List of usage examples for org.apache.commons.cli OptionBuilder withArgName
public static OptionBuilder withArgName(String name)
From source file:io.bfscan.clueweb12.BuildWarcTrecIdMapping.java
@SuppressWarnings("static-access") public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("bz2 Wikipedia XML dump file") .create(INPUT_OPTION));/*from w w w.ja va 2s. c om*/ options.addOption( OptionBuilder.withArgName("dir").hasArg().withDescription("index location").create(INDEX_OPTION)); options.addOption(OptionBuilder.withArgName("num").hasArg() .withDescription("maximum number of documents to index").create(MAX_OPTION)); options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("number of indexing threads") .create(THREADS_OPTION)); options.addOption(new Option(OPTIMIZE_OPTION, "merge indexes into a single segment")); CommandLine cmdline = null; CommandLineParser parser = new GnuParser(); try { cmdline = parser.parse(options, args); } catch (ParseException exp) { System.err.println("Error parsing command line: " + exp.getMessage()); System.exit(-1); } if (!cmdline.hasOption(INPUT_OPTION) || !cmdline.hasOption(INDEX_OPTION)) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(BuildWarcTrecIdMapping.class.getCanonicalName(), options); System.exit(-1); } String indexPath = cmdline.getOptionValue(INDEX_OPTION); int maxdocs = cmdline.hasOption(MAX_OPTION) ? Integer.parseInt(cmdline.getOptionValue(MAX_OPTION)) : Integer.MAX_VALUE; int threads = cmdline.hasOption(THREADS_OPTION) ? Integer.parseInt(cmdline.getOptionValue(THREADS_OPTION)) : DEFAULT_NUM_THREADS; long startTime = System.currentTimeMillis(); String path = cmdline.getOptionValue(INPUT_OPTION); PrintStream out = new PrintStream(System.out, true, "UTF-8"); Directory dir = FSDirectory.open(new File(indexPath)); IndexWriterConfig config = new IndexWriterConfig(Version.LUCENE_43, ANALYZER); config.setOpenMode(OpenMode.CREATE); IndexWriter writer = new IndexWriter(dir, config); LOG.info("Creating index at " + indexPath); LOG.info("Indexing with " + threads + " threads"); FileInputStream fis = null; BufferedReader br = null; try { fis = new FileInputStream(new File(path)); byte[] ignoreBytes = new byte[2]; fis.read(ignoreBytes); // "B", "Z" bytes from commandline tools br = new BufferedReader(new InputStreamReader(new CBZip2InputStream(fis), "UTF8")); ExecutorService executor = Executors.newFixedThreadPool(threads); int cnt = 0; String s; while ((s = br.readLine()) != null) { Runnable worker = new AddDocumentRunnable(writer, s); executor.execute(worker); cnt++; if (cnt % 1000000 == 0) { LOG.info(cnt + " articles added"); } if (cnt >= maxdocs) { break; } } executor.shutdown(); // Wait until all threads are finish while (!executor.isTerminated()) { } LOG.info("Total of " + cnt + " articles indexed."); if (cmdline.hasOption(OPTIMIZE_OPTION)) { LOG.info("Merging segments..."); writer.forceMerge(1); LOG.info("Done!"); } LOG.info("Total elapsed time: " + (System.currentTimeMillis() - startTime) + "ms"); } catch (Exception e) { e.printStackTrace(); } finally { writer.close(); dir.close(); out.close(); br.close(); fis.close(); } }
From source file:com.frostvoid.trekwar.server.TrekwarServer.java
public static void main(String[] args) { // load language try {/*w w w.j ava 2s . c om*/ lang = new Language(Language.ENGLISH); } catch (IOException ioe) { System.err.println("FATAL ERROR: Unable to load language file!"); System.exit(1); } System.out.println(lang.get("trekwar_server") + " " + VERSION); System.out.println("==============================================".substring(0, lang.get("trekwar_server").length() + 1 + VERSION.length())); // Handle parameters Options options = new Options(); options.addOption(OptionBuilder.withArgName("file").withLongOpt("galaxy").hasArg() .withDescription("the galaxy file to load").create("g")); //"g", "galaxy", true, "the galaxy file to load"); options.addOption(OptionBuilder.withArgName("port number").withLongOpt("port").hasArg() .withDescription("the port number to bind to (default 8472)").create("p")); options.addOption(OptionBuilder.withArgName("number").withLongOpt("save-interval").hasArg() .withDescription("how often (in turns) to save the galaxy to disk (default: 5)").create("s")); options.addOption(OptionBuilder.withArgName("log level").withLongOpt("log").hasArg() .withDescription("sets the log level: ALL, FINEST, FINER, FINE, CONFIG, INFO, WARNING, SEVERE, OFF") .create("l")); options.addOption("h", "help", false, "prints this help message"); CommandLineParser cliParser = new BasicParser(); try { CommandLine cmd = cliParser.parse(options, args); String portStr = cmd.getOptionValue("p"); String galaxyFileStr = cmd.getOptionValue("g"); String saveIntervalStr = cmd.getOptionValue("s"); String logLevelStr = cmd.getOptionValue("l"); if (cmd.hasOption("h")) { HelpFormatter help = new HelpFormatter(); help.printHelp("TrekwarServer", options); System.exit(0); } if (cmd.hasOption("g") && galaxyFileStr != null) { galaxyFileName = galaxyFileStr; } else { throw new ParseException("galaxy file not specified"); } if (cmd.hasOption("p") && portStr != null) { port = Integer.parseInt(portStr); if (port < 1 || port > 65535) { throw new NumberFormatException(lang.get("port_number_out_of_range")); } } else { port = 8472; } if (cmd.hasOption("s") && saveIntervalStr != null) { saveInterval = Integer.parseInt(saveIntervalStr); if (saveInterval < 1 || saveInterval > 100) { throw new NumberFormatException("Save Interval out of range (1-100)"); } } else { saveInterval = 5; } if (cmd.hasOption("l") && logLevelStr != null) { if (logLevelStr.equalsIgnoreCase("finest")) { LOG.setLevel(Level.FINEST); } else if (logLevelStr.equalsIgnoreCase("finer")) { LOG.setLevel(Level.FINER); } else if (logLevelStr.equalsIgnoreCase("fine")) { LOG.setLevel(Level.FINE); } else if (logLevelStr.equalsIgnoreCase("config")) { LOG.setLevel(Level.CONFIG); } else if (logLevelStr.equalsIgnoreCase("info")) { LOG.setLevel(Level.INFO); } else if (logLevelStr.equalsIgnoreCase("warning")) { LOG.setLevel(Level.WARNING); } else if (logLevelStr.equalsIgnoreCase("severe")) { LOG.setLevel(Level.SEVERE); } else if (logLevelStr.equalsIgnoreCase("off")) { LOG.setLevel(Level.OFF); } else if (logLevelStr.equalsIgnoreCase("all")) { LOG.setLevel(Level.ALL); } else { System.err.println("ERROR: invalid log level: " + logLevelStr); System.err.println("Run again with -h flag to see valid log level values"); System.exit(1); } } else { LOG.setLevel(Level.INFO); } // INIT LOGGING try { LOG.setUseParentHandlers(false); initLogging(); } catch (IOException ex) { System.err.println("Unable to initialize logging to file"); System.err.println(ex); System.exit(1); } } catch (Exception ex) { System.err.println("ERROR: " + ex.getMessage()); System.err.println("use -h for help"); System.exit(1); } LOG.log(Level.INFO, "Trekwar2 server " + VERSION + " starting up"); // LOAD GALAXY File galaxyFile = new File(galaxyFileName); if (galaxyFile.exists()) { try { long timer = System.currentTimeMillis(); LOG.log(Level.INFO, "Loading galaxy file {0}", galaxyFileName); ObjectInputStream ois = new ObjectInputStream(new FileInputStream(galaxyFile)); galaxy = (Galaxy) ois.readObject(); timer = System.currentTimeMillis() - timer; LOG.log(Level.INFO, "Galaxy file loaded in {0} ms", timer); ois.close(); } catch (IOException ioe) { LOG.log(Level.SEVERE, "IO error while trying to load galaxy file", ioe); } catch (ClassNotFoundException cnfe) { LOG.log(Level.SEVERE, "Unable to find class while loading galaxy", cnfe); } } else { System.err.println("Error: file " + galaxyFileName + " not found"); System.exit(1); } // if turn == 0 (start of game), execute first turn to update fog of war. if (galaxy.getCurrentTurn() == 0) { TurnExecutor.executeTurn(galaxy); } LOG.log(Level.INFO, "Current turn : {0}", galaxy.getCurrentTurn()); LOG.log(Level.INFO, "Turn speed : {0} seconds", galaxy.getTurnSpeed() / 1000); LOG.log(Level.INFO, "Save Interval : {0}", saveInterval); LOG.log(Level.INFO, "Users / max : {0} / {1}", new Object[] { galaxy.getUserCount(), galaxy.getMaxUsers() }); // START SERVER try { server = new ServerSocket(port); LOG.log(Level.INFO, "Server listening on port {0}", port); } catch (BindException be) { LOG.log(Level.SEVERE, "Error: Unable to bind to port {0}", port); System.err.println(be); System.exit(1); } catch (IOException ioe) { LOG.log(Level.SEVERE, "Error: IO error while binding to port {0}", port); System.err.println(ioe); System.exit(1); } galaxy.startup(); Thread timerThread = new Thread(new Runnable() { @Override @SuppressWarnings("SleepWhileInLoop") public void run() { while (true) { try { Thread.sleep(1000); // && galaxy.getLoggedInUsers().size() > 0 will make server pause when nobody is logged in (TESTING) if (System.currentTimeMillis() > galaxy.nextTurnDate) { StringBuffer loggedInUsers = new StringBuffer(); for (User u : galaxy.getLoggedInUsers()) { loggedInUsers.append(u.getUsername()).append(", "); } long time = TurnExecutor.executeTurn(galaxy); LOG.log(Level.INFO, "Turn {0} executed in {1} ms", new Object[] { galaxy.getCurrentTurn(), time }); LOG.log(Level.INFO, "Logged in users: " + loggedInUsers.toString()); LOG.log(Level.INFO, "===================================================================================="); if (galaxy.getCurrentTurn() % saveInterval == 0) { saveGalaxy(); } galaxy.lastTurnDate = System.currentTimeMillis(); galaxy.nextTurnDate = galaxy.lastTurnDate + galaxy.turnSpeed; } } catch (InterruptedException e) { LOG.log(Level.SEVERE, "Error in main server loop, interrupted", e); } } } }); timerThread.start(); // ACCEPT CONNECTIONS AND DELEGATE TO CLIENT SESSIONS while (true) { Socket clientConnection; try { clientConnection = server.accept(); ClientSession c = new ClientSession(clientConnection, galaxy); Thread t = new Thread(c); t.start(); } catch (IOException ex) { LOG.log(Level.SEVERE, "IO Exception while trying to handle incoming client connection", ex); } } }
From source file:de.prozesskraft.pkraft.Createmap.java
public static void main(String[] args) throws org.apache.commons.cli.ParseException, IOException { // try/* w ww .j av a 2 s . c om*/ // { // if (args.length != 3) // { // System.out.println("Please specify processdefinition file (xml) and an outputfilename"); // } // // } // catch (ArrayIndexOutOfBoundsException e) // { // System.out.println("***ArrayIndexOutOfBoundsException: Please specify processdefinition.xml, openoffice_template.od*, newfile_for_processdefinitions.odt\n" + e.toString()); // } /*---------------------------- get options from ini-file ----------------------------*/ File inifile = new java.io.File( WhereAmI.getInstallDirectoryAbsolutePath(Createmap.class) + "/" + "../etc/pkraft-createmap.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); } /*---------------------------- create boolean options ----------------------------*/ Option ohelp = new Option("help", "print this message"); /*---------------------------- create argument options ----------------------------*/ Option ooutput = OptionBuilder.withArgName("FILE").hasArg() .withDescription("[mandatory; default: process.dot] file for generated map.") // .isRequired() .create("output"); Option odefinition = OptionBuilder.withArgName("FILE").hasArg() .withDescription("[mandatory] process definition file.") // .isRequired() .create("definition"); /*---------------------------- create options object ----------------------------*/ Options options = new Options(); options.addOption(ohelp); options.addOption(ooutput); options.addOption(odefinition); /*---------------------------- create the parser ----------------------------*/ CommandLineParser parser = new GnuParser(); try { // parse the command line arguments commandline = parser.parse(options, args); } catch (Exception exp) { // oops, something went wrong System.err.println("Parsing failed. Reason: " + exp.getMessage()); exiter(); } /*---------------------------- usage/help ----------------------------*/ if (commandline.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("createmap", options); System.out.println(""); System.out.println("author: " + author + " | version: " + version + " | date: " + date); System.exit(0); } /*---------------------------- ueberpruefen ob eine schlechte kombination von parametern angegeben wurde ----------------------------*/ if (!