List of usage examples for org.apache.commons.cli HelpFormatter setWidth
public void setWidth(int width)
From source file:com.nextdoor.bender.Bender.java
/** * Main entrypoint for the Bender CLI tool - handles the argument parsing and triggers the * appropriate methods for ultimately invoking a Bender Handler. * * @param args/*from w w w .ja v a 2s. com*/ * @throws ParseException */ public static void main(String[] args) throws ParseException { /* * Create the various types of options that we support */ Option help = Option.builder("H").longOpt("help").desc("Print this message").build(); Option handler = Option.builder("h").longOpt("handler").hasArg() .desc("Which Event Handler do you want to simulate? \n" + "Your options are: KinesisHandler, S3Handler. \n" + "Default: KinesisHandler") .build(); Option source_file = Option.builder("s").longOpt("source_file").required().hasArg() .desc("Reference to the file that you want to process. Usage depends " + "on the Handler you chose. If you chose KinesisHandler " + "then this is a local file (file://path/to/file). If you chose " + "S3Handler, then this is the path to the file in S3 that you want to process " + "(s3://bucket/file...)") .build(); Option kinesis_stream_name = Option.builder().longOpt("kinesis_stream_name").hasArg() .desc("What stream name should we mimic? " + "Default: " + KINESIS_STREAM_NAME + " (Kinesis Handler Only)") .build(); /* * Build out the option handler and parse the options */ Options options = new Options(); options.addOption(help); options.addOption(handler); options.addOption(kinesis_stream_name); options.addOption(source_file); /* * Prepare our help formatter */ HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(100); formatter.setSyntaxPrefix("usage: BENDER_CONFIG=file://config.yaml java -jar"); /* * Parse the options themselves. Throw an error and help if necessary. */ CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (UnrecognizedOptionException | MissingOptionException | MissingArgumentException e) { logger.error(e.getMessage()); formatter.printHelp(name, options); System.exit(1); } /* * The CLI tool doesn't have any configuration files built into it. We require that the user set * BENDER_CONFIG to something reasonable. */ if (System.getenv("BENDER_CONFIG") == null) { logger.error("You must set the BENDER_CONFIG environment variable. \n" + "Valid options include: file://<file>"); formatter.printHelp(name, options); System.exit(1); } if (cmd.hasOption("help")) { formatter.printHelp(name, options); System.exit(0); } /* * Depending on the desired Handler, we invoke a specific method and pass in the options (or * defaults) required for that handler. */ String handler_value = cmd.getOptionValue(handler.getLongOpt(), KINESIS); try { switch (handler_value.toLowerCase()) { case KINESIS: invokeKinesisHandler(cmd.getOptionValue(kinesis_stream_name.getLongOpt(), KINESIS_STREAM_NAME), cmd.getOptionValue(source_file.getLongOpt())); break; case S3: invokeS3Handler(cmd.getOptionValue(source_file.getLongOpt())); break; /* * Error out if an invalid handler was supplied. */ default: logger.error("Invalid Handler Option (" + handler_value + "), valid options are: " + KINESIS); formatter.printHelp(name, options); System.exit(1); } } catch (HandlerException e) { logger.error("Error executing handler: " + e); System.exit(1); } }
From source file:baldrickv.s3streamingtool.S3StreamingTool.java
public static void main(String args[]) throws Exception { BasicParser p = new BasicParser(); Options o = getOptions();/*from www . j a v a 2 s. c o m*/ CommandLine cl = p.parse(o, args); if (cl.hasOption('h')) { HelpFormatter hf = new HelpFormatter(); hf.setWidth(80); StringBuilder sb = new StringBuilder(); sb.append("\n"); sb.append("Upload:\n"); sb.append(" -u -r creds -s 50M -b my_bucket -f hda1.dump -t 10\n"); sb.append("Download:\n"); sb.append(" -d -r creds -s 50M -b my_bucket -f hda1.dump -t 10\n"); sb.append("Upload encrypted:\n"); sb.append(" -u -r creds -z -k secret_key -s 50M -b my_bucket -f hda1.dump -t 10\n"); sb.append("Download encrypted:\n"); sb.append(" -d -r creds -z -k secret_key -s 50M -b my_bucket -f hda1.dump -t 10\n"); sb.append("Cleanup in-progress multipart uploads\n"); sb.append(" -c -r creds -b my_bucket\n"); System.out.println(sb.toString()); hf.printHelp("See above", o); return; } int n = 0; if (cl.hasOption('d')) n++; if (cl.hasOption('u')) n++; if (cl.hasOption('c')) n++; if (cl.hasOption('m')) n++; if (n != 1) { System.err.println("Must specify at exactly one of -d, -u, -c or -m"); System.exit(-1); } if (cl.hasOption('m')) { //InputStream in = new java.io.BufferedInputStream(System.in,1024*1024*2); InputStream in = System.in; System.out.println(TreeHashGenerator.calculateTreeHash(in)); return; } require(cl, 'b'); if (cl.hasOption('d') || cl.hasOption('u')) { require(cl, 'f'); } if (cl.hasOption('z')) { require(cl, 'k'); } AWSCredentials creds = null; if (cl.hasOption('r')) { creds = Utils.loadAWSCredentails(cl.getOptionValue('r')); } else { if (cl.hasOption('i') && cl.hasOption('e')) { creds = new BasicAWSCredentials(cl.getOptionValue('i'), cl.getOptionValue('e')); } else { System.out.println("Must specify either credential file (-r) or AWS key ID and secret (-i and -e)"); System.exit(-1); } } S3StreamConfig config = new S3StreamConfig(); config.setEncryption(false); if (cl.hasOption('z')) { config.setEncryption(true); config.setSecretKey(Utils.loadSecretKey(cl.getOptionValue("k"))); } if (cl.hasOption("encryption-mode")) { config.setEncryptionMode(cl.getOptionValue("encryption-mode")); } config.setS3Bucket(cl.getOptionValue("bucket")); if (cl.hasOption("file")) { config.setS3File(cl.getOptionValue("file")); } if (cl.hasOption("threads")) { config.setIOThreads(Integer.parseInt(cl.getOptionValue("threads"))); } if (cl.hasOption("blocksize")) { String s = cl.getOptionValue("blocksize"); s = s.toUpperCase(); int multi = 1; int end = 0; while ((end < s.length()) && (s.charAt(end) >= '0') && (s.charAt(end) <= '9')) { end++; } int size = Integer.parseInt(s.substring(0, end)); if (end < s.length()) { String m = s.substring(end); if (m.equals("K")) multi = 1024; else if (m.equals("M")) multi = 1048576; else if (m.equals("G")) multi = 1024 * 1024 * 1024; else if (m.equals("KB")) multi = 1024; else if (m.equals("MB")) multi = 1048576; else if (m.equals("GB")) multi = 1024 * 1024 * 1024; else { System.out.println("Unknown suffix on block size. Only K,M and G understood."); System.exit(-1); } } size *= multi; config.setBlockSize(size); } Logger.getLogger("").setLevel(Level.FINE); S3StreamingDownload.log.setLevel(Level.FINE); S3StreamingUpload.log.setLevel(Level.FINE); config.setS3Client(new AmazonS3Client(creds)); config.setGlacierClient(new AmazonGlacierClient(creds)); config.getGlacierClient().setEndpoint("glacier.us-west-2.amazonaws.com"); if (cl.hasOption("glacier")) { config.setGlacier(true); config.setStorageInterface(new StorageGlacier(config.getGlacierClient())); } else { config.setStorageInterface(new StorageS3(config.getS3Client())); } if (cl.hasOption("bwlimit")) { config.setMaxBytesPerSecond(Double.parseDouble(cl.getOptionValue("bwlimit"))); } if (cl.hasOption('c')) { if (config.getGlacier()) { GlacierCleanupMultipart.cleanup(config); } else { S3CleanupMultipart.cleanup(config); } return; } if (cl.hasOption('d')) { config.setOutputStream(System.out); S3StreamingDownload.download(config); return; } if (cl.hasOption('u')) { config.setInputStream(System.in); S3StreamingUpload.upload(config); return; } }
