List of usage examples for java.io File delete
public boolean delete()
From source file:fi.jasoft.plugin.LibSassCompiler.java
public static void main(String[] args) throws Exception { File inputFile = new File(args[0]); File outputFile = new File(args[1]); if (!outputFile.exists()) { outputFile.createNewFile();//from w w w. jav a 2 s . com } File sourceMapFile = new File(args[1] + ".map"); if (!sourceMapFile.exists()) { sourceMapFile.createNewFile(); } File unpackedThemes = new File(args[2]); File unpackedInputFile = Paths .get(unpackedThemes.getCanonicalPath(), inputFile.getParentFile().getName(), inputFile.getName()) .toFile(); Compiler compiler = new Compiler(); Options options = new Options(); try { Output output = compiler.compileFile(unpackedInputFile.toURI(), outputFile.toURI(), options); FileUtils.write(outputFile, output.getCss(), StandardCharsets.UTF_8.name()); FileUtils.write(sourceMapFile, output.getSourceMap(), StandardCharsets.UTF_8.name()); } catch (CompilationException e) { outputFile.delete(); sourceMapFile.delete(); throw e; } }
From source file:edu.stanford.muse.launcher.Main.java
public static void main(String args[]) throws Exception { // set javawebstart.version to a dummy value if not already set (might happen when running with java -jar from cmd line) // exit.jsp doesn't allow us to showdown unless this prop is set if (System.getProperty("javawebstart.version") == null) System.setProperty("javawebstart.version", "UNKNOWN"); final int TIMEOUT_SECS = 60; if (args.length > 0) { out.print(args.length + " argument(s): "); for (int i = 0; i < args.length; i++) out.print(args[i] + " "); out.println();/*from www .j av a2 s . c o m*/ } Options options = getOpt(); CommandLineParser parser = new PosixParser(); CommandLine cmd = parser.parse(options, args); if (cmd.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Muse batch mode", options); return; } boolean debug = false; if (cmd.hasOption("debug")) { URL url = ClassLoader.getSystemResource("log4j.properties.debug"); out.println("Loading logging configuration from url: " + url); PropertyConfigurator.configure(url); debug = true; } else if (cmd.hasOption("debug-address-book")) { URL url = ClassLoader.getSystemResource("log4j.properties.debug.ab"); out.println("Loading logging configuration from url: " + url); PropertyConfigurator.configure(url); debug = false; } else if (cmd.hasOption("debug-groups")) { URL url = ClassLoader.getSystemResource("log4j.properties.debug.groups"); out.println("Loading logging configuration from url: " + url); PropertyConfigurator.configure(url); debug = false; } if (cmd.hasOption("no-browser-open")) browserOpen = false; if (cmd.hasOption("port")) { String portStr = cmd.getOptionValue('p'); try { PORT = Integer.parseInt(portStr); String mesg = " Running on port: " + PORT; out.println(mesg); } catch (NumberFormatException nfe) { out.println("invalid port number " + portStr); } } if (cmd.hasOption("start-page")) startPage = cmd.getOptionValue("start-page"); if (cmd.hasOption("base-dir")) baseDir = cmd.getOptionValue("base-dir"); if (cmd.hasOption("search-mode")) searchMode = true; if (cmd.hasOption("amuse-mode")) amuseMode = true; System.setSecurityManager(null); // this is important WebAppContext webapp0 = null; // deployWarAt("root.war", "/"); // for redirecting String path = "/muse"; WebAppContext webapp1 = deployWarAt("muse.war", path); if (webapp1 == null) { System.err.println("Aborting... no webapp"); return; } // if in any debug mode, turn blurring off if (debug) webapp1.setAttribute("noblur", true); // we set this and its read by JSPHelper within the webapp System.setProperty("muse.container", "jetty"); // need to copy crossdomain.xml file for String tmp = System.getProperty("java.io.tmpdir"); final URL url = Main.class.getClassLoader().getResource("crossdomain.xml"); try { InputStream is = url.openStream(); String file = tmp + File.separatorChar + "crossdomain.xml"; copy_stream_to_file(is, file); } catch (Exception e) { System.err.println("Aborting..." + e); return; } server = new Server(PORT); ResourceHandler resource_handler = new ResourceHandler(); // resource_handler.setWelcomeFiles(new String[]{ "index.html" }); resource_handler.setResourceBase(tmp); // set the header buffer size in the connectors, default is a ridiculous 4K, which causes failures any time there is // is a large request, such as selecting a few hundred folders. (even for posts!) // usually there is only one SocketConnector, so we just put the setHeaderBufferSize in a loop. Connector conns[] = server.getConnectors(); for (Connector conn : conns) { int NEW_BUFSIZE = 1000000; // out.println ("Connector " + conn + " buffer size is " + conn.getHeaderBufferSize() + " setting to " + NEW_BUFSIZE); conn.setHeaderBufferSize(NEW_BUFSIZE); } BASE_URL = "http://localhost:" + PORT + path; String MUSE_CHECK_URL = BASE_URL + "/js/muse.js"; // for quick check of existing muse or successful start up. BASE_URL may take some time to run and may not always be available now that we set dirAllowed to false and public mode does not serve /muse. String debugFile = tmp + File.separatorChar + "debug.txt"; HandlerList hl = new HandlerList(); if (webapp0 != null) hl.setHandlers(new Handler[] { webapp1, webapp0, resource_handler }); else hl.setHandlers(new Handler[] { webapp1, resource_handler }); out.println("Starting up Muse on the local computer at " + BASE_URL + ", " + formatDateLong(new GregorianCalendar())); out.println("***For troubleshooting information, see this file: " + debugFile + "***\n"); out.println("Current directory = " + System.getProperty("user.dir") + ", home directory = " + System.getProperty("user.home")); out.println("Memory status at the beginning: " + getMemoryStats()); if (Runtime.getRuntime().maxMemory() / MB < 512) aggressiveWarn( "You are probably running Muse without enough memory. \nIf you launched Muse from the command line, you can increase memory with an option like java -Xmx1g", 2000); server.setHandler(hl); // handle frequent error of user trying to launch another server when its already on // server.start() usually takes a few seconds to return // after that it takes a few seconds for the webapp to deploy // ignore any exceptions along the way and assume not if we can't prove it is alive boolean urlAlive = false; try { urlAlive = isURLAlive(MUSE_CHECK_URL); } catch (Exception e) { out.println("Exception: e"); e.printStackTrace(out); } boolean disableStart = false; if (urlAlive) { out.println("Oh! Muse is already running at the URL: " + BASE_URL + ", will have to kill it!"); killRunningServer(BASE_URL); Thread.sleep(3000); try { urlAlive = isURLAlive(MUSE_CHECK_URL); } catch (Exception e) { out.println("Exception: e"); e.printStackTrace(out); } if (!urlAlive) out.println("Good. Kill succeeded, will restart"); else { String message = "Previously running Muse still alive despite attempt to kill it, disabling fresh restart!