Example usage for org.apache.commons.cli DefaultParser DefaultParser

List of usage examples for org.apache.commons.cli DefaultParser DefaultParser

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

Prototype

DefaultParser

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Usage

From source file:CTmousetrack.java

public static void main(String[] args) {

    String outLoc = new String("." + File.separator + "CTdata"); // Location of the base output data folder; only used when writing out CT data to a local folder
    String srcName = "CTmousetrack"; // name of the output CT source
    long blockPts = 10; // points per block flush
    long sampInterval = 10; // time between sampling updates, msec
    double trimTime = 0.0; // amount of data to keep (trim time), sec
    boolean debug = false; // turn on debug?

    // Specify the CT output connection
    CTWriteMode writeMode = CTWriteMode.LOCAL; // The selected mode for writing out CT data
    String serverHost = ""; // Server (FTP or HTTP/S) host:port
    String serverUser = ""; // Server (FTP or HTTPS) username
    String serverPassword = ""; // Server (FTP or HTTPS) password

    // For UDP output mode
    DatagramSocket udpServerSocket = null;
    InetAddress udpServerAddress = null;
    String udpHost = "";
    int udpPort = -1;

    // Concatenate all of the CTWriteMode types
    String possibleWriteModes = "";
    for (CTWriteMode wm : CTWriteMode.values()) {
        possibleWriteModes = possibleWriteModes + ", " + wm.name();
    }//from ww  w.j  a va 2 s  .com
    // Remove ", " from start of string
    possibleWriteModes = possibleWriteModes.substring(2);

    //
    // Argument processing using Apache Commons CLI
    //
    // 1. Setup command line options
    Options options = new Options();
    options.addOption("h", "help", false, "Print this message.");
    options.addOption(Option.builder("o").argName("base output dir").hasArg().desc(
            "Base output directory when writing data to local folder (i.e., this is the location of CTdata folder); default = \""
                    + outLoc + "\".")
            .build());
    options.addOption(Option.builder("s").argName("source name").hasArg()
            .desc("Name of source to write data to; default = \"" + srcName + "\".").build());
    options.addOption(Option.builder("b").argName("points per block").hasArg()
            .desc("Number of points per block; UDP output mode will use 1 point/block; default = "
                    + Long.toString(blockPts) + ".")
            .build());
    options.addOption(Option.builder("dt").argName("samp interval msec").hasArg()
            .desc("Sampling period in msec; default = " + Long.toString(sampInterval) + ".").build());
    options.addOption(Option.builder("t").argName("trim time sec").hasArg().desc(
            "Trim (ring-buffer loop) time (sec); this is only used when writing data to local folder; specify 0 for indefinite; default = "
                    + Double.toString(trimTime) + ".")
            .build());
    options.addOption(
            Option.builder("w").argName("write mode").hasArg()
                    .desc("Type of write connection; one of " + possibleWriteModes
                            + "; all but UDP mode write out to CT; default = " + writeMode.name() + ".")
                    .build());
    options.addOption(Option.builder("host").argName("host[:port]").hasArg()
            .desc("Host:port when writing via FTP, HTTP, HTTPS, UDP.").build());
    options.addOption(Option.builder("u").argName("username,password").hasArg()
            .desc("Comma-delimited username and password when writing to CT via FTP or HTTPS.").build());
    options.addOption("x", "debug", false, "Enable CloudTurbine debug output.");

    // 2. Parse command line options
    CommandLineParser parser = new DefaultParser();
    CommandLine line = null;
    try {
        line = parser.parse(options, args);
    } catch (ParseException exp) { // oops, something went wrong
        System.err.println("Command line argument parsing failed: " + exp.getMessage());
        return;
    }

