List of usage examples for org.apache.commons.cli Option Option
public Option(String opt, String longOpt, boolean hasArg, String description) throws IllegalArgumentException
From source file:LNISmokeTest.java
/** * Execute command line. See Usage string for options and arguments. * /*from w w w . jav a 2 s. co m*/ * @param argv the argv * * @throws Exception the exception */ public static void main(String[] argv) throws Exception { Options options = new Options(); OptionGroup func = new OptionGroup(); func.addOption(new Option("c", "copy", true, "copy <Item> to -C <Collection>")); func.addOption(new Option("s", "submit", true, "submit <collection> -P <packager> -i <file>")); func.addOption(new Option("d", "disseminate", true, "disseminate <item> -P <packager> -o <file>")); func.addOption(new Option("f", "propfind", true, "propfind of all properties or -N <propname>")); func.addOption(new Option("r", "rpropfind", true, "recursive propfind, only collections")); func.addOption(new Option("n", "names", true, "list all property names on resource")); func.addOption(new Option("p", "proppatch", true, "set property: <handle> -N <property> -V <newvalue>")); func.setRequired(true); options.addOptionGroup(func); options.addOption("h", "help", false, "show help message"); options.addOption("e", "endpoint", true, "SOAP endpoint URL (REQUIRED)"); options.addOption("P", "packager", true, "Packager to use to import/export a package."); options.addOption("C", "collection", true, "Target collection of -c copy"); options.addOption("o", "output", true, "file to create for new package"); options.addOption("i", "input", true, "file containing package to submit"); options.addOption("N", "name", true, "name of property to query/set"); options.addOption("V", "value", true, "new value for property being set"); try { CommandLine line = (new PosixParser()).parse(options, argv); if (line.hasOption("h")) { usage(options, 0, null); } // get SOAP client connection, using the endpoint URL String endpoint = line.getOptionValue("e"); if (endpoint == null) { usage(options, 2, "Missing the required -e endpoint argument"); } LNISoapServletServiceLocator loc = new LNISoapServletServiceLocator(); LNISoapServlet lni = loc.getDSpaceLNI(new URL(endpoint)); // propfind - with optional single-property Name if (line.hasOption("f")) { String pfXml = (line.hasOption("N")) ? specificPropPrefix + line.getOptionValue("N") + specificPropSuffix : allProp; doPropfind(lni, line.getOptionValue("f"), pfXml, 0, null); } // recursive propfind limited to collection, community objects else if (line.hasOption("r")) { doPropfind(lni, line.getOptionValue("r"), someProp, -1, "collection,community"); } else if (line.hasOption("n")) { doPropfind(lni, line.getOptionValue("n"), nameProp, 0, null); } else if (line.hasOption("p")) { if (line.hasOption("N") && line.hasOption("V")) { doProppatch(lni, line.getOptionValue("p"), line.getOptionValue("N"), line.getOptionValue("V")); } else { usage(options, 13, "Missing required args: -N <name> -V <value>n"); } } // submit a package else if (line.hasOption("s")) { if (line.hasOption("P") && line.hasOption("i")) { doPut(lni, line.getOptionValue("s"), line.getOptionValue("P"), line.getOptionValue("i"), endpoint); } else { usage(options, 13, "Missing required args after -s: -P <packager> -i <file>"); } } // Disseminate (GET) item as package else if (line.hasOption("d")) { if (line.hasOption("P") && line.hasOption("o")) { doGet(lni, line.getOptionValue("d"), line.getOptionValue("P"), line.getOptionValue("o"), endpoint); } else { usage(options, 13, "Missing required args after -d: -P <packager> -o <file>"); } } // copy from src to dst else if (line.hasOption("c")) { if (line.hasOption("C")) { doCopy(lni, line.getOptionValue("c"), line.getOptionValue("C")); } else { usage(options, 13, "Missing required args after -c: -C <collection>\n"); } } else { usage(options, 14, "Missing command option.\n"); } } catch (ParseException pe) { usage(options, 1, "Error in arguments: " + pe.toString()); } catch (java.rmi.RemoteException de) { System.out.println("ERROR, got RemoteException, message=" + de.getMessage()); de.printStackTrace(); die(1, " Exception class=" + de.getClass().getName()); } }
From source file:com.basistech.ninja.Train.java
/** * Command line interface to train a model. * * <pre>/*from w w w.java 2s . c o m*/ * usage: Train [options] * --batch-size <arg> batch size (default = 10) * --epochs <arg> epochs (default = 5) * --examples <arg> input examples file (required) * --layer-sizes <arg> layer sizes, including input/output, e.g. 3 4 2 (required) * --learning-rate <arg> learning-rate (default = 0.7) * --model <arg> output model file (required) * </pre> * * @param args command line arguments * @throws IOException */ public static void main(String[] args) throws IOException { String defaultBatchSize = "10"; String deafaultEpochs = "5"; String defaultLearningRate = "0.7"; Options options = new Options(); Option option; option = new Option(null, "examples", true, "input examples file (required)"); option.setRequired(true); options.addOption(option); option = new Option(null, "model", true, "output model file (required)"); option.setRequired(true); options.addOption(option); option = new Option(null, "layer-sizes", true, "layer sizes, including input/output, e.g. 3 4 2 (required)"); option.setRequired(true); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); option = new Option(null, "batch-size", true, String.format("batch size (default = %s)", defaultBatchSize)); options.addOption(option); option = new Option(null, "epochs", true, String.format("epochs (default = %s)", deafaultEpochs)); options.addOption(option); option = new Option(null, "learning-rate", true, String.format("learning-rate (default = %s)", defaultLearningRate)); options.addOption(option); CommandLineParser parser = new GnuParser(); CommandLine cmdline = null; try { cmdline = parser.parse(options, args); } catch (org.apache.commons.cli.ParseException e) { System.err.println(e.getMessage()); usage(options); System.exit(1); } String[] remaining = cmdline.getArgs(); if (remaining == null) { usage(options); System.exit(1); } List<Integer> layerSizes = Lists.newArrayList(); for (String s : cmdline.getOptionValues("layer-sizes")) { layerSizes.add(Integer.parseInt(s)); } File examplesFile = new File(cmdline.getOptionValue("examples")); Train that = new Train(layerSizes, examplesFile); int batchSize = Integer.parseInt(cmdline.getOptionValue("batch-size", defaultBatchSize)); int epochs = Integer.parseInt(cmdline.getOptionValue("epochs", deafaultEpochs)); double learningRate = Double.parseDouble(cmdline.getOptionValue("learning-rate", defaultLearningRate)); File modelFile = new File(cmdline.getOptionValue("model")); that.train(batchSize, epochs, learningRate, modelFile); }
