List of usage examples for java.io File exists
public boolean exists()
From source file:de.prozesskraft.pkraft.Manager.java
public static void main(String[] args) throws org.apache.commons.cli.ParseException, CloneNotSupportedException { // try/* w w w . j a va 2s . co m*/ // { // if (args.length != 1) // { // System.out.println("Please specify Inputfile and Outputfile (prozessinstanz.lri)"); // } // // } // catch (ArrayIndexOutOfBoundsException e) // { // System.out.println("***ArrayIndexOutOfBoundsException: Please specify procesdefinition.lrd and processinstance.lri\n" + e.toString()); // } /*---------------------------- get options from ini-file ----------------------------*/ File inifile = new java.io.File( WhereAmI.getInstallDirectoryAbsolutePath(Manager.class) + "/" + "../etc/pkraft-manager.ini"); if (inifile.exists()) { try { ini = new Ini(inifile); } catch (InvalidFileFormatException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } catch (IOException e1) { // TODO Auto-generated catch block e1.printStackTrace(); } } else { System.err.println("ini file does not exist: " + inifile.getAbsolutePath()); System.exit(1); exit = true; } /*---------------------------- create boolean options ----------------------------*/ Option help = new Option("help", "print this message"); Option v = new Option("v", "prints version and build-date"); /*---------------------------- create argument options ----------------------------*/ Option instance = OptionBuilder.withArgName("instance").hasArg() .withDescription("[mandatory] process instance file") // .isRequired() .create("instance"); Option stop = OptionBuilder.withArgName("stop") // .hasArg() .withDescription("[optional] stops a running manager for given instance") // .isRequired() .create("stop"); Option kill = OptionBuilder.withArgName("kill") // .hasArg() .withDescription("[optional] kills all applications that have been started by steps") // .isRequired() .create("kill"); /*---------------------------- create options object ----------------------------*/ Options options = new Options(); options.addOption(help); options.addOption(v); options.addOption(instance); options.addOption(stop); options.addOption(kill); /*---------------------------- create the parser ----------------------------*/ CommandLineParser parser = new GnuParser(); try { // parse the command line arguments line = parser.parse(options, args); } // catch ( ParseException exp ) catch (Exception exp) { // oops, something went wrong System.err.println("Parsing failed. Reason: " + exp.getMessage()); exiter(); } /*---------------------------- usage/help ----------------------------*/ if (line.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("manager", options); exit = true; System.exit(0); } else if (line.hasOption("v")) { System.out.println("author: info@prozesskraft.de"); System.out.println("version: [% version %]"); System.out.println("date: [% date %]"); exit = true; System.exit(0); } else if (!(line.hasOption("instance"))) { exiter(); } /*---------------------------- die lizenz ueberpruefen und ggf abbrechen ----------------------------*/ // check for valid license ArrayList<String> allPortAtHost = new ArrayList<String>(); allPortAtHost.add(ini.get("license-server", "license-server-1")); allPortAtHost.add(ini.get("license-server", "license-server-2")); allPortAtHost.add(ini.get("license-server", "license-server-3")); MyLicense lic = new MyLicense(allPortAtHost, "1", "user-edition", "0.1"); // lizenz-logging ausgeben for (String actLine : (ArrayList<String>) lic.getLog()) { System.err.println(actLine); } // abbruch, wenn lizenz nicht valide if (!lic.isValid()) { exit = true; System.exit(1); } /*---------------------------- business logic ----------------------------*/ Process actualProcess = null; try { Process p1 = new Process(); // die dauer des loops festlegen. Dies soll kein standardwert sein, da sonst bei vielen subprozessen die Prozessorlast stark oszilliert // zwischen 12 und 17 sekunden // Random rand = new Random(System.currentTimeMillis()); // int loop_period_seconds = rand.nextInt((17 - 12) + 1) + 12; // System.err.println("loop period is randomly set to: "+loop_period_seconds); fileBinary = new java.io.File(line.getOptionValue("instance")); String pathBinary = ""; if (fileBinary.exists()) { pathBinary = fileBinary.getAbsolutePath(); System.err.println("file does exist: " + pathBinary); } else { System.err.println("file does not exist: " + fileBinary.getAbsolutePath()); exiter(); } if (line.hasOption("stop") || line.hasOption("kill")) { p1.setInfilebinary(pathBinary); Process p2 = p1.readBinary(); p2.log("debug", "setting new manager-Id (0) to signal actual manager (" + p2.getManagerid() + ") that he is no longer in charge "); System.err.println("info: stopping instance"); System.err.println("debug: setting new manager-Id (0) to signal actual manager (" + p2.getManagerid() + ") that he is no longer in charge "); p2.setManagerid(0); p2.run = false; p2.setOutfilebinary(pathBinary); p2.writeBinary(); if (line.hasOption("kill")) { System.err.println("info: killing all steps of instance"); String returnStringOfKills = p2.kill(); System.err.println("info: killing returns: " + returnStringOfKills); } boolean pradar = (!(p2.isWrapper())); // pradar checkout if (pradar) { pradarAttend(p2.getRootdir() + "/process.pmb"); // pradarCheckout(p2.getId(), p2.getName(), "0"); } exit = true; System.exit(0); } startZyklischerThread(0); // prozessinstanz einlesen p1.setInfilebinary(pathBinary); managerid = p1.genManagerid(); Process p2; p2 = p1.readBinary(); // beim aufruf des programms wird erstmal die instanz occupiert p2.setManagerid(managerid); System.err.println("debug: manager " + managerid + ": occupying instance."); p2.log("info", "manager " + managerid + ": occupying instance."); p2.log("debug", "manager " + managerid + ": setting new manager-id to signal other running managers that they are not longer needed."); p2.log("debug", "manager " + managerid + ": setting binary file for input to: " + pathBinary); // System.out.println("setting binary file for input to: "+line.getOptionValue("instance")); p2.log("debug", "manager " + managerid + ": reading binary file: " + pathBinary); p2.setInfilebinary(pathBinary); p2.setOutfilebinary(pathBinary); p2.log("debug", "manager " + managerid + ": setting binary file for output: " + pathBinary); // instanz auf platte schreiben (um anderen managern zu signalisieren, dass sie nicht mehr gebraucht werden // System.out.println("setting manager-id to: "+managerid); p2.log("debug", "manager " + managerid + ": writing process to binary file to occupy instance."); // wenn es kein wrapper-prozess ist, dann soll die komunikation mit pradar vom manager uebernommen werden boolean pradar = (!(p2.isWrapper())); System.err.println("debug: setting instance to run"); p2.run = true; // pradar checkin if (pradar && p2.run && p2.touchInMillis == 0) { pradarAttend(p2.getRootdir() + "/process.pmb"); // p2.log("debug", "pradar-checkin id="+p2.getId()+", process="+p2.getName()+", processversion="+p2.getVersion()+", id2="+p2.getId2()+", parentid="+p2.getParentid()+", resource="+p2.getRootdir()+"/process.pmb"); // pradarCheckin(p2.getId(), p2.getName(), p2.getVersion(), p2.getId2(), p2.getParentid(), getPid(), p2.getRootdir()+"/process.pmb"); } System.err.println("debug: writing binary"); p2.writeBinary(); // process weiter schubsen pushProcessAsFarAsPossible(pathBinary, false); // try // { // // der thread soll so lange schlafen, wie die periode lang ist. die schlafdauer wird mit der anzahl multipliziert, wie oft das loadAverage zu hoch war (max 5) // int faktorForPeriod = Math.min(10, p2.counterLoadAverageTooHigh + 1); // // int secondsToSleep = loop_period_seconds * faktorForPeriod; // System.err.println("debug: sleeping for " + secondsToSleep + " seconds"); // // int millisecondsToSleep = secondsToSleep*1000; // System.err.println("debug: sleeping for " + millisecondsToSleep + " milliseconds"); // // Thread.sleep(millisecondsToSleep); // } // catch (InterruptedException e) // { // // TODO Auto-generated catch block // e.printStackTrace(); // // // ausgabe in das debugLogFile // exiterException(actualProcess.getOutfilebinary(), e); // } } catch (Exception e) { if (actualProcess != null) { actualProcess.log("fatal", e.getMessage() + "\n" + Arrays.toString(e.getStackTrace())); updateFile(actualProcess); e.printStackTrace(); // ausgabe in das debugLogFile exiterException(actualProcess.getOutfilebinary(), e); } exit = true; System.exit(10); } }