    // 3. Retrieve the command line values
    if (line.hasOption("help")) { // Display help message and quit
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp("CTmousetrack", "", options,
                "NOTE: UDP output is a special non-CT output mode where single x,y points are sent via UDP to the specified host:port.");
        return;
    }

    outLoc = line.getOptionValue("o", outLoc);
    if (!outLoc.endsWith("\\") && !outLoc.endsWith("/")) {
        outLoc = outLoc + File.separator;
    }
    // Make sure the base output folder location ends in "CTdata"
    if (!outLoc.endsWith("CTdata\\") && !outLoc.endsWith("CTdata/")) {
        outLoc = outLoc + "CTdata" + File.separator;
    }

    srcName = line.getOptionValue("s", srcName);

    blockPts = Long.parseLong(line.getOptionValue("b", Long.toString(blockPts)));

    sampInterval = Long.parseLong(line.getOptionValue("dt", Long.toString(sampInterval)));

    trimTime = Double.parseDouble(line.getOptionValue("t", Double.toString(trimTime)));

    // Type of output connection
    String writeModeStr = line.getOptionValue("w", writeMode.name());
    boolean bMatch = false;
    for (CTWriteMode wm : CTWriteMode.values()) {
        if (wm.name().toLowerCase().equals(writeModeStr.toLowerCase())) {
            writeMode = wm;
            bMatch = true;
        }
    }
    if (!bMatch) {
        System.err.println("Unrecognized write mode, \"" + writeModeStr + "\"; write mode must be one of "
                + possibleWriteModes);
        System.exit(0);
    }
    if (writeMode != CTWriteMode.LOCAL) {
        // User must have specified the host
        // If FTP or HTTPS, they may also specify username/password
        serverHost = line.getOptionValue("host", serverHost);
        if (serverHost.isEmpty()) {
            System.err.println(
                    "When using write mode \"" + writeModeStr + "\", you must specify the server host.");
            System.exit(0);
        }
        if (writeMode == CTWriteMode.UDP) {
            // Force blockPts to be 1
            blockPts = 1;
            // User must have specified both host and port
            int colonIdx = serverHost.indexOf(':');
            if ((colonIdx == -1) || (colonIdx >= serverHost.length() - 1)) {
                System.err.println(
                        "For UDP output mode, both the host and port (<host>:<port>)) must be specified.");
                System.exit(0);
            }
            udpHost = serverHost.substring(0, colonIdx);
            String udpPortStr = serverHost.substring(colonIdx + 1);
            try {
                udpPort = Integer.parseInt(udpPortStr);
            } catch (NumberFormatException nfe) {
                System.err.println("The UDP port must be a positive integer.");
                System.exit(0);
            }
        }
        if ((writeMode == CTWriteMode.FTP) || (writeMode == CTWriteMode.HTTPS)) {
            String userpassStr = line.getOptionValue("u", "");
            if (!userpassStr.isEmpty()) {
                // This string should be comma-delimited username and password
                String[] userpassCSV = userpassStr.split(",");
                if (userpassCSV.length != 2) {
                    System.err.println("When specifying a username and password for write mode \""
                            + writeModeStr + "\", separate the username and password by a comma.");
                    System.exit(0);
                }
                serverUser = userpassCSV[0];
                serverPassword = userpassCSV[1];
            }
        }
    }

    debug = line.hasOption("debug");

    System.err.println("CTmousetrack parameters:");
    System.err.println("\toutput mode = " + writeMode.name());
    if (writeMode == CTWriteMode.UDP) {
        System.err.println("\twrite to " + udpHost + ":" + udpPort);
    } else {
        System.err.println("\tsource = " + srcName);
        System.err.println("\ttrim time = " + trimTime + " sec");
    }
    System.err.println("\tpoints per block = " + blockPts);
    System.err.println("\tsample interval = " + sampInterval + " msec");

