List of usage examples for java.lang String indexOf
public int indexOf(String str)
From source file:net.sf.freecol.FreeCol.java
/** * The entrypoint.// w w w . j a va 2s . c om * * @param args The command-line arguments. * @throws IOException * @throws FontFormatException */ public static void main(String[] args) throws FontFormatException, IOException { freeColRevision = FREECOL_VERSION; JarURLConnection juc; try { juc = getJarURLConnection(FreeCol.class); } catch (IOException ioe) { juc = null; System.err.println("Unable to open class jar: " + ioe.getMessage()); } if (juc != null) { try { String revision = readVersion(juc); if (revision != null) { freeColRevision += " (Revision: " + revision + ")"; } } catch (Exception e) { System.err.println("Unable to load Manifest: " + e.getMessage()); } try { splashStream = getDefaultSplashStream(juc); } catch (Exception e) { System.err.println("Unable to open default splash: " + e.getMessage()); } } // Java bug #7075600 causes BR#2554. The workaround is to set // the following property. Remove if/when they fix Java. System.setProperty("java.util.Arrays.useLegacyMergeSort", "true"); // We can not even emit localized error messages until we find // the data directory, which might have been specified on the // command line. String dataDirectoryArg = findArg("--freecol-data", args); String err = FreeColDirectories.setDataDirectory(dataDirectoryArg); if (err != null) fatal(err); // This must not fail. // Now we have the data directory, establish the base locale. // Beware, the locale may change! String localeArg = findArg("--default-locale", args); if (localeArg == null) { locale = Locale.getDefault(); } else { int index = localeArg.indexOf('.'); // Strip encoding if present if (index > 0) localeArg = localeArg.substring(0, index); locale = Messages.getLocale(localeArg); } Messages.loadMessageBundle(locale); // Now that we can emit error messages, parse the other // command line arguments. handleArgs(args); // Do the potentially fatal system checks as early as possible. if (javaCheck && JAVA_VERSION_MIN.compareTo(JAVA_VERSION) > 0) { fatal(StringTemplate.template("main.javaVersion").addName("%version%", JAVA_VERSION) .addName("%minVersion%", JAVA_VERSION_MIN)); } if (memoryCheck && MEMORY_MAX < MEMORY_MIN * 1000000) { fatal(StringTemplate.template("main.memory").addAmount("%memory%", MEMORY_MAX).addAmount("%minMemory%", MEMORY_MIN)); } // Having parsed the command line args, we know where the user // directories should be, so we can set up the rest of the // file/directory structure. String userMsg = FreeColDirectories.setUserDirectories(); // Now we have the log file path, start logging. final Logger baseLogger = Logger.getLogger(""); final Handler[] handlers = baseLogger.getHandlers(); for (Handler handler : handlers) { baseLogger.removeHandler(handler); } String logFile = FreeColDirectories.getLogFilePath(); try { baseLogger.addHandler(new DefaultHandler(consoleLogging, logFile)); Logger freecolLogger = Logger.getLogger("net.sf.freecol"); freecolLogger.setLevel(logLevel); } catch (FreeColException e) { System.err.println("Logging initialization failure: " + e.getMessage()); e.printStackTrace(); } Thread.setDefaultUncaughtExceptionHandler((Thread thread, Throwable e) -> { baseLogger.log(Level.WARNING, "Uncaught exception from thread: " + thread, e); }); // Now we can find the client options, allow the options // setting to override the locale, if no command line option // had been specified. // We have users whose machines default to Finnish but play // FreeCol in English. // If the user has selected automatic language selection, do // nothing, since we have already set up the default locale. if (localeArg == null) { String clientLanguage = ClientOptions.getLanguageOption(); Locale clientLocale; if (clientLanguage != null && !Messages.AUTOMATIC.equalsIgnoreCase(clientLanguage) && (clientLocale = Messages.getLocale(clientLanguage)) != locale) { locale = clientLocale; Messages.loadMessageBundle(locale); logger.info("Loaded messages for " + locale); } } // Now we have the user mods directory and the locale is now // stable, load the mods and their messages. Mods.loadMods(); Messages.loadModMessageBundle(locale); // Report on where we are. if (userMsg != null) logger.info(Messages.message(userMsg)); logger.info(getConfiguration().toString()); // Ready to specialize into client or server. if (standAloneServer) { startServer(); } else { startClient(userMsg); } startYourAddition(); }
From source file:com.joliciel.jochre.Jochre.java
public static void main(String[] args) throws Exception { Map<String, String> argMap = new HashMap<String, String>(); for (String arg : args) { int equalsPos = arg.indexOf('='); String argName = arg.substring(0, equalsPos); String argValue = arg.substring(equalsPos + 1); argMap.put(argName, argValue);/*from ww w.ja v a 2 s . c o m*/ } Jochre jochre = new Jochre(); jochre.execute(argMap); }
From source file:org.jets3t.apps.uploader.Uploader.java
/** * Run the Uploader as a stand-alone application. * * @param args//from w w w . j ava 2 s .c om * @throws Exception */ public static void main(String args[]) throws Exception { JFrame ownerFrame = new JFrame("JetS3t Uploader"); ownerFrame.addWindowListener(new WindowListener() { public void windowOpened(WindowEvent e) { } public void windowClosing(WindowEvent e) { e.getWindow().dispose(); } public void windowClosed(WindowEvent e) { } public void windowIconified(WindowEvent e) { } public void windowDeiconified(WindowEvent e) { } public void windowActivated(WindowEvent e) { } public void windowDeactivated(WindowEvent e) { } }); // Read arguments as properties of the form: <propertyName>'='<propertyValue> Properties argumentProperties = new Properties(); if (args.length > 0) { for (int i = 0; i < args.length; i++) { String arg = args[i]; int delimIndex = arg.indexOf("="); if (delimIndex >= 0) { String name = arg.substring(0, delimIndex); String value = arg.substring(delimIndex + 1); argumentProperties.put(name, value); } else { System.out.println("Ignoring property argument with incorrect format: " + arg); } } } new Uploader(ownerFrame, argumentProperties); }
From source file:DcmQR.java