From source file:edu.ksu.cis.indus.staticanalyses.flow.instances.ofa.OFAXMLizerCLI.java
/** * The entry point to the program via command line. * /*from www . ja v a 2s . com*/ * @param args is the command line arguments. * @throws RuntimeException when object flow analysis fails. */ public static void main(final String[] args) { final Options _options = new Options(); Option _option = new Option("c", "cumulative", false, "Consider all root methods in the same execution."); _options.addOption(_option); _option = new Option("o", "output", true, "Directory into which xml files will be written into."); _option.setArgs(1); _options.addOption(_option); _option = new Option("j", "jimple", false, "Dump xmlized jimple."); _options.addOption(_option); _option = new Option("h", "help", false, "Display message."); _options.addOption(_option); _option = new Option("p", "soot-classpath", false, "Prepend this to soot class path."); _option.setArgs(1); _option.setArgName("classpath"); _option.setOptionalArg(false); _options.addOption(_option); _option = new Option("t", "ofa-type", false, "Type of analysis : fioi, fsoi, fios, fsos, fioirt, fsoirt."); _option.setArgs(1); _option.setArgName("type"); _option.setOptionalArg(false); _option.setRequired(true); _options.addOption(_option); _option = new Option("S", "scope", true, "The scope that should be analyzed."); _option.setArgs(1); _option.setArgName("scope"); _option.setRequired(false); _options.addOption(_option); final PosixParser _parser = new PosixParser(); try { final CommandLine _cl = _parser.parse(_options, args); if (_cl.hasOption("h")) { printUsage(_options); System.exit(1); } String _outputDir = _cl.getOptionValue('o'); if (_outputDir == null) { if (LOGGER.isWarnEnabled()) { LOGGER.warn("Defaulting to current directory for output."); } _outputDir = "."; } if (_cl.getArgList().isEmpty()) { throw new MissingArgumentException("Please specify atleast one class."); } final OFAXMLizerCLI _cli = new OFAXMLizerCLI(); _cli.xmlizer.setXmlOutputDir(_outputDir); _cli.xmlizer.setGenerator(new UniqueJimpleIDGenerator()); _cli.setCumulative(_cl.hasOption('c')); _cli.setClassNames(_cl.getArgList()); _cli.type = _cl.getOptionValue('t'); if (_cl.hasOption('p')) { _cli.addToSootClassPath(_cl.getOptionValue('p')); } if (_cl.hasOption('S')) { _cli.setScopeSpecFile(_cl.getOptionValue('S')); } _cli.initialize(); _cli.<ITokens>execute(_cl.hasOption('j')); } catch (final ParseException _e) { LOGGER.error("Error while parsing command line.", _e); System.out.println("Error while parsing command line. \n" + _e); printUsage(_options); } catch (final Throwable _e) { LOGGER.error("Beyond our control. May day! May day!", _e); throw new RuntimeException(_e); } }
From source file:ar.edu.taco.TacoMain.java
/** * @param args/*from w ww. j av a2s. c om*/ */ @SuppressWarnings({ "static-access" }) public static void main(String[] args) { @SuppressWarnings("unused") int loopUnrolling = 3; String tacoVersion = getManifestAttribute(Attributes.Name.IMPLEMENTATION_VERSION); String tacoCreatedBy = getManifestAttribute(new Name("Created-By")); System.out.println("TACO: Taco static analysis tool."); System.out.println("Created By: " + tacoCreatedBy); System.out.println("Version: " + tacoVersion); System.out.println(""); System.out.println(""); Option helpOption = new Option("h", "help", false, "print this message"); Option versionOption = new Option("v", "version", false, "shows version"); Option configFileOption = OptionBuilder.withArgName("path").withLongOpt("configFile").hasArg() .withDescription("set the configuration file").create("cf"); Option classToCheckOption = OptionBuilder.withArgName("classname").withLongOpt("classToCheck").hasArg() .withDescription("set the class to be checked").create('c'); Option methodToCheckOption = OptionBuilder.withArgName("methodname").withLongOpt("methodToCheck").hasArg() .withDescription("set the method to be checked").create('m'); Option dependenciesOption = OptionBuilder.withArgName("classname").withLongOpt("dependencies").hasArgs() .withDescription("additional sources to be parsed").create('d'); Option relevantClassesOption = OptionBuilder.withArgName("classname").withLongOpt("relevantClasses") .hasArgs().withDescription("Set the relevant classes to be used").create("rd"); Option loopsOptions = OptionBuilder.withArgName("integer").withLongOpt("unroll").hasArg() .withDescription("set number of loop unrollings").create('u'); Option bitOptions = OptionBuilder.withArgName("integer").withLongOpt("width").hasArg() .withDescription("set bit width").create('w'); Option instOptions = OptionBuilder.withArgName("integer").withLongOpt("bound").hasArg() .withDescription("set class bound").create('b'); Option skolemizeOption = OptionBuilder.withLongOpt("skolemize") .withDescription("set whether or not skolemize").create("sk"); Option simulateOption = OptionBuilder.withLongOpt("simulate") .withDescription("run method instead of checking").create("r"); Option modularReasoningOption = OptionBuilder.withLongOpt("modularReasoning") .withDescription("check method using modular reasoning").create("mr"); Option relevancyAnalysisOption = OptionBuilder.withLongOpt("relevancyAnalysis") .withDescription("calculate the needed relevantClasses").create("ra"); Option scopeRestrictionOption = OptionBuilder.withLongOpt("scopeRestriction") .withDescription("restrict signature scope to value set in -b option").create("sr"); /* * Option noVerifyOption = OptionBuilder.withLongOpt( * "noVerify").withDescription( * "builds output but does not invoke verification engine").create( * "nv"); */ Options options = new Options(); options.addOption(helpOption); options.addOption(versionOption); options.addOption(configFileOption); options.addOption(classToCheckOption); options.addOption(methodToCheckOption); options.addOption(dependenciesOption); options.addOption(relevantClassesOption); options.addOption(loopsOptions); options.addOption(bitOptions); options.addOption(instOptions); options.addOption(skolemizeOption); options.addOption(simulateOption); options.addOption(modularReasoningOption); options.addOption(relevancyAnalysisOption); options.addOption(scopeRestrictionOption); // options.addOption(noVerifyOption) String configFileArgument = null; Properties overridingProperties = new Properties(); TacoCustomScope tacoScope = new TacoCustomScope(); // create the parser CommandLineParser parser = new PosixParser(); try { // parse the command line arguments CommandLine line = parser.parse(options, args); // help if (line.hasOption(helpOption.getOpt())) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(120, CMD, HEADER, options, FOOTER, true); return; } // version if (line.hasOption(versionOption.getOpt())) { System.out.println(FOOTER); System.out.println(""); return; } // Configuration