Example usage for org.apache.commons.cli CommandLine getOptionValue

List of usage examples for org.apache.commons.cli CommandLine getOptionValue

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Introduction

In this page you can find the example usage for org.apache.commons.cli CommandLine getOptionValue.

Prototype

public String getOptionValue(char opt)

Source Link

Document

Retrieve the argument, if any, of this option.

Usage

From source file:edu.umass.cs.gnsclient.client.testing.CreateGuidTest.java

/**
 * The main routine run from the command line.
 *
 * @param args/*from   w w w.  j a va  2s.co  m*/
 * @throws Exception
 */
public static void main(String args[]) throws Exception {
    try {
        CommandLine parser = initializeOptions(args);
        if (parser.hasOption("help") || args.length == 0) {
            printUsage();
            System.exit(1);
        }
        String alias = parser.getOptionValue("alias");
        new CreateGuidTest(alias != null ? alias : ACCOUNT_ALIAS);
        System.exit(0);
    } catch (HeadlessException e) {
        System.out
                .println("When running headless you'll need to specify the host and port on the command line");
        printUsage();
        System.exit(1);
    }
}

From source file:fr.inria.atlanmod.kyanos.benchmarks.ase2015.NeoEMFMapQueryGetBranchStatements.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 ava2s . 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(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

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

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

        Class<?> inClazz = NeoEMFMapQueryGetBranchStatements.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>();

        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());
            }
        }
        // Add the LoadedObjectCounter store
        List<StoreOption> storeOptions = new ArrayList<StoreOption>();
        //         storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING);
        storeOptions.add(MapResourceOptions.EStoreMapOption.AUTOCOMMIT);
        storeOptions.add(PersistentResourceOptions.EStoreOption.ESTRUCUTRALFEATURE_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.IS_SET_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.SIZE_CACHING);
        loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions);
        resource.load(loadOpts);
        {
            Runtime.getRuntime().gc();
            long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}",
                    MessageUtil.byteCountToDisplaySize(initialUsedMemory)));
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            Set<TextElement> list = ASE2015JavaQueries.getCommentsTagContent(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)));
            Runtime.getRuntime().gc();
            long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory)));
            LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));
        }

        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.ase2015.NeoEMFMapQueryGrabats09.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  w w. j  a v  a2s.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(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

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

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

        Class<?> inClazz = NeoEMFMapQueryGrabats09.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>();

        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());
            }
        }
        // Add the LoadedObjectCounter store
        List<StoreOption> storeOptions = new ArrayList<StoreOption>();
        //         storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING);
        storeOptions.add(MapResourceOptions.EStoreMapOption.AUTOCOMMIT);
        storeOptions.add(PersistentResourceOptions.EStoreOption.ESTRUCUTRALFEATURE_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.IS_SET_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.SIZE_CACHING);
        loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions);
        resource.load(loadOpts);
        {
            Runtime.getRuntime().gc();
            long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}",
                    MessageUtil.byteCountToDisplaySize(initialUsedMemory)));
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<ClassDeclaration> list = ASE2015JavaQueries.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)));
            Runtime.getRuntime().gc();
            long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory)));
            LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));
        }

        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.ase2015.NeoEMFMapQueryInvisibleMethodDeclarations.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 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);

    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(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

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

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

        Class<?> inClazz = NeoEMFMapQueryInvisibleMethodDeclarations.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>();

        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());
            }
        }
        // Add the LoadedObjectCounter store
        List<StoreOption> storeOptions = new ArrayList<StoreOption>();
        //         storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING);
        storeOptions.add(MapResourceOptions.EStoreMapOption.AUTOCOMMIT);
        storeOptions.add(PersistentResourceOptions.EStoreOption.ESTRUCUTRALFEATURE_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.IS_SET_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.SIZE_CACHING);
        loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions);
        resource.load(loadOpts);
        {
            Runtime.getRuntime().gc();
            long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}",
                    MessageUtil.byteCountToDisplaySize(initialUsedMemory)));
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<MethodDeclaration> list = ASE2015JavaQueries.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)));
            Runtime.getRuntime().gc();
            long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory)));
            LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));
        }

