List of usage examples for org.apache.commons.cli HelpFormatter HelpFormatter
HelpFormatter
From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapQueryRenameAllMethods.java
public static void main(String[] args) { Options options = new Options(); Option inputOpt = OptionBuilder.create(IN); inputOpt.setArgName("INPUT"); inputOpt.setDescription("Input Kyanos resource directory"); inputOpt.setArgs(1);// www . j a v a 2 s .c o m inputOpt.setRequired(true); Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS); inClassOpt.setArgName("CLASS"); inClassOpt.setDescription("FQN of EPackage implementation class"); inClassOpt.setArgs(1); inClassOpt.setRequired(true); options.addOption(inputOpt); options.addOption(inClassOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME, new MapPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN))); Class<?> inClazz = KyanosMapQueryRenameAllMethods.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME, PersistentResourceFactory.eINSTANCE); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); resource.load(loadOpts); String name = UUID.randomUUID().toString(); { LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); JavaQueries.renameAllMethods(resource, name); long end = System.currentTimeMillis(); resource.save(Collections.emptyMap()); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); } if (resource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource); } else { resource.unload(); } } catch (ParseException e) { MessageUtil.showError(e.toString()); MessageUtil.showError("Current arguments: " + Arrays.toString(args)); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("java -jar <this-file.jar>", options, true); } catch (Throwable e) { MessageUtil.showError(e.toString()); } }
From source file:com.bytelightning.opensource.pokerface.PokerFaceApp.java
public static void main(String[] args) { if (JavaVersionAsFloat() < (1.8f - Float.MIN_VALUE)) { System.err.println("PokerFace requires at least Java v8 to run."); return;//from w ww . j a v a2s .c o m } // Configure the command line options parser Options options = new Options(); options.addOption("h", false, "help"); options.addOption("listen", true, "(http,https,secure,tls,ssl,CertAlias)=Address:Port for https."); options.addOption("keystore", true, "Filepath for PokerFace certificate keystore."); options.addOption("storepass", true, "The store password of the keystore."); options.addOption("keypass", true, "The key password of the keystore."); options.addOption("target", true, "Remote Target requestPattern=targetUri"); // NOTE: targetUri may contain user-info and if so will be interpreted as the alias of a cert to be presented to the remote target options.addOption("servercpu", true, "Number of cores the server should use."); options.addOption("targetcpu", true, "Number of cores the http targets should use."); options.addOption("trustany", false, "Ignore certificate identity errors from target servers."); options.addOption("files", true, "Filepath to a directory of static files."); options.addOption("config", true, "Path for XML Configuration file."); options.addOption("scripts", true, "Filepath for root scripts directory."); options.addOption("library", true, "JavaScript library to load into global context."); options.addOption("watch", false, "Dynamically watch scripts directory for changes."); options.addOption("dynamicTargetScripting", false, "WARNING! This option allows scripts to redirect requests to *any* other remote server."); CommandLine cmdLine = null; // parse the command line. try { CommandLineParser parser = new PosixParser(); cmdLine = parser.parse(options, args); if (args.length == 0 || cmdLine.hasOption('h')) { HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(120); formatter.printHelp(PokerFaceApp.class.getSimpleName(), options); return; } } catch (ParseException exp) { System.err.println("Parsing failed. Reason: " + exp.getMessage()); return; } catch (Exception ex) { ex.printStackTrace(System.err); return; } XMLConfiguration config = new XMLConfiguration(); try { if (cmdLine.hasOption("config")) { Path tmp = Utils.MakePath(cmdLine.getOptionValue("config")); if (!Files.exists(tmp)) throw new FileNotFoundException("Configuration file does not exist."); if (Files.isDirectory(tmp)) throw new FileNotFoundException("'config' path is not a file."); // This is a bit of a pain, but but let's make sure we have a valid configuration file before we actually try to use it. config.setEntityResolver(new DefaultEntityResolver() { @Override public InputSource resolveEntity(String publicId, String systemId) throws SAXException { InputSource retVal = super.resolveEntity(publicId, systemId); if ((retVal == null) && (systemId != null)) { try { URL entityURL; if (systemId.endsWith("/PokerFace_v1Config.xsd")) entityURL = PokerFaceApp.class.getResource("/PokerFace_v1Config.xsd"); else entityURL = new URL(systemId); URLConnection connection = entityURL.openConnection(); connection.setUseCaches(false); InputStream stream = connection.getInputStream(); retVal = new InputSource(stream); retVal.setSystemId(entityURL.toExternalForm()); } catch (Throwable e) { return retVal; } } return retVal; } }); config.setSchemaValidation(true); config.setURL(tmp.toUri().toURL()); config.load(); if (cmdLine.hasOption("listen")) System.out.println("IGNORING 'listen' option because a configuration file was supplied."); if (cmdLine.hasOption("target")) System.out.println("IGNORING 'target' option(s) because a configuration file was supplied."); if (cmdLine.hasOption("scripts")) System.out.println("IGNORING 'scripts' option because a configuration file was supplied."); if (cmdLine.hasOption("library")) System.out.println("IGNORING 'library' option(s) because a configuration file was supplied."); } else { String[] serverStrs; String[] addr = { null }; String[] port = { null }; serverStrs = cmdLine.getOptionValues("listen"); if (serverStrs == null) throw new MissingOptionException("No listening addresses specified specified"); for (int i = 0; i < serverStrs.length; i++) { String addrStr; String alias = null; String protocol = null; Boolean https = null; int addrPos = serverStrs[i].indexOf('='); if (addrPos >= 0) { if (addrPos < 2) throw new IllegalArgumentException("Invalid http argument."); else if (addrPos + 1 >= serverStrs[i].length()) throw new IllegalArgumentException("Invalid http argument."); addrStr = serverStrs[i].substring(addrPos + 1, serverStrs[i].length()); String[] types = serverStrs[i].substring(0, addrPos).split(","); for (String type : types) { if (type.equalsIgnoreCase("http")) break; else if (type.equalsIgnoreCase("https") || type.equalsIgnoreCase("secure")) https = true; else if (type.equalsIgnoreCase("tls") || type.equalsIgnoreCase("ssl")) protocol = type.toUpperCase(); else alias = type; } } else addrStr = serverStrs[i]; ParseAddressString(addrStr, addr, port, alias != null ? 443 : 80); config.addProperty("server.listen(" + i + ")[@address]", addr[0]); config.addProperty("server.listen(" + i + ")[@port]", port[0]); if (alias != null) config.addProperty("server.listen(" + i + ")[@alias]", alias); if (protocol != null) config.addProperty("server.listen(" + i + ")[@protocol]", protocol); if (https != null) config.addProperty("server.listen(" + i + ")[@secure]", https); } String servercpu = cmdLine.getOptionValue("servercpu"); if (servercpu != null) config.setProperty("server[@cpu]", servercpu); String clientcpu = cmdLine.getOptionValue("targetcpu"); if (clientcpu != null) config.setProperty("targets[@cpu]", clientcpu); // Configure static files if (cmdLine.hasOption("files")) { Path tmp = Utils.MakePath(cmdLine.getOptionValue("files")); if (!Files.exists(tmp)) throw new FileNotFoundException("Files directory does not exist."); if (!Files.isDirectory(tmp)) throw new FileNotFoundException("'files' path is not a directory."); config.setProperty("files.rootDirectory", tmp.toAbsolutePath().toUri()); } // Configure scripting if (cmdLine.hasOption("scripts")) { Path tmp = Utils.MakePath(cmdLine.getOptionValue("scripts")); if (!Files.exists(tmp)) throw new FileNotFoundException("Scripts directory does not exist."); if (!Files.isDirectory(tmp)) throw new FileNotFoundException("'scripts' path is not a directory."); config.setProperty("scripts.rootDirectory", tmp.toAbsolutePath().toUri()); config.setProperty("scripts.dynamicWatch", cmdLine.hasOption("watch")); String[] libraries = cmdLine.getOptionValues("library"); if (libraries != null) { for (int i = 0; i < libraries.length; i++) { Path lib = Utils.MakePath(libraries[i]); if (!Files.exists(lib)) throw new FileNotFoundException( "Script library does not exist [" + libraries[i] + "]."); if (Files.isDirectory(lib)) throw new FileNotFoundException( "Script library is not a file [" + libraries[i] + "]."); config.setProperty("scripts.library(" + i + ")", lib.toAbsolutePath().toUri()); } } } else if (cmdLine.hasOption("watch")) System.out.println("IGNORING 'watch' option as no 'scripts' directory was specified."); else if (cmdLine.hasOption("library")) System.out.println("IGNORING 'library' option as no 'scripts' directory was specified."); } String keyStorePath = cmdLine.getOptionValue("keystore"); if (keyStorePath != null) config.setProperty("keystore", keyStorePath); String keypass = cmdLine.getOptionValue("keypass"); if (keypass != null) config.setProperty("keypass", keypass); String storepass = cmdLine.getOptionValue("storepass"); if (storepass != null) config.setProperty("storepass", keypass); if (cmdLine.hasOption("trustany")) config.setProperty("targets[@trustAny]", true); config.setProperty("scripts.dynamicTargetScripting", cmdLine.hasOption("dynamicTargetScripting")); String[] targetStrs = cmdLine.getOptionValues("target"); if (targetStrs != null) { for (int i = 0; i < targetStrs.length; i++) { int uriPos = targetStrs[i].indexOf('='); if (uriPos < 2) throw new IllegalArgumentException("Invalid target argument."); else if (uriPos + 1 >= targetStrs[i].length()) throw new IllegalArgumentException("Invalid target argument."); String patternStr = targetStrs[i].substring(0, uriPos); String urlStr = targetStrs[i].substring(uriPos + 1, targetStrs[i].length()); String alias; try { URL url = new URL(urlStr); alias = url.getUserInfo(); String scheme = url.getProtocol(); if ((!"http".equals(scheme)) && (!"https".equals(scheme))) throw new IllegalArgumentException("Invalid target uri scheme."); int port = url.getPort(); if (port < 0) port = url.getDefaultPort(); urlStr = scheme + "://" + url.getHost() + ":" + port + url.getPath(); String ref = url.getRef(); if (ref != null) urlStr += "#" + ref; } catch (MalformedURLException ex) { throw new IllegalArgumentException("Malformed target uri"); } config.addProperty("targets.target(" + i + ")[@pattern]", patternStr); config.addProperty("targets.target(" + i + ")[@url]", urlStr); if (alias != null) config.addProperty("targets.target(" + i + ")[@alias]", alias); } } // config.save(System.out); } catch (Throwable e) { e.printStackTrace(System.err); return; } // If we get here, we have a possibly valid configuration. try { final PokerFace p = new PokerFace(); p.config(config); if (p.start()) { PokerFace.Logger.warn("Started!"); Runtime.getRuntime().addShutdownHook(new Thread() { public void run() { try { PokerFace.Logger.warn("Initiating shutdown..."); p.stop(); PokerFace.Logger.warn("Shutdown completed!"); } catch (Throwable e) { PokerFace.Logger.error("Failed to shutdown cleanly!"); e.printStackTrace(System.err); } } }); } else { PokerFace.Logger.error("Failed to start!"); System.exit(-1); } } catch (Throwable e) { e.printStackTrace(System.err); } }
From source file:DokeosConverter.java
public static void main(String[] arguments) throws Exception { CommandLineParser commandLineParser = new PosixParser(); CommandLine commandLine = commandLineParser.parse(OPTIONS, arguments); int port = SocketOpenOfficeConnection.DEFAULT_PORT; if (commandLine.hasOption(OPTION_PORT.getOpt())) { port = Integer.parseInt(commandLine.getOptionValue(OPTION_PORT.getOpt())); }// w w w . j a va 2s. c o m String outputFormat = null; if (commandLine.hasOption(OPTION_OUTPUT_FORMAT.getOpt())) { outputFormat = commandLine.getOptionValue(OPTION_OUTPUT_FORMAT.getOpt()); } boolean verbose = false; if (commandLine.hasOption(OPTION_VERBOSE.getOpt())) { verbose = true; } String dokeosMode = "woogie"; if (commandLine.hasOption(OPTION_DOKEOS_MODE.getOpt())) { dokeosMode = commandLine.getOptionValue(OPTION_DOKEOS_MODE.getOpt()); } int width = 800; if (commandLine.hasOption(OPTION_WIDTH.getOpt())) { width = Integer.parseInt(commandLine.getOptionValue(OPTION_WIDTH.getOpt())); } int height = 600; if (commandLine.hasOption(OPTION_HEIGHT.getOpt())) { height = Integer.parseInt(commandLine.getOptionValue(OPTION_HEIGHT.getOpt())); } String[] fileNames = commandLine.getArgs(); if ((outputFormat == null && fileNames.length != 2 && dokeosMode != null) || fileNames.length < 1) { String syntax = "convert [options] input-file output-file; or\n" + "[options] -f output-format input-file [input-file...]"; HelpFormatter helpFormatter = new HelpFormatter(); helpFormatter.printHelp(syntax, OPTIONS); System.exit(EXIT_CODE_TOO_FEW_ARGS); } OpenOfficeConnection connection = new DokeosSocketOfficeConnection(port); try { if (verbose) { System.out.println("-- connecting to OpenOffice.org on port " + port); } connection.connect(); } catch (ConnectException officeNotRunning) { System.err.println( "ERROR: connection failed. Please make sure OpenOffice.org is running and listening on port " + port + "."); System.exit(EXIT_CODE_CONNECTION_FAILED); } try { // choose the good constructor to deal with the conversion DocumentConverter converter; if (dokeosMode.equals("oogie")) { converter = new OogieDocumentConverter(connection, new DokeosDocumentFormatRegistry(), width, height); } else if (dokeosMode.equals("woogie")) { converter = new WoogieDocumentConverter(connection, new DokeosDocumentFormatRegistry(), width, height); } else { converter = new OpenOfficeDocumentConverter(connection); } if (outputFormat == null) { File inputFile = new File(fileNames[0]); File outputFile = new File(fileNames[1]); convertOne(converter, inputFile, outputFile, verbose); } else { for (int i = 0; i < fileNames.length; i++) { File inputFile = new File(fileNames[i]); File outputFile = new File(FilenameUtils.getFullPath(fileNames[i]) + FilenameUtils.getBaseName(fileNames[i]) + "." + outputFormat); convertOne(converter, inputFile, outputFile, verbose); } } } catch (com.artofsolving.jodconverter.openoffice.connection.OpenOfficeException e) { connection.disconnect(); System.err.println("ERROR: conversion failed."); System.exit(EXIT_CODE_CONVERSION_FAILED); } finally { if (verbose) { System.out.println("-- disconnecting"); } connection.disconnect(); } }