From source file:com.enioka.jqm.tools.Main.java
/** * Startup method for the packaged JAR/*from w ww . ja v a2 s .com*/ * * @param args * 0 is node name */ @SuppressWarnings("static-access") public static void main(String[] args) { Helpers.setLogFileName("cli"); Option o00 = OptionBuilder.withArgName("nodeName").hasArg().withDescription("name of the JQM node to start") .isRequired().create("startnode"); Option o01 = OptionBuilder.withDescription("display help").withLongOpt("help").create("h"); Option o11 = OptionBuilder.withArgName("applicationname").hasArg() .withDescription("name of the application to launch").isRequired().create("enqueue"); Option o21 = OptionBuilder.withArgName("xmlpath").hasArg() .withDescription("path of the XML configuration file to import").isRequired() .create("importjobdef"); Option o31 = OptionBuilder.withArgName("xmlpath").hasArg() .withDescription("export all queue definitions into an XML file").isRequired() .create("exportallqueues"); OptionBuilder.withArgName("xmlpath").hasArg() .withDescription("export some queue definitions into an XML file").isRequired() .create("exportqueuefile"); OptionBuilder.withArgName("queues").hasArg().withDescription("queues to export").withValueSeparator(',') .isRequired().create("queue"); Option o51 = OptionBuilder.withArgName("xmlpath").hasArg() .withDescription("import all queue definitions from an XML file").isRequired() .create("importqueuefile"); Option o61 = OptionBuilder.withArgName("nodeName").hasArg() .withDescription("creates a JQM node of this name, or updates it if it exists. Implies -u.") .isRequired().create("createnode"); Option o71 = OptionBuilder.withDescription("display JQM engine version").withLongOpt("version").create("v"); Option o81 = OptionBuilder.withDescription("upgrade JQM database").withLongOpt("upgrade").create("u"); Option o91 = OptionBuilder.withArgName("jobInstanceId").hasArg() .withDescription("get job instance status by ID").isRequired().withLongOpt("getstatus").create("g"); Option o101 = OptionBuilder.withArgName("password").hasArg() .withDescription("creates or resets root admin account password").isRequired().withLongOpt("root") .create("r"); Option o111 = OptionBuilder.withArgName("option").hasArg() .withDescription( "ws handling. Possible values are: enable, disable, ssl, nossl, internalpki, externalapi") .isRequired().withLongOpt("gui").create("w"); Option o121 = OptionBuilder.withArgName("id[,logfilepath]").hasArg().withDescription("single launch mode") .isRequired().withLongOpt("gui").create("s"); Option o131 = OptionBuilder.withArgName("resourcefile").hasArg() .withDescription("resource parameter file to use. Default is resources.xml") .withLongOpt("resources").create("p"); Option o141 = OptionBuilder.withArgName("login,password,role1,role2,...").hasArgs(Option.UNLIMITED_VALUES) .withValueSeparator(',') .withDescription("Create or update a JQM account. Roles must exist beforehand.").create("U"); Options options = new Options(); OptionGroup og1 = new OptionGroup(); og1.setRequired(true); og1.addOption(o00); og1.addOption(o01); og1.addOption(o11); og1.addOption(o21); og1.addOption(o31); og1.addOption(o51); og1.addOption(o61); og1.addOption(o71); og1.addOption(o81); og1.addOption(o91); og1.addOption(o101); og1.addOption(o111); og1.addOption(o121); og1.addOption(o141); options.addOptionGroup(og1); OptionGroup og2 = new OptionGroup(); og2.addOption(o131); options.addOptionGroup(og2); HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(160); try { // Parse arguments CommandLineParser parser = new BasicParser(); CommandLine line = parser.parse(options, args); // Other db connection? if (line.getOptionValue(o131.getOpt()) != null) { jqmlogger.info("Using resource XML file " + line.getOptionValue(o131.getOpt())); Helpers.resourceFile = line.getOptionValue(o131.getOpt()); } // Set db connection Helpers.registerJndiIfNeeded(); // Enqueue if (line.getOptionValue(o11.getOpt()) != null) { enqueue(line.getOptionValue(o11.getOpt())); } // Get status if (line.getOptionValue(o91.getOpt()) != null) { getStatus(Integer.parseInt(line.getOptionValue(o91.getOpt()))); } // Import XML else if (line.getOptionValue(o21.getOpt()) != null) { importJobDef(line.getOptionValue(o21.getOpt())); } // Start engine else if (line.getOptionValue(o00.getOpt()) != null) { startEngine(line.getOptionValue(o00.getOpt())); } // Export all Queues else if (line.getOptionValue(o31.getOpt()) != null) { exportAllQueues(line.getOptionValue(o31.getOpt())); } // Import queues else if (line.getOptionValue(o51.getOpt()) != null) { importQueues(line.getOptionValue(o51.getOpt())); } // Create node else if (line.getOptionValue(o61.getOpt()) != null) { createEngine(line.getOptionValue(o61.getOpt())); } // Upgrade else if (line.hasOption(o81.getOpt())) { upgrade(); } // Help else if (line.hasOption(o01.getOpt())) { formatter.printHelp("java -jar jqm-engine.jar", options, true); } // Version else if (line.hasOption(o71.getOpt())) { jqmlogger.info("Engine version: " + Helpers.getMavenVersion()); } // Root password else if (line.hasOption(o101.getOpt())) { root(line.getOptionValue(o101.getOpt())); } // Web options else if (line.hasOption(o111.getOpt())) { ws(line.getOptionValue(o111.getOpt())); } // Web options else if (line.hasOption(o121.getOpt())) { single(line.getOptionValue(o121.getOpt())); } // User handling else if (line.hasOption(o141.getOpt())) { user(line.getOptionValues(o141.getOpt())); } } catch (ParseException exp) { jqmlogger.fatal("Could not read command line: " + exp.getMessage()); formatter.printHelp("java -jar jqm-engine.jar", options, true); return; } }