@SuppressWarnings("unchecked") public static void main(String[] args) { CommandLine cl = parse(args);/* w ww. ja va2 s .c o m*/ DcmQR dcmqr = new DcmQR(); final List<String> argList = cl.getArgList(); String remoteAE = argList.get(0); String[] calledAETAddress = split(remoteAE, '@'); dcmqr.setCalledAET(calledAETAddress[0], cl.hasOption("reuseassoc")); if (calledAETAddress[1] == null) { dcmqr.setRemoteHost("127.0.0.1"); dcmqr.setRemotePort(104); } else { String[] hostPort = split(calledAETAddress[1], ':'); dcmqr.setRemoteHost(hostPort[0]); dcmqr.setRemotePort(toPort(hostPort[1])); } if (cl.hasOption("L")) { String localAE = cl.getOptionValue("L"); String[] localPort = split(localAE, ':'); if (localPort[1] != null) { dcmqr.setLocalPort(toPort(localPort[1])); } String[] callingAETHost = split(localPort[0], '@'); dcmqr.setCalling(callingAETHost[0]); if (callingAETHost[1] != null) { dcmqr.setLocalHost(callingAETHost[1]); } } if (cl.hasOption("username")) { String username = cl.getOptionValue("username"); UserIdentity userId; if (cl.hasOption("passcode")) { String passcode = cl.getOptionValue("passcode"); userId = new UserIdentity.UsernamePasscode(username, passcode.toCharArray()); } else { userId = new UserIdentity.Username(username); } userId.setPositiveResponseRequested(cl.hasOption("uidnegrsp")); dcmqr.setUserIdentity(userId); } if (cl.hasOption("connectTO")) dcmqr.setConnectTimeout(parseInt(cl.getOptionValue("connectTO"), "illegal argument of option -connectTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("reaper")) dcmqr.setAssociationReaperPeriod(parseInt(cl.getOptionValue("reaper"), "illegal argument of option -reaper", 1, Integer.MAX_VALUE)); if (cl.hasOption("cfindrspTO")) dcmqr.setDimseRspTimeout(parseInt(cl.getOptionValue("cfindrspTO"), "illegal argument of option -cfindrspTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("cmoverspTO")) dcmqr.setRetrieveRspTimeout(parseInt(cl.getOptionValue("cmoverspTO"), "illegal argument of option -cmoverspTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("cgetrspTO")) dcmqr.setRetrieveRspTimeout(parseInt(cl.getOptionValue("cgetrspTO"), "illegal argument of option -cgetrspTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("acceptTO")) dcmqr.setAcceptTimeout(parseInt(cl.getOptionValue("acceptTO"), "illegal argument of option -acceptTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("releaseTO")) dcmqr.setReleaseTimeout(parseInt(cl.getOptionValue("releaseTO"), "illegal argument of option -releaseTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("soclosedelay")) dcmqr.setSocketCloseDelay(parseInt(cl.getOptionValue("soclosedelay"), "illegal argument of option -soclosedelay", 1, 10000)); if (cl.hasOption("rcvpdulen")) dcmqr.setMaxPDULengthReceive( parseInt(cl.getOptionValue("rcvpdulen"), "illegal argument of option -rcvpdulen", 1, 10000) * KB); if (cl.hasOption("sndpdulen")) dcmqr.setMaxPDULengthSend( parseInt(cl.getOptionValue("sndpdulen"), "illegal argument of option -sndpdulen", 1, 10000) * KB); if (cl.hasOption("sosndbuf")) dcmqr.setSendBufferSize( parseInt(cl.getOptionValue("sosndbuf"), "illegal argument of option -sosndbuf", 1, 10000) * KB); if (cl.hasOption("sorcvbuf")) dcmqr.setReceiveBufferSize( parseInt(cl.getOptionValue("sorcvbuf"), "illegal argument of option -sorcvbuf", 1, 10000) * KB); if (cl.hasOption("filebuf")) dcmqr.setFileBufferSize( parseInt(cl.getOptionValue("filebuf"), "illegal argument of option -filebuf", 1, 10000) * KB); dcmqr.setPackPDV(!cl.hasOption("pdv1")); dcmqr.setTcpNoDelay(!cl.hasOption("tcpdelay")); dcmqr.setMaxOpsInvoked(cl.hasOption("async") ? parseInt(cl.getOptionValue("async"), "illegal argument of option -async", 0, 0xffff) : 1); dcmqr.setMaxOpsPerformed(cl.hasOption("cstoreasync") ? parseInt(cl.getOptionValue("cstoreasync"), "illegal argument of option -cstoreasync", 0, 0xffff) : 0); if (cl.hasOption("C")) dcmqr.setCancelAfter( parseInt(cl.getOptionValue("C"), "illegal argument of option -C", 1, Integer.MAX_VALUE)); if (cl.hasOption("lowprior")) dcmqr.setPriority(CommandUtils.LOW); if (cl.hasOption("highprior")) dcmqr.setPriority(CommandUtils.HIGH); if (cl.hasOption("cstore")) { String[] storeTCs = cl.getOptionValues("cstore"); for (String storeTC : storeTCs) { String cuid; String[] tsuids; int colon = storeTC.indexOf(':'); if (colon == -1) { cuid = storeTC; tsuids = DEF_TS; } else { cuid = storeTC.substring(0, colon); String ts = storeTC.substring(colon + 1); try { tsuids = TS.valueOf(ts).uids; } catch (IllegalArgumentException e) { tsuids = ts.split(","); } } try { cuid = CUID.valueOf(cuid).uid; } catch (IllegalArgumentException e) { // assume cuid already contains UID } dcmqr.addStoreTransferCapability(cuid, tsuids); } if (cl.hasOption("cstoredest")) dcmqr.setStoreDestination(cl.getOptionValue("cstoredest")); } dcmqr.setCGet(cl.hasOption("cget")); if (cl.hasOption("cmove")) dcmqr.setMoveDest(cl.getOptionValue("cmove")); if (cl.hasOption("evalRetrieveAET")) dcmqr.setEvalRetrieveAET(true); if (cl.hasOption("P")) dcmqr.setQueryLevel(QueryRetrieveLevel.PATIENT); else if (cl.hasOption("S")) dcmqr.setQueryLevel(QueryRetrieveLevel.SERIES); else if (cl.hasOption("I")) dcmqr.setQueryLevel(QueryRetrieveLevel.IMAGE); else dcmqr.setQueryLevel(QueryRetrieveLevel.STUDY); if (cl.hasOption("noextneg")) dcmqr.setNoExtNegotiation(true); if (cl.hasOption("rel")) dcmqr.setRelationQR(true); if (cl.hasOption("datetime")) dcmqr.setDateTimeMatching(true); if (cl.hasOption("fuzzy")) dcmqr.setFuzzySemanticPersonNameMatching(true); if (!cl.hasOption("P")) { if (cl.hasOption("retall")) dcmqr.addPrivate(UID.PrivateStudyRootQueryRetrieveInformationModelFIND); if (cl.hasOption("blocked")) dcmqr.addPrivate(UID.PrivateBlockedStudyRootQueryRetrieveInformationModelFIND); if (cl.hasOption("vmf")) dcmqr.addPrivate(UID.PrivateVirtualMultiframeStudyRootQueryRetrieveInformationModelFIND); } if (cl.hasOption("q")) { String[] matchingKeys = cl.getOptionValues("q"); for (int i = 1; i < matchingKeys.length; i++, i++) dcmqr.addMatchingKey(Tag.toTagPath(matchingKeys[i - 1]), matchingKeys[i]); } if (cl.hasOption("r")) { String[] returnKeys = cl.getOptionValues("r"); for (int i = 0; i < returnKeys.length; i++) dcmqr.addReturnKey(Tag.toTagPath(returnKeys[i])); } dcmqr.configureTransferCapability(cl.hasOption("ivrle")); int repeat = cl.hasOption("repeat") ? parseInt(cl.getOptionValue("repeat"), "illegal argument of option -repeat", 1, Integer.MAX_VALUE) : 0; int interval = cl.hasOption("repeatdelay") ? parseInt(cl.getOptionValue("repeatdelay"), "illegal argument of option -repeatdelay", 1, Integer.MAX_VALUE) : 0; boolean closeAssoc = cl.hasOption("closeassoc"); if (cl.hasOption("tls")) { String cipher = cl.getOptionValue("tls"); if ("NULL".equalsIgnoreCase(cipher)) { dcmqr.setTlsWithoutEncyrption(); } else if ("3DES".equalsIgnoreCase(cipher)) { dcmqr.setTls3DES_EDE_CBC(); } else if ("AES".equalsIgnoreCase(cipher)) { dcmqr.setTlsAES_128_CBC(); } else { exit("Invalid parameter for option -tls: " + cipher); } if (cl.hasOption("nossl2")) { dcmqr.disableSSLv2Hello(); } dcmqr.setTlsNeedClientAuth(!cl.hasOption("noclientauth")); if (cl.hasOption("keystore")) { dcmqr.setKeyStoreURL(cl.getOptionValue("keystore")); } if (cl.hasOption("keystorepw")) { dcmqr.setKeyStorePassword(cl.getOptionValue("keystorepw")); } if (cl.hasOption("keypw")) { dcmqr.setKeyPassword(cl.getOptionValue("keypw")); } if (cl.hasOption("truststore")) { dcmqr.setTrustStoreURL(cl.getOptionValue("truststore")); } if (cl.hasOption("truststorepw")) { dcmqr.setTrustStorePassword(cl.getOptionValue("truststorepw")); } long t1 = System.currentTimeMillis(); try { dcmqr.initTLS(); } catch (Exception e) { System.err.println("ERROR: Failed to initialize TLS context:" + e.getMessage()); System.exit(2); } long t2 = System.currentTimeMillis(); LOG.info("Initialize TLS context in {} s", Float.valueOf((t2 - t1) / 1000f)); } try { dcmqr.start(); } catch (Exception e) { System.err.println( "ERROR: Failed to start server for receiving " + "requested objects:" + e.getMessage()); System.exit(2); } try { long t1 = System.currentTimeMillis(); try { dcmqr.open(); } catch (Exception e) { LOG.error("Failed to establish association:", e); System.exit(2); } long t2 = System.currentTimeMillis(); LOG.info("Connected to {} in {} s", remoteAE, Float.valueOf((t2 - t1) / 1000f)); for (;;) { List<DicomObject> result = dcmqr.query(); long t3 = System.currentTimeMillis(); LOG.info("Received {} matching entries in {} s", Integer.valueOf(result.size()), Float.valueOf((t3 - t2) / 1000f)); if (dcmqr.isCMove() || dcmqr.isCGet()) { if (dcmqr.isCMove()) dcmqr.move(result); else dcmqr.get(result); long t4 = System.currentTimeMillis(); LOG.info("Retrieved {} objects (warning: {}, failed: {}) in {}s", new Object[] { Integer.valueOf(dcmqr.getTotalRetrieved()), Integer.valueOf(dcmqr.getWarning()), Integer.valueOf(dcmqr.getFailed()), Float.valueOf((t4 - t3) / 1000f) }); } if (repeat == 0 || closeAssoc) { try { dcmqr.close(); } catch (InterruptedException e) { LOG.error(e.getMessage(), e); } LOG.info("Released connection to {}", remoteAE); } if (repeat-- == 0) break; Thread.sleep(interval); long t4 = System.currentTimeMillis(); dcmqr.open(); t2 = System.currentTimeMillis(); LOG.info("Reconnect or reuse connection to {} in {} s", remoteAE, Float.valueOf((t2 - t4) / 1000f)); } } catch (IOException e) { LOG.error(e.getMessage(), e); } catch (InterruptedException e) { LOG.error(e.getMessage(), e); } catch (ConfigurationException e) { LOG.error(e.getMessage(), e); } finally { dcmqr.stop(); } }
From source file:codesample.AuthenticationSample.java
/***************************************************************************************************************** * * The main method.//from www . java 2 s . c o m * * @param args Not used. * @throws IOException If it fails to create log files. * ***************************************************************************************************************** */ public static void main(String[] args) throws IOException { // Return codes final int SUCCESS = 0; final int FAILURE = 1; int returnCode = SUCCESS; // Hostname to use when connecting to web service. Must contain the fully qualified domain name. String bwsHostname = "<bwsHostName>"; // e.g. bwsHostname = "server01.example.net". // Port to use when connecting to web service. The same port is used to access the // management console in BDS and UDS. Default ports: BDS=38443, UDS=18082, UEM12=18084 String bwsPort = "<bwsPort>"; // e.g. bwsPort = "18084". // Credential type used in the authentication process. CredentialType credentialType = new CredentialType(); credentialType.setPASSWORD(true); credentialType.setValue("PASSWORD"); /* * BWS Host certificate must be installed on the client machine before running this sample code, otherwise a * SSL/TLS secure channel error will be thrown. For more information, see the BlackBerry Web Services for * Enterprise Administration For Java Developers Getting Started Guide. * * To test authentication populate the methods below with the appropriate credentials and information */ // Select which authentication methods you would like to test by setting the variables to true boolean useAD = true; // Active Directory boolean useLDAP = true; // LDAP try { if (bwsHostname.indexOf('.') < 1) { throw new Exception("Invalid bwsHostname format. Expected format is \"server01.example.net\""); } // bwsPort, if not null, must be a positive integer if (bwsPort != null) { int port = Integer.parseInt(bwsPort); if (port < 1) { throw new Exception("Invalid bwsPort. Expecting a positive integer string or null"); } } returnCode = (demonstrateBlackBerryAdministrationServiceAuthentication(bwsHostname, bwsPort, credentialType)) ? SUCCESS : FAILURE; logMessage(""); if (useAD && returnCode == SUCCESS) { returnCode = (demonstrateActiveDirectoryAuthentication(bwsHostname, bwsPort, credentialType)) ? SUCCESS : FAILURE; logMessage(""); } if (useLDAP && returnCode == SUCCESS) { returnCode = (demonstrateLDAPAuthentication(bwsHostname, bwsPort, credentialType)) ? SUCCESS : FAILURE; logMessage(""); } } catch (Exception e) { logMessage("Exception: \"%s\"%n", e.getMessage()); e.printStackTrace(); returnCode = FAILURE; } System.err.format("Exiting sample.%nPress Enter to exit%n"); System.in.read(); System.exit(returnCode); }
From source file:mod.org.dcm4che2.tool.DcmQR.java
@SuppressWarnings("unchecked") public static void main(String[] args) { CommandLine cl = parse(args);/*from w w w . j av a 2 s.com*/ DcmQR dcmqr = new DcmQR(cl.hasOption("device") ? cl.getOptionValue("device") : "DCMQR"); final List<String> argList = cl.getArgList(); String remoteAE = argList.get(0); String[] calledAETAddress = split(remoteAE, '@'); dcmqr.setCalledAET(calledAETAddress[0], cl.hasOption("reuseassoc")); if (calledAETAddress[1] == null) { dcmqr.setRemoteHost("127.0.0.1"); dcmqr.setRemotePort(104); } else { String[] hostPort = split(calledAETAddress[1], ':'); dcmqr.setRemoteHost(hostPort[0]); dcmqr.setRemotePort(toPort(hostPort[1])); } if (cl.hasOption("L")) { String localAE = cl.getOptionValue("L"); String[] localPort = split(localAE, ':'); if (localPort[1] != null) { dcmqr.setLocalPort(toPort(localPort[1])); } String[] callingAETHost = split(localPort[0], '@'); dcmqr.setCalling(callingAETHost[0]); if (callingAETHost[1] != null) { dcmqr.setLocalHost(callingAETHost[1]); } } if (cl.hasOption("username")) { String username = cl.getOptionValue("username"); UserIdentity userId; if (cl.hasOption("passcode")) { String passcode = cl.getOptionValue("passcode"); userId = new UserIdentity.UsernamePasscode(username, passcode.toCharArray()); } else { userId = new UserIdentity.Username(username); } userId.setPositiveResponseRequested(cl.hasOption("uidnegrsp")); dcmqr.setUserIdentity(userId); } if (cl.hasOption("connectTO")) dcmqr.setConnectTimeout(parseInt(cl.getOptionValue("connectTO"), "illegal argument of option -connectTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("reaper")) dcmqr.setAssociationReaperPeriod(parseInt(cl.getOptionValue("reaper"), "illegal argument of option -reaper", 1, Integer.MAX_VALUE)); if (cl.hasOption("cfindrspTO")) dcmqr.setDimseRspTimeout(parseInt(cl.getOptionValue("cfindrspTO"), "illegal argument of option -cfindrspTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("cmoverspTO")) dcmqr.setRetrieveRspTimeout(parseInt(cl.getOptionValue("cmoverspTO"), "illegal argument of option -cmoverspTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("cgetrspTO")) dcmqr.setRetrieveRspTimeout(parseInt(cl.getOptionValue("cgetrspTO"), "illegal argument of option -cgetrspTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("acceptTO")) dcmqr.setAcceptTimeout(parseInt(cl.getOptionValue("acceptTO"), "illegal argument of option -acceptTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("releaseTO")) dcmqr.setReleaseTimeout(parseInt(cl.getOptionValue("releaseTO"), "illegal argument of option -releaseTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("soclosedelay")) dcmqr.setSocketCloseDelay(parseInt(cl.getOptionValue("soclosedelay"), "illegal argument of option -soclosedelay", 1, 10000)); if (cl.hasOption("rcvpdulen")) dcmqr.setMaxPDULengthReceive( parseInt(cl.getOptionValue("rcvpdulen"), "illegal argument of option -rcvpdulen", 1, 10000) * KB); if (cl.hasOption("sndpdulen")) dcmqr.setMaxPDULengthSend( parseInt(cl.getOptionValue("sndpdulen"), "illegal argument of option -sndpdulen", 1, 10000) * KB); if (cl.hasOption("sosndbuf")) dcmqr.setSendBufferSize( parseInt(cl.getOptionValue("sosndbuf"), "illegal argument of option -sosndbuf", 1, 10000) * KB); if (cl.hasOption("sorcvbuf")) dcmqr.setReceiveBufferSize( parseInt(cl.getOptionValue("sorcvbuf"), "illegal argument of option -sorcvbuf", 1, 10000) * KB); if (cl.hasOption("filebuf")) dcmqr.setFileBufferSize( parseInt(cl.getOptionValue("filebuf"), "illegal argument of option -filebuf", 1, 10000) * KB); dcmqr.setPackPDV(!cl.hasOption("pdv1")); dcmqr.setTcpNoDelay(!cl.hasOption("tcpdelay")); dcmqr.setMaxOpsInvoked(cl.hasOption("async") ? parseInt(cl.getOptionValue("async"), "illegal argument of option -async", 0, 0xffff) : 1); dcmqr.setMaxOpsPerformed(cl.hasOption("cstoreasync") ? parseInt(cl.getOptionValue("cstoreasync"), "illegal argument of option -cstoreasync", 0, 0xffff) : 0); if (cl.hasOption("C")) dcmqr.setCancelAfter( parseInt(cl.getOptionValue("C"), "illegal argument of option -C", 1, Integer.MAX_VALUE)); if (cl.hasOption("lowprior")) dcmqr.setPriority(CommandUtils.LOW); if (cl.hasOption("highprior")) dcmqr.setPriority(CommandUtils.HIGH); if (cl.hasOption("cstore")) { String[] storeTCs = cl.getOptionValues("cstore"); for (String storeTC : storeTCs) { String cuid; String[] tsuids; int colon = storeTC.indexOf(':'); if (colon == -1) { cuid = storeTC; tsuids = DEF_TS; } else { cuid = storeTC.substring(0, colon); String ts = storeTC.substring(colon + 1); try { tsuids = TS.valueOf(ts).uids; } catch (IllegalArgumentException e) { tsuids = ts.split(","); } } try { cuid = CUID.valueOf(cuid).uid; } catch (IllegalArgumentException e) { // assume cuid already contains UID } dcmqr.addStoreTransferCapability(cuid, tsuids); } if (cl.hasOption("cstoredest")) dcmqr.setStoreDestination(cl.getOptionValue("cstoredest")); } dcmqr.setCFind(!cl.hasOption("nocfind")); dcmqr.setCGet(cl.hasOption("cget")); if (cl.hasOption("cmove")) dcmqr.setMoveDest(cl.getOptionValue("cmove")); if (cl.hasOption("evalRetrieveAET")) dcmqr.setEvalRetrieveAET(true); dcmqr.setQueryLevel(cl.hasOption("P") ? QueryRetrieveLevel.PATIENT : cl.hasOption("S") ? QueryRetrieveLevel.SERIES : cl.hasOption("I") ? QueryRetrieveLevel.IMAGE : QueryRetrieveLevel.STUDY); if (cl.hasOption("noextneg")) dcmqr.setNoExtNegotiation(true); if (cl.hasOption("rel")) dcmqr.setRelationQR(true); if (cl.hasOption("datetime")) dcmqr.setDateTimeMatching(true); if (cl.hasOption("fuzzy")) dcmqr.setFuzzySemanticPersonNameMatching(true); if (!cl.hasOption("P")) { if (cl.hasOption("retall")) dcmqr.addPrivate(UID.PrivateStudyRootQueryRetrieveInformationModelFIND); if (cl.hasOption("blocked")) dcmqr.addPrivate(UID.PrivateBlockedStudyRootQueryRetrieveInformationModelFIND); if (cl.hasOption("vmf")) dcmqr.addPrivate(UID.PrivateVirtualMultiframeStudyRootQueryRetrieveInformationModelFIND); } if (cl.hasOption("cfind")) { String[] cuids = cl.getOptionValues("cfind"); for (int i = 0; i < cuids.length; i++) dcmqr.addPrivate(cuids[i]); } if (!cl.hasOption("nodefret")) dcmqr.addDefReturnKeys(); if (cl.hasOption("r")) { String[] returnKeys = cl.getOptionValues("r"); for (int i = 0; i < returnKeys.length; i++) dcmqr.addReturnKey(Tag.toTagPath(returnKeys[i])); } if (cl.hasOption("q")) { String[] matchingKeys = cl.getOptionValues("q"); for (int i = 1; i < matchingKeys.length; i++, i++) dcmqr.addMatchingKey(Tag.toTagPath(matchingKeys[i - 1]), matchingKeys[i]); } dcmqr.configureTransferCapability(cl.hasOption("ivrle")); int repeat = cl.hasOption("repeat") ? parseInt(cl.getOptionValue("repeat"), "illegal argument of option -repeat", 1, Integer.MAX_VALUE) : 0; int interval = cl.hasOption("repeatdelay") ? parseInt(cl.getOptionValue("repeatdelay"), "illegal argument of option -repeatdelay", 1, Integer.MAX_VALUE) : 0; boolean closeAssoc = cl.hasOption("closeassoc"); if (cl.hasOption("tls")) { String cipher = cl.getOptionValue("tls"); if ("NULL".equalsIgnoreCase(cipher)) { dcmqr.setTlsWithoutEncyrption(); } else if ("3DES".equalsIgnoreCase(cipher)) { dcmqr.setTls3DES_EDE_CBC(); } else if ("AES".equalsIgnoreCase(cipher)) { dcmqr.setTlsAES_128_CBC(); } else { exit("Invalid parameter for option -tls: " + cipher); } if (cl.hasOption("tls1")) { dcmqr.setTlsProtocol(TLS1); } else if (cl.hasOption("ssl3")) { dcmqr.setTlsProtocol(SSL3); } else if (cl.hasOption("no_tls1")) { dcmqr.setTlsProtocol(NO_TLS1); } else if (cl.hasOption("no_ssl3")) { dcmqr.setTlsProtocol(NO_SSL3); } else if (cl.hasOption("no_ssl2")) { dcmqr.setTlsProtocol(NO_SSL2); } dcmqr.setTlsNeedClientAuth(!cl.hasOption("noclientauth")); if (cl.hasOption("keystore")) { dcmqr.setKeyStoreURL(cl.getOptionValue("keystore")); } if (cl.hasOption("keystorepw")) { dcmqr.setKeyStorePassword(cl.getOptionValue("keystorepw")); } if (cl.hasOption("keypw")) { dcmqr.setKeyPassword(cl.getOptionValue("keypw")); } if (cl.hasOption("truststore")) { dcmqr.setTrustStoreURL(cl.getOptionValue("truststore")); } if (cl.hasOption("truststorepw")) { dcmqr.setTrustStorePassword(cl.getOptionValue("truststorepw")); } long t1 = System.currentTimeMillis(); try { dcmqr.initTLS(); } catch (Exception e) { System.err.println("ERROR: Failed to initialize TLS context:" + e.getMessage()); System.exit(2); } long t2 = System.currentTimeMillis(); LOG.info("Initialize TLS context in {} s", Float.valueOf((t2 - t1) / 1000f)); } try { dcmqr.start(); } catch (Exception e) { System.err.println( "ERROR: Failed to start server for receiving " + "requested objects:" + e.getMessage()); System.exit(2); } try { long t1 = System.currentTimeMillis(); try { dcmqr.open(); } catch (Exception e) { LOG.error("Failed to establish association:", e); System.exit(2); } long t2 = System.currentTimeMillis(); LOG.info("Connected to {} in {} s", remoteAE, Float.valueOf((t2 - t1) / 1000f)); for (;;) { List<DicomObject> result; if (dcmqr.isCFind()) { result = dcmqr.query(); long t3 = System.currentTimeMillis(); LOG.info("Received {} matching entries in {} s", Integer.valueOf(result.size()), Float.valueOf((t3 - t2) / 1000f)); t2 = t3; } else { result = Collections.singletonList(dcmqr.getKeys()); } if (dcmqr.isCMove() || dcmqr.isCGet()) { if (dcmqr.isCMove()) dcmqr.move(result); else dcmqr.get(result); long t4 = System.currentTimeMillis(); LOG.info("Retrieved {} objects (warning: {}, failed: {}) in {}s", new Object[] { Integer.valueOf(dcmqr.getTotalRetrieved()), Integer.valueOf(dcmqr.getWarning()), Integer.valueOf(dcmqr.getFailed()), Float.valueOf((t4 - t2) / 1000f) }); } if (repeat == 0 || closeAssoc) { try { dcmqr.close(); } catch (InterruptedException e) { LOG.error(e.getMessage(), e); } LOG.info("Released connection to {}", remoteAE); } if (repeat-- == 0) break; Thread.sleep(interval); long t4 = System.currentTimeMillis(); dcmqr.open(); t2 = System.currentTimeMillis(); LOG.info("Reconnect or reuse connection to {} in {} s", remoteAE, Float.valueOf((t2 - t4) / 1000f)); } } catch (IOException e) { LOG.error(e.getMessage(), e); } catch (InterruptedException e) { LOG.error(e.getMessage(), e); } catch (ConfigurationException e) { LOG.error(e.getMessage(), e); } finally { dcmqr.stop(); } }
From source file:main.DOORS_Service.java
/** * Login to the DWA server and perform some OSLC actions * @param args//w ww .jav a2 s. co m * @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:GoogleImages.java
public static void main(String[] args) throws InterruptedException { String searchTerm = "s woman"; // term to search for (use spaces to separate terms) int offset = 40; // we can only 20 results at a time - use this to offset and get more! String fileSize = "50mp"; // specify file size in mexapixels (S/M/L not figured out yet) String source = null; // string to save raw HTML source code // format spaces in URL to avoid problems searchTerm = searchTerm.replaceAll(" ", "%20"); // get Google image search HTML source code; mostly built from PhyloWidget example: // http://code.google.com/p/phylowidget/source/browse/trunk/PhyloWidget/src/org/phylowidget/render/images/ImageSearcher.java int offset2 = 0; Set urlsss = new HashSet<String>(); while (offset2 < 600) { try {// w w w .j av a 2s.c o m URL query = new URL("https://www.google.ru/search?start=" + offset2 + "&q=angry+woman&newwindow=1&client=opera&hs=bPE&source=lnms&tbm=isch&sa=X&ved=0ahUKEwiAgcKozIfNAhWoHJoKHSb_AUoQ_AUIBygB&biw=1517&bih=731&dpr=0.9#imgrc=G_1tH3YOPcc8KM%3A"); HttpURLConnection urlc = (HttpURLConnection) query.openConnection(); // start connection... urlc.setInstanceFollowRedirects(true); urlc.setRequestProperty("User-Agent", ""); urlc.connect(); BufferedReader in = new BufferedReader(new InputStreamReader(urlc.getInputStream())); // stream in HTTP source to file StringBuffer response = new StringBuffer(); char[] buffer = new char[1024]; while (true) { int charsRead = in.read(buffer); if (charsRead == -1) { break; } response.append(buffer, 0, charsRead); } in.close(); // close input stream (also closes network connection) source = response.toString(); } // any problems connecting? let us know catch (Exception e) { e.printStackTrace(); } // print full source code (for debugging) // println(source); // extract image URLs only, starting with 'imgurl' if (source != null) { // System.out.println(source); int c = StringUtils.countMatches(source, "http://www.vmir.su"); System.out.println(c); int index = source.indexOf("src="); System.out.println(source.subSequence(index, index + 200)); while (index >= 0) { System.out.println(index); index = source.indexOf("src=", index + 1); if (index == -1) { break; } String rr = source.substring(index, index + 200 > source.length() ? source.length() : index + 200); if (rr.contains("\"")) { rr = rr.substring(5, rr.indexOf("\"", 5)); } System.out.println(rr); urlsss.add(rr); } } offset2 += 20; Thread.sleep(1000); System.out.println("off set = " + offset2); } System.out.println(urlsss); urlsss.forEach(new Consumer<String>() { public void accept(String s) { try { saveImage(s, "C:\\Users\\Java\\Desktop\\ang\\" + UUID.randomUUID().toString() + ".jpg"); } catch (IOException ex) { Logger.getLogger(GoogleImages.class.getName()).log(Level.SEVERE, null, ex); } } }); // String[][] m = matchAll(source, "img height=\"\\d+\" src=\"([^\"]+)\""); // older regex, no longer working but left for posterity // built partially from: http://www.mkyong.com/regular-expressions/how-to-validate-image-file-extension-with-regular-expression // String[][] m = matchAll(source, "imgurl=(.*?\\.(?i)(jpg|jpeg|png|gif|bmp|tif|tiff))"); // (?i) means case-insensitive // for (int i = 0; i < m.length; i++) { // iterate all results of the match // println(i + ":\t" + m[i][1]); // print (or store them)** // } }
From source file:de.citec.csra.elancsv.parser.SimpleParser.java
