List of usage examples for org.apache.commons.cli DefaultParser DefaultParser
DefaultParser
From source file:com.act.biointerpretation.l2expansion.L2ExpansionDriver.java
public static void main(String[] args) throws Exception { // Build command line parser. Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());/*from w w w.j av a 2s.c o m*/ } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { LOGGER.error("Argument parsing failed: %s", e.getMessage()); HELP_FORMATTER.printHelp(L2ExpansionDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } // Print help. if (cl.hasOption(OPTION_HELP)) { HELP_FORMATTER.printHelp(L2ExpansionDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } // Get output files. String outputPath = cl.getOptionValue(OPTION_OUTPUT_PATH); File outputFile = new File(outputPath); if (outputFile.isDirectory() || outputFile.exists()) { LOGGER.error("Supplied output file is a directory or already exists."); System.exit(1); } outputFile.createNewFile(); File inchiOutputFile = new File(outputPath + ".inchis"); if (inchiOutputFile.isDirectory() || inchiOutputFile.exists()) { LOGGER.error("Supplied inchi output file is a directory or already exists."); System.exit(1); } inchiOutputFile.createNewFile(); Optional<OutputStream> maybeProgressStream = Optional.empty(); if (cl.hasOption(OPTION_PROGRESS_PATH)) { String progressPath = cl.getOptionValue(OPTION_PROGRESS_PATH); File progressFile = new File(progressPath); LOGGER.info("Writing incremental results to file at %s", progressFile.getAbsolutePath()); if (progressFile.isDirectory() || progressFile.exists()) { LOGGER.error("Supplied progress file is a directory or already exists."); System.exit(1); } maybeProgressStream = Optional.of(new FileOutputStream(progressFile)); } // Get metabolite list L2InchiCorpus inchiCorpus = getInchiCorpus(cl, OPTION_METABOLITES); LOGGER.info("%d substrate inchis.", inchiCorpus.getInchiList().size()); Integer maxMass = NO_MASS_THRESHOLD; if (cl.hasOption(OPTION_MASS_THRESHOLD)) { maxMass = Integer.parseInt(cl.getOptionValue(OPTION_MASS_THRESHOLD)); LOGGER.info("Filtering out substrates with mass more than %d daltons.", maxMass); } inchiCorpus.filterByMass(maxMass); LOGGER.info("%d substrate inchis that are importable as molecules.", inchiCorpus.getInchiList().size()); PredictionGenerator generator = new AllPredictionsGenerator(new ReactionProjector()); L2Expander expander = buildExpander(cl, inchiCorpus, generator); L2PredictionCorpus predictionCorpus = expander.getPredictions(maybeProgressStream); LOGGER.info("Done with L2 expansion. Produced %d predictions.", predictionCorpus.getCorpus().size()); LOGGER.info("Writing corpus to file."); predictionCorpus.writePredictionsToJsonFile(outputFile); L2InchiCorpus productInchis = new L2InchiCorpus(predictionCorpus.getUniqueProductInchis()); productInchis.writeToFile(inchiOutputFile); LOGGER.info("L2ExpansionDriver complete!"); }
From source file:com.twitter.heron.scheduler.SubmitterMain.java
public static void main(String[] args) throws Exception { Options options = constructOptions(); Options helpOptions = constructHelpOptions(); CommandLineParser parser = new DefaultParser(); // parse the help options first. CommandLine cmd = parser.parse(helpOptions, args, true); if (cmd.hasOption("h")) { usage(options);/*from ww w. ja va 2 s .c o m*/ return; } try { // Now parse the required options cmd = parser.parse(options, args); } catch (ParseException e) { usage(options); throw new RuntimeException("Error parsing command line options: ", e); } Boolean verbose = false; Level logLevel = Level.INFO; if (cmd.hasOption("v")) { logLevel = Level.ALL; verbose = true; } // init log LoggingHelper.loggerInit(logLevel, false); String cluster = cmd.getOptionValue("cluster"); String role = cmd.getOptionValue("role"); String environ = cmd.getOptionValue("environment"); String heronHome = cmd.getOptionValue("heron_home"); String configPath = cmd.getOptionValue("config_path"); String overrideConfigFile = cmd.getOptionValue("override_config_file"); String releaseFile = cmd.getOptionValue("release_file"); String topologyPackage = cmd.getOptionValue("topology_package"); String topologyDefnFile = cmd.getOptionValue("topology_defn"); String topologyJarFile = cmd.getOptionValue("topology_jar"); // load the topology definition into topology proto TopologyAPI.Topology topology = TopologyUtils.getTopology(topologyDefnFile); // first load the defaults, then the config from files to override it // next add config parameters from the command line // load the topology configs // build the final config by expanding all the variables Config config = Config.expand(Config.newBuilder().putAll(defaultConfigs(heronHome, configPath, releaseFile)) .putAll(overrideConfigs(overrideConfigFile)) .putAll(commandLineConfigs(cluster, role, environ, verbose)) .putAll(topologyConfigs(topologyPackage, topologyJarFile, topologyDefnFile, topology)).build()); LOG.fine("Static config loaded successfully "); LOG.fine(config.toString()); SubmitterMain submitterMain = new SubmitterMain(config, topology); boolean isSuccessful = submitterMain.submitTopology(); // Log the result and exit if (!isSuccessful) { throw new RuntimeException(String.format("Failed to submit topology %s", topology.getName())); } else { LOG.log(Level.FINE, "Topology {0} submitted successfully", topology.getName()); } }
From source file:com.twitter.heron.apiserver.Runtime.java
@SuppressWarnings({ "IllegalCatch", "RegexpSinglelineJava" })
public static void main(String[] args) throws Exception {
final Options options = createOptions();
final Options helpOptions = constructHelpOptions();
CommandLineParser parser = new DefaultParser();
// parse the help options first.
