Example usage for java.lang String endsWith

List of usage examples for java.lang String endsWith

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Introduction

In this page you can find the example usage for java.lang String endsWith.

Prototype

public boolean endsWith(String suffix)

Source Link

Document

Tests if this string ends with the specified suffix.

Usage

From source file:com.jswitch.reporte.controlador.JasperViewer2.java

/**
* @param args the command line arguments
*///from   ww w  .j  a  v  a2  s . c om
public static void main(String args[]) {
    String fileName = null;
    boolean isXMLFile = false;

    for (int i = 0; i < args.length; i++) {
        if (args[i].startsWith("-XML")) {
            isXMLFile = true;
        } else if (args[i].startsWith("-F")) {
            fileName = args[i].substring(2);
        } else {
            fileName = args[i];
        }
    }

    if (fileName == null) {
        usage();
        return;
    }

    if (!isXMLFile && fileName.endsWith(".jrpxml")) {
        isXMLFile = true;
    }

    try {
        viewReport(fileName, isXMLFile);
    } catch (JRException e) {
        if (log.isErrorEnabled()) {
            log.error("Error viewing report.", e);
        }
        System.exit(1);
    }
}

From source file:br.bireme.tb.URLS.java

public static void main(final String[] args) throws IOException {
    if (args.length != 1) {
        usage();//from  ww  w  .j  av a 2 s .c om
    }

    final String out = args[0].trim();
    final String outDir = (out.endsWith("/")) ? out : out + "/";
    final String LOG_DIR = "log";
    final File logDir = new File(LOG_DIR);
    if (!logDir.exists()) {
        if (!logDir.mkdir()) {
            throw new IOException("log directory [" + LOG_DIR + "] creation error");
        }
    }

    final Logger logger = Logger.getLogger(Logger.GLOBAL_LOGGER_NAME);
    final FileHandler fh = new FileHandler(getLogFileName(LOG_DIR), false);
    logger.addHandler(fh);

    final String URL = URLS.ROOT_URL;
    final TimeString time = new TimeString();

    time.start();
    generateFileStructure(URL, outDir + "celulasIDB");

    System.out.println("Total time: " + time.getTime());
}

From source file:HLA.java

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

    if (!isVersionOrHigher()) {
        System.err.println("JRE of 1.8+ is required to run Kourami. Exiting.");
        System.exit(1);//www  .j  av a  2 s  . c o  m
    }

    CommandLineParser parser = new DefaultParser();
    Options options = HLA.createOption();
    Options helponlyOpts = HLA.createHelpOption();
    String[] bams = null;
    CommandLine line = null;
    boolean exitRun = false;
    try {
        CommandLine helpcheck = new DefaultParser().parse(helponlyOpts, args, true);
        if (helpcheck.getOptions().length > 0)
            HLA.help(options);
        else {
            line = parser.parse(options, args);
            if (line.hasOption("h"))//help"))
                HLA.help(options);
            else {
                if (line.hasOption("a"))
                    HLA.TYPEADDITIONAL = true;

                HLA.OUTPREFIX = line.getOptionValue("o");//outfilePrefix");
                String tmploc = line.getOptionValue("d");//msaDirectory");
                HLA.MSAFILELOC = tmploc;
                if (tmploc.endsWith(File.separator))
                    HLA.MSAFILELOC = tmploc.substring(0, tmploc.length() - 1);
                if (!new File(HLA.MSAFILELOC).exists() || !new File(HLA.MSAFILELOC).isDirectory()) {
                    System.err.println("Given msaDirectory: " + HLA.MSAFILELOC
                            + "\t does NOT exist or is NOT a directory.");
                    exitRun = true;
                } else if (!new File(HLA.MSAFILELOC + File.separator + "hla_nom_g.txt").exists()) {
                    System.err.println("hla_nom_g.txt NOT FOUND in " + HLA.MSAFILELOC);
                    System.err
                            .println("Please download hla_nom_g.txt from the same IMGT Release as msa files.");
                    exitRun = true;
                }
            }
            bams = line.getArgs();

            if (bams.length < 1 || (bams.length == 1 && bams[bams.length - 1].equals("DEBUG1228")))
                throw new ParseException("At least 1 bam file is required. See Usage:");
            else {
                if (bams.length > 1 && bams[bams.length - 1].equals("DEBUG1228")) {
                    String[] tmpbams = new String[bams.length - 1];
                    for (int i = 0; i < bams.length - 1; i++)
                        tmpbams[i] = bams[i];
                    bams = tmpbams;
                    HLA.DEBUG = true;
                }

                for (String b : bams)
                    if (!new File(b).exists()) {
                        System.err
                                .println("Input bam : " + b + " DOES NOT exist. Please check the bam exists.");
                        exitRun = true;
                    }
            }