public static void main(String[] args) throws IOException, ParseException { Options opts = new Options(); opts.addOption("file", true, "Tab-separated ELAN export file to load."); opts.addOption("tier", true, "Tier to analyze. Optional: Append ::num to interpret annotations numerically."); opts.addOption("format", true, "How to read information from the file name. %V -> participant, %A -> annoatator, %C -> condition, e.g. \"%V - %A\""); opts.addOption("help", false, "Print this help and exit"); CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(opts, args); if (cmd.hasOption("help")) { helpExit(opts, "where OPTION includes:"); }//from w w w .j av a 2s . c om String infile = cmd.getOptionValue("file"); if (infile == null) { helpExit(opts, "Error: no file given."); } String format = cmd.getOptionValue("format"); if (format == null) { helpExit(opts, "Error: no format given."); } String tier = cmd.getOptionValue("tier"); if (tier == null) { helpExit(opts, "Error: no tier given."); } // TODO count values in annotations (e.g. search all robot occurrences) String[] tn = tier.split("::"); boolean numeric = false; if (tn.length == 2 && tn[1].equals("num")) { numeric = true; tier = tn[0]; } format = "^" + format + "$"; format = format.replaceFirst("%V", "(?<V>.*?)"); format = format.replaceFirst("%A", "(?<A>.*?)"); format = format.replaceFirst("%C", "(?<C>.*?)"); Pattern pa = Pattern.compile(format); Map<String, Participant> participants = new HashMap<>(); BufferedReader br = new BufferedReader(new FileReader(infile)); String line; int lineno = 0; while ((line = br.readLine()) != null) { String[] parts = line.split("\t"); lineno++; if (parts.length < 5) { System.err.println("WARNING: line '" + lineno + "' too short '" + line + "'"); continue; } Annotation a = new Annotation(Long.valueOf(parts[ElanFormat.START.field]), Long.valueOf(parts[ElanFormat.STOP.field]), Long.valueOf(parts[ElanFormat.DURATION.field]), parts[ElanFormat.VALUE.field]); String tname = parts[ElanFormat.TIER.field]; String file = parts[ElanFormat.FILE.field].replaceAll(".eaf", ""); Matcher m = pa.matcher(file); String vp = file; String condition = "?"; String annotator = "?"; String participantID = vp; if (m.find()) { vp = m.group("V"); if (format.indexOf("<A>") > 0) { annotator = m.group("A"); } if (format.indexOf("<C>") > 0) { condition = m.group("C"); } } participantID = vp + ";" + annotator; if (!participants.containsKey(participantID)) { participants.put(participantID, new Participant(vp, condition, annotator)); } Participant p = participants.get(participantID); if (!p.tiers.containsKey(tname)) { p.tiers.put(tname, new Tier(tname)); } p.tiers.get(tname).annotations.add(a); } Map<String, Map<String, Number>> values = new HashMap<>(); Set<String> rownames = new HashSet<>(); String allCountKey = "c: all values"; String allDurationKey = "d: all values"; String allMeanKey = "m: all values"; for (Map.Entry<String, Participant> e : participants.entrySet()) { // System.out.println(e); Tier t = e.getValue().tiers.get(tier); String participantID = e.getKey(); if (!values.containsKey(participantID)) { values.put(participantID, new HashMap<String, Number>()); } Map<String, Number> row = values.get(participantID); //participant id if (t != null) { row.put(allCountKey, 0l); row.put(allDurationKey, 0l); row.put(allMeanKey, 0l); for (Annotation a : t.annotations) { long countAll = (long) row.get(allCountKey) + 1; long durationAll = (long) row.get(allDurationKey) + a.duration; long meanAll = durationAll / countAll; row.put(allCountKey, countAll); row.put(allDurationKey, durationAll); row.put(allMeanKey, meanAll); if (!numeric) { String countKey = "c: " + a.value; String durationKey = "d: " + a.value; String meanKey = "m: " + a.value; if (!row.containsKey(countKey)) { row.put(countKey, 0l); } if (!row.containsKey(durationKey)) { row.put(durationKey, 0l); } if (!row.containsKey(meanKey)) { row.put(meanKey, 0d); } long count = (long) row.get(countKey) + 1; long duration = (long) row.get(durationKey) + a.duration; double mean = duration * 1.0 / count; row.put(countKey, count); row.put(durationKey, duration); row.put(meanKey, mean); rownames.add(countKey); rownames.add(durationKey); rownames.add(meanKey); } else { String countKey = "c: " + t.name; String sumKey = "s: " + t.name; String meanKey = "m: " + t.name; if (!row.containsKey(countKey)) { row.put(countKey, 0l); } if (!row.containsKey(sumKey)) { row.put(sumKey, 0d); } if (!row.containsKey(meanKey)) { row.put(meanKey, 0d); } double d = 0; try { d = Double.valueOf(a.value); } catch (NumberFormatException ex) { } long count = (long) row.get(countKey) + 1; double sum = (double) row.get(sumKey) + d; double mean = sum / count; row.put(countKey, count); row.put(sumKey, sum); row.put(meanKey, mean); rownames.add(countKey); rownames.add(sumKey); rownames.add(meanKey); } } } } ArrayList<String> list = new ArrayList(rownames); Collections.sort(list); StringBuilder header = new StringBuilder("ID;Annotator;"); header.append(allCountKey); header.append(";"); header.append(allDurationKey); header.append(";"); header.append(allMeanKey); header.append(";"); for (String l : list) { header.append(l); header.append(";"); } System.out.println(header); for (Map.Entry<String, Map<String, Number>> e : values.entrySet()) { StringBuilder row = new StringBuilder(e.getKey()); row.append(";"); if (e.getValue().containsKey(allCountKey)) { row.append(e.getValue().get(allCountKey)); } else { row.append("0"); } row.append(";"); if (e.getValue().containsKey(allDurationKey)) { row.append(e.getValue().get(allDurationKey)); } else { row.append("0"); } row.append(";"); if (e.getValue().containsKey(allMeanKey)) { row.append(e.getValue().get(allMeanKey)); } else { row.append("0"); } row.append(";"); for (String l : list) { if (e.getValue().containsKey(l)) { row.append(e.getValue().get(l)); } else { row.append("0"); } row.append(";"); } System.out.println(row); } }
From source file:tuit.java
@SuppressWarnings("ConstantConditions") public static void main(String[] args) { System.out.println(licence);/*w ww. j a v a 2 s. c om*/ //Declare variables File inputFile; File outputFile; File tmpDir; File blastnExecutable; File properties; File blastOutputFile = null; // TUITPropertiesLoader tuitPropertiesLoader; TUITProperties tuitProperties; // String[] parameters = null; // Connection connection = null; MySQL_Connector mySQL_connector; // Map<Ranks, TUITCutoffSet> cutoffMap; // BLASTIdentifier blastIdentifier = null; // RamDb ramDb = null; CommandLineParser parser = new GnuParser(); Options options = new Options(); options.addOption(tuit.IN, "input<file>", true, "Input file (currently fasta-formatted only)"); options.addOption(tuit.OUT, "output<file>", true, "Output file (in " + tuit.TUIT_EXT + " format)"); options.addOption(tuit.P, "prop<file>", true, "Properties file (XML formatted)"); options.addOption(tuit.V, "verbose", false, "Enable verbose output"); options.addOption(tuit.B, "blast_output<file>", true, "Perform on a pre-BLASTed output"); options.addOption(tuit.DEPLOY, "deploy", false, "Deploy the taxonomic databases"); options.addOption(tuit.UPDATE, "update", false, "Update the taxonomic databases"); options.addOption(tuit.USE_DB, "usedb", false, "Use RDBMS instead of RAM-based taxonomy"); Option option = new Option(tuit.REDUCE, "reduce", true, "Pack identical (100% similar sequences) records in the given sample file"); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); option = new Option(tuit.COMBINE, "combine", true, "Combine a set of given reduction files into an HMP Tree-compatible taxonomy"); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); options.addOption(tuit.NORMALIZE, "normalize", false, "If used in combination with -combine ensures that the values are normalized by the root value"); HelpFormatter formatter = new HelpFormatter(); try { //Get TUIT directory final File tuitDir = new File( new File(tuit.