From source file:com.sforce.dataset.DatasetUtilMain.java
public static void main(String[] args) { printBanner();/* w w w. java 2 s.c o m*/ DatasetUtilParams params = new DatasetUtilParams(); if (args.length > 0) params.server = false; System.out.println(""); System.out.println("DatsetUtils called with {" + args.length + "} Params:"); for (int i = 0; i < args.length; i++) { if ((i & 1) == 0) { System.out.print("{" + args[i] + "}"); } else { if (i > 0 && args[i - 1].equalsIgnoreCase("--p")) System.out.println(":{*******}"); else System.out.println(":{" + args[i] + "}"); } if (i > 0 && args[i - 1].equalsIgnoreCase("--server")) { if (args[i] != null && args[i].trim().equalsIgnoreCase("false")) params.server = false; else if (args[i] != null && args[i].trim().equalsIgnoreCase("true")) params.server = true; } } System.out.println(""); if (!printlneula(params.server)) { System.out.println( "You do not have permission to use this software. Please delete it from this computer"); System.exit(-1); } String action = null; if (args.length >= 2) { for (int i = 1; i < args.length; i = i + 2) { if (args[i - 1].equalsIgnoreCase("--help") || args[i - 1].equalsIgnoreCase("-help") || args[i - 1].equalsIgnoreCase("help")) { printUsage(); } else if (args[i - 1].equalsIgnoreCase("--u")) { params.username = args[i]; } else if (args[i - 1].equalsIgnoreCase("--p")) { params.password = args[i]; } else if (args[i - 1].equalsIgnoreCase("--sessionId")) { params.sessionId = args[i]; } else if (args[i - 1].equalsIgnoreCase("--token")) { params.token = args[i]; } else if (args[i - 1].equalsIgnoreCase("--endpoint")) { params.endpoint = args[i]; } else if (args[i - 1].equalsIgnoreCase("--action")) { action = args[i]; } else if (args[i - 1].equalsIgnoreCase("--operation")) { if (args[i] != null) { if (args[i].equalsIgnoreCase("overwrite")) { params.Operation = args[i]; } else if (args[i].equalsIgnoreCase("upsert")) { params.Operation = args[i]; } else if (args[i].equalsIgnoreCase("append")) { params.Operation = args[i]; } else if (args[i].equalsIgnoreCase("delete")) { params.Operation = args[i]; } else { System.out.println("Invalid Operation {" + args[i] + "} Must be Overwrite or Upsert or Append or Delete"); System.exit(-1); } } } else if (args[i - 1].equalsIgnoreCase("--debug")) { params.debug = true; DatasetUtilConstants.debug = true; } else if (args[i - 1].equalsIgnoreCase("--ext")) { DatasetUtilConstants.ext = true; } else if (args[i - 1].equalsIgnoreCase("--inputFile")) { String tmp = args[i]; if (tmp != null) { File tempFile = new File(tmp); if (tempFile.exists()) { params.inputFile = tempFile.toString(); } else { System.out.println("File {" + args[i] + "} does not exist"); System.exit(-1); } } } else if (args[i - 1].equalsIgnoreCase("--dataset")) { params.dataset = args[i]; } else if (args[i - 1].equalsIgnoreCase("--datasetLabel")) { params.datasetLabel = args[i]; } else if (args[i - 1].equalsIgnoreCase("--app")) { params.app = args[i]; } else if (args[i - 1].equalsIgnoreCase("--useBulkAPI")) { if (args[i] != null && args[i].trim().equalsIgnoreCase("true")) params.useBulkAPI = true; } else if (args[i - 1].equalsIgnoreCase("--uploadFormat")) { if (args[i] != null && args[i].trim().equalsIgnoreCase("csv")) params.uploadFormat = "csv"; else if (args[i] != null && args[i].trim().equalsIgnoreCase("binary")) params.uploadFormat = "binary"; } else if (args[i - 1].equalsIgnoreCase("--rowLimit")) { if (args[i] != null && !args[i].trim().isEmpty()) params.rowLimit = (new BigDecimal(args[i].trim())).intValue(); } else if (args[i - 1].equalsIgnoreCase("--rootObject")) { params.rootObject = args[i]; } else if (args[i - 1].equalsIgnoreCase("--fileEncoding")) { params.fileEncoding = args[i]; } else if (args[i - 1].equalsIgnoreCase("--server")) { if (args[i] != null && args[i].trim().equalsIgnoreCase("true")) params.server = true; else if (args[i] != null && args[i].trim().equalsIgnoreCase("false")) params.server = false; } else if (args[i - 1].equalsIgnoreCase("--codingErrorAction")) { if (args[i] != null) { if (args[i].equalsIgnoreCase("IGNORE")) { params.codingErrorAction = CodingErrorAction.IGNORE; } else if (args[i].equalsIgnoreCase("REPORT")) { params.codingErrorAction = CodingErrorAction.REPORT; } else if (args[i].equalsIgnoreCase("REPLACE")) { params.codingErrorAction = CodingErrorAction.REPLACE; } } } else { printUsage(); System.out.println("\nERROR: Invalid argument: " + args[i - 1]); System.exit(-1); } } //end for if (params.username != null) { if (params.endpoint == null || params.endpoint.isEmpty()) { params.endpoint = DatasetUtilConstants.defaultEndpoint; } } } if (params.server) { System.out.println(); System.out.println("\n*******************************************************************************"); try { DatasetUtilServer datasetUtilServer = new DatasetUtilServer(); datasetUtilServer.init(args, true); } catch (Exception e) { e.printStackTrace(); } System.out.println("Server ended, exiting JVM....."); System.out.println("*******************************************************************************\n"); System.out.println("QUITAPP"); System.exit(0); } if (params.sessionId == null) { if (params.username == null || params.username.trim().isEmpty()) { params.username = getInputFromUser("Enter salesforce username: ", true, false); } if (params.username.equals("-1")) { params.sessionId = getInputFromUser("Enter salesforce sessionId: ", true, false); params.username = null; params.password = null; } else { if (params.password == null || params.password.trim().isEmpty()) { params.password = getInputFromUser("Enter salesforce password: ", true, true); } } } if (params.sessionId != null && !params.sessionId.isEmpty()) { while (params.endpoint == null || params.endpoint.trim().isEmpty()) { params.endpoint = getInputFromUser("Enter salesforce instance url: ", true, false); if (params.endpoint == null || params.endpoint.trim().isEmpty()) System.out.println("\nERROR: endpoint must be specified when sessionId is specified"); } while (params.endpoint.toLowerCase().contains("login.salesforce.com") || params.endpoint.toLowerCase().contains("test.salesforce.com") || params.endpoint.toLowerCase().contains("test") || params.endpoint.toLowerCase().contains("prod") || params.endpoint.toLowerCase().contains("sandbox")) { System.out.println("\nERROR: endpoint must be the actual serviceURL and not the login url"); params.endpoint = getInputFromUser("Enter salesforce instance url: ", true, false); } } else { if (params.endpoint == null || params.endpoint.isEmpty()) { params.endpoint = getInputFromUser("Enter salesforce instance url (default=prod): ", false, false); if (params.endpoint == null || params.endpoint.trim().isEmpty()) { params.endpoint = DatasetUtilConstants.defaultEndpoint; } } } try { if (params.endpoint.equalsIgnoreCase("PROD") || params.endpoint.equalsIgnoreCase("PRODUCTION")) { params.endpoint = DatasetUtilConstants.defaultEndpoint; } else if (params.endpoint.equalsIgnoreCase("TEST") || params.endpoint.equalsIgnoreCase("SANDBOX")) { params.endpoint = DatasetUtilConstants.defaultEndpoint.replace("login", "test"); } URL uri = new URL(params.endpoint); String protocol = uri.getProtocol(); String host = uri.getHost(); if (protocol == null || !protocol.equalsIgnoreCase("https")) { if (host == null || !