CommandLine cmd = parser.parse(helpOptions, args, true);
if (cmd.hasOption(Flag.Help.name)) {
usage(options);//from www . j ava 2s. co m
return;
}
try {
cmd = parser.parse(options, args);
} catch (ParseException pe) {
System.err.println(pe.getMessage());
usage(options);
return;
}
final boolean verbose = isVerbose(cmd);
// set and configure logging level
Logging.setVerbose(verbose);
Logging.configure(verbose);
LOG.debug("apiserver overrides:\n {}", cmd.getOptionProperties(Flag.Property.name));
final String toolsHome = getToolsHome();
// read command line flags
final String cluster = cmd.getOptionValue(Flag.Cluster.name);
final String heronConfigurationDirectory = getConfigurationDirectory(toolsHome, cmd);
final String heronDirectory = getHeronDirectory(cmd);
final String releaseFile = getReleaseFile(toolsHome, cmd);
final String configurationOverrides = loadOverrides(cmd);
final int port = getPort(cmd);
final String downloadHostName = getDownloadHostName(cmd);
final String heronCorePackagePath = getHeronCorePackagePath(cmd);
final Config baseConfiguration = ConfigUtils.getBaseConfiguration(heronDirectory,
heronConfigurationDirectory, releaseFile, configurationOverrides);
final ResourceConfig config = new ResourceConfig(Resources.get());
final Server server = new Server(port);
final ServletContextHandler contextHandler = new ServletContextHandler(ServletContextHandler.NO_SESSIONS);
contextHandler.setContextPath("/");
LOG.info("using configuration path: {}", heronConfigurationDirectory);
contextHandler.setAttribute(HeronResource.ATTRIBUTE_CLUSTER, cluster);
contextHandler.setAttribute(HeronResource.ATTRIBUTE_CONFIGURATION, baseConfiguration);
contextHandler.setAttribute(HeronResource.ATTRIBUTE_CONFIGURATION_DIRECTORY, heronConfigurationDirectory);
contextHandler.setAttribute(HeronResource.ATTRIBUTE_CONFIGURATION_OVERRIDE_PATH, configurationOverrides);
contextHandler.setAttribute(HeronResource.ATTRIBUTE_PORT, String.valueOf(port));
contextHandler.setAttribute(HeronResource.ATTRIBUTE_DOWNLOAD_HOSTNAME,
Utils.isNotEmpty(downloadHostName) ? String.valueOf(downloadHostName) : null);
contextHandler.setAttribute(HeronResource.ATTRIBUTE_HERON_CORE_PACKAGE_PATH,
Utils.isNotEmpty(heronCorePackagePath) ? String.valueOf(heronCorePackagePath) : null);
server.setHandler(contextHandler);
final ServletHolder apiServlet = new ServletHolder(new ServletContainer(config));
contextHandler.addServlet(apiServlet, API_BASE_PATH);
try {
server.start();
LOG.info("Heron apiserver started at {}", server.getURI());
server.join();
} catch (Exception ex) {
final String message = getErrorMessage(server, port, ex);
LOG.error(message);
System.err.println(message);
System.exit(1);
} finally {
server.destroy();
}
}
From source file:com.ibm.crail.tools.CrailFsck.java
public static void main(String[] args) throws Exception { String type = ""; String filename = "/tmp.dat"; long offset = 0; long length = 1; boolean randomize = false; int storageClass = 0; int locationClass = 0; Option typeOption = Option.builder("t").desc( "type of experiment [getLocations|directoryDump|namenodeDump|blockStatistics|ping|createDirectory]") .hasArg().build();/*from ww w . j a v a2 s.com*/ Option fileOption = Option.builder("f").desc("filename").hasArg().build(); Option offsetOption = Option.builder("y").desc("offset into the file").hasArg().build(); Option lengthOption = Option.builder("l").desc("length of the file [bytes]").hasArg().build(); Option storageOption = Option.builder("c").desc("storageClass for file [1..n]").hasArg().build(); Option locationOption = Option.builder("p").desc("locationClass for file [1..n]").hasArg().build(); Options options = new Options(); options.addOption(typeOption); options.addOption(fileOption); options.addOption(offsetOption); options.addOption(lengthOption); options.addOption(storageOption); options.addOption(locationOption); CommandLineParser parser = new DefaultParser(); CommandLine line = parser.parse(options, Arrays.copyOfRange(args, 0, args.length)); if (line.hasOption(typeOption.getOpt())) { type = line.getOptionValue(typeOption.getOpt()); } if (line.hasOption(fileOption.getOpt())) { filename = line.getOptionValue(fileOption.getOpt()); } if (line.hasOption(offsetOption.getOpt())) { offset = Long.parseLong(line.getOptionValue(offsetOption.getOpt())); } if (line.hasOption(lengthOption.getOpt())) { length = Long.parseLong(line.getOptionValue(lengthOption.getOpt())); } if (line.hasOption(storageOption.getOpt())) { storageClass = Integer.parseInt(line.getOptionValue(storageOption.getOpt())); } if (line.hasOption(locationOption.getOpt())) { locationClass = Integer.parseInt(line.getOptionValue(locationOption.getOpt())); } CrailFsck fsck = new CrailFsck(); if (type.equals("getLocations")) { fsck.getLocations(filename, offset, length); } else if (type.equals("directoryDump")) { fsck.directoryDump(filename, randomize); } else if (type.equals("namenodeDump")) { fsck.namenodeDump(); } else if (type.equals("blockStatistics")) { fsck.blockStatistics(filename); } else if (type.equals("ping")) { fsck.ping(); } else if (type.equals("createDirectory")) { fsck.createDirectory(filename, storageClass, locationClass); } else { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("crail fsck", options); System.exit(-1); } }
From source file:com.hpe.nv.samples.advanced.AdvAllTestManagerClassMethods.java
