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.CdoQuery.java

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

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input CDO resource directory");
    inputOpt.setArgs(1);/*w w  w .java  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);

    Option repoOpt = OptionBuilder.create(REPO_NAME);
    repoOpt.setArgName("REPO_NAME");
    repoOpt.setDescription("CDO Repository name");
    repoOpt.setArgs(1);
    repoOpt.setRequired(true);

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

    CommandLineParser parser = new PosixParser();

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

        String repositoryDir = commandLine.getOptionValue(IN);
        String repositoryName = commandLine.getOptionValue(REPO_NAME);

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

        EmbeddedCDOServer server = new EmbeddedCDOServer(repositoryDir, repositoryName);
        try {
            server.run();
            CDOSession session = server.openSession();
            CDOTransaction transaction = session.openTransaction();
            Resource resource = transaction.getRootResource();

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

            {
                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)));
            }

            transaction.close();
            session.close();
        } finally {
            server.stop();
        }
    } 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.SDFCatsIndexer.java

/**
 * @param args/*w w  w  . ja v  a 2s .  c o 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);
    opt.setArgName("fn");
    options.addOption(opt);

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

    opt = new Option(OPT_NORMALIZATION, true,
            "Normalization method: Counts|CountsPerAtom|CountsPerFeature(def) multiple allowed");
    opt.setArgName("meth");
    options.addOption(opt);

    opt = new Option(OPT_PRINTDESC, false,
            "Causes the descriptor for describing each linear path in a molceule to be created");
    options.addOption(opt);

    opt = new Option(OPT_RGROUPTYPES, false, "treat RGroup attachement point ([U]) as atom type.");
    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);
    }

    String inFile = cmd.getOptionValue(OPT_INFILE);
    String outFile = cmd.getOptionValue(OPT_OUTFILE);

    AtomTyperInterface[] myTypes = CATSIndexer.typers;
    String tagPrefix = "";
    if (cmd.hasOption(OPT_RGROUPTYPES)) {
        myTypes = CATSIndexer.rgroupTypers;
        tagPrefix = "RG";
    }

    if (cmd.hasOption(OPT_PRINTDESC)) {
        SDFCatsIndexer sdfIndexer = new SDFCatsIndexer(myTypes, tagPrefix);
        sdfIndexer.printDescriptors(inFile, outFile);
        sdfIndexer.close();
        return;
    }

    EnumSet<Normalization> normMeth = EnumSet.noneOf(Normalization.class);
    if (cmd.hasOption(OPT_NORMALIZATION))
        for (String n : cmd.getOptionValues(OPT_NORMALIZATION))
            normMeth.add(Normalization.valueOf(n));
    else
        normMeth.add(Normalization.CountsPerFeature);

    SDFCatsIndexer sdfIndexer = new SDFCatsIndexer(myTypes, tagPrefix);
    sdfIndexer.run(inFile, outFile, normMeth);
    sdfIndexer.close();
}

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

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

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);//from ww  w  .j  ava 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);

    Option optFileOpt = OptionBuilder.create(OPTIONS_FILE);
    optFileOpt.setArgName("FILE");
    optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource");
    optFileOpt.setArgs(1);

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

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

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

        URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN)));

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

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

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

        if (commandLine.hasOption(OPTIONS_FILE)) {
            Properties properties = new Properties();
            properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE))));
            for (final Entry<Object, Object> entry : properties.entrySet()) {
                loadOpts.put((String) entry.getKey(), (String) entry.getValue());
            }
        }
        resource.load(loadOpts);
        {
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<ClassDeclaration> list = JavaQueries.grabats09(resource);
            long end = System.currentTimeMillis();
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size()));
            LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
        }

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

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

From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosGraphQueryInvisibleMethodDeclarations.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);/* ww  w.  j  a  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);

    Option optFileOpt = OptionBuilder.create(OPTIONS_FILE);
    optFileOpt.setArgName("FILE");
    optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource");
    optFileOpt.setArgs(1);

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

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

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

        URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN)));