    try {
        //
        // Setup CTwriter or UDP output
        //
        CTwriter ctw = null;
        CTinfo.setDebug(debug);
        if (writeMode == CTWriteMode.LOCAL) {
            ctw = new CTwriter(outLoc + srcName, trimTime);
            System.err.println("\tdata will be written to local folder \"" + outLoc + "\"");
        } else if (writeMode == CTWriteMode.FTP) {
            CTftp ctftp = new CTftp(srcName);
            try {
                ctftp.login(serverHost, serverUser, serverPassword);
            } catch (Exception e) {
                throw new IOException(
                        new String("Error logging into FTP server \"" + serverHost + "\":\n" + e.getMessage()));
            }
            ctw = ctftp; // upcast to CTWriter
            System.err.println("\tdata will be written to FTP server at " + serverHost);
        } else if (writeMode == CTWriteMode.HTTP) {
            // Don't send username/pw in HTTP mode since they will be unencrypted
            CThttp cthttp = new CThttp(srcName, "http://" + serverHost);
            ctw = cthttp; // upcast to CTWriter
            System.err.println("\tdata will be written to HTTP server at " + serverHost);
        } else if (writeMode == CTWriteMode.HTTPS) {
            CThttp cthttp = new CThttp(srcName, "https://" + serverHost);
            // Username/pw are optional for HTTPS mode; only use them if username is not empty
            if (!serverUser.isEmpty()) {
                try {
                    cthttp.login(serverUser, serverPassword);
                } catch (Exception e) {
                    throw new IOException(new String(
                            "Error logging into HTTP server \"" + serverHost + "\":\n" + e.getMessage()));
                }
            }
            ctw = cthttp; // upcast to CTWriter
            System.err.println("\tdata will be written to HTTPS server at " + serverHost);
        } else if (writeMode == CTWriteMode.UDP) {
            try {
                udpServerSocket = new DatagramSocket();
            } catch (SocketException se) {
                System.err.println("Error creating socket for UDP:\n" + se);
                System.exit(0);
            }
            try {
                udpServerAddress = InetAddress.getByName(udpHost);
            } catch (UnknownHostException uhe) {
                System.err.println("Error getting UDP server host address:\n" + uhe);
                System.exit(0);
            }
        }
        if (writeMode != CTWriteMode.UDP) {
            ctw.setBlockMode(blockPts > 1, blockPts > 1);
            ctw.autoFlush(0); // no autoflush
            ctw.autoSegment(1000);
        }

        // screen dims
        Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
        double width = screenSize.getWidth();
        double height = screenSize.getHeight();

        // use Map for consolidated putData
        Map<String, Object> cmap = new LinkedHashMap<String, Object>();

        // loop and write some output
        for (int i = 0; i < 1000000; i++) { // go until killed
            long currentTime = System.currentTimeMillis();
            Point mousePos = MouseInfo.getPointerInfo().getLocation();
            float x_pt = (float) (mousePos.getX() / width); // normalize
            float y_pt = (float) ((height - mousePos.getY()) / height); // flip Y (so bottom=0)
            if (writeMode != CTWriteMode.UDP) {
                // CT output mode
                ctw.setTime(currentTime);
                cmap.clear();
                cmap.put("x", x_pt);
                cmap.put("y", y_pt);
                ctw.putData(cmap);
                if (((i + 1) % blockPts) == 0) {
                    ctw.flush();
                    System.err.print(".");
                }
            } else {
                // UDP output mode
                // We force blockPts to be 1 for UDP output mode, i.e. we "flush" the data every time
                // Write the following data (21 bytes total):
                //     header = "MOUSE", 5 bytes
                //     current time, long, 8 bytes
                //     2 floats (x,y) 4 bytes each, 8 bytes
                int len = 21;
                ByteBuffer bb = ByteBuffer.allocate(len);
                String headerStr = "MOUSE";
                bb.put(headerStr.getBytes("UTF-8"));
                bb.putLong(currentTime);
                bb.putFloat(x_pt);
                bb.putFloat(y_pt);
                // Might be able to use the following, but not sure:
                //     byte[] sendData = bb.array();
                byte[] sendData = new byte[len];
                bb.position(0);
                bb.get(sendData, 0, len);
                DatagramPacket sendPacket = new DatagramPacket(sendData, sendData.length, udpServerAddress,
                        udpPort);
                try {
                    udpServerSocket.send(sendPacket);
                } catch (IOException e) {
                    System.err.println("Test server caught exception trying to send data to UDP client:\n" + e);
                }
                System.err.print(".");
            }
            try {
                Thread.sleep(sampInterval);
            } catch (Exception e) {
            }
            ;
        }
        if (writeMode != CTWriteMode.UDP) {
            ctw.flush(); // wrap up
        }
    } catch (Exception e) {
        System.err.println("CTmousetrack exception: " + e);
        e.printStackTrace();
    }
}