\n"; message += "If you just want to use the previous instance of Muse, please go to http://localhost:9099/muse\n"; message += "\nTo kill this instance, please go to your computer's task manager and kill running java or javaw processes.\nThen try launching Muse again.\n"; aggressiveWarn(message, 2000); return; } } // else // out.println ("Muse not already alive at URL: ..." + URL); if (!disableStart) { out.println("Starting Muse at URL: ..." + BASE_URL); try { server.start(); } catch (BindException be) { out.println("port busy, but webapp not alive: " + BASE_URL + "\n" + be); throw new RuntimeException("Error: Port in use (Please kill Muse if its already running!)\n" + be); } } // webapp1.start(); -- not needed PrintStream debugOut1 = System.err; try { File f = new File(debugFile); if (f.exists()) f.delete(); // particular problem on windows :-( debugOut1 = new PrintStream(new FileOutputStream(debugFile), false, "UTF-8"); } catch (IOException ioe) { System.err.println("Warning: failed to delete debug file " + debugFile + " : " + ioe); } final PrintStream debugOut = debugOut1; Runtime.getRuntime().addShutdownHook(new Thread(new Runnable() { public void run() { try { server.stop(); server.destroy(); debugOut.close(); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } })); // InfoFrame frame = new InfoFrame(); // frame.doShow(); boolean success = waitTillPageAlive(MUSE_CHECK_URL, TIMEOUT_SECS); // frame.updateText ("Opening a browser window"); if (success) { // best effort to start shutdown thread // out.println ("Starting Muse shutdown listener at port " + JettyShutdownThread.SHUTDOWN_PORT); try { int shutdownPort = PORT + 1; // shut down port is arbitrarily set to port + 1. it is ASSUMED to be free. new JettyShutdownThread(server, shutdownPort).start(); out.println("Listening for Muse shutdown message on port " + shutdownPort); } catch (Exception e) { out.println( "Unable to start shutdown listener, you will have to stop the server manually using Cmd-Q on Mac OS or kill javaw processes on Windows"); } try { setupSystemTrayIcon(); } catch (Exception e) { out.println("Unable to setup system tray icon: " + e); e.printStackTrace(out); } // open browser window if (browserOpen) { preferredBrowser = null; // launch a browser here try { String link; if (System.getProperty("muse.mode.public") != null) link = "http://localhost:" + PORT + "/muse/archives/"; else link = "http://localhost:" + PORT + "/muse/index.jsp"; if (searchMode) { String u = "http://localhost:" + PORT + "/muse/search"; out.println("Launching URL in browser: " + u); link += "?mode=search"; } else if (amuseMode) { String u = "http://localhost:" + PORT + "/muse/amuse.jsp"; out.println("Launching URL in browser: " + u); link = u; } else if (startPage != null) { // startPage has to be absolute link = "http://localhost:" + PORT + "/muse/" + startPage; } if (baseDir != null) link = link + "?cacheDir=" + baseDir; // typically this is used when starting from command line. note: still using name, cacheDir out.println("Launching URL in browser: " + link); launchBrowser(link); } catch (Exception e) { out.println( "Warning: Unable to launch browser due to exception (use the -n option to prevent Muse from trying to launch a browser):"); e.printStackTrace(out); } } if (!cmd.hasOption("no-shutdown")) { // arrange to kill Muse after a period of time, we don't want the server to run forever // i clearly have too much time on my hands right now... long secs = KILL_AFTER_MILLIS / 1000; long hh = secs / 3600; long mm = (secs % 3600) / 60; long ss = secs % (60); out.print("Muse will shut down automatically after "); if (hh != 0) out.print(hh + " hours "); if (mm != 0 || (hh != 0 && ss != 0)) out.print(mm + " minutes"); if (ss != 0) out.print(ss + " seconds"); out.println(); Timer timer = new Timer(); TimerTask tt = new ShutdownTimerTask(); timer.schedule(tt, KILL_AFTER_MILLIS); } } else { out.println("\n\n\nSORRY!!! UNABLE TO DEPLOY WEBAPP, EXITING\n\n\n"); // frame.updateText("Sorry, looks like we are having trouble starting the jetty server\n"); } savedSystemOut = out; savedSystemErr = System.err; System.setOut(debugOut); System.setErr(debugOut); }
From source file:edu.stanford.muse.launcher.Splash.java
public static void main(String args[]) throws Exception { Splash splash = null;//ww w . j a v a 2 s . co m splash = new Splash(); tellUser(splash, "Setting up logging..."); setupLogging(); tellUser(splash, "Setting up shutdown port..."); basicSetup(args); BASE_URL = "http://localhost:" + PORT + "/" + WEBAPP_NAME; MUSE_CHECK_URL = BASE_URL + "/js/muse.js"; // for quick check of existing muse or successful start up. BASE_URL may take some time to run and may not always be available now that we set dirAllowed to false and public mode does not serve /muse. tellUser(splash, "Log file: " + debugFile + "***\n"); out.println("Starting up ePADD on the local computer at " + BASE_URL + ", " + formatDateLong(new GregorianCalendar())); out.println("***For troubleshooting information, see this file: " + debugFile + "***\n"); out.println("Current directory = " + System.getProperty("user.dir") + ", home directory = " + System.getProperty("user.home")); out.println("Memory status at the beginning: " + getMemoryStats()); if (Runtime.getRuntime().maxMemory() / MB < 512) aggressiveWarn( "You are probably running ePADD without enough memory. \nIf you launched ePADD from the command line, you can increase memory with an option like java -Xmx1g", 2000); tellUser(splash, "Memory: " + getMemoryStats()); // handle frequent error of user trying to launch another server when its already on // server.start() usually takes a few