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

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

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

        if (commandLine.hasOption(OPTIONS_FILE)) {
            Properties properties = new Properties();
            properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE))));
            for (final Entry<Object, Object> entry : properties.entrySet()) {
                loadOpts.put((String) entry.getKey(), (String) entry.getValue());
            }
        }
        resource.load(loadOpts);
        {
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<MethodDeclaration> list = JavaQueries.getInvisibleMethodDeclarations(resource);
            long end = System.currentTimeMillis();
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size()));
            LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
        }

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

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

From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosGraphQueryList.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  .  jav  a2 s.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);

    Option optFileOpt = OptionBuilder.create(OPTIONS_FILE);
    optFileOpt.setArgName("FILE");
    optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource");
    optFileOpt.setArgs(1);

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

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

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

        URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN)));

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

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

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

        if (commandLine.hasOption(OPTIONS_FILE)) {
            Properties properties = new Properties();
            properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE))));
            for (final Entry<Object, Object> entry : properties.entrySet()) {
                loadOpts.put((String) entry.getKey(), (String) entry.getValue());
            }
        }
        resource.load(loadOpts);
        {
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<MethodDeclaration> list = JavaQueries.getUnusedMethodsList(resource);
            long end = System.currentTimeMillis();
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO, MessageFormat.format("Query result (list) contains {0} elements", list.size()));
            LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
        }

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

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

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

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

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);//  www.  jav a  2s  .  com
    inputOpt.setRequired(true);

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

    Option optFileOpt = OptionBuilder.create(OPTIONS_FILE);
    optFileOpt.setArgName("FILE");
    optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource");
    optFileOpt.setArgs(1);

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

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

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

        URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN)));

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

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

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

        if (commandLine.hasOption(OPTIONS_FILE)) {
            Properties properties = new Properties();
            properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE))));
            for (final Entry<Object, Object> entry : properties.entrySet()) {
                loadOpts.put((String) entry.getKey(), (String) entry.getValue());
            }
        }
        resource.load(loadOpts);
        {
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<Type> list = JavaQueries.getOrphanNonPrimitivesTypes(resource);
            long end = System.currentTimeMillis();
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size()));
            LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
        }

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

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

From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosGraphQueryThrownExceptionsPerPackage.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  2s  . c  o  m
    inputOpt.setRequired(true);

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

    Option optFileOpt = OptionBuilder.create(OPTIONS_FILE);
    optFileOpt.setArgName("FILE");
    optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource");
    optFileOpt.setArgs(1);

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

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

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

        URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN)));

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

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

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

        if (commandLine.hasOption(OPTIONS_FILE)) {
            Properties properties = new Properties();
            properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE))));
            for (final Entry<Object, Object> entry : properties.entrySet()) {
                loadOpts.put((String) entry.getKey(), (String) entry.getValue());
            }
        }
        resource.load(loadOpts);
        {
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            HashMap<String, EList<TypeAccess>> list = JavaQueries.getThrownExceptionsPerPackage(resource);
            long end = System.currentTimeMillis();
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size()));
            LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin)));
        }

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

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

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

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

    Option inputOpt = OptionBuilder.create(IN);
    inputOpt.setArgName("INPUT");
    inputOpt.setDescription("Input Kyanos resource directory");
    inputOpt.setArgs(1);// www  .  j  av  a2 s .com
    inputOpt.setRequired(true);

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

    Option optFileOpt = OptionBuilder.create(OPTIONS_FILE);
    optFileOpt.setArgName("FILE");
    optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource");
    optFileOpt.setArgs(1);

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

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

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

        URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN)));

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

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

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

        if (commandLine.hasOption(OPTIONS_FILE)) {
            Properties properties = new Properties();
            properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE))));
            for (final Entry<Object, Object> entry : properties.entrySet()) {
                loadOpts.put((String) entry.getKey(), (String) entry.getValue());
            }
        }
        resource.load(loadOpts);
        {
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<MethodDeclaration> list = JavaQueries.getUnusedMethodsList(resource);
            long end = System.currentTimeMillis();
            LOG.log(Level.INFO, "End query");
            LOG.log(Level.INFO, MessageFormat.format("Query result 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:fr.inria.atlanmod.kyanos.benchmarks.MorsaCreator.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  w  w w  . j a va2s  .co  m*/
    inputOpt.setRequired(true);