        }
        if (exitRun)
            throw new ParseException("Exitting . . .");
    } catch (ParseException e) {
        System.err.println(e.getMessage());
        //System.err.println("Failed to parse command line args. Check usage.");
        HLA.help(options);
    }

    String[] list = { "A", "B", "C", "DQA1", "DQB1", "DRB1" };

    String[] extList = { "A", "B", "C", "DQA1", "DQB1", "DRB1", "DOA", "DMA", "DMB", "DPA1", "DPB1", "DRA",
            "DRB3", "DRB5", "F", "G", "H", "J", "L" };
    //,"DPA1", "DPB1", "DRA",  "DRB4", "F", "G" , "H", "J" ,"K", "L", "V"};
    //,"DPA1", "DPB1", "DRA", "DRB3", "DRB4", "F", "G" , "H", "J" ,"K", "L", "V"};

    if (HLA.TYPEADDITIONAL)
        list = extList;

    File[] bamfiles = new File[bams.length];

    for (int i = 0; i < bams.length; i++)
        bamfiles[i] = new File(bams[i]);

    //check if <HLA.OUTPREFIX>.result is writable
    //if not exit.
    BufferedWriter resultWriter = null;
    try {
        resultWriter = new BufferedWriter(new FileWriter(HLA.OUTPREFIX + ".result"));
    } catch (IOException ioe) {
        ioe.printStackTrace();
        System.err.println("\n\n>>> CANNOT open output file: " + HLA.OUTPREFIX + ".result <<<\n\n");
        HLA.help(options);
    }

    HLA.log = new LogHandler();
    for (int i = 0; i < args.length; i++)
        HLA.log.append(" " + args[i]);
    HLA.log.appendln();

    try {
        System.err.println("----------------REF GRAPH CONSTRUCTION--------------");

        HLA.log.appendln("----------------REF GRAPH CONSTRUCTION--------------");
        HLA hla = new HLA(list, HLA.MSAFILELOC + File.separator + "hla_nom_g.txt");

        //1. bubble counting before loading reads.
        //System.err.println("----------------BUBBLE COUNTING: REF GRAPH--------------");
        //HLA.log.appendln("----------------BUBBLE COUNTING: REF GRAPH--------------");
        //hla.countStems();

        System.err.println("----------------     READ LOADING     --------------");

        HLA.log.appendln("----------------     READ LOADING     --------------");

        hla.loadReads(bamfiles);

        System.err.println("----------------    GRAPH CLEANING    --------------");
        HLA.log.appendln("----------------    GRAPH CLEANING    --------------");

        hla.flattenInsertionNodes(list);
        hla.removeUnused(list);
        hla.removeStems(list);

        /*updating error prob*/
        hla.updateErrorProb();

        hla.log.flush();

        StringBuffer resultBuffer = new StringBuffer();

        HLA.DEBUG3 = HLA.DEBUG;

        hla.countBubblesAndMerge(list, resultBuffer);

        hla.writeResults(resultBuffer, resultWriter);
    } catch (Exception e) {
        e.printStackTrace();
        HLA.log.outToFile();
        System.exit(-1);
    }
    /*printingWeights*/
    //hla.printWeights();
    HLA.log.outToFile();
    HLA.log.appendln("NEW_NODE_ADDED:\t" + HLA.NEW_NODE_ADDED);
    HLA.log.appendln("HOPPPING:\t" + HLA.HOPPING);
    HLA.log.appendln("INSERTION_NODE_ADDED:\t" + HLA.INSERTION_NODE_ADDED);
    HLA.log.appendln("INSERTION_WITH_NO_NEW_NODE:\t" + HLA.INSERTION_WITH_NO_NEW_NODE);
    HLA.log.appendln("INSERTION_COUNTS:\t" + HLA.INSERTION);
}