file if (line.hasOption(configFileOption.getOpt())) { configFileArgument = line.getOptionValue(configFileOption.getOpt()); } // class to check if (line.hasOption(classToCheckOption.getOpt())) { overridingProperties.put(TacoConfigurator.CLASS_TO_CHECK_FIELD, line.getOptionValue(classToCheckOption.getOpt())); } // method to check if (line.hasOption(methodToCheckOption.getOpt())) { String methodtoCheck = line.getOptionValue(methodToCheckOption.getOpt()); if (!methodtoCheck.matches("^[A-Za-z0-9_-]+_[0-9]")) { methodtoCheck = methodtoCheck + "_0"; } overridingProperties.put(TacoConfigurator.METHOD_TO_CHECK_FIELD, methodtoCheck); } // Dependencies classes if (line.hasOption(dependenciesOption.getOpt())) { String dependenciesClasses = ""; for (String aDependencyClass : line.getOptionValues(dependenciesOption.getOpt())) { dependenciesClasses += aDependencyClass; } overridingProperties.put(TacoConfigurator.CLASSES_FIELD, dependenciesClasses); } // Relevant classes if (line.hasOption(relevantClassesOption.getOpt())) { String relevantClasses = ""; for (String aRelevantClass : line.getOptionValues(relevantClassesOption.getOpt())) { relevantClasses += aRelevantClass; } overridingProperties.put(TacoConfigurator.RELEVANT_CLASSES, relevantClasses); } // Loop unrolling if (line.hasOption(loopsOptions.getOpt())) { loopUnrolling = Integer.parseInt(line.getOptionValue(loopsOptions.getOpt())); } // Int bitwidth if (line.hasOption(bitOptions.getOpt())) { String alloy_bitwidth_str = line.getOptionValue(bitOptions.getOpt()); overridingProperties.put(TacoConfigurator.BITWIDTH, alloy_bitwidth_str); int alloy_bitwidth = new Integer(alloy_bitwidth_str); tacoScope.setAlloyBitwidth(alloy_bitwidth); } // instances scope if (line.hasOption(instOptions.getOpt())) { String assertionsArguments = "for " + line.getOptionValue(instOptions.getOpt()); overridingProperties.put(TacoConfigurator.ASSERTION_ARGUMENTS, assertionsArguments); } // Skolemize if (line.hasOption(skolemizeOption.getOpt())) { overridingProperties.put(TacoConfigurator.SKOLEMIZE_INSTANCE_INVARIANT, false); overridingProperties.put(TacoConfigurator.SKOLEMIZE_INSTANCE_ABSTRACTION, false); } // Simulation if (line.hasOption(simulateOption.getOpt())) { overridingProperties.put(TacoConfigurator.INCLUDE_SIMULATION_PROGRAM_DECLARATION, true); overridingProperties.put(TacoConfigurator.GENERATE_CHECK, false); overridingProperties.put(TacoConfigurator.GENERATE_RUN, false); } // Modular Reasoning if (line.hasOption(modularReasoningOption.getOpt())) { overridingProperties.put(TacoConfigurator.MODULAR_REASONING, true); } // Relevancy Analysis if (line.hasOption(relevancyAnalysisOption.getOpt())) { overridingProperties.put(TacoConfigurator.RELEVANCY_ANALYSIS, true); } } catch (ParseException e) { System.err.println("Command line parsing failed: " + e.getMessage()); } try { System.out.println("****** Starting Taco (version. " + tacoVersion + ") ****** "); System.out.println(""); File file = new File("config/log4j.xml"); if (file.exists()) { DOMConfigurator.configure("config/log4j.xml"); } else { System.err.println("log4j:WARN File config/log4j.xml not found"); } TacoMain main = new TacoMain(); // BUILD TacoScope // main.run(configFileArgument, overridingProperties); } catch (IllegalArgumentException e) { System.err.println("Error found:"); System.err.println(e.getMessage()); } catch (MethodToCheckNotFoundException e) { System.err.println("Error found:"); System.err.println("Method to check was not found. Please verify config file, or add -m option"); } catch (TacoException e) { System.err.println("Error found:"); System.err.println(e.getMessage()); } }
From source file:com.zimbra.doc.soap.changelog.SoapApiChangeLog.java
/** * Main/*from w w w. j av a 2s. c o m*/ */ public static void main(String[] args) throws Exception { CommandLineParser parser = new PosixParser(); Options options = new Options(); Option opt; opt = new Option("d", ARG_OUTPUT_DIR, true, "Output directory for changelog information"); opt.setRequired(true); options.addOption(opt); opt = new Option("t", ARG_TEMPLATES_DIR, true, "Directory containing Freemarker templates"); opt.setRequired(true); options.addOption(opt); opt = new Option("b", ARG_APIDESC_BASELINE_JSON, true, "JSON file - description of baseline SOAP API"); opt.setRequired(true); options.addOption(opt); opt = new Option("c", ARG_APIDESC_CURRENT_JSON, true, "JSON file - description of current SOAP API"); opt.setRequired(true); options.addOption(opt); CommandLine cl = null; try { cl = parser.parse(options, args, true); } catch (ParseException pe) { System.err.println("error: " + pe.getMessage()); System.exit(2); } String baselineApiDescriptionJson = cl.getOptionValue('b'); String currentApiDescriptionJson = cl.getOptionValue('c'); SoapApiChangeLog clog = new SoapApiChangeLog(cl.getOptionValue('d'), cl.getOptionValue('t')); clog.setBaselineDesc(SoapApiDescription.deserializeFromJson(new File(baselineApiDescriptionJson))); clog.setCurrentDesc(SoapApiDescription.deserializeFromJson(new File(currentApiDescriptionJson))); clog.makeChangeLogDataModel(); clog.writeChangelog(); }
From source file:com.cyberway.issue.io.Arc2Warc.java
/** * Command-line interface to Arc2Warc./* ww w.j ava 2 s . c om*/ * * @param args Command-line arguments. * @throws ParseException Failed parse of the command line. * @throws IOException * @throws java.text.ParseException */ public static void main(String[] args) throws ParseException, IOException, java.text.ParseException { Options options = new Options(); options.addOption(new Option("h", "help", false, "Prints this message and exits.")); options.addOption(new Option("f", "force", false, "Force overwrite of target file.")); PosixParser parser = new PosixParser(); CommandLine cmdline = parser.parse(options, args, false); List cmdlineArgs = cmdline.getArgList(); Option[] cmdlineOptions = cmdline.getOptions(); HelpFormatter formatter = new HelpFormatter(); // If no args, print help. if (cmdlineArgs.size() <= 0) { usage(formatter, options, 0); } // Now look at options passed. boolean force = false; for (int i = 0; i < cmdlineOptions.length; i++) { switch (cmdlineOptions[i].getId()) { case 'h': usage(formatter, options, 0); break; case 'f': force = true; break; default: throw new RuntimeException("Unexpected option: " + +cmdlineOptions[i].getId()); } } // If no args, print help. if (cmdlineArgs.size() != 2) { usage(formatter, options, 0); } (new Arc2Warc()).transform(new File(cmdlineArgs.get(0).toString()), new File(cmdlineArgs.get(1).toString()), force); }
From source file:de.uniwue.info2.main.CommandLineInterpreter.java
