Example usage for org.apache.commons.cli Option setRequired

List of usage examples for org.apache.commons.cli Option setRequired

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Introduction

In this page you can find the example usage for org.apache.commons.cli Option setRequired.

Prototype

public void setRequired(boolean required)

Source Link

Document

Sets whether this Option is mandatory.

Usage

From source file:fr.inria.atlanmod.kyanos.benchmarks.Migrator.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input file");
    inputOpt.setArgs(1);/*from   ww  w . j a  v a 2  s .  c  o m*/
    inputOpt.setRequired(true);

    Option outputOpt = OptionBuilder.create(OUT);
    outputOpt.setArgName("OUTPUT");
    outputOpt.setDescription("Output file");
    outputOpt.setArgs(1);
    outputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(IN_EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of input EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    Option outClassOpt = OptionBuilder.create(OUT_EPACKAGE_CLASS);
    outClassOpt.setArgName("CLASS");
    outClassOpt.setDescription("FQN of output EPackage implementation class");
    outClassOpt.setArgs(1);
    outClassOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(outputOpt);
    options.addOption(inClassOpt);
    options.addOption(outClassOpt);

    CommandLineParser parser = new PosixParser();

    try {
        CommandLine commandLine = parser.parse(options, args);
        URI sourceUri = URI.createFileURI(commandLine.getOptionValue(IN));
        URI targetUri = URI.createFileURI(commandLine.getOptionValue(OUT));
        Class<?> inClazz = Migrator.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(IN_EPACKAGE_CLASS));
        Class<?> outClazz = Migrator.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(OUT_EPACKAGE_CLASS));

        @SuppressWarnings("unused")
        EPackage inEPackage = (EPackage) inClazz.getMethod("init").invoke(null);
        EPackage outEPackage = (EPackage) outClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("xmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("zxmi",
                new XMIResourceFactoryImpl());

        Resource sourceResource = resourceSet.getResource(sourceUri, true);
        Resource targetResource = resourceSet.createResource(targetUri);

        targetResource.getContents().clear();
        LOG.log(Level.INFO, "Start migration");
        targetResource.getContents()
                .add(MigratorUtil.migrate(sourceResource.getContents().get(0), outEPackage));
        LOG.log(Level.INFO, "Migration finished");

        Map<String, Object> saveOpts = new HashMap<String, Object>();
        saveOpts.put(XMIResource.OPTION_ZIP, Boolean.TRUE);
        LOG.log(Level.INFO, "Start saving");
        targetResource.save(saveOpts);
        LOG.log(Level.INFO, "Saving done");
    } catch (ParseException e) {
        showError(e.toString());
        showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        showError(e.toString());
    }
}

From source file:com.genentech.struchk.sdfNormalizer.java

public static void main(String[] args) {
    long start = System.currentTimeMillis();
    int nMessages = 0;
    int nErrors = 0;
    int nStruct = 0;

    // create command line Options object
    Options options = new Options();
    Option opt = new Option("in", true, "input file [.ism,.sdf,...]");
    opt.setRequired(true);
    options.addOption(opt);/*from w w w .j a v  a2 s  . c  o  m*/

    opt = new Option("out", true, "output file");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("mol", true, "molFile used for output: ORIGINAL(def)|NORMALIZED|TAUTOMERIC");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option("shortMessage", false,
            "Limit message to first 80 characters to conform with sdf file specs.");
    opt.setRequired(false);
    options.addOption(opt);

    CommandLineParser parser = new PosixParser();
    CommandLine cmd;
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        exitWithHelp(options, e.getMessage());
        throw new Error(e); // avoid compiler errors
    }
    args = cmd.getArgs();

    if (args.length != 0) {
        System.err.print("Unknown options: " + args + "\n\n");
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("sdfNormalizer", options);
        System.exit(1);
    }