From source file:com.bytelightning.opensource.pokerface.PokerFaceApp.java

public static void main(String[] args) {
    if (JavaVersionAsFloat() < (1.8f - Float.MIN_VALUE)) {
        System.err.println("PokerFace requires at least Java v8 to run.");
        return;//  w  ww  . ja  v a2 s  .c  om
    }
    // Configure the command line options parser
    Options options = new Options();
    options.addOption("h", false, "help");
    options.addOption("listen", true, "(http,https,secure,tls,ssl,CertAlias)=Address:Port for https.");
    options.addOption("keystore", true, "Filepath for PokerFace certificate keystore.");
    options.addOption("storepass", true, "The store password of the keystore.");
    options.addOption("keypass", true, "The key password of the keystore.");
    options.addOption("target", true, "Remote Target requestPattern=targetUri"); // NOTE: targetUri may contain user-info and if so will be interpreted as the alias of a cert to be presented to the remote target
    options.addOption("servercpu", true, "Number of cores the server should use.");
    options.addOption("targetcpu", true, "Number of cores the http targets should use.");
    options.addOption("trustany", false, "Ignore certificate identity errors from target servers.");
    options.addOption("files", true, "Filepath to a directory of static files.");
    options.addOption("config", true, "Path for XML Configuration file.");
    options.addOption("scripts", true, "Filepath for root scripts directory.");
    options.addOption("library", true, "JavaScript library to load into global context.");
    options.addOption("watch", false, "Dynamically watch scripts directory for changes.");
    options.addOption("dynamicTargetScripting", false,
            "WARNING! This option allows scripts to redirect requests to *any* other remote server.");

    CommandLine cmdLine = null;
    // parse the command line.
    try {
        CommandLineParser parser = new PosixParser();
        cmdLine = parser.parse(options, args);
        if (args.length == 0 || cmdLine.hasOption('h')) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.setWidth(120);
            formatter.printHelp(PokerFaceApp.class.getSimpleName(), options);
            return;
        }
    } catch (ParseException exp) {
        System.err.println("Parsing failed.  Reason: " + exp.getMessage());
        return;
    } catch (Exception ex) {
        ex.printStackTrace(System.err);
        return;
    }

    XMLConfiguration config = new XMLConfiguration();
    try {
        if (cmdLine.hasOption("config")) {
            Path tmp = Utils.MakePath(cmdLine.getOptionValue("config"));
            if (!Files.exists(tmp))
                throw new FileNotFoundException("Configuration file does not exist.");
            if (Files.isDirectory(tmp))
                throw new FileNotFoundException("'config' path is not a file.");
            // This is a bit of a pain, but but let's make sure we have a valid configuration file before we actually try to use it.
            config.setEntityResolver(new DefaultEntityResolver() {
                @Override
                public InputSource resolveEntity(String publicId, String systemId) throws SAXException {
                    InputSource retVal = super.resolveEntity(publicId, systemId);
                    if ((retVal == null) && (systemId != null)) {
                        try {
                            URL entityURL;
                            if (systemId.endsWith("/PokerFace_v1Config.xsd"))
                                entityURL = PokerFaceApp.class.getResource("/PokerFace_v1Config.xsd");
                            else
                                entityURL = new URL(systemId);
                            URLConnection connection = entityURL.openConnection();
                            connection.setUseCaches(false);
                            InputStream stream = connection.getInputStream();
                            retVal = new InputSource(stream);
                            retVal.setSystemId(entityURL.toExternalForm());
                        } catch (Throwable e) {
                            return retVal;
                        }
                    }
                    return retVal;
                }

            });
            config.setSchemaValidation(true);
            config.setURL(tmp.toUri().toURL());
            config.load();
            if (cmdLine.hasOption("listen"))
                System.out.println("IGNORING 'listen' option because a configuration file was supplied.");
            if (cmdLine.hasOption("target"))
                System.out.println("IGNORING 'target' option(s) because a configuration file was supplied.");
            if (cmdLine.hasOption("scripts"))
                System.out.println("IGNORING 'scripts' option because a configuration file was supplied.");
            if (cmdLine.hasOption("library"))
                System.out.println("IGNORING 'library' option(s) because a configuration file was supplied.");
        } else {
            String[] serverStrs;
            String[] addr = { null };
            String[] port = { null };
            serverStrs = cmdLine.getOptionValues("listen");
            if (serverStrs == null)
                throw new MissingOptionException("No listening addresses specified specified");
            for (int i = 0; i < serverStrs.length; i++) {
                String addrStr;
                String alias = null;
                String protocol = null;
                Boolean https = null;
                int addrPos = serverStrs[i].indexOf('=');
                if (addrPos >= 0) {
                    if (addrPos < 2)
                        throw new IllegalArgumentException("Invalid http argument.");
                    else if (addrPos + 1 >= serverStrs[i].length())
                        throw new IllegalArgumentException("Invalid http argument.");
                    addrStr = serverStrs[i].substring(addrPos + 1, serverStrs[i].length());
                    String[] types = serverStrs[i].substring(0, addrPos).split(",");
                    for (String type : types) {
                        if (type.equalsIgnoreCase("http"))
                            break;
                        else if (type.equalsIgnoreCase("https") || type.equalsIgnoreCase("secure"))
                            https = true;
                        else if (type.equalsIgnoreCase("tls") || type.equalsIgnoreCase("ssl"))
                            protocol = type.toUpperCase();
                        else
                            alias = type;
                    }
                } else
                    addrStr = serverStrs[i];
                ParseAddressString(addrStr, addr, port, alias != null ? 443 : 80);
                config.addProperty("server.listen(" + i + ")[@address]", addr[0]);
                config.addProperty("server.listen(" + i + ")[@port]", port[0]);
                if (alias != null)
                    config.addProperty("server.listen(" + i + ")[@alias]", alias);
                if (protocol != null)
                    config.addProperty("server.listen(" + i + ")[@protocol]", protocol);
                if (https != null)
                    config.addProperty("server.listen(" + i + ")[@secure]", https);
            }
            String servercpu = cmdLine.getOptionValue("servercpu");
            if (servercpu != null)
                config.setProperty("server[@cpu]", servercpu);
            String clientcpu = cmdLine.getOptionValue("targetcpu");
            if (clientcpu != null)
                config.setProperty("targets[@cpu]", clientcpu);