(host.toLowerCase().endsWith("internal.salesforce.com") || host.toLowerCase().endsWith("localhost"))) { System.out.println("\nERROR: Invalid endpoint. UNSUPPORTED_CLIENT: HTTPS Required in endpoint"); System.exit(-1); } } if (uri.getPath() == null || uri.getPath().isEmpty() || uri.getPath().equals("/")) { uri = new URL(uri.getProtocol(), uri.getHost(), uri.getPort(), DatasetUtilConstants.defaultSoapEndPointPath); } params.endpoint = uri.toString(); } catch (MalformedURLException e) { e.printStackTrace(); System.out.println("\nERROR: endpoint is not a valid URL"); System.exit(-1); } PartnerConnection partnerConnection = null; if (params.username != null || params.sessionId != null) { try { partnerConnection = DatasetUtils.login(0, params.username, params.password, params.token, params.endpoint, params.sessionId, params.debug); } catch (ConnectionException e) { e.printStackTrace(); System.exit(-1); } catch (MalformedURLException e) { e.printStackTrace(); System.exit(-1); } } if (args.length == 0 || action == null) { // System.out.println("\n*******************************************************************************"); //// FileListenerUtil.startAllListener(partnerConnection); // try { // Thread.sleep(1000); // } catch (InterruptedException e) { // } // System.out.println("*******************************************************************************\n"); // System.out.println(); // System.out.println("\n*******************************************************************************"); // try { // DatasetUtilServer datasetUtilServer = new DatasetUtilServer(); // datasetUtilServer.init(args, false); // } catch (Exception e) { // e.printStackTrace(); // } // System.out.println("*******************************************************************************\n"); // System.out.println(); while (true) { action = getActionFromUser(); if (action == null || action.isEmpty()) { System.exit(-1); } params = new DatasetUtilParams(); getRequiredParams(action, partnerConnection, params); @SuppressWarnings("unused") boolean status = doAction(action, partnerConnection, params); // if(status) // { // if(action.equalsIgnoreCase("load") && params.debug) // createListener(partnerConnection, params); // } } } else { doAction(action, partnerConnection, params); } }
From source file:examples.mail.IMAPExportMbox.java
public static void main(String[] args) throws IOException { int connect_timeout = CONNECT_TIMEOUT; int read_timeout = READ_TIMEOUT; int argIdx = 0; String eol = EOL_DEFAULT;//from ww w.j a v a2 s . c o m boolean printHash = false; boolean printMarker = false; int retryWaitSecs = 0; for (argIdx = 0; argIdx < args.length; argIdx++) { if (args[argIdx].equals("-c")) { connect_timeout = Integer.parseInt(args[++argIdx]); } else if (args[argIdx].equals("-r")) { read_timeout = Integer.parseInt(args[++argIdx]); } else if (args[argIdx].equals("-R")) { retryWaitSecs = Integer.parseInt(args[++argIdx]); } else if (args[argIdx].equals("-LF")) { eol = LF; } else if (args[argIdx].equals("-CRLF")) { eol = CRLF; } else if (args[argIdx].equals("-.")) { printHash = true; } else if (args[argIdx].equals("-X")) { printMarker = true; } else { break; } } final int argCount = args.length - argIdx; if (argCount < 2) { System.err.println("Usage: IMAPExportMbox [-LF|-CRLF] [-c n] [-r n] [-R n] [-.] [-X]" + " imap[s]://user:password@host[:port]/folder/path [+|-]<mboxfile> [sequence-set] [itemnames]"); System.err.println( "\t-LF | -CRLF set end-of-line to LF or CRLF (default is the line.separator system property)"); System.err.println("\t-c connect timeout in seconds (default 10)"); System.err.println("\t-r read timeout in seconds (default 10)"); System.err.println("\t-R temporary failure retry wait in seconds (default 0; i.e. disabled)"); System.err.println("\t-. print a . for each complete message received"); System.err.println("\t-X print the X-IMAP line for each complete message received"); System.err.println( "\tthe mboxfile is where the messages are stored; use '-' to write to standard output."); System.err.println( "\tPrefix filename with '+' to append to the file. Prefix with '-' to allow overwrite."); System.err.println( "\ta sequence-set is a list of numbers/number ranges e.g. 1,2,3-10,20:* - default 1:*"); System.err .println("\titemnames are the message data item name(s) e.g. BODY.PEEK[HEADER.FIELDS (SUBJECT)]" + " or a macro e.g. ALL - default (INTERNALDATE BODY.PEEK[])"); System.exit(1); } final URI uri = URI.create(args[argIdx++]); final String file = args[argIdx++]; String sequenceSet = argCount > 2 ? args[argIdx++] : "1:*"; final String itemNames; // Handle 0, 1 or multiple item names if (argCount > 3) { if (argCount > 4) { StringBuilder sb = new StringBuilder(); sb.append("("); for (int i = 4; i <= argCount; i++) { if (i > 4) { sb.append(" "); } sb.append(args[argIdx++]); } sb.append(")"); itemNames = sb.toString(); } else { itemNames = args[argIdx++]; } } else { itemNames = "(INTERNALDATE BODY.PEEK[])"; } final boolean checkSequence = sequenceSet.matches("\\d+:(\\d+|\\*)"); // are we expecting a sequence? final MboxListener chunkListener; if (file.equals("-")) { chunkListener = null; } else if (file.startsWith("+")) { final File mbox = new File(file.substring(1)); System.out.println("Appending to file " + mbox); chunkListener = new MboxListener(new BufferedWriter(new FileWriter(mbox, true)), eol, printHash, printMarker, checkSequence); } else if (file.startsWith("-")) { final File mbox = new File(file.substring(1)); System.out.println("Writing to file " + mbox); chunkListener = new MboxListener(new BufferedWriter(new FileWriter(mbox, false)), eol, printHash, printMarker, checkSequence); } else { final File mbox = new File(file); if (mbox.exists()) { throw new IOException("mailbox file: " + mbox + " already exists!"); } System.out.println("Creating file " + mbox); chunkListener = new MboxListener(new BufferedWriter(new FileWriter(mbox)), eol, printHash, printMarker, checkSequence); } String path = uri.getPath(); if (path == null || path.length() < 1) { throw new IllegalArgumentException("Invalid folderPath: '" + path + "'"); } String folder = path.substring(1); // skip the leading / // suppress login details final PrintCommandListener listener = new PrintCommandListener(System.out, true) { @Override public void protocolReplyReceived(ProtocolCommandEvent event) { if (event.getReplyCode() != IMAPReply.PARTIAL) { // This is dealt with by the chunk listener super.protocolReplyReceived(event); } } }; // Connect and login final IMAPClient imap = IMAPUtils.imapLogin(uri, connect_timeout * 1000, listener); String maxIndexInFolder = null; try { imap.setSoTimeout(read_timeout * 1000); if (!imap.select(folder)) { throw new IOException("Could not select folder: " + folder); } for (String line : imap.getReplyStrings()) { maxIndexInFolder = matches(line, PATEXISTS, 1); if (maxIndexInFolder != null) { break; } } if (chunkListener != null) { imap.setChunkListener(chunkListener); } // else the command listener displays the full output without processing while (true) { boolean ok = imap.fetch(sequenceSet, itemNames); // If the fetch failed, can we retry? if (!ok && retryWaitSecs > 0 && chunkListener != null && checkSequence) { final String replyString = imap.getReplyString(); //includes EOL if (startsWith(replyString, PATTEMPFAIL)) { System.err.println("Temporary error detected, will retry in " + retryWaitSecs + "seconds"); sequenceSet = (chunkListener.lastSeq + 1) + ":*"; try { Thread.sleep(retryWaitSecs * 1000); } catch (InterruptedException e) { // ignored } } else { throw new IOException( "FETCH " + sequenceSet + " " + itemNames + " failed with " + replyString); } } else { break; } } } catch (IOException ioe) { String count = chunkListener == null ? "?" : Integer.toString(chunkListener.total); System.err.println("FETCH " + sequenceSet + " " + itemNames + " failed after processing " + count + " complete messages "); if (chunkListener != null) { System.err.println("Last complete response seen: " + chunkListener.lastFetched); } throw ioe; } finally { if (printHash) { System.err.println(); } if (chunkListener != null) { chunkListener.close(); final Iterator<String> missingIds = chunkListener.missingIds.iterator(); if (missingIds.hasNext()) { StringBuilder sb = new StringBuilder(); for (;;) { sb.append(missingIds.next()); if (!missingIds.hasNext()) { break; } sb.append(","); } System.err.println("*** Missing ids: " + sb.toString()); } } imap.logout(); imap.disconnect(); } if (chunkListener != null) { System.out.println("Processed " + chunkListener.total + " messages."); } if (maxIndexInFolder != null) { System.out.println("Folder contained " + maxIndexInFolder + " messages."); } }