From source file:com.twitter.heron.scheduler.RuntimeManagerMain.java

public static void main(String[] args) throws ClassNotFoundException, IllegalAccessException,
        InstantiationException, IOException, ParseException {

    Options options = constructOptions();
    Options helpOptions = constructHelpOptions();
    CommandLineParser parser = new DefaultParser();
    // parse the help options first.
    CommandLine cmd = parser.parse(helpOptions, args, true);

    if (cmd.hasOption("h")) {
        usage(options);//from  w  w  w. ja va  2  s  .co m
        return;
    }

    try {
        // Now parse the required options
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        usage(options);
        throw new RuntimeException("Error parsing command line options: ", e);
    }

    Boolean verbose = false;
    Level logLevel = Level.INFO;
    if (cmd.hasOption("v")) {
        logLevel = Level.ALL;
        verbose = true;
    }

    // init log
    LoggingHelper.loggerInit(logLevel, false);

    String cluster = cmd.getOptionValue("cluster");
    String role = cmd.getOptionValue("role");
    String environ = cmd.getOptionValue("environment");
    String heronHome = cmd.getOptionValue("heron_home");
    String configPath = cmd.getOptionValue("config_path");
    String overrideConfigFile = cmd.getOptionValue("override_config_file");
    String releaseFile = cmd.getOptionValue("release_file");
    String topologyName = cmd.getOptionValue("topology_name");
    String commandOption = cmd.getOptionValue("command");

    // Optional argument in the case of restart
    // TODO(karthik): convert into CLI
    String containerId = Integer.toString(-1);
    if (cmd.hasOption("container_id")) {
        containerId = cmd.getOptionValue("container_id");
    }

    Command command = Command.makeCommand(commandOption);

    // first load the defaults, then the config from files to override it
    Config.Builder defaultsConfig = Config.newBuilder().putAll(ClusterDefaults.getDefaults())
            .putAll(ClusterConfig.loadConfig(heronHome, configPath, releaseFile));

    // add config parameters from the command line
    Config.Builder commandLineConfig = Config.newBuilder().put(Keys.cluster(), cluster).put(Keys.role(), role)
            .put(Keys.environ(), environ).put(Keys.verbose(), verbose)
            .put(Keys.topologyContainerId(), containerId);

    Config.Builder topologyConfig = Config.newBuilder().put(Keys.topologyName(), topologyName);

    Config.Builder overrideConfig = Config.newBuilder()
            .putAll(ClusterConfig.loadOverrideConfig(overrideConfigFile));

    // build the final config by expanding all the variables
    Config config = Config
            .expand(Config.newBuilder().putAll(defaultsConfig.build()).putAll(overrideConfig.build())
                    .putAll(commandLineConfig.build()).putAll(topologyConfig.build()).build());

    LOG.fine("Static config loaded successfully ");
    LOG.fine(config.toString());

    // Create a new instance of RuntimeManagerMain
    RuntimeManagerMain runtimeManagerMain = new RuntimeManagerMain(config, command);
    boolean isSuccessful = runtimeManagerMain.manageTopology();

    // Log the result and exit
    if (!isSuccessful) {
        throw new RuntimeException(String.format("Failed to %s topology %s", command, topologyName));
    } else {
        LOG.log(Level.FINE, "Topology {0} {1} successfully", new Object[] { topologyName, command });
    }
}

From source file:com.act.lcms.v2.TraceIndexAnalyzer.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*ww w . j  a v a  2  s .  c  o m*/
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HELP_FORMATTER.printHelp(TraceIndexExtractor.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(TraceIndexExtractor.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
    }