seconds to return // after that it takes a few seconds for the webapp to deploy // ignore any exceptions along the way and assume not if we can't prove it is alive boolean urlAlive = false; try { urlAlive = isURLAlive(MUSE_CHECK_URL); } catch (Exception e) { out.println("Exception: e"); e.printStackTrace(out); } boolean disableStart = false; if (urlAlive) { out.println("Oh! ePADD already running at: " + BASE_URL + ", will shut it down!"); tellUser(splash, "ePADD already running at: " + BASE_URL + ", will shut it down!"); killRunningServer(BASE_URL); boolean killed = false; int N_KILL_TRIES = 20, N_KILL_PERIOD_MILLIS = 3000; // check every 3 secs 20 times (total 1 minute) for the previous muse to die // if it doesn't die after a minute, fail for (int i = 0; i < N_KILL_TRIES; i++) { try { Thread.sleep(N_KILL_PERIOD_MILLIS); } catch (InterruptedException ie) { } out.println("Checking " + MUSE_CHECK_URL); tellUser(splash, "Checking " + MUSE_CHECK_URL); try { urlAlive = isURLAlive(MUSE_CHECK_URL); } catch (Exception e) { out.println("Exception: " + e); e.printStackTrace(out); } if (!urlAlive) break; } if (!urlAlive) { out.println("Good. Shutdown succeeded, will restart"); tellUser(splash, "Good. Shutdown succeeded, we'll restart ePADD."); } else { String message = "Previously running ePADD still alive despite attempt to shut it down, disabling fresh restart!\n"; message += "If you just want to use the previous instance of ePADD, please go to " + BASE_URL; message += "\nTo kill this instance, please go to your computer's task manager and kill running java or javaw processes.\nThen try launching ePADD again.\n"; aggressiveWarn(message, 2000); tellUser(splash, "Sorry, unable to kill previous ePADD. Quitting!"); try { Thread.sleep(10000); } catch (InterruptedException ie) { } if (splash != null) splash.close(); return; } } // else // out.println ("Muse not already alive at URL: ..." + URL); if (!disableStart) { setupResources(); out.println("Starting ePADD at URL: ..." + BASE_URL); tellUser(splash, "Starting ePADD at " + BASE_URL); server.start(); PrintStream debugOut1 = err; try { File f = new File(debugFile); if (f.exists()) f.delete(); // particular problem on windows :-( debugOut1 = new PrintStream(new FileOutputStream(debugFile), false, "UTF-8"); } catch (IOException ioe) { err.println("Warning: failed to delete debug file " + debugFile + " : " + ioe); } final PrintStream debugOut = debugOut1; Runtime.getRuntime().addShutdownHook(new Thread(new Runnable() { public void run() { try { shutdownSessions(); server.stop(); server.destroy(); debugOut.close(); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } } })); // InfoFrame frame = new InfoFrame(); // frame.doShow(); boolean success = waitTillPageAlive(MUSE_CHECK_URL, TIMEOUT_SECS); // frame.updateText ("Opening a browser window"); if (success) { try { int shutdownPort = PORT + 1; // shut down port is arbitrarily set to port + 1. it is ASSUMED to be free. new ShutdownThread(server, shutdownPort).start(); out.println("Listening for ePADD shutdown message on port " + shutdownPort); tellUser(splash, "Listening for ePADD shutdown message on port " + shutdownPort); } catch (Exception e) { out.println( "Unable to start shutdown listener, you will have to stop the server manually using Cmd-Q on Mac OS or kill javaw processes on Windows"); } try { setupSystemTrayIcon(); } catch (Exception e) { err.println("Unable to setup system tray icon: " + e); e.printStackTrace(err); } // open browser window if (browserOpen) { preferredBrowser = null; // launch a browser here try { String link; link = "http://localhost:" + PORT + "/muse/index.jsp"; if (startPage != null) { // startPage has to be absolute link = "http://localhost:" + PORT + "/muse/" + startPage; } if (baseDir != null) link = link + "?cacheDir=" + baseDir; // typically this is used when starting from command line. note: still using name, cacheDir launchBrowser(link, splash); } catch (Exception e) { out.println( "Warning: Unable to launch browser due to exception (use the -n option to prevent ePADD from trying to launch a browser):"); e.printStackTrace(out); } } } else { out.println("\n\n\nSORRY!!! UNABLE TO DEPLOY WEBAPP, EXITING\n\n\n"); tellUser(splash, "SORRY!!! UNABLE TO DEPLOY WEBAPP, EXITING"); } savedSystemOut = out; savedSystemErr = err; System.setOut(debugOut); System.setErr(debugOut); if (splash != null) splash.close(); } // splashDemo.closeWindow(); }
From source file:edu.stanford.epadd.launcher.Splash.java
public static void main(String args[]) throws Exception { Splash splash = null;/*w ww . j ava2 s. c o m*/ boolean headless = (System.getProperty("muse.mode.server") != null); if (!headless) splash = new Splash(); else { System.out.println("Muse running in headless mode!"); browserOpen = false; } tellUser(splash, "Setting up logging..."); setupLogging(); basicSetup(args); BASE_URL = "http://localhost:" + PORT + "/" + WEBAPP_NAME; MUSE_CHECK_URL = BASE_URL + "/js/muse.js"; // for quick check of existing muse or successful start up. BASE_URL may take some time to run and may not always be available now that we set dirAllowed to false and public mode does not serve /muse. tellUser(splash, "Log file: " + debugFile + "***\n"); out.println("Starting up ePADD on the local computer at " + BASE_URL + ", " + formatDateLong(new GregorianCalendar())); out.println("***For troubleshooting information, see this file: " + debugFile + "***\n"); out.println("Current directory = " + System.getProperty("user.dir") + ", home directory = " + System.getProperty("user.home")); out.println("Memory status at the beginning: " + getMemoryStats()); if (Runtime.getRuntime().maxMemory() / MB < 512) aggressiveWarn( "You are probably running ePADD without enough memory. \nIf you launched ePADD from the command line, you can increase memory with an option like java -Xmx1g", 2000); tellUser(splash, "Memory: " + getMemoryStats()); // handle frequent error of user trying to launch another server when its already on // server.start() usually takes a few seconds to return // after that it takes a few seconds for the webapp to deploy // ignore any exceptions along the way and assume not if we can't prove it is alive boolean urlAlive = false; try { urlAlive = isURLAlive(MUSE_CHECK_URL); } catch (Exception