    String molOpt = cmd.getOptionValue("mol");
    OUTMolFormat outMol = OUTMolFormat.ORIGINAL;
    if (molOpt == null || "original".equalsIgnoreCase(molOpt))
        outMol = OUTMolFormat.ORIGINAL;
    else if ("NORMALIZED".equalsIgnoreCase(molOpt))
        outMol = OUTMolFormat.NORMALIZED;
    else if ("TAUTOMERIC".equalsIgnoreCase(molOpt))
        outMol = OUTMolFormat.TAUTOMERIC;
    else {
        System.err.printf("Unkown option for -mol: %s\n", molOpt);
        System.exit(1);
    }

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    boolean limitMessage = cmd.hasOption("shortMessage");

    try {
        oemolistream ifs = new oemolistream(inFile);
        oemolostream ofs = new oemolostream(outFile);

        URL cFile = OEStruchk.getResourceURL(OEStruchk.class, "Struchk.xml");

        // create OEStruchk from config file
        OEStruchk strchk = new OEStruchk(cFile, CHECKConfig.ASSIGNStructFlag, false);

        OEGraphMol mol = new OEGraphMol();
        StringBuilder sb = new StringBuilder(2000);
        while (oechem.OEReadMolecule(ifs, mol)) {
            if (!strchk.applyRules(mol, null))
                nErrors++;

            switch (outMol) {
            case NORMALIZED:
                mol.Clear();
                oechem.OEAddMols(mol, strchk.getTransformedMol("parent"));
                break;
            case TAUTOMERIC:
                mol.Clear();
                oechem.OEAddMols(mol, strchk.getTransformedMol(null));
                break;
            case ORIGINAL:
                break;
            }

            oechem.OESetSDData(mol, "CTISMILES", strchk.getTransformedIsoSmiles(null));
            oechem.OESetSDData(mol, "CTSMILES", strchk.getTransformedSmiles(null));
            oechem.OESetSDData(mol, "CISMILES", strchk.getTransformedIsoSmiles("parent"));
            oechem.OESetSDData(mol, "Strutct_Flag", strchk.getStructureFlag().getName());

            List<Message> msgs = strchk.getStructureMessages(null);
            nMessages += msgs.size();
            for (Message msg : msgs)
                sb.append(String.format("\t%s:%s", msg.getLevel(), msg.getText()));
            if (limitMessage)
                sb.setLength(Math.min(sb.length(), 80));

            oechem.OESetSDData(mol, "NORM_MESSAGE", sb.toString());

            oechem.OEWriteMolecule(ofs, mol);

            sb.setLength(0);
            nStruct++;
        }
        strchk.delete();
        mol.delete();
        ifs.close();
        ifs.delete();
        ofs.close();
        ofs.delete();

    } catch (Exception e) {
        throw new Error(e);
    } finally {
        System.err.printf("sdfNormalizer: Checked %d structures %d errors, %d messages in %dsec\n", nStruct,
                nErrors, nMessages, (System.currentTimeMillis() - start) / 1000);
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapQueryClassDeclarationAttributes.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);/*  w ww  .j  a  v a2 s.c  o  m*/
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

        CommandLine commandLine = parser.parse(options, args);

        URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN)));

        Class<?> inClazz = KyanosMapQueryClassDeclarationAttributes.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME,
                PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

        Map<String, Object> loadOpts = new HashMap<String, Object>();
        resource.load(loadOpts);
        {
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            HashMap<String, EList<NamedElement>> list = JavaQueries.getClassDeclarationAttributes(resource);
            long end = System.currentTimeMillis();
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO,
                    MessageFormat.format("Query result contains {0} elements", list.entrySet().size()));
            LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
        }

        if (resource instanceof PersistentResourceImpl) {
            PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource);
        } else {
            resource.unload();
        }

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapQueryRenameAllMethods.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);/*from   w  ww .j  ava  2  s  . c  o  m*/
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

        CommandLine commandLine = parser.parse(options, args);

        URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN)));

        Class<?> inClazz = KyanosMapQueryRenameAllMethods.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME,
                PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