        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.ase2015.NeoEMFMapQueryThrownExceptions.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 va 2  s.co 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(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

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

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

        Class<?> inClazz = NeoEMFMapQueryThrownExceptions.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>();

        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());
            }
        }
        // Add the LoadedObjectCounter store
        List<StoreOption> storeOptions = new ArrayList<StoreOption>();
        //         storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING);
        storeOptions.add(MapResourceOptions.EStoreMapOption.AUTOCOMMIT);
        storeOptions.add(PersistentResourceOptions.EStoreOption.ESTRUCUTRALFEATURE_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.IS_SET_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.SIZE_CACHING);
        loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions);
        resource.load(loadOpts);
        {
            Runtime.getRuntime().gc();
            long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}",
                    MessageUtil.byteCountToDisplaySize(initialUsedMemory)));
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<TypeAccess> list = ASE2015JavaQueries.getThrownExceptions(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)));
            Runtime.getRuntime().gc();
            long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory)));
            LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));
        }

        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.ase2015.NeoEMFMapQuerySpecificInvisibleMethodDeclarations.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 a2  s  .co 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(NeoMapURI.NEO_MAP_SCHEME,
                new MapPersistenceBackendFactory());

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

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

        Class<?> inClazz = NeoEMFMapQuerySpecificInvisibleMethodDeclarations.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>();

        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());
            }
        }
        // Add the LoadedObjectCounter store
        List<StoreOption> storeOptions = new ArrayList<StoreOption>();
        //         storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING);
        storeOptions.add(MapResourceOptions.EStoreMapOption.AUTOCOMMIT);
        storeOptions.add(PersistentResourceOptions.EStoreOption.ESTRUCUTRALFEATURE_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.IS_SET_CACHING);
        storeOptions.add(PersistentResourceOptions.EStoreOption.SIZE_CACHING);
        loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions);
        resource.load(loadOpts);
        {
            Runtime.getRuntime().gc();
            long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}",
                    MessageUtil.byteCountToDisplaySize(initialUsedMemory)));
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            EList<MethodDeclaration> list = ASE2015JavaQueries.getSpecificInvisibleMethodDeclarations(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)));
            Runtime.getRuntime().gc();
            long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory)));
            LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));
        }

        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.ase2015.NeoEMFGraphQueryGetBranchStatements.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  a v 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 = NeoEMFGraphQueryGetBranchStatements.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());
            }
        }
        // Add the LoadedObjectCounter store
        List<StoreOption> storeOptions = new ArrayList<StoreOption>();
        //         storeOptions.add(PersistentResourceOptions.EStoreOption.LOADED_OBJECT_COUNTER_LOGGING);
        storeOptions.add(BlueprintsResourceOptions.EStoreGraphOption.AUTOCOMMIT);
        loadOpts.put(PersistentResourceOptions.STORE_OPTIONS, storeOptions);
        resource.load(loadOpts);
        {
            Runtime.getRuntime().gc();
            long initialUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory before query: {0}",
                    MessageUtil.byteCountToDisplaySize(initialUsedMemory)));
            LOG.log(Level.INFO, "Start query");
            long begin = System.currentTimeMillis();
            Set<TextElement> list = ASE2015JavaQueries.getCommentsTagContent(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)));
            Runtime.getRuntime().gc();
            long finalUsedMemory = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
            LOG.log(Level.INFO, MessageFormat.format("Used memory after query: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory)));
            LOG.log(Level.INFO, MessageFormat.format("Memory use increase: {0}",
                    MessageUtil.byteCountToDisplaySize(finalUsedMemory - initialUsedMemory)));
        }