e) { out.println("Exception: e"); e.printStackTrace(out); } boolean disableStart = false; if (urlAlive) { out.println("Oh! ePADD already running at: " + BASE_URL + ", will shut it down!"); tellUser(splash, "ePADD already running at: " + BASE_URL + ", will shut it down!"); killRunningServer(BASE_URL); boolean killed = false; int N_KILL_TRIES = 20, N_KILL_PERIOD_MILLIS = 3000; // check every 3 secs 20 times (total 1 minute) for the previous epadd to die // if it doesn't die after a minute, fail for (int i = 0; i < N_KILL_TRIES; i++) { try { Thread.sleep(N_KILL_PERIOD_MILLIS); } catch (InterruptedException ie) { } out.println("Checking " + MUSE_CHECK_URL); tellUser(splash, "Checking " + MUSE_CHECK_URL); try { urlAlive = isURLAlive(MUSE_CHECK_URL); } catch (Exception e) { out.println("Exception: " + e); e.printStackTrace(out); } if (!urlAlive) break; } if (!urlAlive) { out.println("Good. Shutdown succeeded, will restart"); tellUser(splash, "Good. Shutdown succeeded, we'll restart ePADD."); } else { String message = "Previously running ePADD still alive despite attempt to shut it down, disabling fresh restart!\n"; message += "If you just want to use the previous instance of ePADD, please go to " + BASE_URL; message += "\nTo kill this instance, please go to your computer's task manager and kill running java or javaw processes.\nThen try launching ePADD again.\n"; aggressiveWarn(message, 2000); tellUser(splash, "Sorry, unable to kill previous ePADD. Quitting!"); try { Thread.sleep(10000); } catch (InterruptedException ie) { } if (splash != null) splash.close(); return; } } // else // out.println ("Muse not already alive at URL: ..." + URL); if (!disableStart) { setupResources(); out.println("Starting ePADD at URL: ..." + BASE_URL); tellUser(splash, "Starting ePADD at " + BASE_URL); server.start(); PrintStream debugOut1 = err; try { File f = new File(debugFile); if (f.exists()) f.delete(); // particular problem on windows :-( debugOut1 = new PrintStream(new FileOutputStream(debugFile), false, "UTF-8"); } catch (IOException ioe) { out.println("Warning: failed to delete debug file " + debugFile + " : " + ioe); } final PrintStream debugOut = debugOut1; Runtime.getRuntime().addShutdownHook(new Thread(new Runnable() { public void run() { try { shutdownSessions(); server.stop(); server.destroy(); debugOut.close(); } catch (Exception e) { e.printStackTrace(); } } })); boolean success = waitTillPageAlive(MUSE_CHECK_URL, TIMEOUT_SECS); if (success) { try { int shutdownPort = PORT + 1; // shut down port is arbitrarily set to port + 1. it is ASSUMED to be free. tellUser(splash, "Setting up shutdown port..."); new ShutdownThread(server, shutdownPort).start(); // this will start a non-daemon thread that keeps the process alive out.println("Listening for ePADD shutdown message on port " + shutdownPort); tellUser(splash, "Listening for ePADD shutdown message on port " + shutdownPort); } catch (Exception e) { out.println( "Unable to start shutdown listener, you will have to stop the server manually using Cmd-Q on Mac OS or kill javaw processes on Windows"); } try { setupSystemTrayIcon(); } catch (Exception e) { out.println("Unable to setup system tray icon: " + e); e.printStackTrace(err); } // open browser window if (browserOpen) { preferredBrowser = null; // launch a browser here try { String link; link = "http://localhost:" + PORT + "/muse/index.jsp"; if (startPage != null) { // startPage has to be absolute link = "http://localhost:" + PORT + "/muse/" + startPage; } if (baseDir != null) link = link + "?cacheDir=" + baseDir; // typically this is used when starting from command line. note: still using name, cacheDir launchBrowser(link, splash); } catch (Exception e) { out.println( "Warning: Unable to launch browser due to exception (use the -n option to prevent ePADD from trying to launch a browser):"); e.printStackTrace(out); } } } else { out.println("\n\n\nSORRY!!! UNABLE TO DEPLOY WEBAPP, EXITING\n\n\n"); tellUser(splash, "SORRY!!! UNABLE TO DEPLOY WEBAPP, EXITING"); } savedSystemOut = out; savedSystemErr = err; System.setOut(debugOut); System.setErr(debugOut); if (splash != null) splash.close(); } // program should not halt here, as ShutdownThread is running as a non-daemon thread. // splashDemo.closeWindow(); }
From source file:com.l2jserver.model.template.NPCTemplateConverter.java
public static void main(String[] args) throws SQLException, IOException, ClassNotFoundException, JAXBException { controllers.put("L2Teleporter", TeleporterController.class); controllers.put("L2CastleTeleporter", TeleporterController.class); controllers.put("L2Npc", BaseNPCController.class); controllers.put("L2Monster", MonsterController.class); controllers.put("L2FlyMonster", MonsterController.class); Class.forName("com.mysql.jdbc.Driver"); final File target = new File("generated/template/npc"); System.out.println("Scaning legacy HTML files..."); htmlScannedFiles = FileUtils.listFiles(L2J_HTML_FOLDER, new String[] { "html", "htm" }, true); final JAXBContext c = JAXBContext.newInstance(NPCTemplate.class, Teleports.class); final Connection conn = DriverManager.getConnection(JDBC_URL, JDBC_USERNAME, JDBC_PASSWORD); {/*from www. j a va 2s .c o m*/ System.out.println("Converting teleport templates..."); teleportation.teleport = CollectionFactory.newList(); final Marshaller m = c.createMarshaller(); m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true); final PreparedStatement st = conn.prepareStatement("SELECT * FROM teleport"); st.execute(); final ResultSet rs = st.getResultSet(); while (rs.next()) { final TeleportationTemplate template = new TeleportationTemplate(); template.id = new TeleportationTemplateID(rs.getInt("id"), null); template.name = rs.getString("Description"); TemplateCoordinate coord = new TemplateCoordinate(); coord.x = rs.getInt("loc_x"); coord.y = rs.getInt("loc_y"); coord.z = rs.getInt("loc_z"); template.point = coord; template.price = rs.getInt("price"); template.item = rs.getInt("itemId"); if (rs.getBoolean("fornoble")) { template.restrictions = new Restrictions(); template.restrictions.restriction = Arrays.asList("NOBLE"); } teleportation.teleport.add(template); } m.marshal(teleportation, getXMLSerializer(new FileOutputStream(new File(target, "../teleports.xml")))); // System.exit(0); } System.out.println("Generating template XML files..."); // c.generateSchema(new SchemaOutputResolver() { // @Override // public Result createOutput(String namespaceUri, // String suggestedFileName) throws IOException { // // System.out.println(new File(target, suggestedFileName)); // // return null; // return new StreamResult(new File(target, suggestedFileName)); // } // }); try { final Marshaller m = c.createMarshaller(); m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true); final PreparedStatement st = conn.prepareStatement( "SELECT npc.