            // Configure static files
            if (cmdLine.hasOption("files")) {
                Path tmp = Utils.MakePath(cmdLine.getOptionValue("files"));
                if (!Files.exists(tmp))
                    throw new FileNotFoundException("Files directory does not exist.");
                if (!Files.isDirectory(tmp))
                    throw new FileNotFoundException("'files' path is not a directory.");
                config.setProperty("files.rootDirectory", tmp.toAbsolutePath().toUri());
            }

            // Configure scripting
            if (cmdLine.hasOption("scripts")) {
                Path tmp = Utils.MakePath(cmdLine.getOptionValue("scripts"));
                if (!Files.exists(tmp))
                    throw new FileNotFoundException("Scripts directory does not exist.");
                if (!Files.isDirectory(tmp))
                    throw new FileNotFoundException("'scripts' path is not a directory.");
                config.setProperty("scripts.rootDirectory", tmp.toAbsolutePath().toUri());
                config.setProperty("scripts.dynamicWatch", cmdLine.hasOption("watch"));
                String[] libraries = cmdLine.getOptionValues("library");
                if (libraries != null) {
                    for (int i = 0; i < libraries.length; i++) {
                        Path lib = Utils.MakePath(libraries[i]);
                        if (!Files.exists(lib))
                            throw new FileNotFoundException(
                                    "Script library does not exist [" + libraries[i] + "].");
                        if (Files.isDirectory(lib))
                            throw new FileNotFoundException(
                                    "Script library is not a file [" + libraries[i] + "].");
                        config.setProperty("scripts.library(" + i + ")", lib.toAbsolutePath().toUri());
                    }
                }
            } else if (cmdLine.hasOption("watch"))
                System.out.println("IGNORING 'watch' option as no 'scripts' directory was specified.");
            else if (cmdLine.hasOption("library"))
                System.out.println("IGNORING 'library' option as no 'scripts' directory was specified.");
        }
        String keyStorePath = cmdLine.getOptionValue("keystore");
        if (keyStorePath != null)
            config.setProperty("keystore", keyStorePath);
        String keypass = cmdLine.getOptionValue("keypass");
        if (keypass != null)
            config.setProperty("keypass", keypass);
        String storepass = cmdLine.getOptionValue("storepass");
        if (storepass != null)
            config.setProperty("storepass", keypass);
        if (cmdLine.hasOption("trustany"))
            config.setProperty("targets[@trustAny]", true);

        config.setProperty("scripts.dynamicTargetScripting", cmdLine.hasOption("dynamicTargetScripting"));