        Map<String, Object> loadOpts = new HashMap<String, Object>();
        resource.load(loadOpts);
        String name = UUID.randomUUID().toString();
        {
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            JavaQueries.renameAllMethods(resource, name);
            long end = System.currentTimeMillis();
            resource.save(Collections.emptyMap());
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
        }

        if (resource instanceof PersistentResourceImpl) {
            PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource);
        } else {
            resource.unload();
        }

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapQueryLoop.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);// w ww  . j av a 2  s . c  o m
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

        CommandLine commandLine = parser.parse(options, args);

        URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN)));

        Class<?> inClazz = KyanosMapQueryLoop.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME,
                PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

        Map<String, Object> loadOpts = new HashMap<String, Object>();
        resource.load(loadOpts);

        {
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<MethodDeclaration> list = JavaQueries.getUnusedMethodsLoop(resource);
            long end = System.currentTimeMillis();
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO,
                    MessageFormat.format("Query result (loops) contains {0} elements", list.size()));
            LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
        }

        if (resource instanceof PersistentResourceImpl) {
            PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource);
        } else {
            resource.unload();
        }

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:com.genentech.chemistry.openEye.apps.SDFALogP.java

/**
 * @param args/*from   w w w . ja va  2 s .  co m*/
 */
public static void main(String... args) throws IOException { // create command line Options object
    Options options = new Options();
    Option opt = new Option(OPT_INFILE, true,
            "input file oe-supported Use .sdf|.smi to specify the file type.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_OUTFILE, true, "output file oe-supported. Use .sdf|.smi to specify the file type.");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option(OPT_SMARTS_FILE, true, "Optional: to overwrite atom type definition file.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_PRINT_COUNTS, false,
            "If set the count of each atom type is added to the output file.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_VALIDATE_ASSIGNMENT, false,
            "Print warning if no atomtype matches an atom in a candidte molecule.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_SUPRESS_ZERO, false, "If given atom type counts with count=0 will not be added.");
    opt.setRequired(false);
    options.addOption(opt);

    opt = new Option(OPT_NEUTRALIZE, true, "y|n to neutralize molecule if possible (default=y)");
    opt.setRequired(false);
    options.addOption(opt);

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        System.err.println(e.getMessage());
        exitWithHelp(options);
    }
    args = cmd.getArgs();

    if (cmd.hasOption("d")) {
        System.err.println("Start debugger and press return:");
        new BufferedReader(new InputStreamReader(System.in)).readLine();
    }

    String inFile = cmd.getOptionValue(OPT_INFILE);
    String outFile = cmd.getOptionValue(OPT_OUTFILE);
    String smartsFile = cmd.getOptionValue(OPT_SMARTS_FILE);
    boolean outputCount = cmd.hasOption(OPT_PRINT_COUNTS);
    boolean outputZero = !cmd.hasOption(OPT_SUPRESS_ZERO);
    boolean neutralize = !"n".equalsIgnoreCase(cmd.getOptionValue(OPT_NEUTRALIZE));
    boolean ValidateAssignment = cmd.hasOption(OPT_VALIDATE_ASSIGNMENT);

    SDFALogP sdfALogP = new SDFALogP(smartsFile, outFile, outputZero, neutralize, ValidateAssignment);

    sdfALogP.run(inFile, outputCount);
    sdfALogP.close();
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.MorsaTraverser.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);/*w  w  w  .  j  av  a  2s .c  om*/
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);

    CommandLineParser parser = new PosixParser();

    try {
        CommandLine commandLine = parser.parse(options, args);

        URI uri = URI.createURI("morsa://" + commandLine.getOptionValue(IN));

        Class<?> inClazz = MorsaTraverser.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put("morsa",
                new MorsaResourceFactoryImpl(new MongoDBMorsaBackendFactory()));

        Resource resource = resourceSet.createResource(uri);