*, npcskills.level AS race " + "FROM npc " + "LEFT JOIN npcskills " + "ON(npc.idTemplate = npcskills.npcid AND npcskills.skillid = ?)"); st.setInt(1, 4416); st.execute(); final ResultSet rs = st.getResultSet(); while (rs.next()) { Object[] result = fillNPC(rs); NPCTemplate t = (NPCTemplate) result[0]; String type = (String) result[1]; String folder = createFolder(type); if (folder.isEmpty()) { m.setProperty(Marshaller.JAXB_SCHEMA_LOCATION, "npc ../npc.xsd"); } else { m.setProperty(Marshaller.JAXB_SCHEMA_LOCATION, "npc ../../npc.xsd"); } final File file = new File(target, "npc/" + folder + "/" + t.getID().getID() + (t.getInfo().getName() != null ? "-" + camelCase(t.getInfo().getName().getValue()) : "") + ".xml"); file.getParentFile().mkdirs(); templates.add(t); try { m.marshal(t, getXMLSerializer(new FileOutputStream(file))); } catch (MarshalException e) { System.err.println("Could not generate XML template file for " + t.getInfo().getName().getValue() + " - " + t.getID()); file.delete(); } } System.out.println("Generated " + templates.size() + " templates"); System.gc(); System.out.println("Free: " + FileUtils.byteCountToDisplaySize(Runtime.getRuntime().freeMemory())); System.out.println("Total: " + FileUtils.byteCountToDisplaySize(Runtime.getRuntime().totalMemory())); System.out.println("Used: " + FileUtils.byteCountToDisplaySize( Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory())); System.out.println("Max: " + FileUtils.byteCountToDisplaySize(Runtime.getRuntime().maxMemory())); } finally { conn.close(); } }
From source file:net.minecraftforge.fml.common.asm.transformers.MarkerTransformer.java
public static void main(String[] args) { if (args.length < 2) { System.out.println("Usage: MarkerTransformer <JarPath> <MapFile> [MapFile2]... "); return;// ww w . j a va 2 s . c o m } boolean hasTransformer = false; MarkerTransformer[] trans = new MarkerTransformer[args.length - 1]; for (int x = 1; x < args.length; x++) { try { trans[x - 1] = new MarkerTransformer(args[x]); hasTransformer = true; } catch (IOException e) { System.out.println("Could not read Transformer Map: " + args[x]); e.printStackTrace(); } } if (!hasTransformer) { System.out.println("Could not find a valid transformer to perform"); return; } File orig = new File(args[0]); File temp = new File(args[0] + ".ATBack"); if (!orig.exists() && !temp.exists()) { System.out.println("Could not find target jar: " + orig); return; } /* if (temp.exists()) { if (orig.exists() && !orig.renameTo(new File(args[0] + (new SimpleDateFormat(".yyyy.MM.dd.HHmmss")).format(new Date())))) { System.out.println("Could not backup existing file: " + orig); return; } if (!temp.renameTo(orig)) { System.out.println("Could not restore backup from previous run: " + temp); return; } } */ if (!orig.renameTo(temp)) { System.out.println("Could not rename file: " + orig + " -> " + temp); return; } try { processJar(temp, orig, trans); } catch (IOException e) { e.printStackTrace(); } if (!temp.delete()) { System.out.println("Could not delete temp file: " + temp); } }
From source file:com.spinn3r.api.Main.java
public static void main(String[] args) throws Exception { // NOTE this could be cleaned up to pass the values into the config // object directly. // parse out propeties. String api = null;/*from w w w . jav a 2 s. co m*/ for (int i = 0; i < args.length; ++i) { String v = args[i]; if (v.startsWith("--api")) { api = getOpt(v); } } if (api == null) api = "permalink"; // First. Determine which API you'd like to use. long after = -1; Format format = Format.PROTOSTREAM; String vendor = null; String remoteFilter = null; Long sleep_duration = null; boolean skip_description = false; String host = "api.spinn3r.com"; for (int i = 0; i < args.length; ++i) { String v = args[i]; if (v.startsWith("--vendor")) { vendor = getOpt(v); continue; } if (v.startsWith("--filter")) { filter = getOpt(v); continue; } if (v.startsWith("--remote-filter")) { remoteFilter = getOpt(v); continue; } if (v.startsWith("--show_results")) { show_results = Integer.parseInt(getOpt(v)); continue; } /* * The code for the --afterTimestamp must come * before the code for --after because --afterTimestamp * also matches startsWith("after"); */ if (v.startsWith("--afterTimestamp")) { after = Long.parseLong(getOpt(v)); continue; } if (v.startsWith("--after")) { after = getOptAsTimeInMillis(v); continue; } /* * The code for the --beforeTimestamp must come * before the code for --before because --beforeTimestamp * also matches startsWith("before"); */ if (v.startsWith("--beforeTimestamp")) { before = Long.parseLong(getOpt(v)); continue; } if (v.startsWith("--before")) { before = getOptAsTimeInMillis(v); continue; } if (v.startsWith("--range")) { range = Long.parseLong(getOpt(v)); continue; } if (v.startsWith("--recover")) { restore = true; continue; } if (v.startsWith("--sleep_duration")) { sleep_duration = Long.parseLong(getOpt(v)); continue; } if (v.startsWith("--save=")) { save = getOpt(v); continue; } if (v.startsWith("--save_method=")) { save_method = getOpt(v); continue; } if (v.startsWith("--skip_description=")) { skip_description = Boolean.parseBoolean(getOpt(v)); continue; } if (v.startsWith("--save_compressed=")) { saveCompressed = Boolean.parseBoolean(getOpt(v)); continue; } if (v.startsWith("--timing")) { timing = "true".equals(getOpt(v)); continue; } if (v.startsWith("--debug")) { logLevel = Level.FINE; debugLogFilePath = getOpt(v); continue; } /* * if ( v.startsWith( "--spam_probability" ) ) { * config.setSpamProbability( Double.parseDouble( getOpt( v ) ) ); * continue; } */ if (v.startsWith("--dump_fields=")) { dumpFields = Boolean.parseBoolean(getOpt(v)); continue; } if (v.startsWith("--dump=")) { dump = Boolean.parseBoolean(getOpt(v)); continue; } if (v.startsWith("--csv=")) { csv = Boolean.parseBoolean(getOpt(v)); continue; } if (v.startsWith("--memory")) { System.out.printf("max memory: %s\n", Runtime.getRuntime().maxMemory()); System.exit(0); } if (v.startsWith("--host")) { host = getOpt(v); continue; } if (v.startsWith("--enable3")) { // is now default continue; } if (v.startsWith("com.spinn3r")) continue; if (v.startsWith("--api")) continue; // That's an unknown command line option. Exit. System.err.printf("Unknown command line option: %s\n", v); syntax(); System.exit(1); } /* * Set the log level */ Logger anonymousLogger = Logger.getAnonymousLogger(); anonymousLogger.setLevel(logLevel); if (debugLogFilePath != null) { anonymousLogger.addHandler(new FileHandler(debugLogFilePath)); } Factory factory = new Factory(); String restoreURL = null; if (save != null && restore) { File savedir = new File(save); Collection<File> logFiles = getLogFiles(savedir); PermalinkLogReaderAdapter adapter = getRestoreURLS(logFiles); restoreURL = adapter.getLastUrl(); long ctr = adapter.getLastCtr(); for (File file : logFiles) { if (!file.delete()) throw new IOException("Failed to delete " + file.toString()); } factory.enableLogging(savedir, 1000000); if (restoreURL != null) { factory.enableRestart(ctr, restoreURL); } logManager = factory.getInjector().getInstance(TransactionHistoryManager.class); } else { logManager = factory.getInjector().getInstance(TransactionHistoryManager.class); } Config<? extends BaseResult> config = null; BaseClient<? extends BaseResult> client = null; if (api.startsWith("feed")) { config = new FeedConfig(); client = new FeedClient(); } else if (api.startsWith("comment")) { config = new CommentConfig(); client = new CommentClient(); } else { config = new PermalinkConfig(); client = new PermalinkClient( restoreURL != null ? ImmutableList.of(restoreURL) : Collections.<String>emptyList()); } config.setCommandLine(StringUtils.join(args, " ")); config.setApi(api); config.setFormat(format); config.setVendor(vendor); config.setHost(host); config.setFilter(remoteFilter); config.setSkipDescription(skip_description); if (sleep_duration != null) client.setSleepDuration(sleep_duration); // assert that we have all required options. if (config.getVendor() == null) { syntax(); System.exit(1); } long maxMemory = Runtime.getRuntime().maxMemory(); long requiredMemory = (save == null) ? PARSE_REQUIRED_MEMORY : SAVE_REQUIRED_MEMORY; if (maxMemory < requiredMemory) { System.out.printf("ERROR: Reference client requires at least 2GB of memory.\n"); System.out.printf("\n"); System.out.printf("Now running with: %s vs %s required\n", maxMemory, requiredMemory); System.out.printf("\n"); System.out.printf("Add -Xmx%dM to your command line and run again.\n", requiredMemory / (1024 * 1024)); System.exit(1); } // use defaults System.out.println("Using vendor: " + config.getVendor()); System.out.println("Using api: " + api); if (after > -1) System.out.printf("After: %s (%s)\n", ISO8601DateParser.toString(Config.timestampToDate(after)), after); if (before > -1) System.out.printf("Before: %s (%s)\n", ISO8601DateParser.toString(Config.timestampToDate(before)), before); System.out.println("Saving results to disk: " + save); // Fetch for the last 5 minutes and then try to get up to date. In // production you'd want to call setFirstRequestURL from the // getLastRequestURL returned from fetch() below if (after == -1) { after = Config.millisecondsToTimestamp(System.currentTimeMillis()); after = after - INTERVAL; } config.setAfterTimestamp(after); new Main().exec(client, config); }
From source file:jhc.redsniff.generation.PackageScanningGenerator.java
public static void main(String[] args) throws Exception { if (args.length != 5) { System.err.println("Args: source-dir package-class-filter parent-class generated-class output-dir"); System.err.println(""); System.err.println(" source-dir : Path to Java source containing matchers to generate sugar for."); System.err.println(" May contain multiple paths, separated by commas."); System.err.println(" e.g. src/java,src/more-java"); System.err.println(/* ww w . java 2 s . c o m*/ " package-class-filter : base of package to look for classes with methods, eg jhc.selenium.matchers"); System.err.println(""); System.err.println( "parent-class : Full name of parent class type to examine - eg org.hamcrest.Matcher, jhc.selenium.seeker.Seeker"); System.err.println(" e.g. org.myproject.MyMatchers"); System.err.println("generated-class : Full name of class to generate."); System.err.println(" e.g. org.myproject.MyMatchers"); System.err.println(""); System.err.println(" output-dir : Where to output generated code (package subdirs will be"); System.err.println(" automatically created)."); System.err.println(" e.g. build/generated-code"); System.exit(-1); } String srcDirs = args[0]; String package_name_prefix = args[1]; String parentClassName = args[2]; String fullClassName = args[3]; File outputDir = new File(args[4]); String fileName = fullClassName.replace('.', File.separatorChar) + ".java"; int dotIndex = fullClassName.lastIndexOf("."); String packageName = dotIndex == -1 ? "" : fullClassName.substring(0, dotIndex); String shortClassName = fullClassName.substring(dotIndex + 1); if (!outputDir.isDirectory()) { System.err.println("Output directory not found : " + outputDir.getAbsolutePath()); System.exit(-1); } Class<?> parentClass = Class.forName(parentClassName); File outputFile = new File(outputDir, fileName); outputFile.getParentFile().mkdirs(); File tmpFile = new File(outputDir, fileName + ".tmp"); SugarGenerator sugarGenerator = new SugarGenerator(); try { sugarGenerator .addWriter(new SeleniumFactoryWriter(packageName, shortClassName, new FileWriter(tmpFile))); sugarGenerator.addWriter(new QuickReferenceWriter(System.out)); PackageScanningGenerator pkgScanningGenerator = new PackageScanningGenerator(sugarGenerator, PackageScanningGenerator.class.getClassLoader(), parentClass); if (srcDirs.trim().length() > 0) { for (String srcDir : srcDirs.split(",")) { pkgScanningGenerator.addSourceDir(new File(srcDir)); } } // could add use of xml just to list filter expressions // pkgScanningGenerator.load(new InputSource(configFile)); pkgScanningGenerator.addClasses(package_name_prefix); System.out.println("Generating " + fullClassName); sugarGenerator.generate(); sugarGenerator.close(); outputFile.delete(); FileUtils.moveFile(tmpFile, outputFile); } finally { tmpFile.delete(); sugarGenerator.close(); } }