        String[] targetStrs = cmdLine.getOptionValues("target");
        if (targetStrs != null) {
            for (int i = 0; i < targetStrs.length; i++) {
                int uriPos = targetStrs[i].indexOf('=');
                if (uriPos < 2)
                    throw new IllegalArgumentException("Invalid target argument.");
                else if (uriPos + 1 >= targetStrs[i].length())
                    throw new IllegalArgumentException("Invalid target argument.");
                String patternStr = targetStrs[i].substring(0, uriPos);
                String urlStr = targetStrs[i].substring(uriPos + 1, targetStrs[i].length());
                String alias;
                try {
                    URL url = new URL(urlStr);
                    alias = url.getUserInfo();
                    String scheme = url.getProtocol();
                    if ((!"http".equals(scheme)) && (!"https".equals(scheme)))
                        throw new IllegalArgumentException("Invalid target uri scheme.");
                    int port = url.getPort();
                    if (port < 0)
                        port = url.getDefaultPort();
                    urlStr = scheme + "://" + url.getHost() + ":" + port + url.getPath();
                    String ref = url.getRef();
                    if (ref != null)
                        urlStr += "#" + ref;
                } catch (MalformedURLException ex) {
                    throw new IllegalArgumentException("Malformed target uri");
                }
                config.addProperty("targets.target(" + i + ")[@pattern]", patternStr);
                config.addProperty("targets.target(" + i + ")[@url]", urlStr);
                if (alias != null)
                    config.addProperty("targets.target(" + i + ")[@alias]", alias);
            }
        }
        //         config.save(System.out);
    } catch (Throwable e) {
        e.printStackTrace(System.err);
        return;
    }
    // If we get here, we have a possibly valid configuration.
    try {
        final PokerFace p = new PokerFace();
        p.config(config);
        if (p.start()) {
            PokerFace.Logger.warn("Started!");
            Runtime.getRuntime().addShutdownHook(new Thread() {
                public void run() {
                    try {
                        PokerFace.Logger.warn("Initiating shutdown...");
                        p.stop();
                        PokerFace.Logger.warn("Shutdown completed!");
                    } catch (Throwable e) {
                        PokerFace.Logger.error("Failed to shutdown cleanly!");
                        e.printStackTrace(System.err);
                    }
                }
            });
        } else {
            PokerFace.Logger.error("Failed to start!");
            System.exit(-1);
        }
    } catch (Throwable e) {
        e.printStackTrace(System.err);
    }
}

From source file:esiptestbed.mudrod.ontology.process.LocalOntology.java

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

    // boolean options
    Option helpOpt = new Option("h", "help", false, "show this help message");
    // argument options
    Option ontDirOpt = Option.builder(ONT_DIR).required(true).numberOfArgs(1).hasArg(true)
            .desc("A directory containing .owl files.").argName(ONT_DIR).build();

    // create the options
    Options options = new Options();
    options.addOption(helpOpt);//from   ww w  .  ja  v  a  2  s . c  o m
    options.addOption(ontDirOpt);

    String ontDir;
    CommandLineParser parser = new DefaultParser();
    try {
        CommandLine line = parser.parse(options, args);

        if (line.hasOption(ONT_DIR)) {
            ontDir = line.getOptionValue(ONT_DIR).replace("\\", "/");
        } else {
            ontDir = LocalOntology.class.getClassLoader().getResource("ontology").getFile();
        }
        if (!ontDir.endsWith("/")) {
            ontDir += "/";
        }
    } catch (Exception e) {
        LOG.error("Error whilst processing main method of LocalOntology.", e);
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("LocalOntology: 'ontDir' argument is mandatory. ", options, true);
        return;
    }
    File fileDir = new File(ontDir);
    //Fail if the input is not a directory.
    if (fileDir.isDirectory()) {
        List<String> owlFiles = new ArrayList<>();
        for (File owlFile : fileDir.listFiles()) {
            owlFiles.add(owlFile.toString());
        }
        MudrodEngine mEngine = new MudrodEngine();
        Properties props = mEngine.loadConfig();
        Ontology ontology = new OntologyFactory(props).getOntology();
        //convert to correct iput for ontology loading.
        String[] owlArray = new String[owlFiles.size()];
        owlArray = owlFiles.toArray(owlArray);
        ontology.load(owlArray);

        String[] terms = new String[] { "Glacier ice" };
        //Demonstrate that we can do basic ontology heirarchy navigation and log output.
        for (Iterator<OntClass> i = getParser().rootClasses(getModel()); i.hasNext();) {

            //print Ontology Class Hierarchy
            OntClass c = i.next();
            renderHierarchy(System.out, c, new LinkedList<>(), 0);

            for (Iterator<OntClass> subClass = c.listSubClasses(true); subClass.hasNext();) {
                OntClass sub = subClass.next();
                //This means that the search term is present as an OntClass
                if (terms[0].equalsIgnoreCase(sub.getLabel(null))) {
                    //Add the search term(s) above to the term cache.
                    for (int j = 0; j < terms.length; j++) {
                        addSearchTerm(terms[j], sub);
                    }

                    //Query the ontology and return subclasses of the search term(s)
                    for (int k = 0; k < terms.length; k++) {
                        Iterator<String> iter = ontology.subclasses(terms[k]);
                        while (iter.hasNext()) {
                            LOG.info("Subclasses >> " + iter.next());
                        }
                    }