(commandline.hasOption("definition"))) { System.err.println("option -definition is mandatory."); exiter(); } if (!(commandline.hasOption("output"))) { System.err.println("option -output is mandatory."); 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()) { System.exit(1); } /*---------------------------- die eigentliche business logic ----------------------------*/ Process p1 = new Process(); java.io.File output = new java.io.File(commandline.getOptionValue("output")); if (output.exists()) { System.err.println("warn: already exists: " + output.getCanonicalPath()); exiter(); } p1.setInfilexml(commandline.getOptionValue("definition")); System.err.println("info: reading process definition " + commandline.getOptionValue("definition")); // dummy process Process p2 = null; try { p2 = p1.readXml(); } catch (JAXBException e) { // TODO Auto-generated catch block e.printStackTrace(); System.err.println("error"); exiter(); } // den wrapper process generieren ArrayList<String> dot = p2.getProcessAsDotGraph(); // dot file rausschreiben writeFile.writeFile(output, dot); }
From source file:de.prozesskraft.pkraft.Wrap.java
public static void main(String[] args) throws org.apache.commons.cli.ParseException, IOException { // try//from ww w.j av a 2 s.c o m // { // if (args.length != 3) // { // System.out.println("Please specify processdefinition file (xml) and an outputfilename"); // } // // } // catch (ArrayIndexOutOfBoundsException e) // { // System.out.println("***ArrayIndexOutOfBoundsException: Please specify processdefinition.xml, openoffice_template.od*, newfile_for_processdefinitions.odt\n" + e.toString()); // } /*---------------------------- get options from ini-file ----------------------------*/ File inifile = new java.io.File( WhereAmI.getInstallDirectoryAbsolutePath(Wrap.class) + "/" + "../etc/pkraft-wrap.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); } /*---------------------------- create boolean options ----------------------------*/ Option ohelp = new Option("help", "print this message"); Option ov = new Option("v", "prints version and build-date"); /*---------------------------- create argument options ----------------------------*/ Option ooutput = OptionBuilder.withArgName("FILE").hasArg() .withDescription("[mandatory; default: .] file for generated wrapper process.") // .isRequired() .create("output"); Option odefinition = OptionBuilder.withArgName("FILE").hasArg() .withDescription("[mandatory] process definition file.") // .isRequired() .create("definition"); /*---------------------------- create options object ----------------------------*/ Options options = new Options(); options.addOption(ohelp); options.addOption(ov); options.addOption(ooutput); options.addOption(odefinition); /*---------------------------- create the parser ----------------------------*/ CommandLineParser parser = new GnuParser(); try { // parse the command line arguments commandline = parser.parse(options, args); } catch (Exception exp) { // oops, something went wrong System.err.println("Parsing failed. Reason: " + exp.getMessage()); exiter(); } /*---------------------------- usage/help ----------------------------*/ if (commandline.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("wrap", options); System.exit(0); } else if (commandline.hasOption("v")) { System.out.println("web: www.prozesskraft.de"); System.out.println("version: [% version %]"); System.out.println("date: [% date %]"); System.exit(0); } /*---------------------------- ueberpruefen ob eine schlechte kombination von parametern angegeben wurde ----------------------------*/ if (!(commandline.hasOption("definition"))) { System.err.println("option -definition is mandatory."); exiter(); } if (!(commandline.hasOption("output"))) { System.err.println("option -output is mandatory."); 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()) { System.exit(1); } /*---------------------------- die eigentliche business logic ----------------------------*/ Process p1 = new Process(); java.io.File output = new java.io.File(commandline.getOptionValue("output")); if (output.exists()) { System.err.println("warn: already exists: " + output.getCanonicalPath()); exiter(); } p1.setInfilexml(commandline.getOptionValue("definition")); System.err.println("info: reading process definition " + commandline.getOptionValue("definition")); // dummy process Process p2 = null; try { p2 = p1.readXml(); } catch (JAXBException e) { // TODO Auto-generated catch block e.printStackTrace(); System.err.println("error"); exiter(); } // den wrapper process generieren Process p3 = p2.getProcessAsWrapper(); p3.setOutfilexml(output.getAbsolutePath()); // den neuen wrap-process rausschreiben p3.writeXml(); }
From source file:apps.quantification.LearnQuantificationSVMLight.java
public static void main(String[] args) throws IOException { String cmdLineSyntax = LearnQuantificationSVMLight.class.getName() + " [OPTIONS] <path to svm_light_learn> <path to svm_light_classify> <trainingIndexDirectory> <outputDirectory>"; Options options = new Options(); OptionBuilder.withArgName("f"); OptionBuilder.withDescription("Number of folds"); OptionBuilder.withLongOpt("f"); OptionBuilder.isRequired(true);// w ww.ja v a2s. c om OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("c"); OptionBuilder.withDescription("The c value for svm_light (default 1)"); OptionBuilder.withLongOpt("c"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("k"); OptionBuilder.withDescription("Kernel type (default 0: linear, 1: polynomial, 2: RBF, 3: sigmoid)"); OptionBuilder.withLongOpt("k"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("t"); OptionBuilder.withDescription("Path for temporary files"); OptionBuilder.withLongOpt("t"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("v"); OptionBuilder.withDescription("Verbose output"); OptionBuilder.withLongOpt("v"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("s"); OptionBuilder.withDescription("Don't delete temporary training file in svm_light format (default: delete)"); OptionBuilder.withLongOpt("s"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); SvmLightLearnerCustomizer