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;/* w w w.j a va 2 s . 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:fr.inria.atlanmod.instantiator.neoEMF.Launcher.java
public static void main(String[] args) throws GenerationException, IOException { ResourceSetImpl resourceSet = new ResourceSetImpl(); { // initializing the registry resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put(EcorePackage.eNS_PREFIX, new EcoreResourceFactoryImpl()); resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap() .put(Resource.Factory.Registry.DEFAULT_EXTENSION, new XMIResourceFactoryImpl()); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoEMFURI.NEOEMF_HBASE_SCHEME, NeoEMFResourceFactory.eINSTANCE); }//from w w w . j a v a2s . co m Options options = new Options(); configureOptions(options); CommandLineParser parser = new GnuParser(); try { CommandLine commandLine = parser.parse(options, args); String epackage_class = commandLine.getOptionValue(E_PACKAGE_CLASS); LOGGER.info("Start loading the package"); Class<?> inClazz = Launcher.class.getClassLoader().loadClass(epackage_class); EPackage _package = (EPackage) inClazz.getMethod("init").invoke(null); Resource metamodelResource = new XMIResourceImpl(URI.createFileURI("dummy")); metamodelResource.getContents().add(_package); LOGGER.info("Finish loading the package"); int size = Launcher.DEFAULT_AVERAGE_MODEL_SIZE; if (commandLine.hasOption(SIZE)) { Number number = (Number) commandLine.getParsedOptionValue(SIZE); size = (int) Math.min(Integer.MAX_VALUE, number.longValue()); } float variation = Launcher.DEFAULT_DEVIATION; if (commandLine.hasOption(VARIATION)) { Number number = (Number) commandLine.getParsedOptionValue(VARIATION); if (number.floatValue() < 0.0f || number.floatValue() > 1.0f) { throw new ParseException(MessageFormat.format("Invalid value for option -{0}: {1}", VARIATION, number.floatValue())); } variation = number.floatValue(); } float propVariation = Launcher.DEFAULT_DEVIATION; if (commandLine.hasOption(PROP_VARIATION)) { Number number = (Number) commandLine.getParsedOptionValue(PROP_VARIATION); if (number.floatValue() < 0.0f || number.floatValue() > 1.0f) { throw new ParseException(MessageFormat.format("Invalid value for option -{0}: {1}", PROP_VARIATION, number.floatValue())); } propVariation = number.floatValue(); } long seed = System.currentTimeMillis(); if (commandLine.hasOption(SEED)) { seed = ((Number) commandLine.getParsedOptionValue(SEED)).longValue(); } Range<Integer> range = Range.between(Math.round(size * (1 - variation)), Math.round(size * (1 + variation))); GenericMetamodelConfig config = new GenericMetamodelConfig(metamodelResource, range, seed); GenericMetamodelGenerator modelGen = new GenericMetamodelGenerator(config); if (commandLine.hasOption(OUTPUT_PATH)) { String outDir = commandLine.getOptionValue(OUTPUT_PATH); //java.net.URI intermediateURI = java.net.URI.create(outDir); modelGen.setSamplesPath(outDir); } int numberOfModels = 1; if (commandLine.hasOption(N_MODELS)) { numberOfModels = ((Number) commandLine.getParsedOptionValue(N_MODELS)).intValue(); } int valuesSize = GenericMetamodelConfig.DEFAULT_AVERAGE_VALUES_LENGTH; if (commandLine.hasOption(VALUES_SIZE)) { Number number = (Number) commandLine.getParsedOptionValue(VALUES_SIZE); valuesSize = (int) Math.min(Integer.MAX_VALUE, number.longValue()); } int referencesSize = GenericMetamodelConfig.DEFAULT_AVERAGE_REFERENCES_SIZE; if (commandLine.hasOption(VALUES_SIZE)) { Number number = (Number) commandLine.getParsedOptionValue(DEGREE); referencesSize = (int) Math.min(Integer.MAX_VALUE, number.longValue()); } config.setValuesRange(Math.round(valuesSize * (1 - propVariation)), Math.round(valuesSize * (1 + propVariation))); config.setReferencesRange(Math.round(referencesSize * (1 - propVariation)), Math.round(referencesSize * (1 + propVariation))); config.setPropertiesRange(Math.round(referencesSize * (1 - propVariation)), Math.round(referencesSize * (1 + propVariation))); long start = System.currentTimeMillis(); modelGen.runGeneration(resourceSet, numberOfModels, size, variation); long end = System.currentTimeMillis(); LOGGER.info( MessageFormat.format("Generation finished after {0} s", Long.toString((end - start) / 1000))); if (commandLine.hasOption(DIAGNOSE)) { for (Resource resource : resourceSet.getResources()) { LOGGER.info( MessageFormat.format("Requested validation for resource ''{0}''", resource.getURI())); BasicDiagnostic diagnosticChain = diagnoseResource(resource); if (!isFailed(diagnosticChain)) { LOGGER.info(MessageFormat.format("Result of the diagnosis of resurce ''{0}'' is ''OK''", resource.getURI())); } else { LOGGER.severe(MessageFormat.format("Found ''{0}'' error(s) in the resource ''{1}''", diagnosticChain.getChildren().size(), resource.getURI())); for (Diagnostic diagnostic : diagnosticChain.getChildren()) { LOGGER.fine(diagnostic.getMessage()); } } } LOGGER.info("Validation finished"); } } catch (ParseException e) { System.err.println(e.getLocalizedMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.setOptionComparator(new OptionComarator<Option>()); try { formatter.setWidth(Math.max(Terminal.getTerminal().getTerminalWidth(), 80)); } catch (Throwable t) { LOGGER.warning("Unable to get console information"); } ; formatter.printHelp("java -jar <this-file.jar>", options, true); System.exit(ERROR); } catch (ClassNotFoundException t) { System.err.println("ERROR: Unable to load class" + t.getLocalizedMessage()); StringWriter stringWriter = new StringWriter(); t.printStackTrace(new PrintWriter(stringWriter)); System.err.println(stringWriter.toString()); } catch (Throwable t) { System.err.println("ERROR: " + t.getLocalizedMessage()); StringWriter stringWriter = new StringWriter(); t.printStackTrace(new PrintWriter(stringWriter)); System.err.println(t); LOGGER.severe(stringWriter.toString()); System.exit(ERROR); } }
From source file:fr.inria.atlanmod.dag.instantiator.Launcher.java