@SuppressWarnings("static-access") public static void main(String[] args) { /*-------------------------------------------------------- */ /*---------------SETTING TARGET LANGUAGE------------------ */ /*-------------------------------------------------------- */ LanguageFactory languageFactory = new LanguageFactory(); CommandLine line = null;/*from ww w . j a va 2s . c o m*/ CommandLineParser parser = new BasicParser(); Options options = new Options(); // options to display in the help page Options options_short = new Options(); // add help option Option help_option = new Option(HELP_OPTION_SHORT, HELP_OPTION, false, HELP_DESCRIPTION); options.addOption(help_option); options_short.addOption(help_option); // add extended help option Option help2_option = new Option(HELP2_OPTION_SHORT, HELP2_OPTION, false, HELP2_DESCRIPTION); options.addOption(help2_option); options_short.addOption(help2_option); // add optional operations option options.addOption(new Option(OPTIONAL_OPTION_SHORT, OPTIONAL_OPTION, false, OPTIONAL_DESCRIPTION)); options.addOption(new Option(BIG_ENDIAN_OPTION_SHORT, BIG_ENDIAN_OPTION, false, BIG_ENDIAN_DESCRIPTION)); options.addOption( new Option(LITTLE_ENDIAN_OPTION_SHORT, LITTLE_ENDIAN_OPTION, false, LITTLE_ENDIAN_DESCRIPTION)); // add optional operations config option options.addOption(OptionBuilder.withLongOpt(OPTIONAL_FUNCTIONS_CONFIG_OPTION) .withArgName(OPTIONAL_FUNCTIONS_CONFIG_ARGUMENT) .withDescription(OPTIONAL_FUNCTIONS_CONFIG_DESCRIPTION).hasArg() .create(OPTIONAL_FUNCTIONS_CONFIG_SHORT)); // add dsl option Option dsl_option = OptionBuilder.withLongOpt(DSL_OPTION).withArgName(DSL_ARGUMENT) .withDescription(DSL_DESCRIPTION).hasArg().isRequired().create(DSL_OPTION_SHORT); options.addOption(dsl_option); options_short.addOption(dsl_option); // add output-folder option Option output_option = OptionBuilder.withLongOpt(OUTPUT_OPTION).isRequired().withArgName(OUTPUT_ARGUMENT) .withDescription(OUTPUT_DESCRIPTION).hasArg().create(OUTPUT_OPTION_SHORT); options.addOption(output_option); options_short.addOption(output_option); // count possible language-specifications short optionCounter = 1; // get all possible language-specifications from language-factory and iterate through them List<LanguageSpecification> lSpecs = languageFactory.getAvailableLanguageSpecifications_(); for (LanguageSpecification lSpec : lSpecs) { // get all possible unit-specifications for current language and iterate through them List<UnitTestLibrarySpecification> uSpecs = languageFactory .getAvailableUnitTestLibraries_(lSpec.getOptionName()); String languageDescriptionAll = LANGUAGE_SPECIFICATION + lSpec.getLanguageName(); String languageCounter = "s" + INDEX.format(optionCounter++); for (UnitTestLibrarySpecification uSpec : uSpecs) { // get all possible arithmetic-library-specifications for current language and iterate through // them List<ArithmeticLibrarySpecification> aSpecs = languageFactory .getAvailableArithmeticLibraries_(lSpec.getOptionName()); for (ArithmeticLibrarySpecification aSpec : aSpecs) { String languageDescription = "Generate unit-test for " + lSpec.getLanguageName() + "\n*[" + uSpec.getLibraryName() + " - " + uSpec.getVersion() + "]\n*[" + aSpec.getLibraryName() + " - " + aSpec.getVersion() + "]"; // if there is more than one option, generate suitable option-names and add them all to // commandline options if (uSpecs.size() > 1 || aSpecs.size() > 1) { options.addOption(OptionBuilder .withLongOpt(lSpec.getOptionName() + "_" + uSpec.getOptionName() + "_" + aSpec.getOptionName()) .withDescription(languageDescription).hasArg(false) .create("s" + INDEX.format(optionCounter++))); } else { // if there is only one option, use language-name as option-name languageDescriptionAll = languageDescription; } } // add specifications to options options.addOption(OptionBuilder.withLongOpt(lSpec.getOptionName()) .withDescription(languageDescriptionAll).hasArg(false).create(languageCounter)); } } /*-------------------------------------------------------- */ /*-------------------PARSE USER INPUT--------------------- */ /*-------------------------------------------------------- */ try { // manual search for help-arguments for (String arg : args) { arg = arg.trim().replace("-", ""); if (arg.equals(HELP_OPTION_SHORT) || arg.equals(HELP_OPTION)) { printHelp(options_short); return; } if (arg.equals(HELP2_OPTION_SHORT) || arg.equals(HELP2_OPTION)) { printExtendedHelp(options); return; } } // parse arguments line = parser.parse(options, args); File dsl_file = null; File output_folder = null; File optional_config = null; Properties optional_operations = null; Boolean optional = false; Boolean little_endian = null; ArrayList<String> optional_exceptions = new ArrayList<String>(); // if help-option found print help if (line.hasOption(HELP2_OPTION_SHORT) || args.length == 0) { printExtendedHelp(options); return; } // if help-option found print help if (line.hasOption(HELP_OPTION_SHORT) || args.length == 0) { System.out.println("\n"); printHelp(options_short); return; } if (line.hasOption(OPTIONAL_OPTION_SHORT)) { optional = true; } if (line.hasOption(LITTLE_ENDIAN_OPTION)) { little_endian = true; } if (line.hasOption(BIG_ENDIAN_OPTION)) { little_endian = false; } // if dsl-option found, check if file exists and is readable // print help if error occurs if (line.hasOption(DSL_OPTION_SHORT)) { dsl_file = new File(line.getOptionValue(DSL_OPTION_SHORT)); if (!dsl_file.exists()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - DSL-file doesn't exist:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } else if (dsl_file.isDirectory()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - DSL-file is a directory:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } else if (!dsl_file.canRead()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Need read-permission for DSL-file:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } } // if output-option found, check if folder exists and if write-permission was granted // print help if error occurs if (line.hasOption(OUTPUT_OPTION_SHORT)) { output_folder = new File(line.getOptionValue(OUTPUT_OPTION_SHORT)); if (!output_folder.exists()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Output-folder doesn't exist:\n" + output_folder + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } else if (!output_folder.isDirectory()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Output-folder is not a directory:\n" + output_folder + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } else if (!output_folder.canWrite() || !output_folder.canRead()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Missing permissions for output-folder:\n" + output_folder + "\n" + SEPERATOR + "\n"); printHelp(options_short); return; } } if (line.hasOption(OPTIONAL_FUNCTIONS_CONFIG_SHORT)) { optional_config = new File(line.getOptionValue(OPTIONAL_FUNCTIONS_CONFIG_OPTION)); if (!dsl_file.exists()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - config-file