From source file:ch.kostceco.tools.kostsimy.KOSTSimy.java
/** Die Eingabe besteht aus 2 Parameter: [0] Original-Ordner [1] Replica-Ordner * //from w w w. java 2s. c om * @param args * @throws IOException */ public static void main(String[] args) throws IOException { ApplicationContext context = new ClassPathXmlApplicationContext("classpath:config/applicationContext.xml"); // Zeitstempel Start java.util.Date nowStart = new java.util.Date(); java.text.SimpleDateFormat sdfStart = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeStart = sdfStart.format(nowStart); KOSTSimy kostsimy = (KOSTSimy) context.getBean("kostsimy"); File configFile = new File("configuration" + File.separator + "kostsimy.conf.xml"); // Ueberprfung des Parameters (Log-Verzeichnis) String pathToLogfile = kostsimy.getConfigurationService().getPathToLogfile(); File directoryOfLogfile = new File(pathToLogfile); if (!directoryOfLogfile.exists()) { directoryOfLogfile.mkdir(); } // Im Logverzeichnis besteht kein Schreibrecht if (!directoryOfLogfile.canWrite()) { System.out.println( kostsimy.getTextResourceService().getText(ERROR_LOGDIRECTORY_NOTWRITABLE, directoryOfLogfile)); System.exit(1); } if (!directoryOfLogfile.isDirectory()) { System.out.println(kostsimy.getTextResourceService().getText(ERROR_LOGDIRECTORY_NODIRECTORY)); System.exit(1); } // Ist die Anzahl Parameter (2) korrekt? if (args.length > 3) { System.out.println(kostsimy.getTextResourceService().getText(ERROR_PARAMETER_USAGE)); System.exit(1); } File origDir = new File(args[0]); File repDir = new File(args[1]); File logDatei = null; logDatei = origDir; // Informationen zum Arbeitsverzeichnis holen String pathToWorkDir = kostsimy.getConfigurationService().getPathToWorkDir(); /* Nicht vergessen in "src/main/resources/config/applicationContext-services.xml" beim * entsprechenden Modul die property anzugeben: <property name="configurationService" * ref="configurationService" /> */ // Konfiguration des Loggings, ein File Logger wird zustzlich erstellt LogConfigurator logConfigurator = (LogConfigurator) context.getBean("logconfigurator"); String logFileName = logConfigurator.configure(directoryOfLogfile.getAbsolutePath(), logDatei.getName()); File logFile = new File(logFileName); // Ab hier kann ins log geschrieben werden... LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_HEADER)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_START, ausgabeStart)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_END)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_INFO)); System.out.println("KOST-Simy"); System.out.println(""); if (!origDir.exists()) { // Das Original-Verzeichnis existiert nicht LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOORIGDIR, origDir.getAbsolutePath()))); System.out .println(kostsimy.getTextResourceService().getText(ERROR_NOORIGDIR, origDir.getAbsolutePath())); System.exit(1); } if (!repDir.exists()) { // Das Replica-Verzeichnis existiert nicht LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOREPDIR1, repDir.getAbsolutePath()))); System.out .println(kostsimy.getTextResourceService().getText(ERROR_NOREPDIR1, repDir.getAbsolutePath())); System.exit(1); } File xslOrig = new File("resources" + File.separator + "kost-simy.xsl"); File xslCopy = new File(directoryOfLogfile.getAbsolutePath() + File.separator + "kost-simy.xsl"); if (!xslCopy.exists()) { Util.copyFile(xslOrig, xslCopy); } // Informationen zur prozentualen Stichprobe holen String randomTest = kostsimy.getConfigurationService().getRandomTest(); /* Nicht vergessen in "src/main/resources/config/applicationContext-services.xml" beim * entsprechenden Modul die property anzugeben: <property name="configurationService" * ref="configurationService" /> */ int iRandomTest = 100; try { iRandomTest = Integer.parseInt(randomTest); } catch (Exception ex) { // unzulaessige Eingabe --> 50 wird gesetzt iRandomTest = 50; } if (iRandomTest > 100 || iRandomTest < 1) { // unzulaessige Eingabe --> 50 wird gesetzt iRandomTest = 50; } File tmpDir = new File(pathToWorkDir); /* bestehendes Workverzeichnis Abbruch wenn nicht leer, da am Schluss das Workverzeichnis * gelscht wird und entsprechend bestehende Dateien gelscht werden knnen */ if (tmpDir.exists()) { if (tmpDir.isDirectory()) { // Get list of file in the directory. When its length is not zero the folder is not empty. String[] files = tmpDir.list(); if (files.length > 0) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir))); System.out.println( kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_EXISTS, pathToWorkDir)); System.exit(1); } } } // Im Pfad keine Sonderzeichen Programme knnen evtl abstrzen String patternStr = "[^!#\\$%\\(\\)\\+,\\-_\\.=@\\[\\]\\{\\}\\~:\\\\a-zA-Z0-9 ]"; Pattern pattern = Pattern.compile(patternStr); String name = tmpDir.getAbsolutePath(); String[] pathElements = name.split("/"); for (int i = 0; i < pathElements.length; i++) { String element = pathElements[i]; Matcher matcher = pattern.matcher(element); boolean matchFound = matcher.find(); if (matchFound) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } // die Anwendung muss mindestens unter Java 6 laufen String javaRuntimeVersion = System.getProperty("java.vm.version"); if (javaRuntimeVersion.compareTo("1.6.0") < 0) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_WRONG_JRE))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_WRONG_JRE)); System.exit(1); } // bestehendes Workverzeichnis wieder anlegen if (!tmpDir.exists()) { tmpDir.mkdir(); File origDirTmp = new File(tmpDir.getAbsolutePath() + File.separator + "orig"); File repDirTmp = new File(tmpDir.getAbsolutePath() + File.separator + "rep"); origDirTmp.mkdir(); repDirTmp.mkdir(); } // Im workverzeichnis besteht kein Schreibrecht if (!tmpDir.canWrite()) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, tmpDir))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_WORKDIRECTORY_NOTWRITABLE, tmpDir)); System.exit(1); } // Im Pfad keine Sonderzeichen --> Absturzgefahr name = origDir.getAbsolutePath(); pathElements = name.split("/"); for (int i = 0; i < pathElements.length; i++) { String element = pathElements[i]; Matcher matcher = pattern.matcher(element); boolean matchFound = matcher.find(); if (matchFound) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } name = repDir.getAbsolutePath(); pathElements = name.split("/"); for (int i = 0; i < pathElements.length; i++) { String element = pathElements[i]; Matcher matcher = pattern.matcher(element); boolean matchFound = matcher.find(); if (matchFound) { LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name))); System.out.println(kostsimy.getTextResourceService().getText(ERROR_SPECIAL_CHARACTER, name)); System.exit(1); } } LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_IMAGE1)); float count = 0; int countNio = 0; int countIo = 0; float countVal = 0; int countNotVal = 0; float percentage = (float) 0.0; if (!origDir.isDirectory()) { // TODO: Bildervergleich zweier Dateien --> erledigt --> nur Marker if (repDir.isDirectory()) { // Das Replica-ist ein Verzeichnis, aber