output_directory"); // The file size does not need to be specified. Therefore a default is provided. final long fileSize = config.getLong("file_size", 120); if (fileSize > MAX_FILE_SIZE) { logger.severe(" A file size over 1000 MB is not supported."); return false; } if (outputDir == null) { throw new NoSuchElementException("The output_directory parameter is not set"); } final Path path = Paths.get(outputDir); if (!Files.isDirectory(path, LinkOption.NOFOLLOW_LINKS)) { logger.severe("The output directory configured is not a path."); return false; } if (!Files.isWritable(path)) { logger.severe("The selected output directory is not writable."); return false; } final String parseLibrary = config.getString("parse_library"); if (!parseLibrary.equals("metal")) { logger.severe("Only the metal library is currently implemented as parse library."); return false; } String[] packetInputLibraryOptions = { "metal", "jnetpcap" }; final String packetInputLibrary = config.getString("packets_input_library"); if (!Arrays.asList(packetInputLibraryOptions).contains(packetInputLibrary)) { logger.severe("Packet Input Library: " + packetInputLibrary + " is not implemented."); } // Test all algorithms and their parameters. testPseudonymizationSettings(config); } catch (NoSuchElementException e) { logger.severe("Input element is missing: " + e.getMessage()); return false; } catch (InvalidPathException e) { logger.severe("The path specified in the config file is invalid: " + e.getMessage()); return false; } catch (ConversionException e) { logger.severe("Conversion failed: " + e.getMessage()); return false; } catch (ClassNotFoundException e) { logger.severe("Error in creating a parameter: the class could not be found: " + e.getMessage()); return false; } catch (ConfigurationException e) { logger.severe(e.getMessage()); return false; } return true; }
From source file:com.tesora.dve.worker.DirectConnectionCache.java
public static CachedConnection checkoutDatasource(EventLoopGroup preferredEventLoop, UserAuthentication auth, AdditionalConnectionInfo additionalConnInfo, StorageSite site) throws PESQLException { try {//from w w w . j a v a 2 s. c o m if (preferredEventLoop == null) preferredEventLoop = SharedEventLoopHolder.getLoop(); DSCacheKey datasourceKey = new DirectConnectionCache.DSCacheKey(preferredEventLoop, auth, additionalConnInfo, site); CachedConnection cacheEntry; if (DirectConnectionCache.suppressConnectionCaching) { cacheEntry = DirectConnectionCache.connect(datasourceKey); } else { cacheEntry = DirectConnectionCache.connectionCache.borrowObject(datasourceKey); } return cacheEntry; } catch (NoSuchElementException e) { if (e.getMessage().matches(".*java.net.ConnectException.*")) throw new PECommunicationsException( "Cannot connect to '" + site.getMasterUrl() + "' as user '" + auth.userid + "'", e); throw new PESQLException( "Unable to connect to site '" + site.getName() + "' as user '" + auth.userid + "'", e); } catch (Exception e) { throw new PESQLException( "Unable to connect to site '" + site.getName() + "' as user '" + auth.userid + "'", e); } }
From source file:com.spokentech.speechdown.server.util.pool.AbstractPoolableObjectFactory.java
/** * Initializes an {@link org.apache.commons.pool.ObjectPool} by borrowing each object from the * pool (thereby triggering activation) and then returning all the objects back to the pool. * @param pool the object pool to be initialized. * @throws InstantiationException if borrowing (or returning) an object from the pool triggers an exception. *///from w w w . j a v a2s . c o m public static void initPool(ObjectPool pool) throws InstantiationException { try { List<Object> objects = new ArrayList<Object>(); while (true) try { objects.add(pool.borrowObject()); } catch (NoSuchElementException e) { // ignore, max active reached break; } for (Object obj : objects) { pool.returnObject(obj); } } catch (Exception e) { try { pool.close(); } catch (Exception e1) { _logger.warn("Encounter expception while attempting to close object pool!", e1); } throw (InstantiationException) new InstantiationException(e.getMessage()).initCause(e); } }
From source file:com.telefonica.euro_iaas.sdc.puppetwrapper.controllers.GenericController.java
@ExceptionHandler(NoSuchElementException.class) @ResponseStatus(HttpStatus.NOT_FOUND)/*ww w . j a v a2 s. c om*/ @ResponseBody public PuppetWrapperError handleNoSuchElementException(NoSuchElementException ex) { logger.error(ex.getMessage()); return new PuppetWrapperError(HttpStatus.NOT_FOUND.value(), ex.getMessage()); }
From source file:com.dream.messaging.sender.socket.LongConnSocketMessageSender.java
@Override protected Message send(Message req) throws ConnectionException { IoSession iosession = null;// w w w . j ava 2 s .com Message response = null; try { iosession = getObjectPool().borrowObject(); IoBuffer buffer = IoBuffer.allocate(4); WriteFuture future = iosession.write(buffer); future.await(); } catch (NoSuchElementException e) { logger.error(e.getMessage(), e); } catch (IllegalStateException e) { logger.error(e.getMessage(), e); } catch (Exception e) { logger.error(e.getMessage(), e); } finally { try { getObjectPool().returnObject(iosession); } catch (Exception e) { logger.error(e.getMessage(), e); } } return response; }