        Map<String, Object> loadOpts = new HashMap<String, Object>();
        loadOpts.put(IMorsaResource.OPTION_SERVER_URI, "localhost");
        loadOpts.put(IMorsaResource.OPTION_MAX_SAVE_CACHE_SIZE, 30000);
        loadOpts.put(IMorsaResource.OPTION_DEMAND_LOAD, false);
        //         loadOpts.put(IMorsaResource.OPTION_CACHE_POLICY, FIFOEObjectCachePolicy.class.getName());
        //         loadOpts.put(IMorsaResource.OPTION_MAX_CACHE_SIZE, 30000);
        //         loadOpts.put(IMorsaResource.OPTION_CACHE_FLUSH_FACTOR, 0.3f);
        //         loadOpts.put(IMorsaResource.OPTION_DEMAND_LOAD_STRATEGY, IMorsaResource.OPTION_SINGLE_LOAD_STRATEGY);
        //         loadOpts.put(IMorsaResource.OPTION_DEMAND_LOAD, true);

        resource.load(loadOpts);

        LOG.log(Level.INFO, "Start counting");
        int count = 0;
        long begin = System.currentTimeMillis();
        for (Iterator<EObject> iterator = resource.getAllContents(); iterator.hasNext(); iterator
                .next(), count++)
            ;
        long end = System.currentTimeMillis();
        LOG.log(Level.INFO, "End counting");
        LOG.log(Level.INFO, MessageFormat.format("Resource {0} contains {1} elements", uri, count));
        LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}

From source file:com.blackducksoftware.tools.nrt.NoticeReportTool.java

/**
 * @param args/*  w  w  w . j a va 2s .  c  om*/
 * @throws Exception
 */
public static void main(String[] args) throws Exception {

    System.out.println("Notice Report Tool for Black Duck Suite");
    CommandLineParser parser = new DefaultParser();

    options.addOption("h", "help", false, "show help.");

    Option applicationOption = new Option(NRTConstants.CL_APPLICATION_TYPE, true,
            "Application type [PROTEX|CODECENTER] (required)");
    applicationOption.setRequired(true);
    options.addOption(applicationOption);

    Option configFileOption = new Option(NRTConstants.CL_CONFIG_FILE, true,
            "Location of configuration file (required)");
    configFileOption.setRequired(true);
    options.addOption(configFileOption);

    Option projectNameOption = new Option(NRTConstants.CL_PROJECT_NAME, true,
            "Name of Protex project (will override configuration file)");
    projectNameOption.setRequired(false);
    options.addOption(projectNameOption);

    File configFile = null;
    APPLICATION applicationType = null;
    String projectName = null;

    try {
        CommandLine cmd = parser.parse(options, args);

        if (cmd.hasOption("h")) {
            help();
        }

        // Config File
        if (cmd.hasOption(NRTConstants.CL_CONFIG_FILE)) {
            String configFilePath = cmd.getOptionValue(NRTConstants.CL_CONFIG_FILE);
            log.info("Config file location: " + configFilePath);
            configFile = new File(configFilePath);
            if (!configFile.exists()) {
                log.error("Configuration file does not exist at location: " + configFile);
                System.exit(-1);
            }
        } else {
            log.error("Must specify configuration file!");
            help();
        }

        if (cmd.hasOption(NRTConstants.CL_APPLICATION_TYPE)) {
            String bdsApplicationType = cmd.getOptionValue(NRTConstants.CL_APPLICATION_TYPE);

            try {
                applicationType = APPLICATION.valueOf(bdsApplicationType);
            } catch (IllegalArgumentException e) {
                log.error("No such application type recognized: " + bdsApplicationType);
                help();
            }

        } else {
            help();
        }

        if (cmd.hasOption(NRTConstants.CL_PROJECT_NAME)) {
            projectName = cmd.getOptionValue(NRTConstants.CL_PROJECT_NAME);
            log.info("User specified project name: " + projectName);
        }

        NoticeReportProcessor processor = new NoticeReportProcessor(configFile.getAbsolutePath(),
                applicationType, projectName);
        try {
            processor.connect();
        } catch (Exception e) {
            log.error("Connection problems: " + e.getMessage());
            throw new Exception(e);
        }
        processor.processReport();