Original eine Datei LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOREPDIR2, repDir.getAbsolutePath()))); System.out.println( kostsimy.getTextResourceService().getText(ERROR_NOREPDIR2, repDir.getAbsolutePath())); System.exit(1); } boolean compFile = compFile(origDir, logFileName, directoryOfLogfile, repDir, tmpDir); float statIo = 0; int statNio = 0; float statUn = 0; if (compFile) { statIo = 100; } else { statNio = 100; } LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_IMAGE2)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_STATISTICS, statIo, statNio, statUn)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Zeitstempel End java.util.Date nowEnd = new java.util.Date(); java.text.SimpleDateFormat sdfEnd = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeEnd = sdfEnd.format(nowEnd); ausgabeEnd = "<End>" + ausgabeEnd + "</End>"; Util.valEnd(ausgabeEnd, logFile); Util.amp(logFile); // Die Konfiguration hereinkopieren try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setExpandEntityReferences(false); Document docConfig = factory.newDocumentBuilder().parse(configFile); NodeList list = docConfig.getElementsByTagName("configuration"); Element element = (Element) list.item(0); Document docLog = factory.newDocumentBuilder().parse(logFile); Node dup = docLog.importNode(element, true); docLog.getDocumentElement().appendChild(dup); FileWriter writer = new FileWriter(logFile); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ElementToStream(docLog.getDocumentElement(), baos); String stringDoc2 = new String(baos.toByteArray()); writer.write(stringDoc2); writer.close(); // Der Header wird dabei leider verschossen, wieder zurck ndern String newstring = kostsimy.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTSimyLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError( "<Error>" + kostsimy.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } if (compFile) { // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Validierte Datei valide System.exit(0); } else { // Lschen des Arbeitsverzeichnisses, falls eines angelegt wurde if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Fehler in Validierte Datei --> invalide System.exit(2); } } else { // TODO: Bildervergleich zweier Verzeichnisse --> in Arbeit --> nur Marker if (!repDir.isDirectory()) { // Das Replica-ist eine Datei, aber Original ein Ordner LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_IOE, kostsimy.getTextResourceService().getText(ERROR_NOREPDIR3, repDir.getAbsolutePath()))); System.out.println( kostsimy.getTextResourceService().getText(ERROR_NOREPDIR3, repDir.getAbsolutePath())); System.exit(1); } Map<String, File> fileMap = Util.getFileMap(origDir, false); Set<String> fileMapKeys = fileMap.keySet(); boolean other = false; for (Iterator<String> iterator = fileMapKeys.iterator(); iterator.hasNext();) { String entryName = iterator.next(); File newFile = fileMap.get(entryName); if (!newFile.isDirectory()) { origDir = newFile; count = count + 1; if ((origDir.getAbsolutePath().toLowerCase().endsWith(".pdf") || origDir.getAbsolutePath().toLowerCase().endsWith(".pdfa") || origDir.getAbsolutePath().toLowerCase().endsWith(".tif") || origDir.getAbsolutePath().toLowerCase().endsWith(".tiff") || origDir.getAbsolutePath().toLowerCase().endsWith(".jpeg") || origDir.getAbsolutePath().toLowerCase().endsWith(".jpg") || origDir.getAbsolutePath().toLowerCase().endsWith(".jpe") || origDir.getAbsolutePath().toLowerCase().endsWith(".jp2") || origDir.getAbsolutePath().toLowerCase().endsWith(".gif") || origDir.getAbsolutePath().toLowerCase().endsWith(".png") || origDir.getAbsolutePath().toLowerCase().endsWith(".bmp"))) { percentage = 100 / count * countVal; if (percentage < iRandomTest) { // if ( 100 / count * (countVal + 1) <= iRandomTest ) { countVal = countVal + 1; String origWithOutExt = FilenameUtils.removeExtension(origDir.getName()); File repFile = new File( repDir.getAbsolutePath() + File.separator + origWithOutExt + ".pdf"); if (!repFile.exists()) { repFile = new File( repDir.getAbsolutePath() + File.separator + origWithOutExt + ".pdfa"); if (!repFile.exists()) { repFile = new File( repDir.getAbsolutePath() + File.separator + origWithOutExt + ".tif"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".tiff"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jpeg"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jpg"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jpe"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".jp2"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".gif"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".png"); if (!repFile.exists()) { repFile = new File(repDir.getAbsolutePath() + File.separator + origWithOutExt + ".bmp"); if (!repFile.exists()) { other = true; LOGGER.logError(kostsimy .getTextResourceService() .getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostsimy .getTextResourceService() .getText(MESSAGE_XML_COMPFILE, origDir)); LOGGER.logError(kostsimy .getTextResourceService().getText( MESSAGE_XML_VALERGEBNIS_NOTVALIDATED)); LOGGER.logError( kostsimy.getTextResourceService() .getText(ERROR_NOREP, origDir.getName())); LOGGER.logError(kostsimy .getTextResourceService().getText( MESSAGE_XML_VALERGEBNIS_CLOSE)); } } } } } } } } } } } if (!other) { boolean compFile = compFile(origDir, logFileName, directoryOfLogfile, repFile, tmpDir); if (compFile) { // Vergleich bestanden countIo = countIo + 1; } else { // Vergleich nicht bestanden countNio = countNio + 1; } } } else { countNotVal = countNotVal + 1; LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_COMPFILE, origDir)); LOGGER.logError(kostsimy.getTextResourceService() .getText(MESSAGE_XML_VALERGEBNIS_NOTVALIDATED)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); } } else { countNotVal = countNotVal + 1; LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_COMPFILE, origDir)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_NOTVALIDATED)); LOGGER.logError( kostsimy.getTextResourceService().getText(ERROR_INCORRECTFILEENDING, origDir)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_VALERGEBNIS_CLOSE)); } } } if (countNio == 0 && countIo == 0) { // keine Dateien verglichen LOGGER.logError(kostsimy.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS)); System.out.println(kostsimy.getTextResourceService().getText(ERROR_INCORRECTFILEENDINGS)); } float statIo = 100 / (float) count * (float) countIo; float statNio = 100 / (float) count * (float) countNio; float statUn = 100 - statIo - statNio; LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_IMAGE2)); LOGGER.logError( kostsimy.getTextResourceService().getText(MESSAGE_XML_STATISTICS, statIo, statNio, statUn)); LOGGER.logError(kostsimy.getTextResourceService().getText(MESSAGE_XML_LOGEND)); // Zeitstempel End java.util.Date nowEnd = new java.util.Date(); java.text.SimpleDateFormat sdfEnd = new java.text.SimpleDateFormat("dd.MM.yyyy HH:mm:ss"); String ausgabeEnd = sdfEnd.format(nowEnd); ausgabeEnd = "<End>" + ausgabeEnd + "</End>"; Util.valEnd(ausgabeEnd, logFile); Util.amp(logFile); // Die Konfiguration hereinkopieren try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setValidating(false); factory.setExpandEntityReferences(false); Document docConfig = factory.newDocumentBuilder().parse(configFile); NodeList list = docConfig.getElementsByTagName("configuration"); Element element = (Element) list.item(0); Document docLog = factory.newDocumentBuilder().parse(logFile); Node dup = docLog.importNode(element, true); docLog.getDocumentElement().appendChild(dup); FileWriter writer = new FileWriter(logFile); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ElementToStream(docLog.getDocumentElement(), baos); String stringDoc2 = new String(baos.toByteArray()); writer.write(stringDoc2); writer.close(); // Der Header wird dabei leider verschossen, wieder zurck ndern String newstring = kostsimy.getTextResourceService().getText(MESSAGE_XML_HEADER); String oldstring = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><KOSTSimyLog>"; Util.oldnewstring(oldstring, newstring, logFile); } catch (Exception e) { LOGGER.logError( "<Error>" + kostsimy.getTextResourceService().getText(ERROR_XML_UNKNOWN, e.getMessage())); System.out.println("Exception: " + e.getMessage()); } if (countNio == 0 && countIo == 0) { // keine Dateien verglichen bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } System.exit(1); } else if (countNio == 0) { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // alle Validierten Dateien valide System.exit(0); } else { // bestehendes Workverzeichnis ggf. lschen if (tmpDir.exists()) { Util.deleteDir(tmpDir); } // Fehler in Validierten Dateien --> invalide System.exit(2); } if (tmpDir.exists()) { Util.deleteDir(tmpDir); tmpDir.deleteOnExit(); } } }