                    //print any synonymic relationships to demonstrate that we can 
                    //undertake synonym-based query expansion
                    for (int l = 0; l < terms.length; l++) {
                        Iterator<String> iter = ontology.synonyms(terms[l]);
                        while (iter.hasNext()) {
                            LOG.info("Synonym >> " + iter.next());
                        }
                    }
                }
            }
        }

        mEngine.end();
    }

}

From source file:gov.nasa.jpl.mudrod.ontology.process.LocalOntology.java

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

    // boolean options
    Option helpOpt = new Option("h", "help", false, "show this help message");
    // argument options
    Option ontDirOpt = OptionBuilder.hasArg(true).withArgName(ONT_DIR)
            .withDescription("A directory containing .owl files.").isRequired(false).create();

    // create the options
    Options options = new Options();
    options.addOption(helpOpt);/* w  w  w . j  av a  2 s  . co m*/
    options.addOption(ontDirOpt);

    String ontDir;
    CommandLineParser parser = new GnuParser();
    try {
        CommandLine line = parser.parse(options, args);

        if (line.hasOption(ONT_DIR)) {
            ontDir = line.getOptionValue(ONT_DIR).replace("\\", "/");
        } else {
            ontDir = LocalOntology.class.getClassLoader().getResource("ontology").getFile();
        }
        if (!ontDir.endsWith("/")) {
            ontDir += "/";
        }
    } catch (Exception e) {
        LOG.error("Error whilst processing main method of LocalOntology.", e);
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("LocalOntology: 'ontDir' argument is mandatory. ", options, true);
        return;
    }
    File fileDir = new File(ontDir);
    //Fail if the input is not a directory.
    if (fileDir.isDirectory()) {
        List<String> owlFiles = new ArrayList<>();
        for (File owlFile : fileDir.listFiles()) {
            owlFiles.add(owlFile.toString());
        }
        MudrodEngine mEngine = new MudrodEngine();
        Properties props = mEngine.loadConfig();
        Ontology ontology = new OntologyFactory(props).getOntology();
        //convert to correct iput for ontology loading.
        String[] owlArray = new String[owlFiles.size()];
        owlArray = owlFiles.toArray(owlArray);
        ontology.load(owlArray);

        String[] terms = new String[] { "Glacier ice" };
        //Demonstrate that we can do basic ontology heirarchy navigation and log output.
        for (Iterator<OntClass> i = getParser().rootClasses(getModel()); i.hasNext();) {

            //print Ontology Class Hierarchy
            OntClass c = i.next();
            renderHierarchy(System.out, c, new LinkedList<>(), 0);

            for (Iterator<OntClass> subClass = c.listSubClasses(true); subClass.hasNext();) {
                OntClass sub = subClass.next();
                //This means that the search term is present as an OntClass
                if (terms[0].equalsIgnoreCase(sub.getLabel(null))) {
                    //Add the search term(s) above to the term cache.
                    for (int j = 0; j < terms.length; j++) {
                        addSearchTerm(terms[j], sub);
                    }

                    //Query the ontology and return subclasses of the search term(s)
                    for (int k = 0; k < terms.length; k++) {
                        Iterator<String> iter = ontology.subclasses(terms[k]);
                        while (iter.hasNext()) {
                            LOG.info("Subclasses >> " + iter.next());
                        }
                    }

                    //print any synonymic relationships to demonstrate that we can 
                    //undertake synonym-based query expansion
                    for (int l = 0; l < terms.length; l++) {
                        Iterator<String> iter = ontology.synonyms(terms[l]);
                        while (iter.hasNext()) {
                            LOG.info("Synonym >> " + iter.next());
                        }
                    }
                }
            }
        }

        mEngine.end();
    }

}

From source file:MainClass.java

public static void main(String args[]) throws Exception {
    SSLServerSocketFactory ssf = (SSLServerSocketFactory) SSLServerSocketFactory.getDefault();
    ServerSocket ss = ssf.createServerSocket(443);
    while (true) {
        Socket s = ss.accept();//from  ww w  .  jav a2  s . c om
        PrintStream out = new PrintStream(s.getOutputStream());
        BufferedReader in = new BufferedReader(new InputStreamReader(s.getInputStream()));
        String info = null;
        String request = null;
        String refer = null;