From source file:com.ctriposs.rest4j.tools.idlgen.Rest4JResourceModelExporterCmdLineApp.java
/** * @param args rest4jexporter -sourcepath sourcepath -resourcepackages packagenames [-name api_name] [-outdir outdir] *//*from w w w. ja v a 2s.com*/ public static void main(String[] args) { // args = new String[] {"-name", "groups", // "-resourcepackages", "com.ctriposs.groups.server.rest1.impl com.ctriposs.groups.server.rest2.impl ", // "-resourceclasses", "com.ctriposs.groups.server.restX.impl.FooResource", // "-sourcepath", "src/main/java", // "-outdir", "src/codegen/idl", // "-split"}; CommandLine cl = null; try { final CommandLineParser parser = new GnuParser(); cl = parser.parse(OPTIONS, args); } catch (ParseException e) { System.err.println("Invalid arguments: " + e.getMessage()); final HelpFormatter formatter = new HelpFormatter(); formatter.printHelp( "rest4jexporter -sourcepath sourcepath [-resourcepackages packagenames] [-resourceclasses classnames]" + "[-name api_name] [-outdir outdir]", OPTIONS); System.exit(0); } try { new Rest4JResourceModelExporter().export(cl.getOptionValue("name"), null, cl.getOptionValues("sourcepath"), cl.getOptionValues("resourcepackages"), cl.getOptionValues("resourceclasses"), cl.getOptionValue("outdir", ".")); } catch (Throwable e) { log.error("Error writing IDL files", e); System.exit(1); } }
From source file:com.ingby.socbox.bischeck.Execute.java
public static void main(String[] args) { // create the command line parser CommandLineParser parser = new GnuParser(); CommandLine line = null;/* w ww . ja v a 2 s .co m*/ // create the Options Options options = new Options(); options.addOption("u", "usage", false, "show usage."); options.addOption("d", "deamon", false, "start as a deamon"); try { // parse the command line arguments line = parser.parse(options, args); } catch (org.apache.commons.cli.ParseException e) { System.out.println("Command parse error:" + e.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Bischeck", options); Util.ShellExit(Util.FAILED); } if (line.hasOption("usage")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Bischeck", options); Util.ShellExit(Util.OKAY); } dumpthread = new Thread() { public void run() { try { CacheFactory.destroy(); } catch (CacheException e) { LOGGER.warn("Cache could not be destoryed", e); } } }; dumpthread.setName("dumpcache"); int retStat = Util.OKAY; do { try { if (line.hasOption("deamon")) { ConfigurationManager.init(); } else { ConfigurationManager.initonce(); } } catch (Exception e) { LOGGER.error("Creating bischeck Configuration Manager failed with: {}", e.getMessage(), e); Util.ShellExit(Util.FAILED); } retStat = Execute.getInstance().deamon(); LOGGER.debug("Method Execute returned {}", retStat); } while (retStat == RESTART); dumpthread.start(); LOGGER.info("******************* Shutdown ********************"); Util.ShellExit(retStat); }
From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapQueryGrabats.java
public static void main(String[] args) { Options options = new Options(); Option inputOpt = OptionBuilder.create(IN); inputOpt.setArgName("INPUT"); inputOpt.setDescription("Input Kyanos resource directory"); inputOpt.setArgs(1);/*from w ww . j a v a 2s . c o m*/ inputOpt.setRequired(true); Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS); inClassOpt.setArgName("CLASS"); inClassOpt.setDescription("FQN of EPackage implementation class"); inClassOpt.setArgs(1); inClassOpt.setRequired(true); options.addOption(inputOpt); options.addOption(inClassOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME, new MapPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN))); Class<?> inClazz = KyanosMapQueryGrabats.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME, PersistentResourceFactory.eINSTANCE); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); resource.load(loadOpts); { LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); EList<ClassDeclaration> list = JavaQueries.grabats09(resource); long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size())); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); } if (resource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource); } else { resource.unload(); } } catch (ParseException e) { MessageUtil.showError(e.toString()); MessageUtil.showError("Current arguments: " + Arrays.toString(args)); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("java -jar <this-file.jar>", options, true); } catch (Throwable e) { MessageUtil.showError(e.toString()); } }