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath()) .getParent()); final File ramDbFile = new File(tuitDir, tuit.RAM_DB); //Setup logger Log.getInstance().setLogName("tuit.log"); //Read command line final CommandLine commandLine = parser.parse(options, args, true); //Check if the REDUCE option is on if (commandLine.hasOption(tuit.REDUCE)) { final String[] fileList = commandLine.getOptionValues(tuit.REDUCE); for (String s : fileList) { final Path path = Paths.get(s); Log.getInstance().log(Level.INFO, "Processing " + path.toString() + "..."); final NucleotideFastaSequenceReductor nucleotideFastaSequenceReductor = NucleotideFastaSequenceReductor .fromPath(path); ReductorFileOperator.save(nucleotideFastaSequenceReductor, path.resolveSibling(path.getFileName().toString() + ".rdc")); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Check if COMBINE is on if (commandLine.hasOption(tuit.COMBINE)) { final boolean normalize = commandLine.hasOption(tuit.NORMALIZE); final String[] fileList = commandLine.getOptionValues(tuit.COMBINE); //TODO: implement a test for format here final List<TreeFormatter.TreeFormatterFormat.HMPTreesOutput> hmpTreesOutputs = new ArrayList<>(); final TreeFormatter treeFormatter = TreeFormatter .newInstance(new TreeFormatter.TuitLineTreeFormatterFormat()); for (String s : fileList) { final Path path = Paths.get(s); Log.getInstance().log(Level.INFO, "Merging " + path.toString() + "..."); treeFormatter.loadFromPath(path); final TreeFormatter.TreeFormatterFormat.HMPTreesOutput output = TreeFormatter.TreeFormatterFormat.HMPTreesOutput .newInstance(treeFormatter.toHMPTree(normalize), s.substring(0, s.indexOf("."))); hmpTreesOutputs.add(output); treeFormatter.erase(); } final Path destination; if (commandLine.hasOption(OUT)) { destination = Paths.get(commandLine.getOptionValue(tuit.OUT)); } else { destination = Paths.get("merge.tcf"); } CombinatorFileOperator.save(hmpTreesOutputs, treeFormatter, destination); Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } if (!commandLine.hasOption(tuit.P)) { throw new ParseException("No properties file option found, exiting."); } else { properties = new File(commandLine.getOptionValue(tuit.P)); } //Load properties tuitPropertiesLoader = TUITPropertiesLoader.newInstanceFromFile(properties); tuitProperties = tuitPropertiesLoader.getTuitProperties(); //Create tmp directory and blastn executable tmpDir = new File(tuitProperties.getTMPDir().getPath()); blastnExecutable = new File(tuitProperties.getBLASTNPath().getPath()); //Check for deploy if (commandLine.hasOption(tuit.DEPLOY)) { if (commandLine.hasOption(tuit.USE_DB)) { NCBITablesDeployer.fastDeployNCBIDatabasesFromNCBI(connection, tmpDir); } else { NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Check for update if (commandLine.hasOption(tuit.UPDATE)) { if (commandLine.hasOption(tuit.USE_DB)) { NCBITablesDeployer.updateDatabasesFromNCBI(connection, tmpDir); } else { //No need to specify a different way to update the database other than just deploy in case of the RAM database NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Connect to the database if (commandLine.hasOption(tuit.USE_DB)) { mySQL_connector = MySQL_Connector.newDefaultInstance( "jdbc:mysql://" + tuitProperties.getDBConnection().getUrl().trim() + "/", tuitProperties.getDBConnection().getLogin().trim(), tuitProperties.getDBConnection().getPassword().trim()); mySQL_connector.connectToDatabase(); connection = mySQL_connector.getConnection(); } else { //Probe for ram database if (ramDbFile.exists() && ramDbFile.canRead()) { Log.getInstance().log(Level.INFO, "Loading RAM taxonomic map..."); try { ramDb = RamDb.loadSelfFromFile(ramDbFile); } catch (IOException ie) { if (ie instanceof java.io.InvalidClassException) throw new IOException("The RAM-based taxonomic database needs to be updated."); } } else { Log.getInstance().log(Level.SEVERE, "The RAM database either has not been deployed, or is not accessible." + "Please use the --deploy option and check permissions on the TUIT directory. " + "If you were looking to use the RDBMS as a taxonomic reference, plese use the -usedb option."); return; } } if (commandLine.hasOption(tuit.B)) { blastOutputFile = new File(commandLine.getOptionValue(tuit.B)); if (!blastOutputFile.exists() || !blastOutputFile.canRead()) { throw new Exception("BLAST output file either does not exist, or is not readable."); } else if (blastOutputFile.isDirectory()) { throw new Exception("BLAST output file points to a directory."); } } //Check vital parameters if (!commandLine.hasOption(tuit.IN)) { throw new ParseException("No input file option found, exiting."); } else { inputFile = new File(commandLine.getOptionValue(tuit.IN)); Log.getInstance().setLogName(inputFile.getName().split("\\.")[0] + ".tuit.log"); } //Correct the output file option if needed if (!commandLine.hasOption(tuit.OUT)) { outputFile = new File((inputFile.getPath()).split("\\.")