classificationLearnerCustomizer = null; SvmLightClassifierCustomizer classificationCustomizer = null; int folds = -1; GnuParser parser = new GnuParser(); String[] remainingArgs = null; try { CommandLine line = parser.parse(options, args); remainingArgs = line.getArgs(); classificationLearnerCustomizer = new SvmLightLearnerCustomizer(remainingArgs[0]); classificationCustomizer = new SvmLightClassifierCustomizer(remainingArgs[1]); folds = Integer.parseInt(line.getOptionValue("f")); if (line.hasOption("c")) classificationLearnerCustomizer.setC(Float.parseFloat(line.getOptionValue("c"))); if (line.hasOption("k")) { System.out.println("Kernel type: " + line.getOptionValue("k")); classificationLearnerCustomizer.setKernelType(Integer.parseInt(line.getOptionValue("k"))); } if (line.hasOption("v")) classificationLearnerCustomizer.printSvmLightOutput(true); if (line.hasOption("s")) classificationLearnerCustomizer.setDeleteTrainingFiles(false); if (line.hasOption("t")) { classificationLearnerCustomizer.setTempPath(line.getOptionValue("t")); classificationCustomizer.setTempPath(line.getOptionValue("t")); } } catch (Exception exp) { System.err.println("Parsing failed. Reason: " + exp.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } assert (classificationLearnerCustomizer != null); if (remainingArgs.length != 4) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } String indexFile = remainingArgs[2]; File file = new File(indexFile); String indexName = file.getName(); String indexPath = file.getParent(); String outputPath = remainingArgs[3]; SvmLightLearner classificationLearner = new SvmLightLearner(); classificationLearner.setRuntimeCustomizer(classificationLearnerCustomizer); FileSystemStorageManager fssm = new FileSystemStorageManager(indexPath, false); fssm.open(); IIndex training = TroveReadWriteHelper.readIndex(fssm, indexName, TroveContentDBType.Full, TroveClassificationDBType.Full); final TextualProgressBar progressBar = new TextualProgressBar("Learning the quantifiers"); IOperationStatusListener status = new IOperationStatusListener() { @Override public void operationStatus(double percentage) { progressBar.signal((int) percentage); } }; QuantificationLearner quantificationLearner = new QuantificationLearner(folds, classificationLearner, classificationLearnerCustomizer, classificationCustomizer, ClassificationMode.PER_CATEGORY, new LogisticFunction(), status); IQuantifier[] quantifiers = quantificationLearner.learn(training); File executableFile = new File(classificationLearnerCustomizer.getSvmLightLearnPath()); IDataManager classifierDataManager = new SvmLightDataManager(new SvmLightClassifierCustomizer( executableFile.getParentFile().getAbsolutePath() + Os.pathSeparator() + "svm_light_classify")); String description = "_SVMLight_C-" + classificationLearnerCustomizer.getC() + "_K-" + classificationLearnerCustomizer.getKernelType(); if (classificationLearnerCustomizer.getAdditionalParameters().length() > 0) description += "_" + classificationLearnerCustomizer.getAdditionalParameters(); String quantifierPrefix = indexName + "_Quantifier-" + folds + description; FileSystemStorageManager fssmo = new FileSystemStorageManager( outputPath + File.separatorChar + quantifierPrefix, true); fssmo.open(); QuantificationLearner.write(quantifiers, fssmo, classifierDataManager); fssmo.close(); BufferedWriter bfs = new BufferedWriter( new FileWriter(outputPath + File.separatorChar + quantifierPrefix + "_rates.txt")); TShortDoubleHashMap simpleTPRs = quantificationLearner.getSimpleTPRs(); TShortDoubleHashMap simpleFPRs = quantificationLearner.getSimpleFPRs(); TShortDoubleHashMap scaledTPRs = quantificationLearner.getScaledTPRs(); TShortDoubleHashMap scaledFPRs = quantificationLearner.getScaledFPRs(); ContingencyTableSet contingencyTableSet = quantificationLearner.getContingencyTableSet(); short[] cats = simpleTPRs.keys(); for (int i = 0; i < cats.length; ++i) { short cat = cats[i]; String catName = training.getCategoryDB().getCategoryName(cat); ContingencyTable contingencyTable = contingencyTableSet.getCategoryContingencyTable(cat); double simpleTPR = simpleTPRs.get(cat); double simpleFPR = simpleFPRs.get(cat); double scaledTPR = scaledTPRs.get(cat); double scaledFPR = scaledFPRs.get(cat); String line = quantifierPrefix + "\ttrain\tsimple\t" + catName + "\t" + cat + "\t" + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n"; bfs.write(line); line = quantifierPrefix + "\ttrain\tscaled\t" + catName + "\t" + cat + "\t" + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn() + "\t" + scaledTPR + "\t" + scaledFPR + "\n"; bfs.write(line); } bfs.close(); }
From source file:apps.quantification.LearnQuantificationSVMPerf.java
public static void main(String[] args) throws IOException { String cmdLineSyntax = LearnQuantificationSVMPerf.class.getName() + " [OPTIONS] <path to svm_perf_learn> <path to svm_perf_classify> <trainingIndexDirectory> <outputDirectory>"; Options options = new Options(); OptionBuilder.withArgName("f"); OptionBuilder.withDescription("Number of folds"); OptionBuilder.withLongOpt("f"); OptionBuilder.isRequired(true);/*from w w w. j av a2s. com*/ OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("c"); OptionBuilder.withDescription("The c value for svm_perf (default 0.01)"); OptionBuilder.withLongOpt("c"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("t"); OptionBuilder.withDescription("Path for temporary files"); OptionBuilder.withLongOpt("t"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("l"); OptionBuilder.withDescription("The loss function to optimize (default 2):\n" + " 0 Zero/one loss: 1 if vector of predictions contains error, 0 otherwise.\n" + " 1 F1: 100 minus the F1-score in percent.\n" + " 2 Errorrate: Percentage of errors in prediction vector.\n" + " 3 Prec/Rec Breakeven: 100 minus PRBEP in percent.\n" + " 4 Prec@p: 100 minus precision at p in percent.\n" + " 5 Rec@p: 100 minus recall at p in percent.