From source file:apps.quantification.QuantifySVMPerf.java
public static void main(String[] args) throws IOException { String cmdLineSyntax = QuantifySVMPerf.class.getName() + " [OPTIONS] <path to svm_perf_classify> <testIndexDirectory> <quantificationModelDirectory>"; Options options = new Options(); OptionBuilder.withArgName("d"); OptionBuilder.withDescription("Dump confidences file"); OptionBuilder.withLongOpt("d"); OptionBuilder.isRequired(false);//from ww w . jav a 2 s .c om OptionBuilder.hasArg(false); 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 files in svm_perf format (default: delete)"); OptionBuilder.withLongOpt("s"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); SvmPerfClassifierCustomizer customizer = null; GnuParser parser = new GnuParser(); String[] remainingArgs = null; try { CommandLine line = parser.parse(options, args); remainingArgs = line.getArgs(); customizer = new SvmPerfClassifierCustomizer(remainingArgs[0]); if (line.hasOption("v")) customizer.printSvmPerfOutput(true); if (line.hasOption("s")) { System.out.println("Keeping temporary files."); customizer.setDeleteTestFiles(false); customizer.setDeletePredictionsFiles(false); } if (line.hasOption("t")) customizer.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); } if (remainingArgs.length != 3) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } String indexFile = remainingArgs[1]; File file = new File(indexFile); String indexName = file.getName(); String indexPath = file.getParent(); String quantifierFilename = remainingArgs[2]; FileSystemStorageManager indexFssm = new FileSystemStorageManager(indexPath, false); indexFssm.open(); IIndex test = TroveReadWriteHelper.readIndex(indexFssm, indexName, TroveContentDBType.Full, TroveClassificationDBType.Full); indexFssm.close(); FileSystemStorageManager quantifierFssm = new FileSystemStorageManager(quantifierFilename, false); quantifierFssm.open(); SvmPerfDataManager classifierDataManager = new SvmPerfDataManager(customizer); FileSystemStorageManager fssm = new FileSystemStorageManager(quantifierFilename, false); fssm.open(); IQuantifier[] quantifiers = QuantificationLearner.read(fssm, classifierDataManager, ClassificationMode.PER_CATEGORY); fssm.close(); quantifierFssm.close(); Quantification ccQuantification = quantifiers[0].quantify(test); Quantification paQuantification = quantifiers[1].quantify(test); Quantification accQuantification = quantifiers[2].quantify(test); Quantification maxQuantification = quantifiers[3].quantify(test); Quantification sccQuantification = quantifiers[4].quantify(test); Quantification spaQuantification = quantifiers[5].quantify(test); Quantification trueQuantification = new Quantification("True", test.getClassificationDB()); File quantifierFile = new File(quantifierFilename); String quantificationName = quantifierFile.getParent() + Os.pathSeparator() + indexName + "_" + quantifierFile.getName() + ".txt"; BufferedWriter writer = new BufferedWriter(new FileWriter(quantificationName)); IShortIterator iterator = test.getCategoryDB().getCategories(); while (iterator.hasNext()) { short category = iterator.next(); String prefix = quantifierFile.getName() + "\t" + indexName + "\t" + test.getCategoryDB().getCategoryName(category) + "\t" + category + "\t" + trueQuantification.getQuantification(category) + "\t"; writer.write(prefix + ccQuantification.getName() + "\t" + ccQuantification.getQuantification(category) + "\n"); writer.write(prefix + paQuantification.getName() + "\t" + paQuantification.getQuantification(category) + "\n"); writer.write(prefix + accQuantification.getName() + "\t" + accQuantification.getQuantification(category) + "\n"); writer.write(prefix + maxQuantification.getName() + "\t" + maxQuantification.getQuantification(category) + "\n"); writer.write(prefix + sccQuantification.getName() + "\t" + sccQuantification.getQuantification(category) + "\n"); writer.write(prefix + spaQuantification.getName() + "\t" + spaQuantification.getQuantification(category) + "\n"); } writer.close(); BufferedWriter bfs = new BufferedWriter(new FileWriter(quantifierFile.getParent() + Os.pathSeparator() + indexName + "_" + quantifierFile.getName() + "_rates.txt")); TShortDoubleHashMap simpleTPRs = ((CCQuantifier) quantifiers[0]).getSimpleTPRs(); TShortDoubleHashMap simpleFPRs = ((CCQuantifier) quantifiers[0]).getSimpleFPRs(); TShortDoubleHashMap maxTPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier()) .getSimpleTPRs(); TShortDoubleHashMap maxFPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier()) .getSimpleFPRs(); TShortDoubleHashMap scaledTPRs = ((PAQuantifier) quantifiers[1]).getScaledTPRs(); TShortDoubleHashMap scaledFPRs = ((PAQuantifier) quantifiers[1]).getScaledFPRs(); ContingencyTableSet simpleContingencyTableSet = ((CCQuantifier) quantifiers[0]).getContingencyTableSet(); ContingencyTableSet maxContingencyTableSet = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]) .getInternalQuantifier()).getContingencyTableSet(); short[] cats = simpleTPRs.keys(); for (int i = 0; i < cats.length; ++i) { short cat = cats[i]; String catName = test.getCategoryDB().getCategoryName(cat); ContingencyTable simpleContingencyTable = simpleContingencyTableSet.getCategoryContingencyTable(cat); ContingencyTable maxContingencyTable = maxContingencyTableSet.getCategoryContingencyTable(cat); double simpleTPR = simpleTPRs.get(cat); double simpleFPR = simpleFPRs.get(cat); double maxTPR = maxTPRs.get(cat); double maxFPR = maxFPRs.get(cat); double scaledTPR = scaledTPRs.get(cat); double scaledFPR = scaledFPRs.get(cat); String line = indexName + "_" + quantifierFile.getName() + "\ttest\tsimple\t" + catName + "\t" + cat + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t" + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n"; bfs.write(line); line = indexName + "_" + quantifierFile.getName() + "\ttest\tmax\t" + catName + "\t" + cat + "\t" + maxContingencyTable.tp() + "\t" + maxContingencyTable.fp() + "\t" + maxContingencyTable.fn() + "\t" + maxContingencyTable.tn() + "\t" + maxTPR + "\t" + maxFPR + "\n"; bfs.write(line); line = indexName + "_" + quantifierFile.getName() + "\ttest\tscaled\t" + catName + "\t" + cat + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t" + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + scaledTPR + "\t" + scaledFPR + "\n"; bfs.write(line); } bfs.close(); }
From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapQueryList.java
public static void main(String[] args) { Options options = new Options(); Option inputOpt = OptionBuilder.create(IN); inputOpt.setArgName("INPUT"); inputOpt.setDescription("Input Kyanos resource directory"); inputOpt.setArgs(1);//from ww w. j ava 2 s .com inputOpt.setRequired(true); Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS); inClassOpt.setArgName("CLASS"); inClassOpt.setDescription("FQN of EPackage implementation class"); inClassOpt.setArgs(1); inClassOpt.setRequired(true); options.addOption(inputOpt); options.addOption(inClassOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME, new MapPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN))); Class<?> inClazz = KyanosMapQueryList.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME, PersistentResourceFactory.eINSTANCE); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); resource.load(loadOpts); { LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); EList<MethodDeclaration> list = JavaQueries.getUnusedMethodsList(resource); long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Query result (list) contains {0} elements", list.size())); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); } if (resource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource); } else { resource.unload(); } } catch (ParseException e) { MessageUtil.showError(e.toString()); MessageUtil.showError("Current arguments: " + Arrays.toString(args)); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("java -jar <this-file.jar>", options, true); } catch (Throwable e) { MessageUtil.showError(e.toString()); } }
From source file:apps.quantification.QuantifySVMLight.java
public static void main(String[] args) throws IOException { String cmdLineSyntax = QuantifySVMLight.class.getName() + " [OPTIONS] <path to svm_light_classify> <testIndexDirectory> <quantificationModelDirectory>"; Options options = new Options(); OptionBuilder.withArgName("d"); OptionBuilder.withDescription("Dump confidences file"); OptionBuilder.withLongOpt("d"); OptionBuilder.isRequired(false);/*from w w w .j a va 2s .com*/ OptionBuilder.hasArg(false); 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 files in svm_light format (default: delete)"); OptionBuilder.withLongOpt("s"); OptionBuilder.isRequired(false); OptionBuilder.hasArg(false); options.addOption(OptionBuilder.create()); SvmLightClassifierCustomizer customizer = null; GnuParser parser = new GnuParser(); String[] remainingArgs = null; try { CommandLine line = parser.parse(options, args); remainingArgs = line.getArgs(); customizer = new SvmLightClassifierCustomizer(remainingArgs[0]); if (line.hasOption("v")) customizer.printSvmLightOutput(true); if (line.hasOption("s")) { System.out.println("Keeping temporary files."); customizer.setDeleteTestFiles(false); customizer.setDeletePredictionsFiles(false); } if (line.hasOption("t")) customizer.