[0] + tuit.TUIT_EXT); } else { outputFile = new File(commandLine.getOptionValue(tuit.OUT)); } //Adjust the output level if (commandLine.hasOption(tuit.V)) { Log.getInstance().setLevel(Level.FINE); Log.getInstance().log(Level.INFO, "Using verbose output for the log"); } else { Log.getInstance().setLevel(Level.INFO); } //Try all files if (inputFile != null) { if (!inputFile.exists() || !inputFile.canRead()) { throw new Exception("Input file either does not exist, or is not readable."); } else if (inputFile.isDirectory()) { throw new Exception("Input file points to a directory."); } } if (!properties.exists() || !properties.canRead()) { throw new Exception("Properties file either does not exist, or is not readable."); } else if (properties.isDirectory()) { throw new Exception("Properties file points to a directory."); } //Create blast parameters final StringBuilder stringBuilder = new StringBuilder(); for (Database database : tuitProperties.getBLASTNParameters().getDatabase()) { stringBuilder.append(database.getUse()); stringBuilder.append(" ");//Gonna insert an extra space for the last database } String remote; String entrez_query; if (tuitProperties.getBLASTNParameters().getRemote().getDelegate().equals("yes")) { remote = "-remote"; entrez_query = "-entrez_query"; parameters = new String[] { "-db", stringBuilder.toString(), remote, entrez_query, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue() }; } else { if (!commandLine.hasOption(tuit.B)) { if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .startsWith("NOT") || tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .startsWith("ALL")) { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), "-negative_gilist", TUITFileOperatorHelper.restrictToEntrez(tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue() .toUpperCase().replace("NOT", "OR")) .getAbsolutePath(), "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } else if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .equals("")) { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } else { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), /*"-gilist", TUITFileOperatorHelper.restrictToEntrez( tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue()).getAbsolutePath(),*/ //TODO remove comment!!!!! "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } } } //Prepare a cutoff Map if (tuitProperties.getSpecificationParameters() != null && tuitProperties.getSpecificationParameters().size() > 0) { cutoffMap = new HashMap<Ranks, TUITCutoffSet>(tuitProperties.getSpecificationParameters().size()); for (SpecificationParameters specificationParameters : tuitProperties .getSpecificationParameters()) { cutoffMap.put(Ranks.valueOf(specificationParameters.getCutoffSet().getRank()), TUITCutoffSet.newDefaultInstance( Double.parseDouble( specificationParameters.getCutoffSet().getPIdentCutoff().getValue()), Double.parseDouble(specificationParameters.getCutoffSet() .getQueryCoverageCutoff().getValue()), Double.parseDouble( specificationParameters.getCutoffSet().getAlpha().getValue()))); } } else { cutoffMap = new HashMap<Ranks, TUITCutoffSet>(); } final TUITFileOperatorHelper.OutputFormat format; if (tuitProperties.getBLASTNParameters().getOutputFormat().getFormat().equals("rdp")) { format = TUITFileOperatorHelper.OutputFormat.RDP_FIXRANK; } else { format = TUITFileOperatorHelper.OutputFormat.TUIT; } try (TUITFileOperator<NucleotideFasta> nucleotideFastaTUITFileOperator = NucleotideFastaTUITFileOperator .newInstance(format, cutoffMap);) { nucleotideFastaTUITFileOperator.setInputFile(inputFile); nucleotideFastaTUITFileOperator.setOutputFile(outputFile); final String cleanupString = tuitProperties.getBLASTNParameters().getKeepBLASTOuts().getKeep(); final boolean cleanup; if (cleanupString.equals("no")) { Log.getInstance().log(Level.INFO, "Temporary BLAST files will be deleted."); cleanup = true; } else { Log.getInstance().log(Level.INFO, "Temporary BLAST files will be kept."); cleanup = false; } //Create blast identifier ExecutorService executorService = Executors.newSingleThreadExecutor(); if (commandLine.hasOption(tuit.USE_DB)) { if (blastOutputFile == null) { blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromFileOperator(tmpDir, blastnExecutable, parameters, nucleotideFastaTUITFileOperator, connection, cutoffMap, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup); } else { try { blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromBLASTOutput( nucleotideFastaTUITFileOperator, connection, cutoffMap, blastOutputFile, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup); } catch (JAXBException e) { Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName() + ", please check input. The file must be XML formatted."); } catch (Exception e) { e.printStackTrace(); } } } else { if (blastOutputFile == null) { blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromFileOperator(tmpDir, blastnExecutable, parameters, nucleotideFastaTUITFileOperator, cutoffMap, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup, ramDb); } else { try { blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromBLASTOutput( nucleotideFastaTUITFileOperator, cutoffMap, blastOutputFile, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup, ramDb); } catch (JAXBException e) { Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName() + ", please check input. The file must be XML formatted."); } catch (Exception e) { e.printStackTrace(); } } } Future<?> runnableFuture = executorService.submit(blastIdentifier); runnableFuture.get(); executorService.shutdown(); } } catch (ParseException pe) { Log.getInstance().log(Level.SEVERE, (pe.getMessage())); formatter.printHelp("tuit", options); } catch (SAXException saxe) { Log.getInstance().log(Level.SEVERE, saxe.getMessage()); } catch (FileNotFoundException fnfe) { Log.getInstance().log(Level.SEVERE, fnfe.getMessage()); } catch (TUITPropertyBadFormatException tpbfe) { Log.getInstance().log(Level.SEVERE, tpbfe.getMessage()); } catch (ClassCastException cce) { Log.getInstance().log(Level.SEVERE, cce.getMessage()); } catch (JAXBException jaxbee) { Log.getInstance().log(Level.SEVERE, "The properties file is not well formatted. Please ensure that the XML is consistent with the io.properties.dtd schema."); } catch (ClassNotFoundException cnfe) { //Probably won't happen unless the library deleted from the .jar Log.getInstance().log(Level.SEVERE, cnfe.getMessage()); //cnfe.printStackTrace(); } catch (SQLException sqle) { Log.getInstance().log(Level.SEVERE, "A database communication error occurred with the following message:\n" + sqle.getMessage()); //sqle.printStackTrace(); if (sqle.getMessage().contains("Access denied for user")) { Log.getInstance().log(Level.SEVERE, "Please use standard database login: " + NCBITablesDeployer.login + " and password: " + NCBITablesDeployer.password); } } catch (Exception e) { Log.getInstance().log(Level.SEVERE, e.getMessage()); e.printStackTrace(); } finally { if (connection != null) { try { connection.close(); } catch (SQLException sqle) { Log.getInstance().log(Level.SEVERE, "Problem closing the database connection: " + sqle); } } Log.getInstance().log(Level.FINE, "Task done, exiting..."); } }