From source file:com.g2inc.scap.library.domain.SCAPContentManager.java
/** * A main method only used for testing//from w w w. j a v a 2 s . co m * * @param args Command-line arguments * */ public static void main(String[] args) throws Exception { BasicConfigurator.configure(); LOG.trace("SchemaParser starting, schemaVersion =" + args[0] + ", xsd File=" + args[1]); File xsdFile = new File(args[1]); if (!xsdFile.exists()) { LOG.error("Usage: java SchemaParser <name of xsd file>"); } SCAPDocumentTypeEnum version = SCAPDocumentTypeEnum.valueOf(args[0]); SCAPContentManager mgr = SCAPContentManager.getInstance(new File(args[1])); // schema-related data should now be populated List<String> platformTypes = mgr.getValidPlatforms(version); LOG.trace("STARTING PLATFORMS"); for (int i = 0; i < platformTypes.size(); i++) { LOG.trace(platformTypes.get(i)); } String[] platforms = { "windows", "independent" }; List<NameDoc> list = null; Iterator<NameDoc> iter = null; LOG.trace("STARTING TESTS"); list = mgr.getValidTestTypes(version, platforms); iter = list.iterator(); while (iter.hasNext()) { NameDoc testName = iter.next(); LOG.trace("\t" + testName); } LOG.trace("STARTING OBJECTS"); list = mgr.getValidObjectTypes(version, platforms); iter = list.iterator(); while (iter.hasNext()) { NameDoc objName = iter.next(); LOG.trace("\t" + objName); LOG.trace("STARTING OBJECT ENTITIES FOR " + objName.getName()); List<OvalEntity> entityList = mgr.getValidObjectEntityTypes(version, "windows", objName.getName()); if (entityList != null && entityList.size() > 0) { for (int i = 0; i < entityList.size(); i++) { LOG.trace("\t\t" + entityList.get(i).toString()); } } } LOG.trace("STARTING STATES"); list = mgr.getValidStateTypes(version, platforms); iter = list.iterator(); while (iter.hasNext()) { NameDoc stateName = iter.next(); LOG.trace("\t" + stateName); LOG.trace("STARTING STATE ENTITIES FOR " + stateName.getName()); List<OvalEntity> entityList = mgr.getValidStateEntityTypes(version, "windows", stateName.getName()); if (entityList != null && entityList.size() > 0) { for (int i = 0; i < entityList.size(); i++) { LOG.trace("\t\t" + entityList.get(i).toString()); } } } }
From source file:DIA_Umpire_Quant.DIA_Umpire_Quant.java
/** * @param args the command line arguments *//* www . ja va 2 s. co m*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire quantitation with targeted re-extraction analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, it should be like: java -jar -Xmx10G DIA_Umpire_Quant.jar diaumpire_quant.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_quant.log"); } catch (Exception e) { } try { Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; String UserMod = ""; String Combined_Prot = ""; String InternalLibID = ""; String ExternalLibPath = ""; String ExternalLibDecoyTag = "DECOY"; boolean DefaultProtFiltering = true; boolean DataSetLevelPepFDR = false; float ProbThreshold = 0.99f; float ExtProbThreshold = 0.99f; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; float MinFragMz = 200f; String FilterWeight = "GW"; float MinWeight = 0.9f; float RTWindow_Int = -1f; float RTWindow_Ext = -1f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean InternalLibSearch = false; boolean ExternalLibSearch = false; boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "TargetedExtraction": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "InternalLibSearch": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "ExternalLibSearch": { ExternalLibSearch = Boolean.parseBoolean(value); break; } case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "UserMod": { UserMod = value; break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } case "DataSetLevelPepFDR": { DataSetLevelPepFDR = Boolean.parseBoolean(value); break; } case "InternalLibID": { InternalLibID = value; break; } case "ExternalLibPath": { ExternalLibPath = value; break; } case "ExtProbThreshold": { ExtProbThreshold = Float.parseFloat(value); break; } case "RTWindow_Int": { RTWindow_Int = Float.parseFloat(value); break; } case "RTWindow_Ext": { RTWindow_Ext = Float.parseFloat(value); break; } case "ExternalLibDecoyTag": { ExternalLibDecoyTag = value; if (ExternalLibDecoyTag.endsWith("_")) { ExternalLibDecoyTag = ExternalLibDecoyTag.substring(0, ExternalLibDecoyTag.length() - 1); } break; } case "ProbThreshold": { ProbThreshold = Float.parseFloat(value); break; } case "ReSearchProb": { //ReSearchProb = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } case "MinFragMz": { MinFragMz = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); if (!UserMod.equals("")) { PTMManager.GetInstance().ImportUserMod(UserMod); } //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } } } LCMSID combinePepID = null; if (DataSetLevelPepFDR) { combinePepID = LCMSID.ReadLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); if (combinePepID == null) { FDR_DataSetLevel fdr = new FDR_DataSetLevel(); fdr.GeneratePepIonList(FileList, tandemPara, WorkFolder + "combinePepID.SerFS"); combinePepID = fdr.combineID; combinePepID.WriteLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); } } //process each DIA file for quantification based on untargeted identifications for (DIAPack DiaFile : FileList) { long time = System.currentTimeMillis(); Logger.getRootLogger().info("Loading identification results " + DiaFile.Filename + "...."); //If the LCMSID serialization is found if (!DiaFile.ReadSerializedLCMSID()) { DiaFile.ParsePepXML(tandemPara, combinePepID); DiaFile.BuildStructure(); if (!DiaFile.MS1FeatureMap.ReadPeakCluster()) { Logger.getRootLogger().info("Loading peak and structure failed, job is incomplete"); System.exit(1); } DiaFile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); //Generate mapping between index of precursor feature and pseudo MS/MS scan index DiaFile.GenerateClusterScanNomapping(); //Doing quantification DiaFile.AssignQuant(); DiaFile.ClearStructure(); } DiaFile.IDsummary.ReduceMemoryUsage(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(DiaFile.Filename + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); } //<editor-fold defaultstate="collapsed" desc="Targete re-extraction using internal library"> Logger.getRootLogger().info( "================================================================================================="); if (InternalLibSearch && FileList.size() > 1) { Logger.getRootLogger().info("Module C: Targeted extraction using internal library"); FragmentLibManager libManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, InternalLibID); if (libManager == null) { Logger.getRootLogger().info("Building internal spectral library"); libManager = new FragmentLibManager(InternalLibID); ArrayList<LCMSID> LCMSIDList = new ArrayList<>(); for (DIAPack dia : FileList) { LCMSIDList.add(dia.IDsummary); } libManager.ImportFragLibTopFrag(LCMSIDList, Freq, TopNFrag); libManager.WriteFragmentLibSerialization(WorkFolder); } libManager.ReduceMemoryUsage(); Logger.getRootLogger() .info("Building retention time prediction model and generate