        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.google.api.codegen.CodeGeneratorTool.java

public static void main(String[] args) throws Exception {
    Options options = new Options();
    options.addOption("h", "help", false, "show usage");
    options.addOption(Option.builder().longOpt("descriptor_set")
            .desc("The descriptor set representing the compiled input protos.").hasArg()
            .argName("DESCRIPTOR-SET").required(true).build());
    options.addOption(//from w w  w.ja  va2s  . co m
            Option.builder().longOpt("service_yaml").desc("The service YAML configuration file or files.")
                    .hasArg().argName("SERVICE-YAML").required(true).build());
    options.addOption(Option.builder().longOpt("gapic_yaml").desc("The GAPIC YAML configuration file or files.")
            .hasArg().argName("GAPIC-YAML").required(true).build());
    options.addOption(Option.builder().longOpt("package_yaml")
            .desc("The package metadata YAML configuration file.").hasArg().argName("PACKAGE-YAML").build());
    options.addOption(Option.builder("o").longOpt("output")
            .desc("The directory in which to output the generated client library.").hasArg()
            .argName("OUTPUT-DIRECTORY").build());
    options.addOption(Option.builder().longOpt("enabled_artifacts")
            .desc("Optional. Artifacts enabled for the generator. "
                    + "Currently supports 'surface' and 'test'.")
            .hasArg().argName("ENABLED_ARTIFACTS").required(false).build());

    CommandLine cl = (new DefaultParser()).parse(options, args);
    if (cl.hasOption("help")) {
        HelpFormatter formater = new HelpFormatter();
        formater.printHelp("CodeGeneratorTool", options);
    }

    int exitCode = generate(cl.getOptionValue("descriptor_set"), cl.getOptionValues("service_yaml"),
            cl.getOptionValues("gapic_yaml"), cl.getOptionValue("package_yaml"),
            cl.getOptionValue("output", ""), cl.getOptionValues("enabled_artifacts"));
    System.exit(exitCode);
}

From source file:edu.msu.cme.rdp.probematch.cli.PrimerMatch.java

public static void main(String[] args) throws Exception {

    PrintStream out = new PrintStream(System.out);
    int maxDist = Integer.MAX_VALUE;

    try {//from  www  . jav a2 s  . c o  m
        CommandLine line = new PosixParser().parse(options, args);
        if (line.hasOption("outFile")) {
            out = new PrintStream(new File(line.getOptionValue("outFile")));
        }
        if (line.hasOption("maxDist")) {
            maxDist = Integer.valueOf(line.getOptionValue("maxDist"));
        }
        args = line.getArgs();

        if (args.length != 2) {
            throw new Exception("Unexpected number of command line arguments");
        }
    } catch (Exception e) {
        System.err.println("Error: " + e.getMessage());
        new HelpFormatter().printHelp("PrimerMatch <primer_list | primer_file> <seq_file>", options);
        return;
    }

    List<PatternBitMask64> primers = new ArrayList();
    if (new File(args[0]).exists()) {
        File primerFile = new File(args[0]);
        SequenceFormat seqformat = SeqUtils.guessFileFormat(primerFile);

        if (seqformat.equals(SequenceFormat.FASTA)) {
            SequenceReader reader = new SequenceReader(primerFile);
            Sequence seq;

            while ((seq = reader.readNextSequence()) != null) {
                primers.add(new PatternBitMask64(seq.getSeqString(), true, seq.getSeqName()));
            }
            reader.close();
        } else {
            BufferedReader reader = new BufferedReader(new FileReader(args[0]));
            String line;

            while ((line = reader.readLine()) != null) {
                line = line.trim();
                if (!line.equals("")) {
                    primers.add(new PatternBitMask64(line, true));
                }
            }
            reader.close();
        }
    } else {
        for (String primer : args[0].split(",")) {
            primers.add(new PatternBitMask64(primer, true));
        }
    }

    SeqReader seqReader = new SequenceReader(new File(args[1]));
    Sequence seq;
    String primerRegion;

    out.println("#seqname\tdesc\tprimer_index\tprimer_name\tposition\tmismatches\tseq_primer_region");
    while ((seq = seqReader.readNextSequence()) != null) {
        for (int index = 0; index < primers.size(); index++) {
            PatternBitMask64 primer = primers.get(index);
            BitVector64Result results = BitVector64.process(seq.getSeqString().toCharArray(), primer, maxDist);

            for (BitVector64Match result : results.getResults()) {
                primerRegion = seq.getSeqString().substring(
                        Math.max(0, result.getPosition() - primer.getPatternLength()), result.getPosition());

                if (result.getPosition() < primer.getPatternLength()) {
                    for (int pad = result.getPosition(); pad < primer.getPatternLength(); pad++) {
                        primerRegion = "x" + primerRegion;
                    }
                }

                out.println(seq.getSeqName() + "\t" + seq.getDesc() + "\t" + (index + 1) + "\t"
                        + primer.getPrimerName() + "\t" + result.getPosition() + "\t" + result.getScore() + "\t"
                        + primerRegion);
            }
        }
    }
    out.close();
    seqReader.close();
}