public static void main(String[] args) throws GenerationException, IOException { ResourceSetImpl resourceSet = new ResourceSetImpl(); { // initializing the registry resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put(EcorePackage.eNS_PREFIX, new EcoreResourceFactoryImpl()); resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap() .put(Resource.Factory.Registry.DEFAULT_EXTENSION, new XMIResourceFactoryImpl()); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoEMFURI.NEOEMF_HBASE_SCHEME, NeoEMFResourceFactory.eINSTANCE); }/* www . j a v a 2 s. c om*/ Options options = new Options(); configureOptions(options); CommandLineParser parser = new GnuParser(); try { CommandLine commandLine = parser.parse(options, args); // String epackage_class = commandLine.getOptionValue(E_PACKAGE_CLASS); // // LOGGER.info("Start loading the package"); // Class<?> inClazz = Launcher.class.getClassLoader().loadClass(epackage_class); // EPackage _package = (EPackage) inClazz.getMethod("init").invoke(null); // // Resource metamodelResource = new XMIResourceImpl(URI.createFileURI("dummy")); // metamodelResource.getContents().add(_package); // LOGGER.info("Finish loading the package"); int size = Launcher.DEFAULT_AVERAGE_MODEL_SIZE; if (commandLine.hasOption(SIZE)) { Number number = (Number) commandLine.getParsedOptionValue(SIZE); size = (int) Math.min(Integer.MAX_VALUE, number.longValue()); } float variation = Launcher.DEFAULT_DEVIATION; if (commandLine.hasOption(VARIATION)) { Number number = (Number) commandLine.getParsedOptionValue(VARIATION); if (number.floatValue() < 0.0f || number.floatValue() > 1.0f) { throw new ParseException(MessageFormat.format("Invalid value for option -{0}: {1}", VARIATION, number.floatValue())); } variation = number.floatValue(); } float propVariation = Launcher.DEFAULT_DEVIATION; if (commandLine.hasOption(PROP_VARIATION)) { Number number = (Number) commandLine.getParsedOptionValue(PROP_VARIATION); if (number.floatValue() < 0.0f || number.floatValue() > 1.0f) { throw new ParseException(MessageFormat.format("Invalid value for option -{0}: {1}", PROP_VARIATION, number.floatValue())); } propVariation = number.floatValue(); } long seed = System.currentTimeMillis(); if (commandLine.hasOption(SEED)) { seed = ((Number) commandLine.getParsedOptionValue(SEED)).longValue(); } Range<Integer> range = Range.between(Math.round(size * (1 - variation)), Math.round(size * (1 + variation))); ISpecimenConfiguration config = new DagMetamodelConfig(range, seed); IGenerator generator = new DagGenerator(config, config.getSeed()); GenericMetamodelGenerator modelGen = new GenericMetamodelGenerator(generator); if (commandLine.hasOption(OUTPUT_PATH)) { String outDir = commandLine.getOptionValue(OUTPUT_PATH); //java.net.URI intermediateURI = java.net.URI.create(outDir); modelGen.setSamplesPath(outDir); } int numberOfModels = 1; if (commandLine.hasOption(N_MODELS)) { numberOfModels = ((Number) commandLine.getParsedOptionValue(N_MODELS)).intValue(); } int valuesSize = GenericMetamodelConfig.DEFAULT_AVERAGE_VALUES_LENGTH; if (commandLine.hasOption(VALUES_SIZE)) { Number number = (Number) commandLine.getParsedOptionValue(VALUES_SIZE); valuesSize = (int) Math.min(Integer.MAX_VALUE, number.longValue()); } int referencesSize = GenericMetamodelConfig.DEFAULT_AVERAGE_REFERENCES_SIZE; if (commandLine.hasOption(DEGREE)) { Number number = (Number) commandLine.getParsedOptionValue(DEGREE); referencesSize = (int) Math.min(Integer.MAX_VALUE, number.longValue()); } config.setValuesRange(Math.round(valuesSize * (1 - propVariation)), Math.round(valuesSize * (1 + propVariation))); config.setReferencesRange(Math.round(referencesSize * (1 - propVariation)), Math.round(referencesSize * (1 + propVariation))); config.setPropertiesRange(Math.round(referencesSize * (1 - propVariation)), Math.round(referencesSize * (1 + propVariation))); long start = System.currentTimeMillis(); modelGen.runGeneration(resourceSet, numberOfModels, size, variation); long end = System.currentTimeMillis(); LOGGER.info( MessageFormat.format("Generation finished after {0} s", Long.toString((end - start) / 1000))); // for (Resource rsc : resourceSet.getResources()) { // if (rsc.getContents().get(0) instanceof DAG) { // // } // // } if (commandLine.hasOption(DIAGNOSE)) { for (Resource resource : resourceSet.getResources()) { LOGGER.info( MessageFormat.format("Requested validation for resource ''{0}''", resource.getURI())); BasicDiagnostic diagnosticChain = diagnoseResource(resource); if (!isFailed(diagnosticChain)) { LOGGER.info(MessageFormat.format("Result of the diagnosis of resurce ''{0}'' is ''OK''", resource.getURI())); } else { LOGGER.severe(MessageFormat.format("Found ''{0}'' error(s) in the resource ''{1}''", diagnosticChain.getChildren().size(), resource.getURI())); for (Diagnostic diagnostic : diagnosticChain.getChildren()) { LOGGER.fine(diagnostic.getMessage()); } } } LOGGER.info("Validation finished"); } } catch (ParseException e) { System.err.println(e.getLocalizedMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.setOptionComparator(new OptionComarator<Option>()); try { formatter.setWidth(Math.max(Terminal.getTerminal().getTerminalWidth(), 80)); } catch (Throwable t) { LOGGER.warning("Unable to get console information"); } ; formatter.printHelp("java -jar <this-file.jar>", options, true); System.exit(ERROR); } catch (Throwable t) { System.err.println("ERROR: " + t.getLocalizedMessage()); StringWriter stringWriter = new StringWriter(); t.printStackTrace(new PrintWriter(stringWriter)); System.err.println(t); LOGGER.severe(stringWriter.toString()); System.exit(ERROR); } }
From source file:CTmousetrack.java
public static void main(String[] args) { String outLoc = new String("." + File.separator + "CTdata"); // Location of the base output data folder; only used when writing out CT data to a local folder String srcName = "CTmousetrack"; // name of the output CT source long blockPts = 10; // points per block flush long sampInterval = 10; // time between sampling updates, msec double trimTime = 0.0; // amount of data to keep (trim time), sec boolean debug = false; // turn on debug? // Specify the CT output connection CTWriteMode writeMode = CTWriteMode.LOCAL; // The selected mode for writing out CT data String serverHost = ""; // Server (FTP or HTTP/S) host:port String serverUser = ""; // Server (FTP or HTTPS) username String serverPassword = ""; // Server (FTP or HTTPS) password // For UDP output mode DatagramSocket udpServerSocket = null; InetAddress udpServerAddress = null; String udpHost = ""; int udpPort = -1; // Concatenate all of the CTWriteMode types String possibleWriteModes = ""; for (CTWriteMode wm : CTWriteMode.values()) { possibleWriteModes = possibleWriteModes + ", " + wm.name(); }/*from w ww .j ava 2 s . c o m*/ // Remove ", " from start of string possibleWriteModes = possibleWriteModes.substring(2); // // Argument processing using Apache Commons CLI // // 1. Setup command line options Options options = new Options(); options.addOption("h", "help", false, "Print this message."); options.addOption(Option.builder("o").argName("base output dir").hasArg().desc( "Base output directory when writing data to