    File rocksDBFile = new File(cl.getOptionValue(OPTION_INDEX_PATH));
    if (!rocksDBFile.exists()) {
        System.err.format("Index file at %s does not exist, nothing to analyze", rocksDBFile.getAbsolutePath());
        HELP_FORMATTER.printHelp(TraceIndexExtractor.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    LOGGER.info("Starting analysis");

    TraceIndexAnalyzer analyzer = new TraceIndexAnalyzer();
    analyzer.runExtraction(rocksDBFile, new File(cl.getOptionValue(OPTION_OUTPUT_PATH)));

    LOGGER.info("Done");
}

From source file:jena.RuleMap.java

/**
 * General command line utility to process one RDF file into another
 * by application of a set of forward chaining rules. 
 * <pre>/*from   w  ww .j a va 2 s. co m*/
 * Usage:  RuleMap [-il inlang] [-ol outlang] -d infile rulefile
 * </pre>
 */
public static void main(String[] args) {
    try {

        // Parse the command line
        String usage = "Usage:  RuleMap [-il inlang] [-ol outlang] [-d] rulefile infile (- for stdin)";
        final CommandLineParser parser = new DefaultParser();
        Options options = new Options().addOption("il", "inputLang", true, "input language")
                .addOption("ol", "outputLang", true, "output language").addOption("d", "Deductions only?");
        CommandLine cl = parser.parse(options, args);
        final List<String> filenameArgs = cl.getArgList();
        if (filenameArgs.size() != 2) {
            System.err.println(usage);
            System.exit(1);
        }

        String inLang = cl.getOptionValue("inputLang");
        String fname = filenameArgs.get(1);
        Model inModel = null;
        if (fname.equals("-")) {
            inModel = ModelFactory.createDefaultModel();
            inModel.read(System.in, null, inLang);
        } else {
            inModel = FileManager.get().loadModel(fname, inLang);
        }

        String outLang = cl.hasOption("outputLang") ? cl.getOptionValue("outputLang") : "N3";

        boolean deductionsOnly = cl.hasOption('d');

        // Fetch the rule set and create the reasoner
        BuiltinRegistry.theRegistry.register(new Deduce());
        Map<String, String> prefixes = new HashMap<>();
        List<Rule> rules = loadRules(filenameArgs.get(0), prefixes);
        Reasoner reasoner = new GenericRuleReasoner(rules);

        // Process
        InfModel infModel = ModelFactory.createInfModel(reasoner, inModel);
        infModel.prepare();
        infModel.setNsPrefixes(prefixes);

        // Output
        try (PrintWriter writer = new PrintWriter(System.out)) {
            if (deductionsOnly) {
                Model deductions = infModel.getDeductionsModel();
                deductions.setNsPrefixes(prefixes);
                deductions.setNsPrefixes(inModel);
                deductions.write(writer, outLang);
            } else {
                infModel.write(writer, outLang);
            }
        }
    } catch (Throwable t) {
        System.err.println("An error occured: \n" + t);
        t.printStackTrace();
    }
}

From source file:edu.ifpb.pos.restletclient.CommandLineApp.java

public static void main(String[] args) {
    try {//  w  w  w  .  j a  v a 2s  .  c  o  m
        CommandLineParser parser = new DefaultParser();
        CommandLine line = parser.parse(getOp(), args);
        execute(line);
    } catch (ParseException ex) {
        System.out.println("ERROR: " + ex.getMessage());
    } catch (IOException ex) {
        Logger.getLogger(CommandLineApp.class.getName()).log(Level.SEVERE, null, ex);
    }