public static void main(String[] args) throws Exception { try {//from ww w . j ava 2s. co m // program arguments Options options = new Options(); options.addOption("i", "server-ip", true, "[mandatory] NV Test Manager IP"); options.addOption("o", "server-port", true, "[mandatory] NV Test Manager port"); options.addOption("u", "username", true, "[mandatory] NV username"); options.addOption("w", "password", true, "[mandatory] NV password"); options.addOption("e", "ssl", true, "[optional] Pass true to use SSL. Default: false"); options.addOption("y", "proxy", true, "[optional] Proxy server host:port"); options.addOption("t", "site-url", true, "[optional] Site under test URL. Default: HPE Network Virtualization site URL. If you change this value, make sure to change the --xpath argument too"); options.addOption("x", "xpath", true, "[optional] Parameter for ExpectedConditions.visibilityOfElementLocated(By.xpath(...)) method. Use an xpath expression of some element in the site. Default: //div[@id='content']"); options.addOption("a", "active-adapter-ip", true, "[optional] Active adapter IP. Default: --server-ip argument"); options.addOption("s", "shunra-file-path", true, "[optional] File path for the .shunra file to analyze"); options.addOption("z", "zip-result-file-path", true, "[optional] File path to store the analysis results as a .zip file"); options.addOption("k", "analysis-ports", true, "[optional] A comma-separated list of ports for test analysis"); options.addOption("f", "first-test-flow-tcp-port", true, "[optional] TCP port for the flow of the first test"); options.addOption("g", "second-test-flow-tcp-port", true, "[optional] TCP port for the flow of the second test"); options.addOption("b", "browser", true, "[optional] The browser for which the Selenium WebDriver is built. Possible values: Chrome and Firefox. Default: Firefox"); options.addOption("d", "debug", true, "[optional] Pass true to view console debug messages during execution. Default: false"); options.addOption("h", "help", false, "[optional] Generates and prints help information"); // parse and validate the command line arguments CommandLineParser parser = new DefaultParser(); CommandLine line = parser.parse(options, args); if (line.hasOption("help")) { // print help if help argument is passed HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("AdvAllTestManagerClassMethods.java", options); return; } if (line.hasOption("server-ip")) { serverIp = line.getOptionValue("server-ip"); if (serverIp.equals("0.0.0.0")) { throw new Exception( "Please replace the server IP argument value (0.0.0.0) with your NV Test Manager IP"); } } else { throw new Exception("Missing argument -i/--server-ip <serverIp>"); } if (line.hasOption("server-port")) { serverPort = Integer.parseInt(line.getOptionValue("server-port")); } else { throw new Exception("Missing argument -o/--server-port <serverPort>"); } if (line.hasOption("username")) { username = line.getOptionValue("username"); } else { throw new Exception("Missing argument -u/--username <username>"); } if (line.hasOption("password")) { password = line.getOptionValue("password"); } else { throw new Exception("Missing argument -w/--password <password>"); } if (line.hasOption("ssl")) { ssl = Boolean.parseBoolean(line.getOptionValue("ssl")); } if (line.hasOption("site-url")) { siteUrl = line.getOptionValue("site-url"); } else { siteUrl = "http://www8.hp.com/us/en/software-solutions/network-virtualization/index.html"; } if (line.hasOption("xpath")) { xpath = line.getOptionValue("xpath"); } else { xpath = "//div[@id='content']"; } if (line.hasOption("zip-result-file-path")) { zipResultFilePath = line.getOptionValue("zip-result-file-path"); } if (line.hasOption("proxy")) { proxySetting = line.getOptionValue("proxy"); } if (line.hasOption("active-adapter-ip")) { activeAdapterIp = line.getOptionValue("active-adapter-ip"); } else { activeAdapterIp = serverIp; } if (line.hasOption("analysis-ports")) { String analysisPortsStr = line.getOptionValue("analysis-ports"); analysisPorts = analysisPortsStr.split(","); } else { analysisPorts = new String[] { "80", "8080" }; } if (line.hasOption("shunra-file-path")) { shunraFilePath = line.getOptionValue("shunra-file-path"); } if (line.hasOption("firstTestFlowTcpPort")) { firstTestFlowTcpPort = Integer.parseInt(line.getOptionValue("firstTestFlowTcpPort")); } else { firstTestFlowTcpPort = 8080; } if (line.hasOption("secondTestFlowTcpPort")) { secondTestFlowTcpPort = Integer.parseInt(line.getOptionValue("secondTestFlowTcpPort")); } else { secondTestFlowTcpPort = 80; } if (line.hasOption("browser")) { browser = line.getOptionValue("browser"); } else { browser = "Firefox"; } if (line.hasOption("debug")) { debug = Boolean.parseBoolean(line.getOptionValue("debug")); } String newLine = System.getProperty("line.separator"); String testDescription = "*** This sample demonstrates all of the TestManager class APIs. These APIs let you: ***" + newLine + "*** * initialize the TestManager object to pass logon credentials, the NV Test Manager IP, the port, and so on ***" + newLine + "*** * set/get the NV configuration and active adapter ***" + newLine + "*** * get the running tests tokens ***" + newLine + "*** * start/stop packet list capture ***" + newLine + "*** * get packet list information ***" + newLine + "*** * stop a specified array of tests or all of the running tests ***" + newLine + "*** * analyze a .shunra file, which is a compressed file that includes an events file, metadata, and packet lists ***" + newLine + "*** ***" + newLine + "*** You can view the actual steps of this sample in the AdvAllTestManagerClassMethods.java file. ***" + newLine; // print the sample's description System.out.println(testDescription); // start console spinner if (!debug) { spinner = new Thread(new Spinner()); spinner.start(); } // sample execution steps /***** Part 1 - Initialize the TestManager object to pass logon credentials, the NV Test Manager IP, the port, and so on *****/ printPartDescription( "\b------ Part 1 - Initialize the TestManager object to pass logon credentials, the NV Test Manager IP, the port, and so on"); initTestManager(); printPartSeparator(); /***** Part 2 - Set/get the NV configuration and active adapter *****/ printPartDescription("------ Part 2 - Set/get the NV configuration and active adapter"); setActiveAdapter(); getActiveAdapter(); setConfiguration(); getConfiguration(); printPartSeparator(); /***** Part 3 - Start tests and get the NV tests' tokens *****/ printPartDescription("------ Part 3 - Start tests and get the NV tests' tokens"); startTest1(); connectTest1ToTransactionManager(); startTest2(); connectTest2ToTransactionManager(); getTestTokens(); printPartSeparator(); /***** Part 4 - Start NV transactions, navigate to the site and start capturing the packet lists *****/ printPartDescription( "------ Part 4 - Start NV transactions, navigate to the site and start capturing the packet lists"); startTransaction1(); startTransaction2(); startPacketListCapture(); buildSeleniumWebDriver(); seleniumNavigateToPage(); printPartSeparator(); /***** Part 5 - Get the packet list information and print it to the console (if the --debug argument is set to true) *****/ printPartDescription( "------ Part 5 - Get the packet list information and print it to the console (if the --debug argument is set to true)"); getPacketListInfo(); printPartSeparator(); /***** Part 6 - Stop capturing packet lists and stop the NV transactions *****/ printPartDescription("------ Part 6 - Stop capturing packet lists and stop the NV transactions"); stopPacketListCapture(); stopTransaction1(); siteTransaction1 = null; stopTransaction2(); siteTransaction2 = null; printPartSeparator(); /***** Part 7 - Stop the first NV test using the "stopTests" method and then stop the second test using the "stopAllTests" method *****/ printPartDescription( "------ Part 7 - Stop the first NV test using the \"stopTests\" method and then stop the second test using the \"stopAllTests\" method"); stopTest1(); siteTest1 = null; driver.manage().timeouts().implicitlyWait(30, TimeUnit.SECONDS); stopAllTests(); siteTest2 = null; printPartSeparator(); /***** Part 8 - Analyze the specified .shunra file and print the results to the console *****/ printPartDescription( "------ Part 8 - Analyze the specified .shunra file and print the results to the console"); analyzeShunra(); printPartSeparator(); doneCallback(); } catch (Exception e) { try { handleError(e.getMessage()); } catch (Exception e2) { System.out.println("Error occurred: " + e2.getMessage()); } } }
From source file:com.act.lcms.db.analysis.BestMoleculesPickerFromLCMSIonAnalysis.java
public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());/* w w w . j a v a 2 s .c o m*/ } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { HELP_FORMATTER.printHelp(BestMoleculesPickerFromLCMSIonAnalysis.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(BestMoleculesPickerFromLCMSIonAnalysis.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } List<String> positiveReplicateResults = new ArrayList<>( Arrays.asList(cl.getOptionValues(OPTION_INPUT_FILES))); if (cl.hasOption(OPTION_MIN_OF_REPLICATES)) { HitOrMissReplicateFilterAndTransformer transformer = new HitOrMissReplicateFilterAndTransformer(); List<IonAnalysisInterchangeModel> models = positiveReplicateResults.stream().map(file -> { try { return IonAnalysisInterchangeModel.loadIonAnalysisInterchangeModelFromFile(file); } catch (IOException e) { throw new UncheckedIOException(e); } }).collect(Collectors.toList()); IonAnalysisInterchangeModel transformedModel = IonAnalysisInterchangeModel .filterAndOperateOnMoleculesFromMultipleReplicateModels(models, transformer); printInchisAndIonsToFile(transformedModel, cl.getOptionValue(OPTION_OUTPUT_FILE), cl.hasOption(OPTION_JSON_FORMAT)); return; } Double minSnrThreshold = Double.parseDouble(cl.getOptionValue(OPTION_MIN_SNR_THRESHOLD)); Double minIntensityThreshold = Double.parseDouble(cl.getOptionValue(OPTION_MIN_INTENSITY_THRESHOLD)); Double minTimeThreshold = Double.parseDouble(cl.getOptionValue(OPTION_MIN_TIME_THRESHOLD)); if (cl.hasOption(OPTION_GET_IONS_SUPERSET)) { List<IonAnalysisInterchangeModel> models = positiveReplicateResults.stream().map(file -> { try { return IonAnalysisInterchangeModel.loadIonAnalysisInterchangeModelFromFile(file); } catch (IOException e) { throw new UncheckedIOException(e); } }).collect(Collectors.toList()); IonAnalysisInterchangeModel transformedModel = IonAnalysisInterchangeModel .getSupersetOfIonicVariants(models, minSnrThreshold, minIntensityThreshold, minTimeThreshold); printInchisAndIonsToFile(transformedModel, cl.getOptionValue(OPTION_OUTPUT_FILE), cl.hasOption(OPTION_JSON_FORMAT)); return; } if (cl.hasOption(OPTION_THRESHOLD_ANALYSIS)) { if (positiveReplicateResults.size() > 1) { LOGGER.error("Since this is a threshold analysis, the number of positive replicates should be 1."); System.exit(1); } // We need to set this variable as a final since it is used in a lambda function below. final Set<String> ions = new HashSet<>(); if (cl.hasOption(OPTION_FILTER_BY_IONS)) { ions.addAll(Arrays.asList(cl.getOptionValues(OPTION_FILTER_BY_IONS))); } HitOrMissSingleSampleFilterAndTransformer hitOrMissSingleSampleTransformer = new HitOrMissSingleSampleFilterAndTransformer( minIntensityThreshold, minSnrThreshold, minTimeThreshold, ions); IonAnalysisInterchangeModel model = IonAnalysisInterchangeModel.filterAndOperateOnMoleculesFromModel( IonAnalysisInterchangeModel.loadIonAnalysisInterchangeModelFromFile( positiveReplicateResults.get(0)), hitOrMissSingleSampleTransformer); printInchisAndIonsToFile(model, cl.getOptionValue(OPTION_OUTPUT_FILE), cl.hasOption(OPTION_JSON_FORMAT)); } }