local folder (i.e., this is the location of CTdata folder); default = \"" + outLoc + "\".") .build()); options.addOption(Option.builder("s").argName("source name").hasArg() .desc("Name of source to write data to; default = \"" + srcName + "\".").build()); options.addOption(Option.builder("b").argName("points per block").hasArg() .desc("Number of points per block; UDP output mode will use 1 point/block; default = " + Long.toString(blockPts) + ".") .build()); options.addOption(Option.builder("dt").argName("samp interval msec").hasArg() .desc("Sampling period in msec; default = " + Long.toString(sampInterval) + ".").build()); options.addOption(Option.builder("t").argName("trim time sec").hasArg().desc( "Trim (ring-buffer loop) time (sec); this is only used when writing data to local folder; specify 0 for indefinite; default = " + Double.toString(trimTime) + ".") .build()); options.addOption( Option.builder("w").argName("write mode").hasArg() .desc("Type of write connection; one of " + possibleWriteModes + "; all but UDP mode write out to CT; default = " + writeMode.name() + ".") .build()); options.addOption(Option.builder("host").argName("host[:port]").hasArg() .desc("Host:port when writing via FTP, HTTP, HTTPS, UDP.").build()); options.addOption(Option.builder("u").argName("username,password").hasArg() .desc("Comma-delimited username and password when writing to CT via FTP or HTTPS.").build()); options.addOption("x", "debug", false, "Enable CloudTurbine debug output."); // 2. Parse command line options CommandLineParser parser = new DefaultParser(); CommandLine line = null; try { line = parser.parse(options, args); } catch (ParseException exp) { // oops, something went wrong System.err.println("Command line argument parsing failed: " + exp.getMessage()); return; } // 3. Retrieve the command line values if (line.hasOption("help")) { // Display help message and quit HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(120); formatter.printHelp("CTmousetrack", "", options, "NOTE: UDP output is a special non-CT output mode where single x,y points are sent via UDP to the specified host:port."); return; } outLoc = line.getOptionValue("o", outLoc); if (!outLoc.endsWith("\\") && !outLoc.endsWith("/")) { outLoc = outLoc + File.separator; } // Make sure the base output folder location ends in "CTdata" if (!outLoc.endsWith("CTdata\\") && !outLoc.endsWith("CTdata/")) { outLoc = outLoc + "CTdata" + File.separator; } srcName = line.getOptionValue("s", srcName); blockPts = Long.parseLong(line.getOptionValue("b", Long.toString(blockPts))); sampInterval = Long.parseLong(line.getOptionValue("dt", Long.toString(sampInterval))); trimTime = Double.parseDouble(line.getOptionValue("t", Double.toString(trimTime))); // Type of output connection String writeModeStr = line.getOptionValue("w", writeMode.name()); boolean bMatch = false; for (CTWriteMode wm : CTWriteMode.values()) { if (wm.name().toLowerCase().equals(writeModeStr.toLowerCase())) { writeMode = wm; bMatch = true; } } if (!bMatch) { System.err.println("Unrecognized write mode, \"" + writeModeStr + "\"; write mode must be one of " + possibleWriteModes); System.exit(0); } if (writeMode != CTWriteMode.LOCAL) { // User must have specified the host // If FTP or HTTPS, they may also specify username/password serverHost = line.getOptionValue("host", serverHost); if (serverHost.isEmpty()) { System.err.println( "When using write mode \"" + writeModeStr + "\", you must specify the server host."); System.exit(0); } if (writeMode == CTWriteMode.UDP) { // Force blockPts to be 1 blockPts = 1; // User must have specified both host and port int colonIdx = serverHost.indexOf(':'); if ((colonIdx == -1) || (colonIdx >= serverHost.length() - 1)) { System.err.println( "For UDP output mode, both the host and port (<host>:<port>)) must be specified."); System.exit(0); } udpHost = serverHost.substring(0, colonIdx); String udpPortStr = serverHost.substring(colonIdx + 1); try { udpPort = Integer.parseInt(udpPortStr); } catch (NumberFormatException nfe) { System.err.println("The UDP port must be a positive integer."); System.exit(0); } } if ((writeMode == CTWriteMode.FTP) || (writeMode == CTWriteMode.HTTPS)) { String userpassStr = line.getOptionValue("u", ""); if (!userpassStr.isEmpty()) { // This string should be comma-delimited username and password String[] userpassCSV = userpassStr.split(","); if (userpassCSV.length != 2) { System.err.println("When specifying a username and password for write mode \"" + writeModeStr + "\", separate the username and password by a comma."); System.exit(0); } serverUser = userpassCSV[0]; serverPassword = userpassCSV[1]; } } } debug = line.hasOption("debug"); System.err.println("CTmousetrack parameters:"); System.err.println("\toutput mode = " + writeMode.name()); if (writeMode == CTWriteMode.UDP) { System.err.println("\twrite to " + udpHost + ":" + udpPort); } else { System.err.println("\tsource = " + srcName); System.err.println("\ttrim time = " + trimTime + " sec"); } System.err.println("\tpoints per block = " + blockPts); System.err.println("\tsample interval = " + sampInterval + " msec"); try { // // Setup CTwriter or UDP output // CTwriter ctw = null; CTinfo.setDebug(debug); if (writeMode == CTWriteMode.LOCAL) { ctw = new CTwriter(outLoc + srcName, trimTime); System.err.println("\tdata will be written to local folder \"" + outLoc + "\""); } else if (writeMode == CTWriteMode.FTP) { CTftp ctftp = new CTftp(srcName); try { ctftp.login(serverHost, serverUser, serverPassword); } catch (Exception e) { throw new IOException( new String("Error logging into FTP server \"" + serverHost + "\":\n" + e.getMessage())); } ctw = ctftp; // upcast to CTWriter System.err.println("\tdata will be written to FTP server at " + serverHost); } else if (writeMode == CTWriteMode.HTTP) { // Don't send username/pw in HTTP mode since they will be unencrypted CThttp cthttp = new CThttp(srcName, "http://" + serverHost); ctw = cthttp; // upcast to CTWriter System.err.println("\tdata will be written to HTTP server at " + serverHost); } else if (writeMode == CTWriteMode.HTTPS) { CThttp cthttp = new CThttp(srcName, "https://" + serverHost); // Username/pw are optional for HTTPS mode; only use them if username is not empty if (!serverUser.isEmpty()) { try { cthttp.login(serverUser, serverPassword); } catch (Exception e) { throw new IOException(new String( "Error logging into HTTP server \"" + serverHost + "\":\n" + e.getMessage())); } } ctw = cthttp; // upcast to CTWriter System.err.println("\tdata will be written to HTTPS server at " + serverHost); } else if (writeMode == CTWriteMode.UDP) { try { udpServerSocket = new DatagramSocket(); } catch (SocketException se) { System.err.println("Error creating socket for UDP:\n" + se); System.exit(0); } try { udpServerAddress = InetAddress.getByName(udpHost); } catch (UnknownHostException uhe) { System.err.println("Error getting UDP server host address:\n" + uhe); System.exit(0); } } if (writeMode != CTWriteMode.UDP) { ctw.setBlockMode(blockPts > 1, blockPts > 1); ctw.autoFlush(0); // no autoflush ctw.autoSegment(1000); } // screen dims Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); double width = screenSize.getWidth(); double height = screenSize.getHeight(); // use Map for consolidated putData Map<String, Object> cmap = new LinkedHashMap<String, Object>(); // loop and write some output for (int i = 0; i < 1000000; i++) { // go until killed long currentTime = System.currentTimeMillis(); Point mousePos = MouseInfo.getPointerInfo().getLocation(); float x_pt = (float) (mousePos.getX() / width); // normalize float y_pt = (float) ((height - mousePos.getY()) / height); // flip Y (so bottom=0) if (writeMode != CTWriteMode.UDP) { // CT output mode ctw.setTime(currentTime); cmap.clear(); cmap.put("x", x_pt); cmap.put("y", y_pt); ctw.putData(cmap); if (((i + 1) % blockPts) == 0) { ctw.flush(); System.err.print("."); } } else { // UDP output mode // We force blockPts to be 1 for UDP output mode, i.e. we "flush" the data every time // Write the following data (21 bytes total): // header = "MOUSE", 5 bytes // current time, long, 8 bytes // 2 floats (x,y) 4 bytes each, 8 bytes int len = 21; ByteBuffer bb = ByteBuffer.allocate(len); String headerStr = "MOUSE"; bb.put(headerStr.getBytes("UTF-8")); bb.putLong(currentTime); bb.putFloat(x_pt); bb.putFloat(y_pt); // Might be able to use the following, but not sure: // byte[] sendData = bb.array(); byte[] sendData = new byte[len]; bb.position(0); bb.get(sendData, 0, len); DatagramPacket sendPacket = new DatagramPacket(sendData, sendData.length, udpServerAddress, udpPort); try { udpServerSocket.send(sendPacket); } catch (IOException e) { System.err.println("Test server caught exception trying to send data to UDP client:\n" + e); } System.err.print("."); } try { Thread.sleep(sampInterval); } catch (Exception e) { } ; } if (writeMode != CTWriteMode.UDP) { ctw.flush(); // wrap up } } catch (Exception e) { System.err.println("CTmousetrack exception: " + e); e.printStackTrace(); } }
From source file:fr.inria.atlanmod.instantiator.SpecimenGenerator.java
public static void main(String[] args) throws GenerationException, IOException { Options options = new Options(); configureOptions(options);/*from www .ja va2 s .c o m*/ CommandLineParser parser = new GnuParser(); try { CommandLine commandLine = parser.parse(options, args); String metamodel = commandLine.getOptionValue(METAMODEL); DefaultModelGenerator modelGen = new DefaultModelGenerator(URI.createFileURI(metamodel)); if (commandLine.hasOption(ADDITIONAL_METAMODEL)) { for (String additionalMetamodel : commandLine.getOptionValues(ADDITIONAL_METAMODEL)) { URI additionalMetamodelUri = URI.createFileURI(additionalMetamodel); Resource resource = new XMIResourceImpl(additionalMetamodelUri); resource.load(Collections.emptyMap()); registerPackages(resource); } } if (commandLine.hasOption(OUTPUT_DIR)) { String outDir = commandLine.getOptionValue(OUTPUT_DIR); modelGen.setSamplesPath(Paths.get(outDir)); } else { modelGen.setSamplesPath(Paths.get(".")); } if (commandLine.hasOption(N_MODELS)) { int models = ((Number) commandLine.getParsedOptionValue(N_MODELS)).intValue(); modelGen.setSetSize(new int[] { models }); } else { modelGen.setSetSize(new int[] { 1 }); } if (commandLine.hasOption(SIZE)) { long size = ((Number) commandLine.getParsedOptionValue(SIZE)).longValue(); modelGen.setModelsSize(new long[] { size }); } else { modelGen.setModelsSize(new long[] { 1000 }); } if (commandLine.hasOption(SEED)) { long seed = ((Number) commandLine.getParsedOptionValue(SEED)).longValue(); modelGen.setSeed(seed); } else { modelGen.setSeed(System.currentTimeMillis()); } modelGen.runGeneration(); } catch (ParseException e) { System.err.println(e.getLocalizedMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.setOptionComparator(new OptionComarator<Option>()); try { formatter.setWidth(Math.max(TerminalFactory.get().getWidth(), 80)); } catch (Throwable t) { // Nothing to do... } ; formatter.printHelp("java -jar <this-file.jar>", options, true); } }
From source file:microbiosima.Microbiosima.java
/** * @param args/*from ww w .j av a 2s . co m*/ * the command line arguments * @throws java.io.FileNotFoundException * @throws java.io.UnsupportedEncodingException */ public static void main(String[] args) throws FileNotFoundException, UnsupportedEncodingException { //Init with default values int populationSize = 500; int microSize = 1000; int numberOfSpecies = 150; int numberOfGeneration = 10000; int numberOfObservation = 100; int numberOfReplication = 1; double pctEnv = 0; double pctPool = 0; Options options = new Options(); Option help = new Option("h", "help", false, "print this message"); Option version = new Option("v", "version", false, "print the version information and exit"); options.addOption(help); options.addOption(version); options.addOption(Option.builder("o").longOpt("obs").hasArg().argName("OBS") .desc("Number generation for observation [default: 100]").build()); options.addOption(Option.builder("r").longOpt("rep").hasArg().argName("REP") .desc("Number of replication [default: 1]").build()); Builder C = Option.builder("c").longOpt("config").numberOfArgs(4).argName("Pop Micro Spec Gen") .desc("Four Parameters in the following orders: " + "(1) population size, (2) microbe size, (3) number of species, (4) number of generation" + " [default: 500 1000 150 10000]"); options.addOption(C.build()); HelpFormatter formatter = new HelpFormatter(); String syntax = "microbiosima pctEnv pctPool"; String header = "\nSimulates the evolutionary and ecological dynamics of microbiomes within a population of hosts.