}

From source file:com.maxpowered.amazon.advertising.api.app.App.java

public static void main(final String... args)
        throws FileNotFoundException, IOException, JAXBException, XMLStreamException, InterruptedException {
    try (ClassPathXmlApplicationContext ctx = new ClassPathXmlApplicationContext("application-context.xml")) {
        /*/*w  w  w.ja va2s  . c  o m*/
         * Get default options based on spring configs
         */
        final String inputDefault = getOptionDefaultBasedOnSpringProperty(ctx, PROPERTY_APP_INPUT, STD_IN_STR);
        final String processedDefault = inputDefault.equals(STD_IN_STR) ? DEFAULT_PROCESSED_FILE_BASE
                : inputDefault + PROCESSED_EXT;
        final String outputDefault = getOptionDefaultBasedOnSpringProperty(ctx, PROPERTY_APP_OUTPUT,
                STD_OUT_STR);
        int throttleDefault = Integer.valueOf(getOptionDefaultBasedOnSpringProperty(ctx, PROPERTY_APP_THROTTLE,
                String.valueOf(DEFAULT_APP_THROTTLE)));
        // Maximum of 25000 requests per hour
        throttleDefault = Math.min(throttleDefault, MAX_APP_THROTTLE);

        /*
         * Get options from the CLI args
         */
        final Options options = new Options();

        options.addOption("h", false, "Display this help.");
        options.addOption("i", true, "Set the file to read ASINs from. " + DEFAULT_STR + inputDefault);
        options.addOption("p", true, "Set the file to store processed ASINs in. " + DEFAULT_STR
                + processedDefault + " or '" + PROCESSED_EXT + "' appended to the input file name.");
        // Add a note that the output depends on the configured processors. If none are configured, it defaults to a
        // std.out processor
        options.addOption("o", true,
                "Set the file to write fetched info xml to via FileProcessor. " + DEFAULT_STR + outputDefault);
        options.addOption("1", false, "Override output file and always output fetched info xml to std.out.");
        options.addOption("t", true, "Set the requests per hour throttle (max of " + MAX_APP_THROTTLE + "). "
                + DEFAULT_STR + throttleDefault);

        final CommandLineParser parser = new DefaultParser();
        CommandLine cmd = null;
        boolean needsHelp = false;

        try {
            cmd = parser.parse(options, args);
        } catch (final ParseException e) {
            needsHelp = true;
        }

        if (cmd.hasOption("h") || needsHelp) {
            final HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("App", options);
            return;
        }

        // Get throttle rate
        final int throttle = Math.min(
                cmd.hasOption("t") ? Integer.valueOf(cmd.getOptionValue("t")) : throttleDefault,
                MAX_APP_THROTTLE);
        LOG.debug("Throttle (default {}) is {} requests per hour", throttleDefault, throttle);
        // We don't want to hit our limit, just under an hour worth of milliseconds
        final int requestWait = 3540000 / throttle;

        // Get input stream
        String input;
        if (cmd.hasOption("i")) {
            input = cmd.getOptionValue("i");
        } else {
            input = inputDefault;
        }
        LOG.debug("Input name (default {}) is {}", inputDefault, input);

        // Get processed file
        String processed;
        if (cmd.hasOption("p")) {
            processed = cmd.getOptionValue("p");
        } else {
            processed = input + PROCESSED_EXT;
        }
        LOG.debug("Processed file name (default {}) is {}", processedDefault, processed);
        final File processedFile = new File(processed);
        processedFile.createNewFile();

        try (final InputStream inputStream = getInputStream(input)) {

            // Get output stream
            String output;
            if (cmd.hasOption("o")) {
                output = cmd.getOptionValue("o");
            } else {
                output = outputDefault;
            }
            if (cmd.hasOption("1")) {
                output = STD_OUT_STR;
            }
            LOG.debug("Output (default {}) name is {}", outputDefault, output);
            // Special logic to set the FileProcessor output
            if (output.equals(STD_OUT_STR)) {
                final FileProcessor fileProcessor = ctx.getBeanFactory().getBean(FileProcessor.class);
                fileProcessor.setOutputStream(System.out);
            } else if (!output.equals(outputDefault)) {
                final FileProcessor fileProcessor = ctx.getBeanFactory().getBean(FileProcessor.class);
                fileProcessor.setOutputFile(output);
            }