\n" + " 10 ROCArea: Percentage of swapped pos/neg pairs (i.e. 100 - ROCArea)."); OptionBuilder.withLongOpt("l"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("w"); OptionBuilder.withDescription("Choice of structural learning algorithm (default 9):\n" + " 0: n-slack algorithm described in [2]\n" + " 1: n-slack algorithm with shrinking heuristic\n" + " 2: 1-slack algorithm (primal) described in [5]\n" + " 3: 1-slack algorithm (dual) described in [5]\n" + " 4: 1-slack algorithm (dual) with constraint cache [5]\n" + " 9: custom algorithm in svm_struct_learn_custom.c"); OptionBuilder.withLongOpt("w"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("p"); OptionBuilder.withDescription("The value of p used by the prec@p and rec@p loss functions (default 0)"); OptionBuilder.withLongOpt("p"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("v"); OptionBuilder.withDescription("Verbose output"); OptionBuilder.withLongOpt("v"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); OptionBuilder.withArgName("s"); OptionBuilder.withDescription("Don't delete temporary training file in svm_perf format (default: delete)"); OptionBuilder.withLongOpt("s"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); SvmPerfLearnerCustomizer classificationLearnerCustomizer = null; SvmPerfClassifierCustomizer classificationCustomizer = null; int folds = -1; GnuParser parser = new GnuParser(); String[] remainingArgs = null; try { CommandLine line = parser.parse(options, args); remainingArgs = line.getArgs(); classificationLearnerCustomizer = new SvmPerfLearnerCustomizer(remainingArgs[0]); classificationCustomizer = new SvmPerfClassifierCustomizer(remainingArgs[1]); folds = Integer.parseInt(line.getOptionValue("f")); if (line.hasOption("c")) classificationLearnerCustomizer.setC(Float.parseFloat(line.getOptionValue("c"))); if (line.hasOption("w")) classificationLearnerCustomizer.setW(Integer.parseInt(line.getOptionValue("w"))); if (line.hasOption("p")) classificationLearnerCustomizer.setP(Integer.parseInt(line.getOptionValue("p"))); if (line.hasOption("l")) classificationLearnerCustomizer.setL(Integer.parseInt(line.getOptionValue("l"))); if (line.hasOption("v")) classificationLearnerCustomizer.printSvmPerfOutput(true); if (line.hasOption("s")) classificationLearnerCustomizer.setDeleteTrainingFiles(false); if (line.hasOption("t")) { classificationLearnerCustomizer.setTempPath(line.getOptionValue("t")); classificationCustomizer.setTempPath(line.getOptionValue("t")); } } catch (Exception exp) { System.err.println("Parsing failed. Reason: " + exp.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } assert (classificationLearnerCustomizer != null); if (remainingArgs.length != 4) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } String indexFile = remainingArgs[2]; File file = new File(indexFile); String indexName = file.getName(); String indexPath = file.getParent(); String outputPath = remainingArgs[3]; SvmPerfLearner classificationLearner = new SvmPerfLearner(); classificationLearner.setRuntimeCustomizer(classificationLearnerCustomizer); FileSystemStorageManager fssm = new FileSystemStorageManager(indexPath, false); fssm.open(); IIndex training = TroveReadWriteHelper.readIndex(fssm, indexName, TroveContentDBType.Full, TroveClassificationDBType.Full); final TextualProgressBar progressBar = new TextualProgressBar("Learning the quantifiers"); IOperationStatusListener status = new IOperationStatusListener() { @Override public void operationStatus(double percentage) { progressBar.signal((int) percentage); } }; QuantificationLearner quantificationLearner = new QuantificationLearner(folds, classificationLearner, classificationLearnerCustomizer, classificationCustomizer, ClassificationMode.PER_CATEGORY, new LogisticFunction(), status); IQuantifier[] quantifiers = quantificationLearner.learn(training); File executableFile = new File(classificationLearnerCustomizer.getSvmPerfLearnPath()); IDataManager classifierDataManager = new SvmPerfDataManager(new SvmPerfClassifierCustomizer( executableFile.getParentFile().getAbsolutePath() + Os.pathSeparator() + "svm_perf_classify")); String description = "_SVMPerf_C-" + classificationLearnerCustomizer.getC() + "_W-" + classificationLearnerCustomizer.getW() + "_L-" + classificationLearnerCustomizer.getL(); if (classificationLearnerCustomizer.getL() == 4 || classificationLearnerCustomizer.getL() == 5) description += "_P-" + classificationLearnerCustomizer.getP(); if (classificationLearnerCustomizer.getAdditionalParameters().length() > 0) description += "_" + classificationLearnerCustomizer.getAdditionalParameters(); String quantifierPrefix = indexName + "_Quantifier-" + folds + description; FileSystemStorageManager fssmo = new FileSystemStorageManager( outputPath + File.separatorChar + quantifierPrefix, true); fssmo.open(); QuantificationLearner.write(quantifiers, fssmo, classifierDataManager); fssmo.close(); BufferedWriter bfs = new BufferedWriter( new FileWriter(outputPath + File.separatorChar + quantifierPrefix + "_rates.txt")); TShortDoubleHashMap simpleTPRs = quantificationLearner.getSimpleTPRs(); TShortDoubleHashMap simpleFPRs = quantificationLearner.getSimpleFPRs(); TShortDoubleHashMap scaledTPRs = quantificationLearner.getScaledTPRs(); TShortDoubleHashMap scaledFPRs = quantificationLearner.getScaledFPRs(); ContingencyTableSet contingencyTableSet = quantificationLearner.getContingencyTableSet(); short[] cats = simpleTPRs.keys(); for (int i = 0; i < cats.length; ++i) { short cat = cats[i]; String catName = training.getCategoryDB().getCategoryName(cat); ContingencyTable contingencyTable = contingencyTableSet.getCategoryContingencyTable(cat); double simpleTPR = simpleTPRs.get(cat); double simpleFPR = simpleFPRs.get(cat); double scaledTPR = scaledTPRs.get(cat); double scaledFPR = scaledFPRs.get(cat); String line = quantifierPrefix + "\ttrain\tsimple\t" + catName + "\t" + cat + "\t" + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n"; bfs.write(line); line = quantifierPrefix + "\ttrain\tscaled\t" + catName + "\t" + cat + "\t" + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn() + "\t" + scaledTPR + "\t" + scaledFPR + "\n"; bfs.write(line); } bfs.close(); }
From source file:edu.duke.igsp.gkde.Main.java