doesn't exist:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printExtendedHelp(options); return; } else if (dsl_file.isDirectory()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - config-file is a directory:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printExtendedHelp(options); return; } else if (!dsl_file.canRead()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Need read-permission for config-file:\n" + dsl_file + "\n" + SEPERATOR + "\n"); printExtendedHelp(options); return; } } if (optional_config != null) { optional_operations = new Properties(); BufferedInputStream stream = new BufferedInputStream(new FileInputStream(optional_config)); optional_operations.load(stream); stream.close(); String optional_prop = optional_operations.getProperty("GENERATE_OPTIONAL"); if (optional_prop != null) { if (optional_prop.trim().toLowerCase().equals("true")) { optional = true; } else if (optional_prop.trim().toLowerCase().equals("false")) { optional = false; } else if (!optional_prop.trim().isEmpty()) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - Syntax incorrect in config-file:\nUse \"true\" or \"false\" for \"GENERATE_OPTIONAL\"\n" + SEPERATOR + "\n"); printExtendedHelp(options); return; } } String exceptions = optional_operations.getProperty("EXCLUSIONS"); if (exceptions != null) { for (String exc : optional_operations.getProperty("EXCLUSIONS").split(";")) { optional_exceptions.add(exc.trim()); } } } /*-------------------------------------------------------- */ /*-------------------START GENERATING--------------------- */ /*-------------------------------------------------------- */ // instantiate generator for unit-tests TestcaseGenerator mainGenerator = new TestcaseGenerator(dsl_file, output_folder); boolean overrideDefaultSpecs = false; // check if user input contains a language-specifications // if user specified language, set overrideDefaultSpecs to true, so that only given specifications // are used for (int i = 1; i <= optionCounter; i++) { String opt = "s" + INDEX.format(i); if (line.hasOption(opt)) { LanguageSpecification targetSpecification = languageFactory .getLanguageSpecification(options.getOption(opt).getLongOpt()); String output = (GENERATING_DIALOG + targetSpecification.getLanguageName()); // finally generate unit-test for current language-specification boolean successful = mainGenerator.generateUnitTest(targetSpecification, optional, optional_exceptions, little_endian); if (successful) { System.out.println(output + "\n--> Successfully generated."); } else { System.err.println(output + "\n--> ERROR - see logfile"); } overrideDefaultSpecs = true; } } // skip, if user already defined one language-specification // if user did not define language-specification, generate unit-tests for all // possible language-specifications (default) if (!overrideDefaultSpecs) { for (int i = 0; i < lSpecs.size(); i++) { LanguageSpecification specification = languageFactory .getLanguageSpecification(lSpecs.get(i).getOptionName()); String output = INDEX.format(i + 1) + " - " + GENERATING_DIALOG + specification.getLanguageName(); // finally generate unit-test for current language-specification boolean successful = mainGenerator.generateUnitTest(specification, optional, optional_exceptions, little_endian); if (successful) { System.out.println(output + "\n--> Successfully generated."); } else { System.err.println(output + "\n--> ERROR - see logfile"); } } } } catch (ParseException | IOException p) { System.err.println("\n" + SEPERATOR + "\n" + "ERROR - WRONG ARGUMENTS:\n" + p.getMessage() + "\n" + SEPERATOR + "\n"); printHelp(options_short); System.out.println("\n"); } }
From source file:tuit.java
@SuppressWarnings("ConstantConditions") public static void main(String[] args) { System.out.println(licence);//from ww w.j a v a2s. c om //Declare variables File inputFile; File outputFile; File tmpDir; File blastnExecutable; File properties; File blastOutputFile = null; // TUITPropertiesLoader tuitPropertiesLoader; TUITProperties tuitProperties; // String[] parameters = null; // Connection connection = null; MySQL_Connector mySQL_connector; // Map<Ranks, TUITCutoffSet> cutoffMap; // BLASTIdentifier blastIdentifier = null; // RamDb ramDb = null; CommandLineParser parser = new GnuParser(); Options options = new Options(); options.addOption(tuit.IN, "input<file>", true, "Input file (currently fasta-formatted only)"); options.addOption(tuit.OUT, "output<file>", true, "Output file (in " + tuit.TUIT_EXT + " format)"); options.addOption(tuit.P, "prop<file>", true, "Properties file (XML formatted)"); options.addOption(tuit.V, "verbose", false, "Enable verbose output"); options.addOption(tuit.B, "blast_output<file>", true, "Perform on a pre-BLASTed output"); options.addOption(tuit.DEPLOY, "deploy", false, "Deploy the taxonomic databases"); options.addOption(tuit.UPDATE, "update", false, "Update the taxonomic databases"); options.addOption(tuit.USE_DB, "usedb", false, "Use RDBMS instead of RAM-based taxonomy"); Option option = new Option(tuit.REDUCE, "reduce", true, "Pack identical (100% similar sequences) records in the given sample file"); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); option = new Option(tuit.COMBINE, "combine", true, "Combine a set of given reduction files into an HMP Tree-compatible taxonomy"); option.setArgs(Option.UNLIMITED_VALUES); options.addOption(option); options.addOption(tuit.NORMALIZE, "normalize", false, "If used in combination with -combine ensures that the values are normalized by the root value"); HelpFormatter formatter = new HelpFormatter(); try { //Get TUIT directory final File tuitDir = new File( new File(tuit.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath()) .getParent()); final File ramDbFile = new File(tuitDir, tuit.RAM_DB); //Setup logger Log.getInstance().setLogName("tuit.log"); //Read command line final CommandLine commandLine = parser.parse(options, args, true); //Check if the REDUCE option is on if (commandLine.hasOption(tuit.REDUCE)) { final String[] fileList = commandLine.getOptionValues(tuit.REDUCE); for (String s : fileList) { final Path path = Paths.get(s); Log.getInstance().log(Level.INFO, "Processing " + path.toString() + "..."); final NucleotideFastaSequenceReductor nucleotideFastaSequenceReductor = NucleotideFastaSequenceReductor .fromPath(path); ReductorFileOperator.save(nucleotideFastaSequenceReductor, path.resolveSibling(path.getFileName().toString() + ".rdc")); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Check if COMBINE is on if (commandLine.hasOption(tuit.COMBINE)) { final boolean normalize = commandLine.hasOption(tuit.NORMALIZE); final String[] fileList = commandLine.getOptionValues(tuit.COMBINE); //TODO: implement a test for format here final