candidate peptide list"); for (int i = 0; i < FileList.size(); i++) { FileList.get(i).IDsummary.ClearMappedPep(); } for (int i = 0; i < FileList.size(); i++) { for (int j = i + 1; j < FileList.size(); j++) { RTAlignedPepIonMapping alignment = new RTAlignedPepIonMapping(WorkFolder, FileList.get(i).GetParameter(), FileList.get(i).IDsummary, FileList.get(j).IDsummary); alignment.GenerateModel(); alignment.GenerateMappedPepIon(); } FileList.get(i).ExportID(); FileList.get(i).IDsummary = null; } Logger.getRootLogger().info("Targeted matching........"); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } if (!diafile.IDsummary.GetMappedPepIonList().isEmpty()) { diafile.UseMappedIon = true; diafile.FilterMappedIonByProb = false; diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); diafile.GenerateMassCalibrationRTMap(); diafile.TargetedExtractionQuant(false, libManager, 1.1f, RTWindow_Int); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); diafile.IDsummary.RemoveLowProbMappedIon(ProbThreshold); diafile.ExportID(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); diafile.ClearStructure(); } diafile.IDsummary = null; System.gc(); } Logger.getRootLogger().info( "================================================================================================="); } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library"> //External library search if (ExternalLibSearch) { Logger.getRootLogger().info("Module C: Targeted extraction using external library"); //Read exteranl library FragmentLibManager ExlibManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, FilenameUtils.getBaseName(ExternalLibPath)); if (ExlibManager == null) { ExlibManager = new FragmentLibManager(FilenameUtils.getBaseName(ExternalLibPath)); //Import traML file ExlibManager.ImportFragLibByTraML(ExternalLibPath, ExternalLibDecoyTag); //Check if there are decoy spectra ExlibManager.CheckDecoys(); //ExlibManager.ImportFragLibBySPTXT(ExternalLibPath); ExlibManager.WriteFragmentLibSerialization(WorkFolder); } Logger.getRootLogger() .info("No. of peptide ions in external lib:" + ExlibManager.PeptideFragmentLib.size()); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } //Generate RT mapping RTMappingExtLib RTmap = new RTMappingExtLib(diafile.IDsummary, ExlibManager, diafile.GetParameter()); RTmap.GenerateModel(); RTmap.GenerateMappedPepIon(); diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.GenerateMassCalibrationRTMap(); //Perform targeted re-extraction diafile.TargetedExtractionQuant(false, ExlibManager, ProbThreshold, RTWindow_Ext); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); //Remove target IDs below the defined probability threshold diafile.IDsummary.RemoveLowProbMappedIon(ExtProbThreshold); diafile.ExportID(); diafile.ClearStructure(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); } } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); diafile.IDsummary.ClearAssignPeakCluster(); //diafile.IDsummary.ClearPSMs(); } if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.MinFragMZ = MinFragMz; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:au.org.ala.delta.key.Key.java
/** * @param args//from w w w .j a v a2s. c o m * specifies the name of the input file to use. */ public static void main(String[] args) throws Exception { System.out.println(generateCreditsString()); File f = handleArgs(args); if (!f.exists()) { Logger.log("File %s does not exist!", f.getName()); return; } new Key(f).calculateKey(); }
From source file:gr.omadak.leviathan.asp.AspParser.java
public static void main(String[] args) { File bDir = null;/*from ww w . j av a 2s . c o m*/ File oDir = null; File sDir = null; boolean gSource = true; boolean defaultVB = true; int i = 0; int argCount = args.length; while (i < argCount) { if (i < argCount - 1) { if (args[i].equals("-o")) { oDir = new File(args[++i]); } else if (args[i].equals("-b")) { bDir = new File(args[++i]); } else if (args[i].equals("-s")) { sDir = new File(args[++i]); } } if (args[i].equals("-ng")) { gSource = false; } else if (args[i].equals("-js")) { defaultVB = false; } i++; } boolean oDirValid = oDir != null && (!oDir.exists() || oDir.isDirectory()); boolean bDirValid = bDir != null && bDir.isDirectory(); boolean isValid = oDirValid && bDirValid; if (isValid && sDir == null) { sDir = bDir; } if (!isValid) { System.err.println("Usage:AspParser -b <base directory> " + "-o <output directory> [-s <source directory> -g -ng -vb -js]\n" + "base directory: the directory where virtual root exists.\n" + "eg <!--#include virtual=\"/someFile.asp\"-->\noutput directory" + ": the directory where generated files will be placed in\n" + "source directory: the root directory where sources are\nIf not " + "defined then the base directory is used\n" + "-ng disables source production\n" + "-js if an asp page has not defined the langugae asume is js"); if (!oDirValid) { if (oDir == null) { System.err.println("Output directory is not defined"); } else { System.err.println("Output directory:" + oDir + " can not be used"); } } if (!bDirValid) { if (bDir == null) { System.err.println("Base directory is not defined"); } else { System.err.println("Base directory:" + bDir + " does not exist or is not a directory"); } } System.exit(1); } AspParser parser = new AspParser(bDir, oDir); parser.setGenerateCode(gSource); parser.parseDir(sDir, defaultVB); System.exit(0); }
From source file:com.seanmadden.fast.ldap.main.Main.java
/** * The Main Event.//from www .j a va 2 s . com * * @param args */ @SuppressWarnings("static-access") public static void main(String[] args) { BasicConfigurator.configure(); log.debug("System initializing"); try { Logger.getRootLogger().addAppender( new FileAppender(new PatternLayout(PatternLayout.TTCC_CONVERSION_PATTERN), "log.log")); } catch (IOException e1) { log.error("Unable to open the log file..?"); } /* * Initialize the configuration engine. */ XMLConfiguration config = new XMLConfiguration(); config.setListDelimiter('|'); /* * Initialize the Command-Line parsing engine. */ CommandLineParser parser = new PosixParser(); Options opts = new Options(); opts.addOption(OptionBuilder.withLongOpt("config-file").hasArg() .withDescription("The configuration file to load").withArgName("config.xml").create("c")); opts.addOption(OptionBuilder.withLongOpt("profile").hasArg().withDescription("The profile to use") .withArgName("Default").create("p")); opts.addOption(OptionBuilder.withLongOpt("password").hasArg().withDescription("Password to connect with") .withArgName("password").create("P")); opts.addOption(OptionBuilder.withLongOpt("debug").hasArg(false).create('d')); opts.addOption(OptionBuilder.withLongOpt("verbose").hasArg(false).create('v')); File configurationFile = new File("config.xml"); try { // Parse the command-line options CommandLine cmds = parser.parse(opts, args); if (!cmds.hasOption('p')) { Logger.getRootLogger().addAppender(new GuiErrorAlerter(Level.ERROR)); } Logger.getRootLogger().setLevel(Level.ERROR); if (cmds.hasOption('v')) { Logger.getRootLogger().setLevel(Level.INFO); } if (cmds.hasOption('d')) { Logger.getRootLogger().setLevel(Level.DEBUG); } log.debug("Enabling configuration file parsing"); // The user has given us a file to parse. if (cmds.hasOption("c")) { configurationFile = new File(cmds.getOptionValue("c")); } log.debug("Config file: " + configurationFile); // Load the configuration file if (configurationFile.exists()) { config.load(configurationFile); } else { log.error("Cannot find config file"); } /* * Convert the profiles into memory */ Vector<ConnectionProfile> profs = new Vector<ConnectionProfile>(); List<?