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); } if (remainingArgs.length != 3) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(cmdLineSyntax, options); System.exit(-1); } String indexFile = remainingArgs[1]; File file = new File(indexFile); String indexName = file.getName(); String indexPath = file.getParent(); String quantifierFilename = remainingArgs[2]; FileSystemStorageManager indexFssm = new FileSystemStorageManager(indexPath, false); indexFssm.open(); IIndex test = TroveReadWriteHelper.readIndex(indexFssm, indexName, TroveContentDBType.Full, TroveClassificationDBType.Full); indexFssm.close(); FileSystemStorageManager quantifierFssm = new FileSystemStorageManager(quantifierFilename, false); quantifierFssm.open(); SvmLightDataManager classifierDataManager = new SvmLightDataManager(customizer); FileSystemStorageManager fssm = new FileSystemStorageManager(quantifierFilename, false); fssm.open(); IQuantifier[] quantifiers = QuantificationLearner.read(fssm, classifierDataManager, ClassificationMode.PER_CATEGORY); fssm.close(); quantifierFssm.close(); Quantification ccQuantification = quantifiers[0].quantify(test); Quantification paQuantification = quantifiers[1].quantify(test); Quantification accQuantification = quantifiers[2].quantify(test); Quantification maxQuantification = quantifiers[3].quantify(test); Quantification sccQuantification = quantifiers[4].quantify(test); Quantification spaQuantification = quantifiers[5].quantify(test); Quantification trueQuantification = new Quantification("True", test.getClassificationDB()); File quantifierFile = new File(quantifierFilename); String quantificationName = quantifierFile.getParent() + Os.pathSeparator() + indexName + "_" + quantifierFile.getName() + ".txt"; BufferedWriter writer = new BufferedWriter(new FileWriter(quantificationName)); IShortIterator iterator = test.getCategoryDB().getCategories(); while (iterator.hasNext()) { short category = iterator.next(); String prefix = quantifierFile.getName() + "\t" + indexName + "\t" + test.getCategoryDB().getCategoryName(category) + "\t" + category + "\t" + trueQuantification.getQuantification(category) + "\t"; writer.write(prefix + ccQuantification.getName() + "\t" + ccQuantification.getQuantification(category) + "\n"); writer.write(prefix + paQuantification.getName() + "\t" + paQuantification.getQuantification(category) + "\n"); writer.write(prefix + accQuantification.getName() + "\t" + accQuantification.getQuantification(category) + "\n"); writer.write(prefix + maxQuantification.getName() + "\t" + maxQuantification.getQuantification(category) + "\n"); writer.write(prefix + sccQuantification.getName() + "\t" + sccQuantification.getQuantification(category) + "\n"); writer.write(prefix + spaQuantification.getName() + "\t" + spaQuantification.getQuantification(category) + "\n"); } writer.close(); BufferedWriter bfs = new BufferedWriter(new FileWriter(quantifierFile.getParent() + Os.pathSeparator() + indexName + "_" + quantifierFile.getName() + "_rates.txt")); TShortDoubleHashMap simpleTPRs = ((CCQuantifier) quantifiers[0]).getSimpleTPRs(); TShortDoubleHashMap simpleFPRs = ((CCQuantifier) quantifiers[0]).getSimpleFPRs(); TShortDoubleHashMap maxTPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier()) .getSimpleTPRs(); TShortDoubleHashMap maxFPRs = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]).getInternalQuantifier()) .getSimpleFPRs(); TShortDoubleHashMap scaledTPRs = ((PAQuantifier) quantifiers[1]).getScaledTPRs(); TShortDoubleHashMap scaledFPRs = ((PAQuantifier) quantifiers[1]).getScaledFPRs(); ContingencyTableSet simpleContingencyTableSet = ((CCQuantifier) quantifiers[0]).getContingencyTableSet(); ContingencyTableSet maxContingencyTableSet = ((CCQuantifier) ((ScaledQuantifier) quantifiers[3]) .getInternalQuantifier()).getContingencyTableSet(); short[] cats = simpleTPRs.keys(); for (int i = 0; i < cats.length; ++i) { short cat = cats[i]; String catName = test.getCategoryDB().getCategoryName(cat); ContingencyTable simpleContingencyTable = simpleContingencyTableSet.getCategoryContingencyTable(cat); ContingencyTable maxContingencyTable = maxContingencyTableSet.getCategoryContingencyTable(cat); double simpleTPR = simpleTPRs.get(cat); double simpleFPR = simpleFPRs.get(cat); double maxTPR = maxTPRs.get(cat); double maxFPR = maxFPRs.get(cat); double scaledTPR = scaledTPRs.get(cat); double scaledFPR = scaledFPRs.get(cat); String line = indexName + "_" + quantifierFile.getName() + "\ttest\tsimple\t" + catName + "\t" + cat + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t" + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n"; bfs.write(line); line = indexName + "_" + quantifierFile.getName() + "\ttest\tmax\t" + catName + "\t" + cat + "\t" + maxContingencyTable.tp() + "\t" + maxContingencyTable.fp() + "\t" + maxContingencyTable.fn() + "\t" + maxContingencyTable.tn() + "\t" + maxTPR + "\t" + maxFPR + "\n"; bfs.write(line); line = indexName + "_" + quantifierFile.getName() + "\ttest\tscaled\t" + catName + "\t" + cat + "\t" + simpleContingencyTable.tp() + "\t" + simpleContingencyTable.fp() + "\t" + simpleContingencyTable.fn() + "\t" + simpleContingencyTable.tn() + "\t" + scaledTPR + "\t" + scaledFPR + "\n"; bfs.write(line); } bfs.close(); }