public static void main(String[] argv) throws Exception { Options opts = new Options(); opts.addOption("s", true, "wiggle track step (default=1)"); opts.addOption("l", true, "feature length (default=600)"); opts.addOption("f", true, "fragment size (default=estimated from data)"); // opts.addOption("b", true, "bandwidth (default=200)"); // opts.addOption("w", true, "window (default=3800"); opts.addOption("wg", true, "wg threshold set (defualt = calculated)"); opts.addOption("c", true, "genomic total read weight (defualt = calculated)"); opts.addOption("h", false, "print usage"); opts.addOption(OptionBuilder.withArgName("input dir").hasArg() .withDescription("input directory (default=current directory)").isRequired(false).create("d")); opts.addOption(OptionBuilder.withArgName("output dir").hasArg() .withDescription("output directory (default=current directory)").isRequired(false).create("o")); opts.addOption(OptionBuilder.withArgName("background dir").hasArg() .withDescription("background directory (default=none)").isRequired(false).create("b")); opts.addOption(OptionBuilder.withArgName("ploidy dir").hasArg() .withDescription("ploidy/input directory (default=none)").isRequired(false).create("p")); opts.addOption(OptionBuilder.withArgName("wig | bed | npf").hasArg() .withDescription("output format (default wig)").isRequired(false).create("of")); opts.addOption(OptionBuilder.withArgName("dnase | chip | faire | atac").hasArg() .withDescription("input data").isRequired(true).create("in")); opts.addOption(OptionBuilder.withArgName("weight clip").hasArg() .withDescription("weight clip value (default none)").isRequired(false).create("wc")); opts.addOption("t", true, "threshold (standard deviations) (default=4.0)"); // opts.addOption("r", true, "background ratio (default=2.0)"); opts.addOption("v", false, "verbose output"); CommandLineParser parser = new GnuParser(); int fragment_size = -1; int fragment_offset = 0; long featureLength = 600l; // float thresh = 2; float threshold = KDEChromosome.Settings.DEFAULT_THRESHOLD; int step = 1; boolean showHelp = false; boolean verbose = false; String inputDirectory = null; String backgroundDirectory = null; String ploidyDirectory = null; String[] files = null;/*w w w .j a v a2s . c om*/ String[] bgfiles = {}; String[] ipfiles = {}; String outputFormat = "wig"; String inputDataType = "dnase"; File outputDirectory = new File(System.getProperty("user.dir")); long bandwidth = 0l; long window = 0l; double ncuts = 0.0d; float temp_threshold = 0f; int weight_clip = 0; System.out.println("F-Seq Version 1.85"); try { CommandLine cmd = parser.parse(opts, argv); showHelp = (cmd.hasOption("h")); verbose = (cmd.hasOption("v")); if (cmd.hasOption("s")) step = Integer.parseInt(cmd.getOptionValue("s")); if (cmd.hasOption("f")) fragment_size = Integer.parseInt(cmd.getOptionValue("f")); if (cmd.hasOption("d")) //input directory inputDirectory = cmd.getOptionValue("d"); if (cmd.hasOption("b")) //background directory backgroundDirectory = cmd.getOptionValue("b"); if (cmd.hasOption("p")) //ploidy|input directory ploidyDirectory = cmd.getOptionValue("p"); if (cmd.hasOption("l")) // bandwidth featureLength = Long.parseLong(cmd.getOptionValue("l")); if (cmd.hasOption("of")) { // output format outputFormat = cmd.getOptionValue("of"); if (!outputFormat.equals("wig") && !outputFormat.equals("bed") && !outputFormat.equals("npf")) { System.out.println("Parameter error: output format must be 'wig' or 'bed'."); showHelp = true; } } if (cmd.hasOption("in")) { // input data type inputDataType = cmd.getOptionValue("in"); if (!inputDataType.equals("dnase") && !inputDataType.equals("chip") && !inputDataType.equals("faire") && !inputDataType.equals("atac")) { System.out.println( "Parameter error: input data type must be 'dnase', 'chip', 'faire', or 'atac'."); showHelp = true; } } if (cmd.hasOption("wc")) { // weight clip weight_clip = Integer.parseInt(cmd.getOptionValue("wc")); } if (cmd.hasOption("t")) { // threshold (standard deviations) threshold = Float.parseFloat(cmd.getOptionValue("t")); } if (cmd.hasOption("o")) { // output directory String out = cmd.getOptionValue("o"); outputDirectory = new File(out); if (!outputDirectory.exists() && !outputDirectory.isDirectory()) { System.out.println("Output directory '" + out + "' is not a valid directory."); showHelp = true; } } if (cmd.hasOption("wg")) temp_threshold = Float.parseFloat(cmd.getOptionValue("wg")); if (cmd.hasOption("c")) ncuts = Double.parseDouble(cmd.getOptionValue("c")); // TESTING ONLY // if(cmd.hasOption("w")) // window // window = Long.parseLong(cmd.getOptionValue("w")); //if(cmd.hasOption("b")) // window // bandwidth = Long.parseLong(cmd.getOptionValue("b")); files = cmd.getArgs(); // input files //bgfiles = cmd.getArgs(); // background files } catch (Exception e) { System.out.println("Error parsing arguments: " + e.getMessage()); e.printStackTrace(); showHelp = true; } if (showHelp || (inputDirectory == null && files.length == 0)) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("fseq [options]... [file(s)]...", opts); System.exit(1); } File[] pfiles = getFiles(inputDirectory, files); File[] background_files = getFiles(backgroundDirectory, bgfiles); File[] ploidy_files = getFiles(ploidyDirectory, ipfiles); KDEChromosome[] chrs = null; // assume all files are of the same type, if not we'll get parsing errors String path = pfiles[0].getPath(); String extension = path.substring(path.lastIndexOf('.')).toLowerCase(); System.out.println("Path: " + path + ", extension: " + extension); if (extension.equals(".bed")) { System.out.println("Parsing BED file."); chrs = BedReader.read(pfiles); } else if (extension.equals(".sam") || extension.equals(".bam")) { System.out.println("Parsing SAM/BAM file."); chrs = SamReader.read(pfiles, weight_clip); } //KDEChromosome[] input = BedReader.read(ifiles); //compute fragment offset if (fragment_size == -1) { fragment_size = wgShiftCalc(chrs); } fragment_offset = (int) (fragment_size / 2); if (ncuts == 0.0d) { for (int i = 0; i < chrs.length; ++i) { // computes the total read weight of all cuts on a chromosome ncuts += chrs[i].getTotalWeight(); } } KDEChromosome.Settings settings = null; if (bandwidth > 0 || window > 0) { settings = new