    } catch (Exception e) {
        log.error("Error: " + e.getMessage());
        help();
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.ReferencesCounter.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input file");
    inputOpt.setArgs(1);/*from  www.j a  v  a 2  s. c om*/
    inputOpt.setRequired(true);

    Option outputOpt = OptionBuilder.create(OUT);
    outputOpt.setArgName("OUTPUT");
    outputOpt.setDescription("Output file");
    outputOpt.setArgs(1);
    outputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(IN_EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of input EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    Option labelOpt = OptionBuilder.create(LABEL);
    labelOpt.setArgName("LABEL");
    labelOpt.setDescription("Label for the data set");
    labelOpt.setArgs(1);
    labelOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(outputOpt);
    options.addOption(inClassOpt);
    options.addOption(labelOpt);

    CommandLineParser parser = new PosixParser();

    try {
        CommandLine commandLine = parser.parse(options, args);
        URI sourceUri = URI.createFileURI(commandLine.getOptionValue(IN));
        Class<?> inClazz = ReferencesCounter.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(IN_EPACKAGE_CLASS));
        @SuppressWarnings("unused")
        EPackage inEPackage = (EPackage) inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("xmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("zxmi",
                new XMIResourceFactoryImpl());

        Resource sourceResource = resourceSet.getResource(sourceUri, true);

        FileWriter writer = new FileWriter(new File(commandLine.getOptionValue(OUT)));
        try {
            writer.write(commandLine.getOptionValue(LABEL));
            writer.write("\n");

            for (Iterator<EObject> iterator = sourceResource.getAllContents(); iterator.hasNext();) {
                EObject eObject = iterator.next();
                for (EStructuralFeature feature : eObject.eClass().getEAllStructuralFeatures()) {
                    if (feature.isMany() && eObject.eIsSet(feature)) {
                        EList<?> value = (EList<?>) eObject.eGet(feature);
                        //                     if (value.size() > 10) 
                        writer.write(String.format("%d\n", value.size()));
                    }
                }
            }
        } finally {
            IOUtils.closeQuietly(writer);
        }

    } catch (ParseException e) {
        showError(e.toString());
        showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        showError(e.toString());
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapTraverser.java

public static void main(String[] args) {
    Options options = new Options();

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);/*from  ww w.  ja v a 2s .  c  om*/
    inputOpt.setRequired(true);

    Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS);
    inClassOpt.setArgName("CLASS");
    inClassOpt.setDescription("FQN of EPackage implementation class");
    inClassOpt.setArgs(1);
    inClassOpt.setRequired(true);

    options.addOption(inputOpt);
    options.addOption(inClassOpt);

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

        CommandLine commandLine = parser.parse(options, args);

        URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN)));

        Class<?> inClazz = KyanosMapTraverser.class.getClassLoader()
                .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS));
        inClazz.getMethod("init").invoke(null);

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME,
                PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

        Map<String, Object> loadOpts = new HashMap<String, Object>();
        resource.load(loadOpts);
        resource.getContents().get(0);

        LOG.log(Level.INFO, "Start counting");
        int count = 0;
        long begin = System.currentTimeMillis();
        for (Iterator<EObject> iterator = resource.getAllContents(); iterator.hasNext(); iterator
                .next(), count++)
            ;
        long end = System.currentTimeMillis();
        LOG.log(Level.INFO, "End counting");
        LOG.log(Level.INFO, MessageFormat.format("Resource {0} contains {1} elements", uri, count));
        LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));

        if (resource instanceof PersistentResourceImpl) {
            PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource);
        } else {
            resource.unload();
        }

    } catch (ParseException e) {
        MessageUtil.showError(e.toString());
        MessageUtil.showError("Current arguments: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java -jar <this-file.jar>", options, true);
    } catch (Throwable e) {
        MessageUtil.showError(e.toString());
    }
}