From source file:ms1quant.MS1Quant.java
/** * @param args the command line arguments MS1Quant parameterfile *///from w ww . j ava2 s. c o m public static void main(String[] args) throws Exception { BufferedReader reader = null; try { System.out.println( "================================================================================================="); System.out.println("Umpire MS1 quantification and feature detection analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length < 3 || !args[1].startsWith("-mode")) { System.out .println("command : java -jar -Xmx10G MS1Quant.jar ms1quant.params -mode[1 or 2] [Option]"); System.out.println("\n-mode"); System.out.println("\t1:Single file mode--> mzXML_file PepXML_file"); System.out.println("\t\tEx: -mode1 file1.mzXML file1.pep.xml"); System.out.println( "\t2:Folder mode--> mzXML_Folder PepXML_Folder, all generated csv tables will be merged into a single csv file"); System.out.println("\t\tEx: -mode2 /data/mzxml/ /data/pepxml/"); System.out.println("\nOptions"); System.out.println( "\t-C\tNo of concurrent files to be processed (only for folder mode), Ex. -C5, default:1"); System.out.println("\t-p\tMinimum probability, Ex. -p0.9, default:0.9"); System.out.println("\t-ID\tDetect identified feature only"); System.out.println("\t-O\toutput folder, Ex. -O/data/"); return; } ConsoleLogger consoleLogger = new ConsoleLogger(); consoleLogger.SetConsoleLogger(Level.DEBUG); consoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "ms1quant_debug.log"); Logger logger = Logger.getRootLogger(); logger.debug("Command: " + Arrays.toString(args)); logger.info("MS1Quant version: " + UmpireInfo.GetInstance().Version); String parameterfile = args[0]; logger.info("Parameter file: " + parameterfile); File paramfile = new File(parameterfile); if (!paramfile.exists()) { logger.error("Parameter file " + paramfile.getAbsolutePath() + " cannot be found. The program will exit."); } reader = new BufferedReader(new FileReader(paramfile.getAbsolutePath())); String line = ""; InstrumentParameter param = new InstrumentParameter(InstrumentParameter.InstrumentType.TOF5600); int NoCPUs = 2; int NoFile = 1; param.DetermineBGByID = false; param.EstimateBG = true; //<editor-fold defaultstate="collapsed" desc="Read parameter file"> while ((line = reader.readLine()) != null) { if (!"".equals(line) && !line.startsWith("#")) { logger.info(line); //System.out.println(line); if (line.split("=").length < 2) { continue; } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); if (type.startsWith("para.")) { type = type.replace("para.", "SE."); } String value = line.split("=")[1].trim(); switch (type) { case "Thread": { NoCPUs = Integer.parseInt(value); break; } //<editor-fold defaultstate="collapsed" desc="instrument parameters"> case "SE.MS1PPM": { param.MS1PPM = Float.parseFloat(value); break; } case "SE.MS2PPM": { param.MS2PPM = Float.parseFloat(value); break; } case "SE.SN": { param.SNThreshold = Float.parseFloat(value); break; } case "SE.MS2SN": { param.MS2SNThreshold = Float.parseFloat(value); break; } case "SE.MinMSIntensity": { param.MinMSIntensity = Float.parseFloat(value); break; } case "SE.MinMSMSIntensity": { param.MinMSMSIntensity = Float.parseFloat(value); break; } case "SE.MinRTRange": { param.MinRTRange = Float.parseFloat(value); break; } case "SE.MaxNoPeakCluster": { param.MaxNoPeakCluster = Integer.parseInt(value); param.MaxMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinNoPeakCluster": { param.MinNoPeakCluster = Integer.parseInt(value); param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinMS2NoPeakCluster": { param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MaxCurveRTRange": { param.MaxCurveRTRange = Float.parseFloat(value); break; } case "SE.Resolution": { param.Resolution = Integer.parseInt(value); break; } case "SE.RTtol": { param.RTtol = Float.parseFloat(value); break; } case "SE.NoPeakPerMin": { param.NoPeakPerMin = Integer.parseInt(value); break; } case "SE.StartCharge": { param.StartCharge = Integer.parseInt(value); break; } case "SE.EndCharge": { param.EndCharge = Integer.parseInt(value); break; } case "SE.MS2StartCharge": { param.MS2StartCharge = Integer.parseInt(value); break; } case "SE.MS2EndCharge": { param.MS2EndCharge = Integer.parseInt(value); break; } case "SE.NoMissedScan": { param.NoMissedScan = Integer.parseInt(value); break; } case "SE.Denoise": { param.Denoise = Boolean.valueOf(value); break; } case "SE.EstimateBG": { param.EstimateBG = Boolean.valueOf(value); break; } case "SE.RemoveGroupedPeaks": { param.RemoveGroupedPeaks = Boolean.valueOf(value); break; } case "SE.MinFrag": { param.MinFrag = Integer.parseInt(value); break; } case "SE.IsoPattern": { param.IsoPattern = Float.valueOf(value); break; } case "SE.StartRT": { param.startRT = Float.valueOf(value); } case "SE.EndRT": { param.endRT = Float.valueOf(value); } //</editor-fold> } } } //</editor-fold> int mode = 1; if (args[1].equals("-mode2")) { mode = 2; } else if (args[1].equals("-mode1")) { mode = 1; } else { logger.error("-mode number not recongized. The program will exit."); } String mzXML = ""; String pepXML = ""; String mzXMLPath = ""; String pepXMLPath = ""; File mzXMLfile = null; File pepXMLfile = null; File mzXMLfolder = null; File pepXMLfolder = null; int idx = 0; if (mode == 1) { mzXML = args[2]; logger.info("Mode1 mzXML file: " + mzXML); mzXMLfile = new File(mzXML); if (!mzXMLfile.exists()) { logger.error("Mode1 mzXML file " + mzXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } pepXML = args[3]; logger.info("Mode1 pepXML file: " + pepXML); pepXMLfile = new File(pepXML); if (!pepXMLfile.exists()) { logger.error("Mode1 pepXML file " + pepXMLfile.getAbsolutePath() + " cannot be found. The program will exit."); return; } idx = 4; } else if (mode == 2) { mzXMLPath = args[2]; logger.info("Mode2 mzXML folder: " + mzXMLPath); mzXMLfolder = new File(mzXMLPath); if (!mzXMLfolder.exists()) { logger.error("Mode2 mzXML folder " + mzXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } pepXMLPath = args[3]; logger.info("Mode2 pepXML