\n\n" + "required arguments:\n" + " pctEnv Percentage of environmental acquisition\n" + " pctPool Percentage of pooled environmental component\n" + "\noptional arguments:\n"; String footer = "\n"; formatter.setWidth(80); CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); String[] pct_config = cmd.getArgs(); if (cmd.hasOption("h") || args.length == 0) { formatter.printHelp(syntax, header, options, footer, true); System.exit(0); } if (cmd.hasOption("v")) { System.out.println("Microbiosima " + VERSION); System.exit(0); } if (pct_config.length != 2) { System.out.println("ERROR! Required exactly two argumennts for pct_env and pct_pool. It got " + pct_config.length + ": " + Arrays.toString(pct_config)); formatter.printHelp(syntax, header, options, footer, true); System.exit(3); } else { pctEnv = Double.parseDouble(pct_config[0]); pctPool = Double.parseDouble(pct_config[1]); if (pctEnv < 0 || pctEnv > 1) { System.out.println( "ERROR: pctEnv (Percentage of environmental acquisition) must be between 0 and 1 (pctEnv=" + pctEnv + ")! EXIT"); System.exit(3); } if (pctPool < 0 || pctPool > 1) { System.out.println( "ERROR: pctPool (Percentage of pooled environmental component must) must be between 0 and 1 (pctPool=" + pctPool + ")! EXIT"); System.exit(3); } } if (cmd.hasOption("config")) { String[] configs = cmd.getOptionValues("config"); populationSize = Integer.parseInt(configs[0]); microSize = Integer.parseInt(configs[1]); numberOfSpecies = Integer.parseInt(configs[2]); numberOfGeneration = Integer.parseInt(configs[3]); } if (cmd.hasOption("obs")) { numberOfObservation = Integer.parseInt(cmd.getOptionValue("obs")); } if (cmd.hasOption("rep")) { numberOfReplication = Integer.parseInt(cmd.getOptionValue("rep")); } } catch (ParseException e) { e.printStackTrace(); System.exit(3); } StringBuilder sb = new StringBuilder(); sb.append("Configuration Summary:").append("\n\tPopulation size: ").append(populationSize) .append("\n\tMicrobe size: ").append(microSize).append("\n\tNumber of species: ") .append(numberOfSpecies).append("\n\tNumber of generation: ").append(numberOfGeneration) .append("\n\tNumber generation for observation: ").append(numberOfObservation) .append("\n\tNumber of replication: ").append(numberOfReplication).append("\n"); System.out.println(sb.toString()); // System.exit(3); // LogNormalDistribution lgd=new LogNormalDistribution(0,1); // environment=lgd.sample(150); // double environment_sum=0; // for (int i=0;i<No;i++){ // environment_sum+=environment[i]; // } // for (int i=0;i<No;i++){ // environment[i]/=environment_sum; // } double[] environment = new double[numberOfSpecies]; for (int i = 0; i < numberOfSpecies; i++) { environment[i] = 1 / (double) numberOfSpecies; } for (int rep = 0; rep < numberOfReplication; rep++) { String prefix = "" + (rep + 1) + "_"; String sufix = "_E" + pctEnv + "_P" + pctPool + ".txt"; System.out.println("Output 5 result files in the format of: " + prefix + "[****]" + sufix); try { PrintWriter file1 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "gamma_diversity" + sufix))); PrintWriter file2 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "alpha_diversity" + sufix))); PrintWriter file3 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "beta_diversity" + sufix))); PrintWriter file4 = new PrintWriter(new BufferedWriter(new FileWriter(prefix + "sum" + sufix))); PrintWriter file5 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "inter_generation_distance" + sufix))); PrintWriter file6 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "environment_population_distance" + sufix))); Population population = new Population(microSize, environment, populationSize, pctEnv, pctPool, 0, 0); while (population.getNumberOfGeneration() < numberOfGeneration) { population.sumSpecies(); if (population.getNumberOfGeneration() % numberOfObservation == 0) { file1.println(population.gammaDiversity(true)); file2.println(population.alphaDiversity(true)); file3.print(population.betaDiversity(true)); file3.print("\t"); file3.println(population.BrayCurtis(true)); file4.println(population.printOut()); file5.println(population.interGenerationDistance()); file6.println(population.environmentPopulationDistance()); } population.getNextGen(); } file1.close(); file2.close(); file3.close(); file4.close(); file5.close(); file6.close(); } catch (IOException e) { e.printStackTrace(); } } }
From source file:microbiosima.SelectiveMicrobiosima.java
/** * @param args//www. ja v a 2s . c om * the command line arguments * @throws java.io.FileNotFoundException * @throws java.io.UnsupportedEncodingException */ public static void main(String[] args) throws FileNotFoundException, UnsupportedEncodingException { int populationSize = 500;//Integer.parseInt(parameters[1]); int microSize = 1000;//Integer.parseInt(parameters[2]); int numberOfSpecies = 150;//Integer.parseInt(parameters[3]); int numberOfGeneration = 10000; int Ngene = 10; int numberOfObservation = 100; int numberOfReplication = 10; double Ngenepm = 5; double pctEnv = 0; double pctPool = 0; double msCoeff = 1; double hsCoeff = 1; boolean HMS_or_TMS = true; Options options = new Options(); Option help = new Option("h", "help", false, "print this message"); Option version = new Option("v", "version", false, "print the version information and exit"); options.addOption(help); options.addOption(version); options.addOption(Option.builder("o").longOpt("obs").hasArg().argName("OBS") .desc("Number generation for observation [default: 100]").build()); options.addOption(Option.builder("r").longOpt("rep").hasArg().argName("REP") .desc("Number of replication [default: 1]").build()); Builder C = Option.builder("c").longOpt("config").numberOfArgs(6).argName("Pop Micro Spec Gen") .desc("Four Parameters in the following orders: " + "(1) population size, (2) microbe size, (3) number of species, (4) number of generation, (5) number of total traits, (6)number of traits per microbe" + " [default: 500 1000 150 10000 10 5]"); options.addOption(C.build()); HelpFormatter formatter = new HelpFormatter(); String syntax = "microbiosima pctEnv pctPool"; String header = "\nSimulates the evolutionary and ecological dynamics of microbiomes within a population of hosts.