From source file:com.rodaxsoft.mailgun.message.tools.MailgunSender.java
/** * Main method/*from w ww .ja v a 2 s. c om*/ * @param args Command line arguments * @throws ConfigurationException if a configuration error occurs */ public static void main(String[] args) { //Parse the command line CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(OPTIONS, args); initializeMailgun(cmd); } catch (ParseException | ContextedException | ConfigurationException e) { System.err.println(e.getMessage()); System.err.println(); printHelp(); System.exit(-1); } //Read the plain text and HTML content files String text = null; String html = null; try { text = readFileToString(cmd.getOptionValue(PLAIN_TXT_OPT)); html = readFileToString(cmd.getOptionValue(HTML_OPT)); } catch (IOException e) { LOG.error("Error reading file", e); System.exit(-1); } if (!cmd.hasOption(RECIPIENTS_FILE_OPT)) { sendMessageToEmailAddress(cmd, text, html); } else { sendMessageToRecipientsInFile(cmd, text, html); } }
From source file:com.tremolosecurity.openunison.util.OpenUnisonUtils.java
public static void main(String[] args) throws Exception { logger = org.apache.logging.log4j.LogManager.getLogger(OpenUnisonUtils.class.getName()); Options options = new Options(); options.addOption("unisonXMLFile", true, "The full path to the Unison xml file"); options.addOption("keystorePath", true, "The full path to the Unison keystore"); options.addOption("chainName", true, "The name of the authentication chain"); options.addOption("mechanismName", true, "The name of the authentication mechanism for SAML2"); options.addOption("idpName", true, "The name of the identity provider application"); options.addOption("pathToMetaData", true, "The full path to the saml2 metadata file"); options.addOption("createDefault", false, "If set, add default parameters"); options.addOption("action", true, "export-sp-metadata, import-sp-metadata, export-secretkey, print-secretkey, import-idp-metadata, export-idp-metadata, clear-dlq, import-secretkey, create-secretkey"); options.addOption("urlBase", true, "Base URL, no URI; https://host:port"); options.addOption("alias", true, "Key alias"); options.addOption("newKeystorePath", true, "Path to the new keystore"); options.addOption("newKeystorePassword", true, "Password for the new keystore"); options.addOption("help", false, "Prints this message"); options.addOption("signMetadataWithKey", true, "Signs the metadata with the specified key"); options.addOption("dlqName", true, "The name of the dead letter queue"); options.addOption("upgradeFrom106", false, "Updates workflows from 1.0.6"); options.addOption("secretkey", true, "base64 encoded secret key"); options.addOption("envFile", true, "Environment variables for parmaterized configs"); CommandLineParser parser = new DefaultParser(); CommandLine cmd = parser.parse(options, args, true); if (args.length == 0 || cmd.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("OpenUnisonUtils", options); }/*from ww w . ja v a2 s. c o m*/ logger.info("Loading Unison Configuration"); String unisonXMLFile = loadOption(cmd, "unisonXMLFile", options); TremoloType ttRead = loadTremoloType(unisonXMLFile, cmd, options); String action = loadOption(cmd, "action", options); TremoloType ttWrite = null; if (action.equalsIgnoreCase("import-sp-metadata") || action.equalsIgnoreCase("import-idp-metadata")) { ttWrite = loadTremoloType(unisonXMLFile); } logger.info("Configuration loaded"); logger.info("Loading the keystore..."); String ksPath = loadOption(cmd, "keystorePath", options); KeyStore ks = loadKeyStore(ksPath, ttRead); logger.info("...loaded"); if (action.equalsIgnoreCase("import-sp-metadata")) { importMetaData(options, cmd, unisonXMLFile, ttRead, ttWrite, ksPath, ks); } else if (action.equalsIgnoreCase("export-sp-metadata")) { exportSPMetaData(options, cmd, ttRead, ks); } else if (action.equalsIgnoreCase("print-secretkey")) { printSecreyKey(options, cmd, ttRead, ks); } else if (action.equalsIgnoreCase("import-secretkey")) { importSecreyKey(options, cmd, ttRead, ks, ksPath); } else if (action.equalsIgnoreCase("create-secretkey")) { Security.addProvider(new BouncyCastleProvider()); logger.info("Creating AES-256 secret key"); String alias = loadOption(cmd, "alias", options); logger.info("Alias : '" + alias + "'"); KeyGenerator kg = KeyGenerator.getInstance("AES", "BC"); kg.init(256, new SecureRandom()); SecretKey sk = kg.generateKey(); ks.setKeyEntry(alias, sk, ttRead.getKeyStorePassword().toCharArray(), null); logger.info("Saving key"); ks.store(new FileOutputStream(ksPath), ttRead.getKeyStorePassword().toCharArray()); logger.info("Finished"); } else if (action.equalsIgnoreCase("export-secretkey")) { logger.info("Export Secret Key"); logger.info("Loading key"); String alias = loadOption(cmd, "alias", options); SecretKey key = (SecretKey) ks.getKey(alias, ttRead.getKeyStorePassword().toCharArray()); logger.info("Loading new keystore path"); String pathToNewKeystore = loadOption(cmd, "newKeystorePath", options); logger.info("Loading new keystore password"); String ksPassword = loadOption(cmd, "newKeystorePassword", options); KeyStore newKS = KeyStore.getInstance("PKCS12"); newKS.load(null, ttRead.getKeyStorePassword().toCharArray()); newKS.setKeyEntry(alias, key, ksPassword.toCharArray(), null); newKS.store(new FileOutputStream(pathToNewKeystore), ksPassword.toCharArray()); logger.info("Exported"); } else if (action.equalsIgnoreCase("import-idp-metadata")) { importIdpMetadata(options, cmd, unisonXMLFile, ttRead, ttWrite, ksPath, ks); } else if (action.equalsIgnoreCase("export-idp-metadata")) { exportIdPMetadata(options, cmd, ttRead, ks); } else if (action.equalsIgnoreCase("clear-dlq")) { logger.info("Getting the DLQ Name..."); String dlqName = loadOption(cmd, "dlqName", options); QueUtils.emptyDLQ(ttRead, dlqName); } else if (action.equalsIgnoreCase("upgradeFrom106")) { logger.info("Upgrading OpenUnison's configuration from 1.0.6"); String backupFileName = unisonXMLFile + ".bak"; logger.info("Backing up to '" + backupFileName + "'"); BufferedReader in = new BufferedReader(new InputStreamReader(new FileInputStream(unisonXMLFile))); PrintWriter out = new PrintWriter(new FileOutputStream(backupFileName)); String line = null; while ((line = in.readLine()) != null) { out.println(line); } out.flush(); out.close(); in.close(); ByteArrayOutputStream bout = new ByteArrayOutputStream(); AddChoiceToTasks.convert(new FileInputStream(unisonXMLFile), bout); FileOutputStream fsout = new FileOutputStream(unisonXMLFile); fsout.write(bout.toByteArray()); fsout.flush(); fsout.close(); } }
From source file:com.yahoo.labs.yamall.local.Yamall.java
public static void main(String[] args) { String[] remainingArgs = null; String inputFile = null;//www . j a va2s . c o m String predsFile = null; String saveModelFile = null; String initialModelFile = null; String lossName = null; String parserName = null; String linkName = null; String invertHashName = null; double learningRate = 1; String minPredictionString = null; String maxPredictionString = null; String fmNumberFactorsString = null; int bitsHash; int numberPasses; int holdoutPeriod = 10; boolean testOnly = false; boolean exponentialProgress; double progressInterval; options.addOption("h", "help", false, "displays this help"); options.addOption("t", false, "ignore label information and just test"); options.addOption(Option.builder().hasArg(false).required(false).longOpt("binary") .desc("reports loss as binary classification with -1,1 labels").build()); options.addOption( Option.builder().hasArg(false).required(false).longOpt("solo").desc("uses SOLO optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("pcsolo") .desc("uses Per Coordinate SOLO optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("pistol") .desc("uses PiSTOL optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("kt") .desc("(EXPERIMENTAL) uses KT optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("pckt") .desc("(EXPERIMENTAL) uses Per Coordinate KT optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("pccocob") .desc("(EXPERIMENTAL) uses Per Coordinate COCOB optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("cocob") .desc("(EXPERIMENTAL) uses COCOB optimizer").build()); options.addOption( Option.builder().hasArg(false).required(false).longOpt("fm").desc("Factorization Machine").build()); options.addOption(Option.builder("f").hasArg(true).required(false).desc("final regressor to save") .type(String.class).longOpt("final_regressor").build()); options.addOption(Option.builder("p").hasArg(true).required(false).desc("file to output predictions to") .longOpt("predictions").type(String.class).build()); options.addOption( Option.builder("i").hasArg(true).required(false).desc("initial regressor(s) to load into memory") .longOpt("initial_regressor").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false).desc( "specify the loss function to be used. Currently available ones are: absolute, squared (default), hinge, logistic") .longOpt("loss_function").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false).desc( "specify the link function used in the output of the predictions. Currently available ones are: identity (default), logistic") .longOpt("link").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("output human-readable final regressor with feature names").longOpt("invert_hash") .type(String.class).build()); options.addOption( Option.builder("l").hasArg(true).required(false).desc("set (initial) learning Rate, default = 1.0") .longOpt("learning_rate").type(String.class).build()); options.addOption(Option.builder("b").hasArg(true).required(false) .desc("number of bits in the feature table, default = 18").longOpt("bit_precision") .type(String.class).build()); options.addOption(Option.builder("P").hasArg(true).required(false) .desc("progress update frequency, integer: additive; float: multiplicative, default = 2.0") .longOpt("progress").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("smallest prediction to output, before the link function, default = -50") .longOpt("min_prediction").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("smallest prediction to output, before the link function, default = 50") .longOpt("max_prediction").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("ignore namespaces beginning with the characters in <arg>").longOpt("ignore") .type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false).desc("number of training passes") .longOpt("passes").type(String.class).build()); options.addOption( Option.builder().hasArg(true).required(false).desc("holdout period for test only, default = 10") .longOpt("holdout_period").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("number of factors for Factorization Machines default = 8").longOpt("fmNumberFactors") .type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("specify the parser to use. Currently available ones are: vw (default), libsvm, tsv") .longOpt("parser").