        while ((info = in.readLine()) != null) {
            if (info.startsWith("GET")) {
                request = info;
            }
            if (info.startsWith("Referer:")) {
                refer = info;
            }
            if (info.equals(""))
                break;
        }
        if (request != null) {
            out.println("HTTP/1.0 200 OK\nMIME_version:1.0\nContent_Type:text/html");
            int sp1 = request.indexOf(' ');
            int sp2 = request.indexOf(' ', sp1 + 1);
            String filename = request.substring(sp1 + 2, sp2);
            if (refer != null) {
                sp1 = refer.indexOf(' ');
                refer = refer.substring(sp1 + 1, refer.length());
                if (!refer.endsWith("/")) {
                    refer = refer + "/";
                }
                filename = refer + filename;
            }
            URL con = new URL(filename);
            InputStream gotoin = con.openStream();
            int n = gotoin.available();
            byte buf[] = new byte[1024];
            out.println("HTTP/1.0 200 OK\nMIME_version:1.0\nContent_Type:text/html");
            out.println("Content_Length:" + n + "\n");
            while ((n = gotoin.read(buf)) >= 0) {
                out.write(buf, 0, n);
            }
            out.close();
            s.close();
            in.close();
        }
    }
}

From source file:de.gbv.ole.Marc21ToOleBulk.java

/**
 * Convertiert eine MARC21-Datei in eine MarcXML-Bulk-Import-SQL-Datei.
 * @param args      Pfad mit auf .mrc endendem Dateinamen der MARC21-Datei.
 * @throws IOException      Fehler beim Dateilesen oder -schreiben
 *//*from w w w.j  av a  2s.c o  m*/
public static void main(final String[] args) throws IOException {
    if (args.length < 1 || args.length > 2) {
        usageExit();
    }

    boolean ppn5 = false;
    if (args.length == 2) {
        if ("-5".equals(args[0])) {
            ppn5 = true;
        } else {
            usageExit();
        }
    }
    String infile = args[args.length - 1];

    if (!infile.endsWith(MRCSUFFIX)) {
        System.err.println("Filename ending in .mrc expected, " + "but found filename: " + infile);
        usageExit();
    }

    InputStream in = new FileInputStream(infile);
    MarcStreamReader reader = new MarcStreamReader(in);

    String filename = infile.substring(0, infile.length() - MRCSUFFIX.length());
    Writer bib = utf8Writer(filename + "-bib.sql");
    Writer holdings = utf8Writer(filename + "-holdings.sql");
    Writer item = utf8Writer(filename + "-item.sql");

    while (reader.hasNext()) {
        MarcWriter writer = new Marc21ToOleBulk(bib, holdings, item, ppn5);
        writer.write(reader.next());
        writer.close();
    }

    in.close();
    item.close();
    holdings.close();
    bib.close();
}

From source file:act.installer.pubchem.PubchemTTLMerger.java

public static void main(String[] args) throws Exception {
    org.apache.commons.cli.Options opts = new org.apache.commons.cli.Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*from  www . jav  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(PubchemTTLMerger.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

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

    PubchemTTLMerger merger = new PubchemTTLMerger();

    File rocksDBFile = new File(cl.getOptionValue(OPTION_INDEX_PATH));

    if (cl.hasOption(OPTION_ONLY_MERGE)) {
        if (!(rocksDBFile.exists() && rocksDBFile.isDirectory())) {
            System.err.format("Must specify an existing RocksDB index when using '%s'.\n", OPTION_ONLY_MERGE);
            HELP_FORMATTER.printHelp(PubchemTTLMerger.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
            System.exit(1);
        }
        merger.finish(merger.merge(rocksDBFile));
        return;
    }

    File rdfDir = new File(cl.getOptionValue(OPTION_RDF_DIRECTORY));
    if (!rdfDir.isDirectory()) {
        System.err.format("Must specify a directory of RDF files to be parsed.\n");
        HELP_FORMATTER.printHelp(PubchemTTLMerger.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    File[] filesInDirectoryArray = rdfDir.listFiles(new FilenameFilter() {
        private static final String TTL_GZ_SUFFIX = ".ttl.gz";

        @Override
        public boolean accept(File dir, String name) {
            return name.endsWith(TTL_GZ_SUFFIX);
        }
    });

    if (filesInDirectoryArray == null || filesInDirectoryArray.length == 0) {
        System.err.format("Found zero compressed TTL files in directory at '%s'.\n", rdfDir.getAbsolutePath());
        HELP_FORMATTER.printHelp(PubchemTTLMerger.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    // Sort files for stability/sanity.
    List<File> filesInDirectory = Arrays.asList(filesInDirectoryArray);
    Collections.sort(filesInDirectory);

    if (cl.hasOption(OPTION_ONLY_SYNONYMS)) {
        filesInDirectory = filterByFileContents(filesInDirectory, PC_RDF_DATA_FILE_CONFIG.HASH_TO_SYNONYM);
    }