List<TreeFormatter.TreeFormatterFormat.HMPTreesOutput> hmpTreesOutputs = new ArrayList<>(); final TreeFormatter treeFormatter = TreeFormatter .newInstance(new TreeFormatter.TuitLineTreeFormatterFormat()); for (String s : fileList) { final Path path = Paths.get(s); Log.getInstance().log(Level.INFO, "Merging " + path.toString() + "..."); treeFormatter.loadFromPath(path); final TreeFormatter.TreeFormatterFormat.HMPTreesOutput output = TreeFormatter.TreeFormatterFormat.HMPTreesOutput .newInstance(treeFormatter.toHMPTree(normalize), s.substring(0, s.indexOf("."))); hmpTreesOutputs.add(output); treeFormatter.erase(); } final Path destination; if (commandLine.hasOption(OUT)) { destination = Paths.get(commandLine.getOptionValue(tuit.OUT)); } else { destination = Paths.get("merge.tcf"); } CombinatorFileOperator.save(hmpTreesOutputs, treeFormatter, destination); Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } if (!commandLine.hasOption(tuit.P)) { throw new ParseException("No properties file option found, exiting."); } else { properties = new File(commandLine.getOptionValue(tuit.P)); } //Load properties tuitPropertiesLoader = TUITPropertiesLoader.newInstanceFromFile(properties); tuitProperties = tuitPropertiesLoader.getTuitProperties(); //Create tmp directory and blastn executable tmpDir = new File(tuitProperties.getTMPDir().getPath()); blastnExecutable = new File(tuitProperties.getBLASTNPath().getPath()); //Check for deploy if (commandLine.hasOption(tuit.DEPLOY)) { if (commandLine.hasOption(tuit.USE_DB)) { NCBITablesDeployer.fastDeployNCBIDatabasesFromNCBI(connection, tmpDir); } else { NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Check for update if (commandLine.hasOption(tuit.UPDATE)) { if (commandLine.hasOption(tuit.USE_DB)) { NCBITablesDeployer.updateDatabasesFromNCBI(connection, tmpDir); } else { //No need to specify a different way to update the database other than just deploy in case of the RAM database NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile); } Log.getInstance().log(Level.FINE, "Task done, exiting..."); return; } //Connect to the database if (commandLine.hasOption(tuit.USE_DB)) { mySQL_connector = MySQL_Connector.newDefaultInstance( "jdbc:mysql://" + tuitProperties.getDBConnection().getUrl().trim() + "/", tuitProperties.getDBConnection().getLogin().trim(), tuitProperties.getDBConnection().getPassword().trim()); mySQL_connector.connectToDatabase(); connection = mySQL_connector.getConnection(); } else { //Probe for ram database if (ramDbFile.exists() && ramDbFile.canRead()) { Log.getInstance().log(Level.INFO, "Loading RAM taxonomic map..."); try { ramDb = RamDb.loadSelfFromFile(ramDbFile); } catch (IOException ie) { if (ie instanceof java.io.InvalidClassException) throw new IOException("The RAM-based taxonomic database needs to be updated."); } } else { Log.getInstance().log(Level.SEVERE, "The RAM database either has not been deployed, or is not accessible." + "Please use the --deploy option and check permissions on the TUIT directory. " + "If you were looking to use the RDBMS as a taxonomic reference, plese use the -usedb option."); return; } } if (commandLine.hasOption(tuit.B)) { blastOutputFile = new File(commandLine.getOptionValue(tuit.B)); if (!blastOutputFile.exists() || !blastOutputFile.canRead()) { throw new Exception("BLAST output file either does not exist, or is not readable."); } else if (blastOutputFile.isDirectory()) { throw new Exception("BLAST output file points to a directory."); } } //Check vital parameters if (!commandLine.hasOption(tuit.IN)) { throw new ParseException("No input file option found, exiting."); } else { inputFile = new File(commandLine.getOptionValue(tuit.IN)); Log.getInstance().setLogName(inputFile.getName().split("\\.")[0] + ".tuit.log"); } //Correct the output file option if needed if (!commandLine.hasOption(tuit.OUT)) { outputFile = new File((inputFile.getPath()).split("\\.")[0] + tuit.TUIT_EXT); } else { outputFile = new File(commandLine.getOptionValue(tuit.OUT)); } //Adjust the output level if (commandLine.hasOption(tuit.V)) { Log.getInstance().setLevel(Level.FINE); Log.getInstance().log(Level.INFO, "Using verbose output for the log"); } else { Log.getInstance().setLevel(Level.INFO); } //Try all files if (inputFile != null) { if (!inputFile.exists() || !inputFile.canRead()) { throw new Exception("Input file either does not exist, or is not readable."); } else if (inputFile.isDirectory()) { throw new Exception("Input file points to a directory."); } } if (!properties.exists() || !properties.canRead()) { throw new Exception("Properties file either does not exist, or is not readable."); } else if (properties.isDirectory()) { throw new Exception("Properties file points to a directory."); } //Create blast parameters final StringBuilder stringBuilder = new StringBuilder(); for (Database database : tuitProperties.getBLASTNParameters().getDatabase()) { stringBuilder.append(database.getUse()); stringBuilder.append(" ");//Gonna insert an extra space for the last database } String remote; String entrez_query; if (tuitProperties.getBLASTNParameters().getRemote().getDelegate().equals("yes")) { remote = "-remote"; entrez_query = "-entrez_query"; parameters = new String[] { "-db", stringBuilder.toString(), remote, entrez_query, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue() }; } else { if (!commandLine.hasOption(tuit.B)) { if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .startsWith("NOT") || tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .startsWith("ALL")) { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), "-negative_gilist", TUITFileOperatorHelper.restrictToEntrez(tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue() .toUpperCase().replace("NOT", "OR")) .getAbsolutePath(), "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } else if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase() .equals("")) { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } else { parameters = new String[] { "-db", stringBuilder.toString(), "-evalue", tuitProperties.getBLASTNParameters().getExpect().getValue(), /*"-gilist", TUITFileOperatorHelper.restrictToEntrez( tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue()).getAbsolutePath(),*/ //TODO remove comment!!!!! "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() }; } } } //Prepare a cutoff Map if (tuitProperties.getSpecificationParameters() != null && tuitProperties.getSpecificationParameters().size() > 0) { cutoffMap = new HashMap<Ranks, TUITCutoffSet>(tuitProperties.getSpecificationParameters().size()); for (SpecificationParameters specificationParameters : tuitProperties .getSpecificationParameters()) { cutoffMap.put(Ranks.valueOf(specificationParameters.getCutoffSet().getRank()), TUITCutoffSet.newDefaultInstance( Double.parseDouble( specificationParameters.getCutoffSet().getPIdentCutoff().getValue()), Double.parseDouble(specificationParameters.getCutoffSet() .getQueryCoverageCutoff().getValue()), Double.parseDouble( specificationParameters.getCutoffSet().getAlpha().getValue()))); } } else { cutoffMap = new HashMap<Ranks, TUITCutoffSet>(); } final TUITFileOperatorHelper.OutputFormat format; if (tuitProperties.getBLASTNParameters().getOutputFormat().getFormat().equals("rdp")) { format = TUITFileOperatorHelper.OutputFormat.RDP_FIXRANK; } else { format = TUITFileOperatorHelper.OutputFormat.TUIT; } try (TUITFileOperator<NucleotideFasta> nucleotideFastaTUITFileOperator = NucleotideFastaTUITFileOperator .newInstance(format, cutoffMap);) { nucleotideFastaTUITFileOperator.setInputFile(inputFile); nucleotideFastaTUITFileOperator.setOutputFile(outputFile); final String cleanupString = tuitProperties.getBLASTNParameters().getKeepBLASTOuts().getKeep(); final boolean cleanup; if (cleanupString.equals("no")) { Log.getInstance().log(Level.INFO, "Temporary BLAST files will be deleted."); cleanup = true; } else { Log.getInstance().log(Level.INFO, "Temporary BLAST files will be kept."); cleanup = false; } //Create blast identifier ExecutorService executorService = Executors.newSingleThreadExecutor(); if (commandLine.hasOption(tuit.USE_DB)) { if (blastOutputFile == null) { blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromFileOperator(tmpDir, blastnExecutable, parameters, nucleotideFastaTUITFileOperator, connection, cutoffMap, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup); } else { try { blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromBLASTOutput( nucleotideFastaTUITFileOperator, connection, cutoffMap, blastOutputFile, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup); } catch (JAXBException e) { Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName() + ", please check input. The file must be XML formatted."); } catch (Exception e) { e.printStackTrace(); } } } else { if (blastOutputFile == null) { blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromFileOperator(tmpDir, blastnExecutable, parameters, nucleotideFastaTUITFileOperator, cutoffMap, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup, ramDb); } else { try { blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromBLASTOutput( nucleotideFastaTUITFileOperator, cutoffMap, blastOutputFile, Integer.parseInt( tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()), cleanup, ramDb); } catch (JAXBException e) { Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName() + ", please check input. The file must be XML formatted."); } catch (Exception e) { e.printStackTrace(); } } } Future<?> runnableFuture = executorService.submit(blastIdentifier); runnableFuture.get(); executorService.shutdown(); } } catch (ParseException pe) { Log.getInstance().log(Level.SEVERE, (pe.getMessage())); formatter.printHelp("tuit", options); } catch (SAXException saxe) { Log.getInstance().log(Level.SEVERE, saxe.getMessage()); } catch (FileNotFoundException fnfe) { Log.getInstance().log(Level.SEVERE, fnfe.getMessage()); } catch (TUITPropertyBadFormatException tpbfe) { Log.getInstance().log(Level.SEVERE, tpbfe.getMessage()); } catch (ClassCastException cce) { Log.getInstance().log(Level.SEVERE, cce.getMessage()); } catch (JAXBException jaxbee) { Log.getInstance().log(Level.SEVERE, "The properties file is not well formatted. Please ensure that the XML is consistent with the io.properties.dtd schema."); } catch (ClassNotFoundException cnfe) { //Probably won't happen unless the library deleted from the .jar Log.getInstance().log(Level.SEVERE, cnfe.getMessage()); //cnfe.printStackTrace(); } catch (SQLException sqle) { Log.getInstance().log(Level.SEVERE, "A database communication error occurred with the following message:\n" + sqle.getMessage()); //sqle.printStackTrace(); if (sqle.getMessage().contains("Access denied for user")) { Log.getInstance().log(Level.SEVERE, "Please use standard database login: " + NCBITablesDeployer.login + " and password: " + NCBITablesDeployer.password); } } catch (Exception e) { Log.getInstance().log(Level.SEVERE, e.getMessage()); e.printStackTrace(); } finally { if (connection != null) { try { connection.close(); } catch (SQLException sqle) { Log.getInstance().log(Level.SEVERE, "Problem closing the database connection: " + sqle); } } Log.getInstance().log(Level.FINE, "Task done, exiting..."); } }
From source file:edu.ksu.cis.indus.staticanalyses.dependency.DependencyXMLizerCLI.java
/** * This is the entry point via command-line. * //w w w . j a v a 2 s.co m * @param args is the command line arguments. * @throws RuntimeException when an Throwable exception beyond our control occurs. * @pre args != null */ public static void main(final String[] args) { final Options _options = new Options(); Option _option = new Option("o", "output", true, "Directory into which xml files will be written into. Defaults to current directory if omitted"); _option.setArgs(1); _option.setArgName("output-directory"); _options.addOption(_option); _option = new Option("j", "jimple", false, "Dump xmlized jimple."); _options.addOption(_option); final DivergenceDA _fidda = DivergenceDA.getDivergenceDA(IDependencyAnalysis.Direction.FORWARD_DIRECTION); _fidda.setConsiderCallSites(true); final DivergenceDA _bidda = DivergenceDA.getDivergenceDA(IDependencyAnalysis.Direction.BACKWARD_DIRECTION); _bidda.setConsiderCallSites(true); final NonTerminationSensitiveEntryControlDA _ncda = new NonTerminationSensitiveEntryControlDA(); final Object[][] _dasOptions = { { "ibdda1", "Identifier based data dependence (Soot)", new IdentifierBasedDataDA() }, { "ibdda2", "Identifier based data dependence (Indus)", new IdentifierBasedDataDAv2() }, { "ibdda3", "Identifier based data dependence (Indus Optimized)", new IdentifierBasedDataDAv3() }, { "rbdda", "Reference based data dependence", new ReferenceBasedDataDA() }, { "nscda", "Non-termination sensitive Entry control dependence", _ncda }, { "nicda", "Non-termination insensitive Entry control dependence", new NonTerminationInsensitiveEntryControlDA(), }, { "xcda", "Exit control dependence", new ExitControlDA() }, { "sda", "Synchronization dependence", new SynchronizationDA() }, { "frda1", "Forward Ready dependence v1", ReadyDAv1.getForwardReadyDA() }, { "brda1", "Backward Ready dependence v1", ReadyDAv1.getBackwardReadyDA() }, { "frda2", "Forward Ready dependence v2", ReadyDAv2.getForwardReadyDA() }, { "brda2", "Backward Ready dependence v2", ReadyDAv2.getBackwardReadyDA() }, { "frda3", "Forward Ready dependence v3", ReadyDAv3.getForwardReadyDA() }, { "brda3", "Backward Ready dependence v3", ReadyDAv3.getBackwardReadyDA() }, { "ida1", "Interference dependence v1", new InterferenceDAv1() }, { "ida2", "Interference dependence v2", new InterferenceDAv2() }, { "ida3", "Interference