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false).desc("schema file for the TSV input") .longOpt("schema").type(String.class).build()); CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (ParseException e) { System.out.println("Unrecognized option"); help(); } if (cmd.hasOption("h")) help(); if (cmd.hasOption("t")) testOnly = true; if (cmd.hasOption("binary")) { binary = true; System.out.println("Reporting binary loss"); } initialModelFile = cmd.getOptionValue("i"); predsFile = cmd.getOptionValue("p"); lossName = cmd.getOptionValue("loss_function", "squared"); linkName = cmd.getOptionValue("link", "identity"); saveModelFile = cmd.getOptionValue("f"); learningRate = Double.parseDouble(cmd.getOptionValue("l", "1.0")); bitsHash = Integer.parseInt(cmd.getOptionValue("b", "18")); invertHashName = cmd.getOptionValue("invert_hash"); minPredictionString = cmd.getOptionValue("min_prediction", "-50"); maxPredictionString = cmd.getOptionValue("max_prediction", "50"); fmNumberFactorsString = cmd.getOptionValue("fmNumberFactors", "8"); parserName = cmd.getOptionValue("parser", "vw"); numberPasses = Integer.parseInt(cmd.getOptionValue("passes", "1")); System.out.println("Number of passes = " + numberPasses); if (numberPasses > 1) { holdoutPeriod = Integer.parseInt(cmd.getOptionValue("holdout_period", "10")); System.out.println("Holdout period = " + holdoutPeriod); } remainingArgs = cmd.getArgs(); if (remainingArgs.length == 1) inputFile = remainingArgs[0]; InstanceParser instanceParser = null; if (parserName.equals("vw")) instanceParser = new VWParser(bitsHash, cmd.getOptionValue("ignore"), (invertHashName != null)); else if (parserName.equals("libsvm")) instanceParser = new LIBSVMParser(bitsHash, (invertHashName != null)); else if (parserName.equals("tsv")) { String schema = cmd.getOptionValue("schema"); if (schema == null) { System.out.println("TSV parser requires a schema file."); System.exit(0); } else { String spec = null; try { spec = new String(Files.readAllBytes(Paths.get(schema))); } catch (IOException e) { System.out.println("Error reading the TSV schema file."); e.printStackTrace(); System.exit(0); } instanceParser = new TSVParser(bitsHash, cmd.getOptionValue("ignore"), (invertHashName != null), spec); } } else { System.out.println("Unknown parser."); System.exit(0); } System.out.println("Num weight bits = " + bitsHash); // setup progress String progress = cmd.getOptionValue("P", "2.0"); if (progress.indexOf('.') >= 0) { exponentialProgress = true; progressInterval = (double) Double.parseDouble(progress); } else { exponentialProgress = false; progressInterval = (double) Integer.parseInt(progress); } // min and max predictions minPrediction = (double) Double.parseDouble(minPredictionString); maxPrediction = (double) Double.parseDouble(maxPredictionString); // number of factors for Factorization Machines fmNumberFactors = (int) Integer.parseInt(fmNumberFactorsString); // configure the learner Loss lossFnc = null; LinkFunction link = null; if (initialModelFile == null) { if (cmd.hasOption("kt")) { learner = new KT(bitsHash); } else if (cmd.hasOption("pckt")) { learner = new PerCoordinateKT(bitsHash); } else if (cmd.hasOption("pcsolo")) { learner = new PerCoordinateSOLO(bitsHash); } else if (cmd.hasOption("solo")) { learner = new SOLO(bitsHash); } else if (cmd.hasOption("pccocob")) { learner = new PerCoordinateCOCOB(bitsHash); } else if (cmd.hasOption("cocob")) { learner = new COCOB(bitsHash); } else if (cmd.hasOption("pistol")) { learner = new PerCoordinatePiSTOL(bitsHash); } else if (cmd.hasOption("fm")) { learner = new SGD_FM(bitsHash, fmNumberFactors); } else learner = new SGD_VW(bitsHash); } else { learner = IOLearner.loadLearner(initialModelFile); } // setup link function if (linkName.equals("identity")) { link = new IdentityLinkFunction(); } else if (linkName.equals("logistic")) { link = new LogisticLinkFunction(); } else { System.out.println("Unknown link function."); System.exit(0); } // setup loss function if (lossName.equals("squared")) { lossFnc = new SquareLoss(); } else if (lossName.equals("hinge")) { lossFnc = new HingeLoss(); } else if (lossName.equals("logistic")) { lossFnc = new LogisticLoss(); } else if (lossName.equals("absolute")) { lossFnc = new AbsLoss(); } else { System.out.println("Unknown loss function."); System.exit(0); } learner.setLoss(lossFnc); learner.setLearningRate(learningRate); // maximum range predictions System.out.println("Max prediction = " + maxPrediction + ", Min Prediction = " + minPrediction); // print information about the learner System.out.println(learner.toString()); // print information about the link function System.out.println(link.toString()); // print information about the parser System.out.println(instanceParser.toString()); // print information about ignored namespaces System.out.println("Ignored namespaces = " + cmd.getOptionValue("ignore", "")); long start = System.nanoTime(); FileInputStream fstream; try { BufferedReader br = null; if (inputFile != null) { fstream = new FileInputStream(inputFile); System.out.println("Reading datafile = " + inputFile); br = new BufferedReader(new InputStreamReader(fstream)); } else { System.out.println("Reading from console"); br = new BufferedReader(new InputStreamReader(System.in)); } File fout = null; FileOutputStream fos = null; BufferedWriter bw = null; if (predsFile != null) { fout = new File(predsFile); fos = new FileOutputStream(fout); bw = new BufferedWriter(new OutputStreamWriter(fos)); } try { System.out.println("average example current current current"); System.out.println("loss counter label predict features"); int iter = 0; double cumLoss = 0; double weightedSampleSum = 0; double sPlus = 0; double sMinus = 0; Instance sample = null; boolean justPrinted = false; int pass = 0; ObjectOutputStream ooutTr = null; ObjectOutputStream ooutHO = null; ObjectInputStream oinTr = null; double pred = 0; int limit = 1; double hError = Double.MAX_VALUE; double lastHError = Double.MAX_VALUE; int numTestSample = 0; int numTrainingSample = 0; int idx = 0; if (numberPasses > 1) { ooutTr = new ObjectOutputStream(new FileOutputStream("cache_training.bin")); ooutHO = new ObjectOutputStream(new FileOutputStream("cache_holdout.bin")); oinTr = new ObjectInputStream(new FileInputStream("cache_training.bin")); } do { while (true) { double score; if (pass > 0 && numberPasses > 1) { Instance tmp = (Instance) oinTr.readObject(); if (tmp != null) sample = tmp; else break; } else { String strLine = br.readLine(); if (strLine != null) sample = instanceParser.parse(strLine); else break; } justPrinted = false; idx++; if (numberPasses > 1 && pass == 0 && idx % holdoutPeriod == 0) { // store the current sample for the holdout set ooutHO.writeObject(sample); ooutHO.reset(); numTestSample++; } else { if (numberPasses > 1 && pass == 0) { ooutTr.writeObject(sample); ooutTr.reset(); numTrainingSample++; } iter++; if (testOnly) { // predict the sample score = learner.predict(sample); } else { // predict the sample and update the classifier using the sample score = learner.update(sample); } score = Math.min(Math.max(score, minPrediction), maxPrediction); pred = link.apply(score); if (!binary) cumLoss += learner.getLoss().lossValue(score, sample.getLabel()) * sample.getWeight(); else if (Math.signum(score) != sample.getLabel()) cumLoss += sample.getWeight(); weightedSampleSum += sample.getWeight(); if (sample.getLabel() > 0) sPlus = sPlus + sample.getWeight(); else sMinus = sMinus + sample.getWeight(); // output predictions to file if (predsFile != null) { bw.write(String.format("%.6f %s", pred, sample.getTag())); bw.newLine(); } // print statistics to screen if (iter == limit) { justPrinted = true; System.out.printf("%.6f %12d % .4f % .4f %d\n", cumLoss / weightedSampleSum, iter, sample.getLabel(), pred, sample.getVector().size()); if (exponentialProgress) limit *= progressInterval; else limit += progressInterval; } } } if (numberPasses > 1) { if (pass == 0) { // finished first pass of many // write a null at the end of the files ooutTr.writeObject(null); ooutHO.writeObject(null); ooutTr.flush(); ooutHO.flush(); ooutTr.close(); ooutHO.close(); System.out.println("finished first epoch"); System.out.println(numTrainingSample + " training samples"); System.out.println(numTestSample + " holdout samples saved"); } lastHError = hError; hError = evalHoldoutError(); } if (numberPasses > 1) { System.out.printf("Weighted loss on holdout on epoch %d = %.6f\n", pass + 1, hError); oinTr.close(); oinTr = new ObjectInputStream(new FileInputStream("cache_training.bin")); if (hError > lastHError) { System.out.println("Early stopping"); break; } } pass++; } while (pass < numberPasses); if (justPrinted == false) { System.out.printf("%.6f %12d % .4f % .4f %d\n", cumLoss / weightedSampleSum, iter, sample.getLabel(), pred, sample.getVector().size()); } System.out.println("finished run"); System.out.println(String.format("average loss best constant predictor: %.6f", lossFnc.lossConstantBinaryLabels(sPlus, sMinus))); if (saveModelFile != null) IOLearner.saveLearner(learner, saveModelFile); if (invertHashName != null) IOLearner.saveInvertHash(learner.getWeights(), instanceParser.getInvertHashMap(), invertHashName); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ClassNotFoundException e) { // TODO Auto-generated catch block e.printStackTrace(); } // close the input stream try { br.close(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } // close the output stream if (predsFile != null) { try { bw.close(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } long millis = System.nanoTime() - start; System.out.printf("Elapsed time: %d min, %d sec\n", TimeUnit.NANOSECONDS.toMinutes(millis), TimeUnit.NANOSECONDS.toSeconds(millis) - 60 * TimeUnit.NANOSECONDS.toMinutes(millis)); } catch ( FileNotFoundException e) { System.out.println("Error opening the input file"); e.printStackTrace(); } }
From source file:act.installer.bing.BingSearchRanker.java
public static void main(final String[] args) throws Exception { // Parse the command line options Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build());//from w ww.j a v a 2 s. c om } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s\n", e.getMessage()); HELP_FORMATTER.printHelp(BingSearchRanker.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(BingSearchRanker.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } String inputPath = cl.getOptionValue(OPTION_INPUT_FILEPATH); String outputPath = cl.getOptionValue(OPTION_OUTPUT_FILEPATH); Boolean isTSVInput = cl.hasOption(OPTION_TSV_INPUT); // Read the molecule corpus LOGGER.info("Reading the input molecule corpus"); MoleculeCorpus moleculeCorpus = new MoleculeCorpus(); if (isTSVInput) { LOGGER.info("Input format is TSV"); moleculeCorpus.buildCorpusFromTSVFile(inputPath); } else { LOGGER.info("Input format is raw InChIs"); moleculeCorpus.buildCorpusFromRawInchis(inputPath); } // Get the inchi set Set<String> inchis = moleculeCorpus.getMolecules(); LOGGER.info("Found %d molecules in the input corpus", inchis.size()); // Update the Bing Search results in the Installer database BingSearchRanker bingSearchRanker = new BingSearchRanker(cl.hasOption(OPTION_INCLUDE_CHEBI_APPLICATIONS), cl.hasOption(OPTION_INCLUDE_WIKIPEDIA_URL), cl.hasOption(OPTION_INCLUDE_USAGE_EXPLORER_URL), cl.hasOption(OPTION_FORCE_UPDATE)); LOGGER.info("Updating the Bing Search results in the Installer database"); bingSearchRanker.addBingSearchResults(inchis); LOGGER.info("Done updating the Bing Search results"); // Write the results in a TSV file LOGGER.info("Writing results to output file"); bingSearchRanker.writeBingSearchRanksAsTSV(inchis, outputPath); LOGGER.info("Bing Search ranker is done. \"I'm tired, boss.\""); }