KDEChromosome.Settings(bandwidth, window, threshold, fragment_offset, ncuts, inputDataType); } else { settings = new KDEChromosome.Settings(featureLength, threshold, fragment_offset, ncuts, inputDataType); } float wg_threshold = wgThreshold(settings, chrs); if (temp_threshold != 0f) { wg_threshold = temp_threshold; } //KDEChromosome.Settings bg_settings = null; //bg_settings = new KDEChromosome.Settings(featureLength*2, threshold, fragment_offset); //int background_size = 0; //int input_size = 0; //float bg_ratio = 0; //float sd = 0; if (verbose) { System.out.println("Settings: "); System.out.println("\twindow=" + (settings.window * 2)); System.out.println("\tbandwidth=" + (settings.bandwidth)); //System.out.println("\tfragment offset=" + (settings.offset)); System.out.println("\tthreshold = " + wg_threshold); System.out.println("\test. fragment size = " + fragment_size); System.out.println("\tsequence length = " + chrs[0].getSequenceLength()); } // if(backgroundDirectory != null) { // for(int i = 0; i < input.length; ++i) { // background_size += input[i].getLength(); // } // for(int i = 0; i < chrs.length; ++i) { // input_size += chrs[i].getLength(); // } // bg_ratio = (float)input_size/(float)background_size; // sd = computeSD(bg_settings, input); // //System.out.println("Sample Ratio: " + bg_ratio); // //System.out.println("Input Size: " + input_size); // //System.out.println("Background Size: " + background_size); // //System.out.println("Input standard deviation: " + (settings.threshold * (float)Math.sqrt((double)bg_ratio * (double)sd * (double)sd))); // //System.out.println("Data standard deviation: " + settings.threshold * computeSD(settings, chrs)); // } for (int i = 0; i < chrs.length; ++i) { if (chrs[i].getFirstPos() == chrs[i].getLastPos()) { System.out.println("Warning: " + chrs[i].getChromosome() + " has size zero. Skipping."); continue; } File ofile = Util.makeUniqueFileWithExtension(outputDirectory, chrs[i].getChromosome(), outputFormat); DensityWriter dw = null; if (outputFormat.equals("wig")) { dw = new WiggleDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step); } else { if (outputFormat.equals("npf")) { dw = new NpfDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step); } else { dw = new BedDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step); } } //Function takes all? or new function for each? // if(backgroundDirectory != null) { // boolean hit = false; // for(int j = 0; j < background_files.length; ++j) { // if(background_files[j].getName().equals(chrs[i].getChromosome() + ".bff")) { // System.out.println("Running background on Chromosome " + chrs[i].getChromosome()); // chrs[i].runBG(settings, dw, verbose, wg_threshold, background_files[j]); // hit = true; // } // } // if(!hit) // System.out.println("No background for Chromosome " + chrs[i].getChromosome()); // } else { // if(ploidyDirectory !=) // chrs[i].run(settings, dw, verbose, wg_threshold); // } chrs[i].run(settings, dw, verbose, wg_threshold, background_files, ploidy_files); dw.close(); } //kde.showGraph(); }
From source file:com.github.r351574nc3.amex.assignment1.App.java
public static void main(final String... args) { if (args.length < 1) { printUsage();//from w ww . j a va 2 s .c o m System.exit(0); } final Options options = new Options(); options.addOption(OptionBuilder.withArgName("output").hasArg(true).withDescription("Path for CSV output") .create("o")); options.addOption( OptionBuilder.withArgName("input").hasArg(true).withDescription("Path for CSV input").create("i")); final CommandLineParser parser = new BasicParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.out.println(e.getMessage()); printUsage(); System.exit(0); } if ((cmd.hasOption('o') && cmd.hasOption('i')) || !(cmd.hasOption('o') || cmd.hasOption('i')) || (cmd.hasOption('o') && cmd.getArgs().length < 1)) { printUsage(); System.exit(0); } if (cmd.hasOption('o') && cmd.getArgs().length > 0) { final String outputName = cmd.getOptionValue("o"); final int iterations = Integer.parseInt(cmd.getArgs()[cmd.getArgs().length - 1]); new App().run(new File(outputName), iterations); } else if (cmd.hasOption('i')) { final String inputName = cmd.getOptionValue("i"); new App().run(new File(inputName)); } System.exit(0); }
From source file:jp.primecloud.auto.tool.management.main.Main.java
public static void main(String args[]) { Options options = new Options(); options.addOption("Z", false, "Zabbix mode"); options.addOption("U", false, "UPDATE mode"); options.addOption("S", false, "SELECT mode"); options.addOption("C", false, "Create Mode"); options.addOption("P", false, "Show Platform"); options.addOption("L", false, "Show Users"); options.addOption("E", false, "Ecrypt UserPassword"); options.addOption("I", false, "IaasGateway Mode"); options.addOption("A", false, "PCC-API Genarate ID or Key Mode"); options.addOption("W", false, "Decrypt UserPassword"); options.addOption("username", true, "Create the username"); options.addOption("password", true, "Create the password"); options.addOption("firstname", true, "Create the firstname"); options.addOption("familyname", true, "Create the familyname"); options.addOption("userno", true, "Create the userno"); options.addOption("dburl", "connectionurl", true, "PrimeCloud Controller database url"); options.addOption("dbuser", "username", true, "PrimeCloud Controller database username"); options.addOption("dbpass", "password", true, "PrimeCloud Controller database password"); options.addOption("sql", true, "SQL"); options.addOption("columnname", true, "columnName"); options.addOption("columntype", true, "columnType"); options.addOption("salt", true, "Salt"); OptionBuilder.withLongOpt("prepared"); OptionBuilder.hasArgs();// w ww . jav a 2s . c o m OptionBuilder.withDescription("execute as PreparedStatement"); OptionBuilder.withArgName("params"); Option optionPrepared = OptionBuilder.create(); options.addOption(optionPrepared); // for Zabbix options.addOption("enable", false, "enable"); options.addOption("disable", false, "disable"); options.addOption("get", false, "getUser from zabbix"); options.addOption("check", false, "API setting check for