From source file:com.nextdoor.bender.S3SnsNotifier.java

public static void main(String[] args) throws ParseException, InterruptedException, IOException {
    formatter = DateTimeFormat.forPattern("yyyy-MM-dd'T'HH:mm:ss.SSS'Z'").withZoneUTC();

    /*/*from   w  w  w .ja  v a 2  s  .  c o m*/
     * Parse cli arguments
     */
    Options options = new Options();
    options.addOption(Option.builder().longOpt("bucket").hasArg().required()
            .desc("Name of S3 bucket to list s3 objects from").build());
    options.addOption(Option.builder().longOpt("key-file").hasArg().required()
            .desc("Local file of S3 keys to process").build());
    options.addOption(
            Option.builder().longOpt("sns-arn").hasArg().required().desc("SNS arn to publish to").build());
    options.addOption(Option.builder().longOpt("throttle-ms").hasArg()
            .desc("Amount of ms to wait between publishing to SNS").build());
    options.addOption(Option.builder().longOpt("processed-file").hasArg()
            .desc("Local file to use to store procssed S3 object names").build());
    options.addOption(Option.builder().longOpt("skip-processed").hasArg(false)
            .desc("Whether to skip S3 objects that have been processed").build());
    options.addOption(
            Option.builder().longOpt("dry-run").hasArg(false).desc("If set do not publish to SNS").build());

    CommandLineParser parser = new DefaultParser();
    CommandLine cmd = parser.parse(options, args);

    String bucket = cmd.getOptionValue("bucket");
    String keyFile = cmd.getOptionValue("key-file");
    String snsArn = cmd.getOptionValue("sns-arn");
    String processedFile = cmd.getOptionValue("processed-file", null);
    boolean skipProcessed = cmd.hasOption("skip-processed");
    dryRun = cmd.hasOption("dry-run");
    long throttle = Long.parseLong(cmd.getOptionValue("throttle-ms", "-1"));

    if (processedFile != null) {
        File file = new File(processedFile);

        if (!file.exists()) {
            logger.debug("creating local file to store processed s3 object names: " + processedFile);
            file.createNewFile();
        }
    }

    /*
     * Import S3 keys that have been processed
     */
    if (skipProcessed && processedFile != null) {
        try (BufferedReader br = new BufferedReader(new FileReader(processedFile))) {
            String line;
            while ((line = br.readLine()) != null) {
                alreadyPublished.add(line.trim());
            }
        }
    }

    /*
     * Setup writer for file containing processed S3 keys
     */
    FileWriter fw = null;
    BufferedWriter bw = null;
    if (processedFile != null) {
        fw = new FileWriter(processedFile, true);
        bw = new BufferedWriter(fw);
    }

    /*
     * Create clients
     */
    AmazonS3Client s3Client = new AmazonS3Client();
    AmazonSNSClient snsClient = new AmazonSNSClient();

    /*
     * Get S3 object list
     */
    try (BufferedReader br = new BufferedReader(new FileReader(keyFile))) {
        String line;
        while ((line = br.readLine()) != null) {
            String key = line.trim();

            if (alreadyPublished.contains(key)) {
                logger.info("skipping " + key);
            }

            ObjectMetadata om = s3Client.getObjectMetadata(bucket, key);

            S3EventNotification s3Notification = getS3Notification(key, bucket, om.getContentLength());

            String json = s3Notification.toJson();

            /*
             * Publish to SNS
             */
            if (publish(snsArn, json, snsClient, key) && processedFile != null) {
                bw.write(key + "\n");
                bw.flush();
            }

            if (throttle != -1) {
                Thread.sleep(throttle);
            }

        }
    }

    if (processedFile != null) {
        bw.close();
        fw.close();
    }
}