\n\n" + "required arguments:\n" + " pctEnv Percentage of environmental acquisition\n" + " pctPool Percentage of pooled environmental component\n" + " msCoeff Parameter related to microbe selection strength\n" + " hsCoeff Parameter related to host selection strength\n" + " HMS_or_TMS String HMS or TMS to specify host-mediated or trait-mediated microbe selection\n" + "\noptional arguments:\n"; String footer = "\n"; formatter.setWidth(80); CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); String[] pct_config = cmd.getArgs(); if (cmd.hasOption("h") || args.length == 0) { formatter.printHelp(syntax, header, options, footer, true); System.exit(0); } if (cmd.hasOption("v")) { System.out.println("Microbiosima " + VERSION); System.exit(0); } if (pct_config.length != 5) { System.out.println( "ERROR! Required exactly five argumennts for pct_env, pct_pool, msCoeff, hsCoeff and HMS_or_TMS. It got " + pct_config.length + ": " + Arrays.toString(pct_config)); formatter.printHelp(syntax, header, options, footer, true); System.exit(3); } else { pctEnv = Double.parseDouble(pct_config[0]); pctPool = Double.parseDouble(pct_config[1]); msCoeff = Double.parseDouble(pct_config[2]); hsCoeff = Double.parseDouble(pct_config[3]); if (pct_config[4].equals("HMS")) HMS_or_TMS = true; if (pct_config[4].equals("TMS")) HMS_or_TMS = false; if (pctEnv < 0 || pctEnv > 1) { System.out.println( "ERROR: pctEnv (Percentage of environmental acquisition) must be between 0 and 1 (pctEnv=" + pctEnv + ")! EXIT"); System.exit(3); } if (pctPool < 0 || pctPool > 1) { System.out.println( "ERROR: pctPool (Percentage of pooled environmental component must) must be between 0 and 1 (pctPool=" + pctPool + ")! EXIT"); System.exit(3); } if (msCoeff < 1) { System.out.println( "ERROR: msCoeff (parameter related to microbe selection strength) must be not less than 1 (msCoeff=" + msCoeff + ")! EXIT"); System.exit(3); } if (hsCoeff < 1) { System.out.println( "ERROR: hsCoeff (parameter related to host selection strength) must be not less than 1 (hsCoeff=" + hsCoeff + ")! EXIT"); System.exit(3); } if (!(pct_config[4].equals("HMS") || pct_config[4].equals("TMS"))) { System.out.println( "ERROR: HMS_or_TMS (parameter specifying host-mediated or trait-mediated selection) must be either 'HMS' or 'TMS' (HMS_or_TMS=" + pct_config[4] + ")! EXIT"); System.exit(3); } } if (cmd.hasOption("config")) { String[] configs = cmd.getOptionValues("config"); populationSize = Integer.parseInt(configs[0]); microSize = Integer.parseInt(configs[1]); numberOfSpecies = Integer.parseInt(configs[2]); numberOfGeneration = Integer.parseInt(configs[3]); Ngene = Integer.parseInt(configs[4]); Ngenepm = Double.parseDouble(configs[5]); if (Ngenepm > Ngene) { System.out.println( "ERROR: number of traits per microbe must not be greater than number of total traits! EXIT"); System.exit(3); } } if (cmd.hasOption("obs")) { numberOfObservation = Integer.parseInt(cmd.getOptionValue("obs")); } if (cmd.hasOption("rep")) { numberOfReplication = Integer.parseInt(cmd.getOptionValue("rep")); } } catch (ParseException e) { e.printStackTrace(); System.exit(3); } StringBuilder sb = new StringBuilder(); sb.append("Configuration Summary:").append("\n\tPopulation size: ").append(populationSize) .append("\n\tMicrobe size: ").append(microSize).append("\n\tNumber of species: ") .append(numberOfSpecies).append("\n\tNumber of generation: ").append(numberOfGeneration) .append("\n\tNumber generation for observation: ").append(numberOfObservation) .append("\n\tNumber of replication: ").append(numberOfReplication) .append("\n\tNumber of total traits: ").append(Ngene).append("\n\tNumber of traits per microbe: ") .append(Ngenepm).append("\n"); System.out.println(sb.toString()); double[] environment = new double[numberOfSpecies]; for (int i = 0; i < numberOfSpecies; i++) { environment[i] = 1 / (double) numberOfSpecies; } int[] fitnessToHost = new int[Ngene]; int[] fitnessToMicrobe = new int[Ngene]; for (int rep = 0; rep < numberOfReplication; rep++) { String prefix = "" + (rep + 1) + "_"; String sufix; if (HMS_or_TMS) sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_HMS" + msCoeff + ".txt"; else sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_TMS" + msCoeff + ".txt"; System.out.println("Output 5 result files in the format of: " + prefix + "[****]" + sufix); try { PrintWriter file1 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "gamma_diversity" + sufix))); PrintWriter file2 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "alpha_diversity" + sufix))); PrintWriter file3 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "beta_diversity" + sufix))); PrintWriter file4 = new PrintWriter(new BufferedWriter(new FileWriter(prefix + "sum" + sufix))); PrintWriter file5 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "inter_generation_distance" + sufix))); PrintWriter file6 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "environment_population_distance" + sufix))); PrintWriter file7 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "host_fitness" + sufix))); PrintWriter file8 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "cos_theta" + sufix))); PrintWriter file9 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "host_fitness_distribution" + sufix))); PrintWriter file10 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "microbiome_fitness_distribution" + sufix))); PrintWriter file11 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "bacteria_contents" + sufix))); PrintWriter file12 = new PrintWriter( new BufferedWriter(new FileWriter(prefix + "individual_bacteria_contents" + sufix))); for (int i = 0; i < Ngene; i++) { fitnessToMicrobe[i] = MathUtil.getNextInt(2) - 1; fitnessToHost[i] = MathUtil.getNextInt(2) - 1; } MathUtil.setSeed(rep % numberOfReplication); SelectiveSpeciesRegistry ssr = new SelectiveSpeciesRegistry(numberOfSpecies, Ngene, Ngenepm, msCoeff, fitnessToHost, fitnessToMicrobe); MathUtil.setSeed(); SelectivePopulation population = new SelectivePopulation(microSize, environment, populationSize, pctEnv, pctPool, 0, 0, ssr, hsCoeff, HMS_or_TMS); while (population.getNumberOfGeneration() < numberOfGeneration) { population.sumSpecies(); if (population.getNumberOfGeneration() % numberOfObservation == 0) { //file1.print(population.gammaDiversity(false)); //file2.print(population.alphaDiversity(false)); //file1.print("\t"); //file2.print("\t"); file1.println(population.gammaDiversity(true)); file2.println(population.alphaDiversity(true)); //file3.print(population.betaDiversity(true)); //file3.print("\t"); file3.println(population.BrayCurtis(true)); file4.println(population.printOut()); file5.println(population.interGenerationDistance()); file6.println(population.environmentPopulationDistance()); file7.print(population.averageHostFitness()); file7.print("\t"); file7.println(population.varianceHostFitness()); file8.println(population.cosOfMH()); file9.println(population.printOutHFitness()); file10.println(population.printOutMFitness()); file11.println(population.printBacteriaContents()); } population.getNextGen(); } for (SelectiveIndividual host : population.getIndividuals()) { file12.println(host.printBacteriaContents()); } file1.close(); file2.close(); file3.close(); file4.close(); file5.close(); file6.close(); file7.close(); file8.close(); file9.close(); file10.close(); file11.close(); file12.close(); } catch (IOException e) { e.printStackTrace(); } } }