> profList = config.configurationAt("Profiles").configurationsAt("Profile"); for (Object p : profList) { SubnodeConfiguration profile = (SubnodeConfiguration) p; String name = profile.getString("[@name]"); String auth = profile.getString("LdapAuthString"); String server = profile.getString("LdapServerString"); String group = profile.getString("LdapGroupsLocation"); ConnectionProfile prof = new ConnectionProfile(name, server, auth, group); profs.add(prof); } ConnectionProfile prof = null; if (!cmds.hasOption('p')) { /* * Deploy the profile selector, to select a profile */ ProfileSelector profSel = new ProfileSelector(profs); prof = profSel.getSelection(); if (prof == null) { return; } /* * Empty the profiles and load a clean copy - then save it back * to the file */ config.clearTree("Profiles"); for (ConnectionProfile p : profSel.getProfiles()) { config.addProperty("Profiles.Profile(-1)[@name]", p.getName()); config.addProperty("Profiles.Profile.LdapAuthString", p.getLdapAuthString()); config.addProperty("Profiles.Profile.LdapServerString", p.getLdapServerString()); config.addProperty("Profiles.Profile.LdapGroupsLocation", p.getLdapGroupsString()); } config.save(configurationFile); } else { for (ConnectionProfile p : profs) { if (p.getName().equals(cmds.getOptionValue('p'))) { prof = p; break; } } } log.info("User selected " + prof); String password = ""; if (cmds.hasOption('P')) { password = cmds.getOptionValue('P'); } else { password = PasswordPrompter.promptForPassword("Password?"); } if (password.equals("")) { return; } LdapInterface ldap = new LdapInterface(prof.getLdapServerString(), prof.getLdapAuthString(), prof.getLdapGroupsString(), password); /* * Gather options information from the configuration engine for the * specified report. */ Hashtable<String, Hashtable<String, ReportOption>> reportDataStructure = new Hashtable<String, Hashtable<String, ReportOption>>(); List<?> repConfig = config.configurationAt("Reports").configurationsAt("Report"); for (Object p : repConfig) { SubnodeConfiguration repNode = (SubnodeConfiguration) p; // TODO Do something with the report profile. // Allowing the user to deploy "profiles" is a nice feature // String profile = repNode.getString("[@profile]"); String reportName = repNode.getString("[@report]"); Hashtable<String, ReportOption> reportOptions = new Hashtable<String, ReportOption>(); reportDataStructure.put(reportName, reportOptions); // Loop through the options and add each to the table. for (Object o : repNode.configurationsAt("option")) { SubnodeConfiguration option = (SubnodeConfiguration) o; String name = option.getString("[@name]"); String type = option.getString("[@type]"); String value = option.getString("[@value]"); ReportOption ro = new ReportOption(); ro.setName(name); if (type.toLowerCase().equals("boolean")) { ro.setBoolValue(Boolean.parseBoolean(value)); } else if (type.toLowerCase().equals("integer")) { ro.setIntValue(Integer.valueOf(value)); } else { // Assume a string type here then. ro.setStrValue(value); } reportOptions.put(name, ro); log.debug(ro); } } System.out.println(reportDataStructure); /* * At this point, we now need to deploy the reports window to have * the user pick a report and select some happy options to allow * that report to work. Let's go. */ /* * Deploy the Reports selector, to select a report */ Reports.getInstance().setLdapConnection(ldap); ReportsWindow reports = new ReportsWindow(Reports.getInstance().getAllReports(), reportDataStructure); Report report = reports.getSelection(); if (report == null) { return; } /* * Empty the profiles and load a clean copy - then save it back to * the file */ config.clearTree("Reports"); for (Report r : Reports.getInstance().getAllReports()) { config.addProperty("Reports.Report(-1)[@report]", r.getClass().getCanonicalName()); config.addProperty("Reports.Report[@name]", "Standard"); for (ReportOption ro : r.getOptions().values()) { config.addProperty("Reports.Report.option(-1)[@name]", ro.getName()); config.addProperty("Reports.Report.option[@type]", ro.getType()); config.addProperty("Reports.Report.option[@value]", ro.getStrValue()); } } config.save(configurationFile); ProgressBar bar = new ProgressBar(); bar.start(); report.execute(); ASCIIFormatter format = new ASCIIFormatter(); ReportResult res = report.getResult(); format.format(res, new File(res.getForName() + "_" + res.getReportName() + ".txt")); bar.stop(); JOptionPane.showMessageDialog(null, "The report is at " + res.getForName() + "_" + res.getReportName() + ".txt", "Success", JOptionPane.INFORMATION_MESSAGE); } catch (ParseException e) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("FAST Ldap Searcher", opts); } catch (ConfigurationException e) { e.printStackTrace(); log.fatal("OH EM GEES! Configuration errors."); } catch (Exception e) { e.printStackTrace(); } }
From source file:com.maxl.java.aips2xml.Aips2Xml.java
public static void main(String[] args) { Options options = new Options(); addOption(options, "help", "print this message", false, false); addOption(options, "version", "print the version information and exit", false, false); addOption(options, "quiet", "be extra quiet", false, false); addOption(options, "verbose", "be extra verbose", false, false); addOption(options, "zip", "generate zip file", false, false); addOption(options, "lang", "use given language", true, false); addOption(options, "alpha", "only include titles which start with option value", true, false); addOption(options, "nodown", "no download, parse only", false, false); commandLineParse(options, args);// w ww .ja va2s . c o m // Download all files and save them in appropriate directories if (DOWNLOAD_ALL) { System.out.println(""); allDown(); } DateFormat df = new SimpleDateFormat("ddMMyy"); String date_str = df.format(new Date()); System.out.println(""); if (!DB_LANGUAGE.isEmpty()) { extractPackageInfo(); List<MedicalInformations.MedicalInformation> med_list = readAipsFile(); if (SHOW_LOGS) { System.out.println(""); System.out.println("- Generating xml and html files ... "); } long startTime = System.currentTimeMillis(); int counter = 0; String fi_complete_xml = ""; for (MedicalInformations.MedicalInformation m : med_list) { if (m.getLang().equals(DB_LANGUAGE) && m.getType().equals("fi")) { if (m.getTitle().startsWith(MED_TITLE)) { if (SHOW_LOGS) System.out.println(++counter + ": " + m.getTitle()); String[] html_str = extractHtmlSection(m); // html_str[0] -> registration numbers // html_str[1] -> content string String xml_str = convertHtmlToXml(m.getTitle(), html_str[1], html_str[0]); if (DB_LANGUAGE.equals("de")) { if (!html_str[0].isEmpty()) { String name = m.getTitle(); // Replace all "Sonderzeichen" name = name.replaceAll("[/%:]", "_"); writeToFile(html_str[1], "./fis/fi_de_html/", name + "_fi_de.html"); writeToFile(xml_str, "./fis/fi_de_xml/", name + "_fi_de.xml"); fi_complete_xml += (xml_str + "\n"); } } else if (DB_LANGUAGE.equals("fr")) { if (!html_str[0].isEmpty()) { String name = m.getTitle(); // Replace all "Sonderzeichen" name = name.replaceAll("[/%:]", "_"); writeToFile(html_str[1], "./fis/fi_fr_html/", name + "_fi_fr.html"); writeToFile(xml_str, "./fis/fi_fr_xml/", name + "_fi_fr.xml"); fi_complete_xml += (xml_str + "\n"); } } } } } // Add header to huge xml fi_complete_xml = addHeaderToXml(fi_complete_xml); // Dump to file if (DB_LANGUAGE.equals("de")) { writeToFile(fi_complete_xml, "./fis/", "fi_de.xml"); if (ZIP_XML) zipToFile("./fis/", "fi_de.xml"); } else if (DB_LANGUAGE.equals("fr")) { writeToFile(fi_complete_xml, "./fis/", "fi_fr.xml"); if (ZIP_XML) zipToFile("./fis/", "fi_fr.xml"); } // Move stylesheet file to ./fis/ folders try { File src = new File("./css/amiko_stylesheet.css"); File dst_de = new File("./fis/fi_de_html/"); File dst_fr = new File("./fis/fi_fr_html/"); if (src.exists()) { if (dst_de.exists()) FileUtils.copyFileToDirectory(src, dst_de); if (dst_fr.exists()) FileUtils.copyFileToDirectory(src, dst_fr); } } catch (IOException e) { // Unhandled! } if (SHOW_LOGS) { long stopTime = System.currentTimeMillis(); System.out.println("- Generated " + counter + " xml and html files in " + (stopTime - startTime) / 1000.0f + " sec"); } } System.exit(0); }