dependence v3", new InterferenceDAv3() }, { "fdda", "Forward Intraprocedural Divergence dependence", DivergenceDA.getDivergenceDA(IDependencyAnalysis.Direction.FORWARD_DIRECTION), }, { "bdda", "Backward Intraprocedural Divergence dependence", DivergenceDA.getDivergenceDA(IDependencyAnalysis.Direction.BACKWARD_DIRECTION), }, { "fidda", "Forward Intra+Interprocedural Divergence dependence", _fidda }, { "bidda", "Backward Intra+Interprocedural Divergence dependence", _bidda }, { "fpidda", "Forward Interprocedural Divergence dependence", InterProceduralDivergenceDA .getDivergenceDA(IDependencyAnalysis.Direction.FORWARD_DIRECTION), }, { "bpidda", "Backward Interprocedural Divergence dependence", InterProceduralDivergenceDA .getDivergenceDA(IDependencyAnalysis.Direction.BACKWARD_DIRECTION), }, }; _option = new Option("h", "help", false, "Display message."); _option.setOptionalArg(false); _options.addOption(_option); _option = new Option("p", "soot-classpath", false, "Prepend this to soot class path."); _option.setArgs(1); _option.setArgName("classpath"); _option.setOptionalArg(false); _options.addOption(_option); _option = new Option("aliasedusedefv1", false, "Use version 1 of aliased use-def info."); _options.addOption(_option); _option = new Option("safelockanalysis", false, "Use safe-lock-analysis for ready dependence."); _options.addOption(_option); _option = new Option("ofaforinterference", false, "Use OFA for interference dependence."); _options.addOption(_option); _option = new Option("ofaforready", false, "Use OFA for ready dependence."); _options.addOption(_option); _option = new Option("exceptionalexits", false, "Consider exceptional exits for control dependence."); _options.addOption(_option); _option = new Option("commonuncheckedexceptions", false, "Consider common unchecked exceptions."); _options.addOption(_option); _option = new Option("S", "scope", true, "The scope that should be analyzed."); _option.setArgs(1); _option.setArgName("scope"); _option.setRequired(false); _options.addOption(_option); for (int _i = 0; _i < _dasOptions.length; _i++) { final String _shortOption = _dasOptions[_i][0].toString(); final String _description = _dasOptions[_i][1].toString(); _option = new Option(_shortOption, false, _description); _options.addOption(_option); } final CommandLineParser _parser = new GnuParser(); try { final CommandLine _cl = _parser.parse(_options, args); if (_cl.hasOption("h")) { printUsage(_options); System.exit(1); } final DependencyXMLizerCLI _xmlizerCLI = new DependencyXMLizerCLI(); String _outputDir = _cl.getOptionValue('o'); if (_outputDir == null) { if (LOGGER.isWarnEnabled()) { LOGGER.warn("Defaulting to current directory for output."); } _outputDir = "."; } _xmlizerCLI.xmlizer.setXmlOutputDir(_outputDir); if (_cl.hasOption('p')) { _xmlizerCLI.addToSootClassPath(_cl.getOptionValue('p')); } if (_cl.hasOption('S')) { _xmlizerCLI.setScopeSpecFile(_cl.getOptionValue('S')); } _xmlizerCLI.dumpJimple = _cl.hasOption('j'); _xmlizerCLI.useAliasedUseDefv1 = _cl.hasOption("aliasedusedefv1"); _xmlizerCLI.useSafeLockAnalysis = _cl.hasOption("safelockanalysis"); _xmlizerCLI.exceptionalExits = _cl.hasOption("exceptionalexits"); _xmlizerCLI.commonUncheckedException = _cl.hasOption("commonuncheckedexceptions"); final List<String> _classNames = _cl.getArgList(); if (_classNames.isEmpty()) { throw new MissingArgumentException("Please specify atleast one class."); } _xmlizerCLI.setClassNames(_classNames); final int _exitControlDAIndex = 6; if (_cl.hasOption(_dasOptions[_exitControlDAIndex][0].toString())) { _xmlizerCLI.das.add(_ncda); for (final Iterator<DependenceSort> _i = _ncda.getIds().iterator(); _i.hasNext();) { final DependenceSort _id = _i.next(); MapUtils.putIntoCollectionInMapUsingFactory(_xmlizerCLI.info, _id, _ncda, SetUtils.getFactory()); } } if (!parseForDependenceOptions(_dasOptions, _cl, _xmlizerCLI)) { throw new ParseException("Atleast one dependence analysis must be requested."); } _xmlizerCLI.<ITokens>execute(); } catch (final ParseException _e) { LOGGER.error("Error while parsing command line.", _e); System.out.println("Error while parsing command line." + _e); printUsage(_options); } catch (final Throwable _e) { LOGGER.error("Beyond our control. May day! May day!", _e); throw new RuntimeException(_e); } }
From source file:com.example.dlp.Redact.java
/** Command line application to redact strings, images using the Data Loss Prevention API. */ public static void main(String[] args) throws Exception { OptionGroup optionsGroup = new OptionGroup(); optionsGroup.setRequired(true);// www . ja v a 2s. co m Option stringOption = new Option("s", "string", true, "redact string"); optionsGroup.addOption(stringOption); Option fileOption = new Option("f", "file path", true, "redact input file path"); optionsGroup.addOption(fileOption); Options commandLineOptions = new Options(); commandLineOptions.addOptionGroup(optionsGroup); Option minLikelihoodOption = Option.builder("minLikelihood").hasArg(true).required(false).build(); commandLineOptions.addOption(minLikelihoodOption); Option replaceOption = Option.builder("r").longOpt("replace string").hasArg(true).required(false).build(); commandLineOptions.addOption(replaceOption); Option infoTypesOption = Option.builder("infoTypes").hasArg(true).required(false).build(); infoTypesOption.setArgs(Option.UNLIMITED_VALUES); commandLineOptions.addOption(infoTypesOption); Option outputFilePathOption = Option.builder("o").hasArg(true).longOpt("outputFilePath").required(false) .build(); commandLineOptions.addOption(outputFilePathOption); CommandLineParser parser = new DefaultParser(); HelpFormatter formatter = new HelpFormatter(); CommandLine cmd; try { cmd = parser.parse(commandLineOptions, args); } catch (ParseException e) { System.out.println(e.getMessage()); formatter.printHelp(Redact.class.getName(), commandLineOptions); System.exit(1); return; } String replacement = cmd.getOptionValue(replaceOption.getOpt(), "_REDACTED_"); List<InfoType> infoTypesList = new ArrayList<>(); String[] infoTypes = cmd.getOptionValues(infoTypesOption.getOpt()); if (infoTypes != null) { for (String infoType : infoTypes) { infoTypesList.add(InfoType.newBuilder().setName(infoType).build()); } } Likelihood minLikelihood = Likelihood.valueOf( cmd.getOptionValue(minLikelihoodOption.getOpt(), Likelihood.LIKELIHOOD_UNSPECIFIED.name())); // string inspection if (cmd.hasOption("s")) { String source = cmd.getOptionValue(stringOption.getOpt()); redactString(source, replacement, minLikelihood, infoTypesList); } else if (cmd.hasOption("f")) { String filePath = cmd.getOptionValue(fileOption.getOpt()); String outputFilePath = cmd.getOptionValue(outputFilePathOption.getOpt()); redactImage(filePath, minLikelihood, infoTypesList, outputFilePath); } }