    Option outputOpt = OptionBuilder.create(OUT);
    outputOpt.setArgName("OUTPUT");
    outputOpt.setDescription("Output directory");
    outputOpt.setArgs(1);
    outputOpt.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(outputOpt);
    options.addOption(inClassOpt);

    CommandLineParser parser = new PosixParser();

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

        URI sourceUri = URI.createFileURI(commandLine.getOptionValue(IN));
        URI targetUri = URI.createURI("morsa://" + commandLine.getOptionValue(OUT));

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

        ResourceSet resourceSet = new ResourceSetImpl();

        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("xmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put("zxmi",
                new XMIResourceFactoryImpl());
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put("morsa",
                new MorsaResourceFactoryImpl(new MongoDBMorsaBackendFactory()));

        Resource sourceResource = resourceSet.createResource(sourceUri);
        Map<String, Object> loadOpts = new HashMap<String, Object>();
        if ("zxmi".equals(sourceUri.fileExtension())) {
            loadOpts.put(XMIResource.OPTION_ZIP, Boolean.TRUE);
        }

        Runtime.getRuntime().gc();
        long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
        LOG.log(Level.INFO, MessageFormat.format("Used memory before loading: {0}",
                MessageUtil.byteCountToDisplaySize(initialUsedMemory)));
        LOG.log(Level.INFO, "Loading source resource");
        sourceResource.load(loadOpts);
        LOG.log(Level.INFO, "Source resource loaded");
        Runtime.getRuntime().gc();
        long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
        LOG.log(Level.INFO, MessageFormat.format("Used memory after loading: {0}",
                MessageUtil.byteCountToDisplaySize(finalUsedMemory)));
        LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));

        Resource targetResource = resourceSet.createResource(targetUri);

        Map<String, Object> saveOpts = new HashMap<String, Object>();
        //URI of the MongoDB database (e.g. localhost)
        saveOpts.put(IMorsaResource.OPTION_SERVER_URI, "localhost");
        saveOpts.put(IMorsaResource.OPTION_MAX_SAVE_CACHE_SIZE, 30000);
        saveOpts.put(IMorsaResource.OPTION_DEMAND_LOAD, false);
        targetResource.save(saveOpts);

        LOG.log(Level.INFO, "Start moving elements");
        targetResource.getContents().clear();
        targetResource.getContents().addAll(sourceResource.getContents());
        LOG.log(Level.INFO, "End moving elements");
        LOG.log(Level.INFO, "Start saving");
        targetResource.save(saveOpts);
        LOG.log(Level.INFO, "Saved");

        targetResource.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.KyanosGraphQueryClassDeclarationAttributes.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  a  v a  2 s. 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);

    Option optFileOpt = OptionBuilder.create(OPTIONS_FILE);
    optFileOpt.setArgName("FILE");
    optFileOpt.setDescription("Properties file holding the options to be used in the Kyanos Resource");
    optFileOpt.setArgs(1);

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

    CommandLineParser parser = new PosixParser();

    try {
        PersistenceBackendFactoryRegistry.getFactories().put(NeoBlueprintsURI.NEO_GRAPH_SCHEME,
                new BlueprintsPersistenceBackendFactory());

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

        URI uri = NeoBlueprintsURI.createNeoGraphURI(new File(commandLine.getOptionValue(IN)));

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

        ResourceSet resourceSet = new ResourceSetImpl();
        resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap()
                .put(NeoBlueprintsURI.NEO_GRAPH_SCHEME, PersistentResourceFactory.eINSTANCE);

        Resource resource = resourceSet.createResource(uri);

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

        if (commandLine.hasOption(OPTIONS_FILE)) {
            Properties properties = new Properties();
            properties.load(new FileInputStream(new File(commandLine.getOptionValue(OPTIONS_FILE))));
            for (final Entry<Object, Object> entry : properties.entrySet()) {
                loadOpts.put((String) entry.getKey(), (String) entry.getValue());
            }
        }
        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());
    }
}