            // This could be easily configured through CLI or properties
            final List<String> responseGroups = Lists.newArrayList();
            for (final ResponseGroup responseGroup : new ResponseGroup[] { ResponseGroup.IMAGES,
                    ResponseGroup.ITEM_ATTRIBUTES }) {
                responseGroups.add(responseGroup.getResponseGroupName());
            }
            final String responseGroupString = Joiner.on(",").join(responseGroups);

            // Search the list of remaining ASINs
            final ProductFetcher fetcher = ctx.getBeanFactory().getBean(ProductFetcher.class);
            fetcher.setProcessedFile(processedFile);
            fetcher.setRequestWait(requestWait);
            fetcher.setInputStream(inputStream);
            fetcher.setResponseGroups(responseGroupString);

            // This ensures that statistics of processed asins should almost always get printed at the end
            Runtime.getRuntime().addShutdownHook(new Thread() {
                @Override
                public void run() {
                    fetcher.logStatistics();
                }
            });

            fetcher.fetchProductInformation();
        }
    }
}

From source file:com.act.analysis.surfactant.SurfactantLabeler.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());//from   w w w  . ja  v a  2 s  . c o  m
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        return;
    }

    File inputFile = new File(cl.getOptionValue(OPTION_INPUT_FILE));
    if (!inputFile.isFile()) {
        System.err.format("No input file at: %s\n", inputFile.getAbsolutePath());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    File outputFile = new File(cl.getOptionValue(OPTION_OUTPUT_FILE));
    if (outputFile.exists()) {
        System.err.format("WARNING: output file at %s already exists\n", outputFile.getAbsolutePath());
    }

    /* Sometimes the InChIs might not appear in the input file (like in regression results).  Instead a corpus of
     * names and InChIs can be specified in a separate file and looked up as molecules are read/visualized.  The join
     * field is the key on which the InChI for a given row in the input file is found. */
    File inchiSourceFile = null;
    if (cl.hasOption(OPTION_INCHI_SOURCE)) {
        inchiSourceFile = new File(cl.getOptionValue(OPTION_INCHI_SOURCE));
        boolean err = false;
        if (!inchiSourceFile.isFile()) {
            System.err.format("No inchi source file at: %s\n", inchiSourceFile.getAbsolutePath());
            err = true;
        }
        if (!cl.hasOption(OPTION_INCHI_SOURCE_JOIN_FIELD)) {
            System.err.format("Must specify a join field when using an inchi source file.\n");
            err = true;
        }
        if (err) {
            HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts,
                    null, true);
            System.exit(1);
        }
    }

    SurfactantLabeler surfactantLabeler = new SurfactantLabeler();
    surfactantLabeler.runAnalysis(cl.getOptionValue(OPTION_LICENSE_FILE), inputFile, outputFile,
            inchiSourceFile, cl.getOptionValue(OPTION_INCHI_SOURCE_JOIN_FIELD));
}

From source file:com.act.utils.parser.UniprotInterpreter.java

public static void main(String[] args)
        throws ParserConfigurationException, IOException, SAXException, CompoundNotFoundException {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*from w  w  w . j  ava  2 s.com*/
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        LOGGER.error("Argument parsing failed: %s", e.getMessage());
        HELP_FORMATTER.printHelp(UniprotInterpreter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(UniprotInterpreter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    File uniprotFile = new File(cl.getOptionValue(OPTION_UNIPROT_PATH));

    if (!uniprotFile.exists()) {
        String msg = "Uniprot file path is null";
        LOGGER.error(msg);
        throw new RuntimeException(msg);
    } else {
        UniprotInterpreter reader = new UniprotInterpreter(uniprotFile);
        reader.init();
    }
}

From source file:com.act.reachables.ConditionalReachabilityInterpreter.java

public static void main(String[] args) throws Exception {
    // Parse the command line options
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());//from ww  w .  ja v a2 s. com
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HELP_FORMATTER.printHelp(BingSearchRanker.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(BingSearchRanker.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
    }

    String inputPath = cl.getOptionValue(OPTION_INPUT_ACT_FILEPATH);
    String outputPath = cl.getOptionValue(OPTION_OUTPUT_FILEPATH);
    String dbName = cl.getOptionValue(OPTION_DB_NAME);