From source file:eu.freme.bpt.Main.java
public static void main(String[] args) { final List<String> services = new ArrayList<>(); for (EService eService : EService.values()) { services.add(eService.getName()); }//from ww w .ja v a2 s .c om Pair<EService, String[]> serviceAndArgs = extractService(args, services); EService service = serviceAndArgs.getName(); // create options that will be parsed from the args /////// General BPT options /////// Option helpOption = new Option("h", "help", false, "Prints this message"); Option inputOption = Option.builder("if").longOpt("input-file").argName("input file").desc( "The input file or directory to process. In case of a directory, each file in that directory is processed. " + "If not given, standard in is used.") .hasArg().build(); Option outputOption = Option.builder("od").longOpt("output-dir").argName("output dir") .desc("The output directory. If not given, output is written to standard out.").hasArg().build(); Option propertiesOption = Option.builder("prop").longOpt("properties").argName("properties file") .desc("The properties file that contains configuration of the tool.").hasArg().build(); Options options = new Options().addOption(helpOption).addOption(inputOption).addOption(outputOption) .addOption(propertiesOption); /////// Common service options /////// Option informatOption = Option.builder("f").longOpt("informat").argName("FORMAT") .desc("The format of the input document(s). Defaults to 'turtle'").hasArg().build(); Option outformatOption = Option.builder("o").longOpt("outformat").argName("FORMAT") .desc("The desired output format of the service. Defaults to 'turtle'").hasArg().build(); options.addOption(informatOption).addOption(outformatOption); /////// Service specific options /////// if (service != null) { switch (service) { case E_TRANSLATION: ETranslation.addOptions(options); break; case E_ENTITY: EEntity.addOptions(options); break; case E_LINK: ELink.addOptions(options); break; case E_TERMINOLOGY: ETerminology.addOptions(options); break; case PIPELINING: Pipelining.addOptions(options); break; case E_PUBLISHING: // TODO ! default: logger.warn("Unknown service {}. Skipping!", service); break; } } else { ETranslation.addOptions(options); EEntity.addOptions(options); ELink.addOptions(options); ETerminology.addOptions(options); Pipelining.addOptions(options); } CommandLine commandLine = null; int exitValue; try { CommandLineParser parser = new DefaultParser(); commandLine = parser.parse(options, serviceAndArgs.getValue()); exitValue = 0; } catch (ParseException e) { System.err.println(e.getMessage()); exitValue = 1; } if ((exitValue != 0) || commandLine.hasOption("h") || service == null) { HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(132); formatter.printHelp("java -jar <this jar file> <e-service> ", options, true); System.exit(exitValue); } logger.debug("Commandline successfully parsed!"); try { BPT batchProcessingTool = new BPT(); if (commandLine.hasOption("prop")) { batchProcessingTool.loadProperties(commandLine.getOptionValue("prop")); } if (commandLine.hasOption("if")) { batchProcessingTool.setInput(commandLine.getOptionValue("if")); } if (commandLine.hasOption("od")) { batchProcessingTool.setOutput(commandLine.getOptionValue("od")); } if (commandLine.hasOption('f')) { batchProcessingTool.setInFormat(Format.valueOf(commandLine.getOptionValue('f').replace('-', '_'))); } if (commandLine.hasOption('o')) { batchProcessingTool.setOutFormat(Format.valueOf(commandLine.getOptionValue('o').replace('-', '_'))); } switch (service) { case E_TRANSLATION: batchProcessingTool.eTranslation(commandLine.getOptionValue("source-lang"), commandLine.getOptionValue("target-lang"), commandLine.getOptionValue("system"), commandLine.getOptionValue("domain"), commandLine.getOptionValue("key")); break; case E_ENTITY: batchProcessingTool.eEntity(commandLine.getOptionValue("language"), commandLine.getOptionValue("dataset"), commandLine.getOptionValue("mode")); break; case E_LINK: batchProcessingTool.eLink(commandLine.getOptionValue("templateid")); break; case E_TERMINOLOGY: batchProcessingTool.eTerminology(commandLine.getOptionValue("source-lang"), commandLine.getOptionValue("target-lang"), commandLine.getOptionValue("collection"), commandLine.getOptionValue("domain"), commandLine.getOptionValue("key"), commandLine.getOptionValue("mode")); break; case PIPELINING: batchProcessingTool.pipelining(commandLine.getOptionValue("templateid")); break; case E_PUBLISHING: default: logger.error("Unknown service {}. Aborting!", service); System.exit(3); } } catch (Exception e) { logger.error("Cannot handle input or output. Reason: ", e); System.exit(2); } }