    if (cl.hasOption(OPTION_ONLY_MESH)) {
        filesInDirectory = filterByFileContents(filesInDirectory, PC_RDF_DATA_FILE_CONFIG.HASH_TO_MESH);
    }

    if (cl.hasOption(OPTION_ONLY_PUBCHEM_IDS)) {
        filesInDirectory = filterByFileContents(filesInDirectory, PC_RDF_DATA_FILE_CONFIG.HASH_TO_CID);
    }

    if (filesInDirectory.size() == 0) {
        System.err.format(
                "Arrived at index initialization with no files to process.  "
                        + "Maybe too many filters were specified?  synonyms: %s, MeSH: %s, Pubchem ids: %s\n",
                cl.hasOption(OPTION_ONLY_SYNONYMS), cl.hasOption(OPTION_ONLY_MESH),
                cl.hasOption(OPTION_ONLY_PUBCHEM_IDS));
        HELP_FORMATTER.printHelp(PubchemTTLMerger.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
        System.exit(1);
    }

    RocksDB.loadLibrary();
    Pair<RocksDB, Map<COLUMN_FAMILIES, ColumnFamilyHandle>> dbAndHandles = null;
    try {
        if (rocksDBFile.exists()) {
            if (!cl.hasOption(OPTION_OPEN_EXISTING_OKAY)) {
                System.err.format(
                        "Index directory at '%s' already exists, delete before retrying or add '%s' option to reuse.\n",
                        rocksDBFile.getAbsolutePath(), OPTION_OPEN_EXISTING_OKAY);
                HELP_FORMATTER.printHelp(PubchemTTLMerger.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                        true);
                System.exit(1);
            } else {
                LOGGER.info("Reusing existing index at %s", rocksDBFile.getAbsolutePath());
                dbAndHandles = openExistingRocksDB(rocksDBFile);
            }
        } else {
            LOGGER.info("Creating new index at %s", rocksDBFile.getAbsolutePath());
            dbAndHandles = createNewRocksDB(rocksDBFile);
        }
        merger.buildIndex(dbAndHandles, filesInDirectory);

        merger.merge(dbAndHandles);
    } finally {
        if (dbAndHandles != null) {
            merger.finish(dbAndHandles);
        }
    }
}

From source file:data_gen.Data_gen.java

public static void main(String[] args) throws FileNotFoundException, IOException {
    long startTime = System.nanoTime();
    if (args.length < 2) {
        System.out.println("Usage:");
        System.out.println(/*from  ww w  .j a v  a  2s  . c  o  m*/
                "java -jar \"jarfile\" [Directory of text source folder] [Dierctory of configration file]"
                        + "\n");
        System.exit(0);
    }

    String Dir = args[0]; // get text source dir from user
    String config_dir = args[1];
    File folder = new File(Dir);
    if (folder.isDirectory() == false) {
        System.out.println("Text souce folder is not a Directory." + "\n");
        System.exit(0);
    }
    if (!config_dir.endsWith(".properties") && !config_dir.endsWith(".PROPERTIES")) {
        System.out.println("\n"
                + "There was error parsing dataset parameters from configuration file, make sure you have the 4 parameters specified and the right type of file"
                + "\n");
        System.exit(0);
    }

    listOfFiles = folder.listFiles(new FilenameFilter() {
        @Override
        public boolean accept(File dir, String name) {
            return name.toLowerCase().endsWith(".txt");
        }
    });

    if (listOfFiles.length == 0) {
        System.out.println("Text source folder is empty ! Have at least one .txt file there" + "\n");
        System.exit(0);
    }

    System.out.println("\n");
    Parse_Document_values(config_dir);// parse config file to get class attribute values
    document_size = Docments_Total_size / documents_count; // to get each document size 
    max = (long) ((double) document_size * 1.8);
    min = (long) ((double) document_size * 0.2);

    schema_fields = Parse_Document_fields(config_dir);

    try {
        LineIterator it = FileUtils.lineIterator(listOfFiles[0]);

        while (it.hasNext()) {
            tx.add(it.nextLine());
        }
    } catch (NullPointerException | FileNotFoundException e) {
        System.out.println("The text source file could not be found." + "\n");
        System.exit(0);
    }

    new File(output_dir).mkdir();
    //////////////////////////////////////////////////////////////// build json or .dat
    ////////////////////////////////////////////////////////////////////     
    if (Default_DataSet_name.endsWith(".json")) {
        Build_json_file(config_dir, startTime);
    }

    if (Default_DataSet_name.endsWith(".dat")) {
        Build_dat_file(config_dir, startTime);
    }

    generate_xml();
    generate_field_map();

}