    LOGGER.info("Starting to deserialize reachables forest.");
    ActData.instance().deserialize(inputPath);
    ActData actData = ActData.instance();
    LOGGER.info("Finished deserializing reachables forest.");

    NoSQLAPI db = new NoSQLAPI(dbName, dbName);
    ConditionalReachabilityInterpreter conditionalReachabilityInterpreter = new ConditionalReachabilityInterpreter(
            actData, db);
    conditionalReachabilityInterpreter.run(outputPath);
}

From source file:com.act.biointerpretation.BiointerpretationDriver.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());//ww  w  . j ava2s  .c  om
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(ReactionDesalter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        return;
    }

    if (cl.hasOption(OPTION_CONFIGURATION_FILE)) {
        List<BiointerpretationStep> steps;
        File configFile = new File(cl.getOptionValue(OPTION_CONFIGURATION_FILE));
        if (!configFile.exists()) {
            String msg = String.format("Cannot find configuration file at %s", configFile.getAbsolutePath());
            LOGGER.error(msg);
            throw new RuntimeException(msg);
        }
        // Read the whole config file.
        try (InputStream is = new FileInputStream(configFile)) {
            steps = OBJECT_MAPPER.readValue(is, new TypeReference<List<BiointerpretationStep>>() {
            });
        } catch (IOException e) {
            LOGGER.error("Caught IO exception when attempting to read configuration file: %s", e.getMessage());
            throw e; // Crash after logging if the config file can't be read.
        }

        // Ask for explicit confirmation before dropping databases.
        LOGGER.info("Biointerpretation plan:");
        for (BiointerpretationStep step : steps) {
            crashIfInvalidDBName(step.getReadDBName());
            crashIfInvalidDBName(step.getWriteDBName());
            LOGGER.info("%s: %s -> %s", step.getOperation(), step.getReadDBName(), step.getWriteDBName());
        }
        LOGGER.warn("WARNING: each DB to be written will be dropped before the writing step commences");
        LOGGER.info("Proceed? [y/n]");
        String readLine;
        try (BufferedReader reader = new BufferedReader(new InputStreamReader(System.in))) {
            readLine = reader.readLine();
        }
        readLine.trim();
        if ("y".equalsIgnoreCase(readLine) || "yes".equalsIgnoreCase(readLine)) {
            LOGGER.info("Biointerpretation plan confirmed, commencing");
            for (BiointerpretationStep step : steps) {
                performOperation(step, true);
            }
            LOGGER.info("Biointerpretation plan completed");
        } else {
            LOGGER.info("Biointerpretation plan not confirmed, exiting");
        }
    } else if (cl.hasOption(OPTION_SINGLE_OPERATION)) {
        if (!cl.hasOption(OPTION_SINGLE_READ_DB) || !cl.hasOption(OPTION_SINGLE_WRITE_DB)) {
            String msg = "Must specify read and write DB names when performing a single operation";
            LOGGER.error(msg);
            throw new RuntimeException(msg);
        }
        BiointerpretationOperation operation;
        try {
            operation = BiointerpretationOperation.valueOf(cl.getOptionValue(OPTION_SINGLE_OPERATION));
        } catch (IllegalArgumentException e) {
            LOGGER.error("Caught IllegalArgumentException when trying to parse operation '%s': %s",
                    cl.getOptionValue(OPTION_SINGLE_OPERATION), e.getMessage());
            throw e; // Crash if we can't interpret the operation.
        }
        String readDB = crashIfInvalidDBName(cl.getOptionValue(OPTION_SINGLE_READ_DB));
        String writeDB = crashIfInvalidDBName(cl.getOptionValue(OPTION_SINGLE_WRITE_DB));

        performOperation(new BiointerpretationStep(operation, readDB, writeDB), false);
    } else {
        String msg = "Must specify either a config file or a single operation to perform.";
        LOGGER.error(msg);
        throw new RuntimeException(msg);
    }
}