folder: " + pepXMLPath); pepXMLfolder = new File(pepXMLPath); if (!pepXMLfolder.exists()) { logger.error("Mode2 pepXML folder " + pepXMLfolder.getAbsolutePath() + " does not exist. The program will exit."); return; } idx = 4; } String outputfolder = ""; float MinProb = 0f; for (int i = idx; i < args.length; i++) { if (args[i].startsWith("-")) { if (args[i].equals("-ID")) { param.TargetIDOnly = true; logger.info("Detect ID feature only: true"); } if (args[i].startsWith("-O")) { outputfolder = args[i].substring(2); logger.info("Output folder: " + outputfolder); File outputfile = new File(outputfolder); if (!outputfolder.endsWith("\\") | outputfolder.endsWith("/")) { outputfolder += "/"; } if (!outputfile.exists()) { outputfile.mkdir(); } } if (args[i].startsWith("-C")) { try { NoFile = Integer.parseInt(args[i].substring(2)); logger.info("No of concurrent files: " + NoFile); } catch (Exception ex) { logger.error(args[i] + " is not a correct integer format, will process only one file at a time."); } } if (args[i].startsWith("-p")) { try { MinProb = Float.parseFloat(args[i].substring(2)); logger.info("probability threshold: " + MinProb); } catch (Exception ex) { logger.error(args[i] + " is not a correct format, will use 0 as threshold instead."); } } } } reader.close(); TandemParam tandemparam = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); PTMManager.GetInstance(); if (param.TargetIDOnly) { param.EstimateBG = false; param.ApexDelta = 1.5f; param.NoMissedScan = 10; param.MiniOverlapP = 0.2f; param.RemoveGroupedPeaks = false; param.CheckMonoIsotopicApex = false; param.DetectByCWT = false; param.FillGapByBK = false; param.IsoCorrThreshold = -1f; param.SmoothFactor = 3; } if (mode == 1) { logger.info("Processing " + mzXMLfile.getAbsolutePath() + "...."); long time = System.currentTimeMillis(); LCMSPeakMS1 LCMS1 = new LCMSPeakMS1(mzXMLfile.getAbsolutePath(), NoCPUs); LCMS1.SetParameter(param); LCMS1.Resume = false; if (!param.TargetIDOnly) { LCMS1.CreatePeakFolder(); } LCMS1.ExportPeakClusterTable = true; if (pepXMLfile.exists()) { tandemparam.InteractPepXMLPath = pepXMLfile.getAbsolutePath(); LCMS1.ParsePepXML(tandemparam, MinProb); logger.info("No. of PSMs included: " + LCMS1.IDsummary.PSMList.size()); logger.info("No. of Peptide ions included: " + LCMS1.IDsummary.GetPepIonList().size()); } if (param.TargetIDOnly) { LCMS1.SaveSerializationFile = false; } if (param.TargetIDOnly || !LCMS1.ReadPeakCluster()) { LCMS1.PeakClusterDetection(); } if (pepXMLfile.exists()) { LCMS1.AssignQuant(false); LCMS1.IDsummary.ExportPepID(outputfolder); } time = System.currentTimeMillis() - time; logger.info(LCMS1.ParentmzXMLName + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); LCMS1.BaseClearAllPeaks(); LCMS1.SetSpectrumParser(null); LCMS1.IDsummary = null; LCMS1 = null; System.gc(); } else if (mode == 2) { LCMSID IDsummary = new LCMSID("", "", ""); logger.info("Parsing all pepXML files in " + pepXMLPath + "...."); for (File file : pepXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("pep.xml") || file.getName().toLowerCase().endsWith("pepxml")) { PepXMLParser pepXMLParser = new PepXMLParser(IDsummary, file.getAbsolutePath(), MinProb); } } HashMap<String, LCMSID> LCMSIDMap = IDsummary.GetLCMSIDFileMap(); ExecutorService executorPool = null; executorPool = Executors.newFixedThreadPool(NoFile); logger.info("Processing all mzXML files in " + mzXMLPath + "...."); for (File file : mzXMLfolder.listFiles()) { if (file.getName().toLowerCase().endsWith("mzxml")) { LCMSID id = LCMSIDMap.get(FilenameUtils.getBaseName(file.getName())); if (id == null || id.PSMList == null) { logger.warn("No IDs found in :" + FilenameUtils.getBaseName(file.getName()) + ". Quantification for this file is skipped"); continue; } if (!id.PSMList.isEmpty()) { MS1TargetQuantThread thread = new MS1TargetQuantThread(file, id, NoCPUs, outputfolder, param); executorPool.execute(thread); } } } LCMSIDMap.clear(); LCMSIDMap = null; IDsummary = null; executorPool.shutdown(); try { executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS); } catch (InterruptedException e) { logger.info("interrupted.."); } if (outputfolder == null | outputfolder.equals("")) { outputfolder = mzXMLPath; } logger.info("Merging PSM files.."); File output = new File(outputfolder); FileWriter writer = new FileWriter(output.getAbsolutePath() + "/PSM_merge.csv"); boolean header = false; for (File csvfile : output.listFiles()) { if (csvfile.getName().toLowerCase().endsWith("_psms.csv")) { BufferedReader outreader = new BufferedReader(new FileReader(csvfile)); String outline = outreader.readLine(); if (!header) { writer.write(outline + "\n"); header = true; } while ((outline = outreader.readLine()) != null) { writer.write(outline + "\n"); } outreader.close(); csvfile.delete(); } } writer.close(); } logger.info("MS1 quant module is complete."); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:IndexService.IndexServer.java
public static void main(String[] args) { File stop = new File("/tmp/.indexstop"); File running = new File("/tmp/.indexrunning"); if (args != null && args.length > 0 && args[0].equals("stop")) { try {/*from w w w . ja v a 2 s . c o m*/ stop.createNewFile(); running.delete(); } catch (IOException e) { e.printStackTrace(); } return; } if (running.exists() && (System.currentTimeMillis() - running.lastModified() < 15000)) { long time = running.lastModified(); try { Thread.sleep(10000); } catch (InterruptedException e) { e.printStackTrace(); } if (running.lastModified() == time) { running.delete(); } else { return; } } if (stop.exists()) { try { Thread.sleep(5000); } catch (InterruptedException e) { e.printStackTrace(); } if (stop.exists()) stop.delete(); } Configuration conf = new Configuration(); IndexServer server = new IndexServer(conf); if (args != null && args.length > 0 && args[0].equals("test")) { server.testmode = true; } server.start(); try { running.createNewFile(); } catch (IOException e) { e.printStackTrace(); } new UserCmdProc(server).start(); while (true) { stop = new File("/tmp/.indexstop"); if (stop.exists()) { server.close(); running.delete(); stop.delete(); break; } try { Thread.sleep(5000); } catch (InterruptedException e1) { e1.printStackTrace(); } running.setLastModified(System.currentTimeMillis()); } }