zabbix"); options.addOption("config", true, "Property can obtain from management-config.properties"); options.addOption("platformkind", true, "Platform kind. e.g. ec2 and ec2_vpc or vmware"); options.addOption("platformname", true, "Platform can obtain from auto-config.xml"); options.addOption("platformno", true, "Platform can obtain from auto-config.xml"); // for IaasGateway(AWS, Cloudstack) options.addOption("keyname", true, "import your key pair as keyName"); options.addOption("publickey", true, "import your public key"); // for PCC options.addOption("accessid", true, "accessid for PCC-API"); options.addOption("secretkey", true, "secretkey for PCC-API"); options.addOption("generatetype", true, "genarateType for PCC-API"); options.addOption("h", "help", false, "help"); CommandLineParser parser = new BasicParser(); CommandLine commandLine; try { commandLine = parser.parse(options, args); } catch (ParseException e) { System.out.println( "???????? -h?????????"); return; } if (commandLine.hasOption("h")) { HelpFormatter f = new HelpFormatter(); f.printHelp("PCC script ", options); } ManagementConfigLoader.init(); //? //Zabbix? if (commandLine.hasOption("Z")) { if (commandLine.hasOption("C")) { //Zabbix? ZabbixMain.createExecute(commandLine); } else if (commandLine.hasOption("U")) { //Zabbix ZabbixMain.updateExecute(commandLine); } else if (commandLine.hasOption("disable")) { //Zabbix ZabbixMain.disableExecute(commandLine); } else if (commandLine.hasOption("enable")) { //Zabbix ZabbixMain.enableExecute(commandLine); } else if (commandLine.hasOption("get")) { //Zabbix? ZabbixMain.getUser(commandLine); } else if (commandLine.hasOption("check")) { //Zabbix?? ZabbixMain.checkApiVersion(); } //PCC? } else if (commandLine.hasOption("U")) { if (commandLine.hasOption("prepared")) { SQLMain.updateExecutePrepared(commandLine); } else { //Update? SQLMain.updateExecute(commandLine); } } else if (commandLine.hasOption("S")) { //Select? SQLMain.selectExecute(commandLine); } else if (commandLine.hasOption("P")) { //? ConfigMain.showPlatforms(); } else if (commandLine.hasOption("L")) { //PCC? UserService.showUserPlatform(); } else if (commandLine.hasOption("config")) { //??? ConfigMain.getProperty(commandLine.getOptionValue("config")); } else if (commandLine.hasOption("platformname") && commandLine.hasOption("platformkind")) { //?????? ConfigMain.getPlatformNo(commandLine.getOptionValue("platformname"), commandLine.getOptionValue("platformkind")); } else if (commandLine.hasOption("E")) { //PCC?? UserService.encryptUserPassword(commandLine.getOptionValue("password")); } else if (commandLine.hasOption("I")) { //IaasGatewayCall??AWS or Cloudstack??? IaasGatewayMain.importExecute(commandLine); } else if (commandLine.hasOption("A")) { PccApiGenerateService.genarate(commandLine); } else if (commandLine.hasOption("W")) { //PCC?? UserService.decryptUserPassword(commandLine.getOptionValue("password"), commandLine.getOptionValue("salt")); } }
From source file:cc.wikitools.lucene.IndexWikipediaDump.java
@SuppressWarnings("static-access") public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("bz2 Wikipedia XML dump file") .create(INPUT_OPTION));/* www .j a v a2 s. co m*/ options.addOption( OptionBuilder.withArgName("dir").hasArg().withDescription("index location").create(INDEX_OPTION)); options.addOption(OptionBuilder.withArgName("num").hasArg() .withDescription("maximum number of documents to index").create(MAX_OPTION)); options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("number of indexing threads") .create(THREADS_OPTION)); options.addOption(new Option(OPTIMIZE_OPTION, "merge indexes into a single segment")); CommandLine cmdline = null; CommandLineParser parser = new GnuParser(); try { cmdline = parser.parse(options, args); } catch (ParseException exp) { System.err.println("Error parsing command line: " + exp.getMessage()); System.exit(-1); } if (!cmdline.hasOption(INPUT_OPTION) || !cmdline.hasOption(INDEX_OPTION)) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(IndexWikipediaDump.class.getCanonicalName(), options); System.exit(-1); } String indexPath = cmdline.getOptionValue(INDEX_OPTION); int maxdocs = cmdline.hasOption(MAX_OPTION) ? Integer.parseInt(cmdline.getOptionValue(MAX_OPTION)) : Integer.MAX_VALUE; int threads = cmdline.hasOption(THREADS_OPTION) ? Integer.parseInt(cmdline.getOptionValue(THREADS_OPTION)) : DEFAULT_NUM_THREADS; long startTime = System.currentTimeMillis(); String path = cmdline.getOptionValue(INPUT_OPTION); PrintStream out = new PrintStream(System.out, true, "UTF-8"); WikiClean cleaner = new WikiCleanBuilder().withTitle(true).build(); Directory dir = FSDirectory.open(new File(indexPath)); IndexWriterConfig config = new IndexWriterConfig(Version.LUCENE_43, ANALYZER); config.setOpenMode(OpenMode.CREATE); IndexWriter writer = new IndexWriter(dir, config); LOG.info("Creating index at " + indexPath); LOG.info("Indexing with " + threads + " threads"); try { WikipediaBz2DumpInputStream stream = new WikipediaBz2DumpInputStream(path); ExecutorService executor = Executors.newFixedThreadPool(threads); int cnt = 0; String page; while ((page = stream.readNext()) != null) { String title = cleaner.getTitle(page); // These are heuristic specifically for filtering out non-articles in enwiki-20120104. if (title.startsWith("Wikipedia:") || title.startsWith("Portal:") || title.startsWith("File:")) { continue; } if (page.contains("#REDIRECT") || page.contains("#redirect") || page.contains("#Redirect")) { continue; } Runnable worker = new AddDocumentRunnable(writer, cleaner, page); executor.execute(worker); cnt++; if (cnt % 10000 == 0) { LOG.info(cnt + " articles added"); } if (cnt >= maxdocs) { break; } } executor.shutdown(); // Wait until all threads are finish while (!executor.isTerminated()) { } LOG.info("Total of " + cnt + " articles indexed."); if (cmdline.hasOption(OPTIMIZE_OPTION)) { LOG.info("Merging segments..."); writer.forceMerge(1); LOG.info("Done!"); } LOG.info("Total elapsed time: " + (System.currentTimeMillis() - startTime) + "ms"); } catch (Exception e) { e.printStackTrace(); } finally { writer.close(); dir.close(); out.close(); } }