Example usage for java.nio.file Path getFileName

List of usage examples for java.nio.file Path getFileName

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Introduction

In this page you can find the example usage for java.nio.file Path getFileName.

Prototype

Path getFileName();

Source Link

Document

Returns the name of the file or directory denoted by this path as a Path object.

Usage

From source file:com.datazuul.iiif.presentation.api.ManifestGenerator.java

public static void main(String[] args)
        throws ParseException, JsonProcessingException, IOException, URISyntaxException {
    Options options = new Options();
    options.addOption("d", true, "Absolute file path to the directory containing the image files.");

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

    if (cmd.hasOption("d")) {
        String imageDirectoryPath = cmd.getOptionValue("d");
        Path imageDirectory = Paths.get(imageDirectoryPath);
        final List<Path> files = new ArrayList<>();
        try {/*from   w  w  w.jav  a2  s.  c  o  m*/
            Files.walkFileTree(imageDirectory, new SimpleFileVisitor<Path>() {
                @Override
                public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
                    if (!attrs.isDirectory()) {
                        // TODO there must be a more elegant solution for filtering jpeg files...
                        if (file.getFileName().toString().endsWith("jpg")) {
                            files.add(file);
                        }
                    }
                    return FileVisitResult.CONTINUE;
                }
            });
        } catch (IOException e) {
            e.printStackTrace();
        }
        Collections.sort(files, new Comparator() {
            @Override
            public int compare(Object fileOne, Object fileTwo) {
                String filename1 = ((Path) fileOne).getFileName().toString();
                String filename2 = ((Path) fileTwo).getFileName().toString();

                try {
                    // numerical sorting
                    Integer number1 = Integer.parseInt(filename1.substring(0, filename1.lastIndexOf(".")));
                    Integer number2 = Integer.parseInt(filename2.substring(0, filename2.lastIndexOf(".")));
                    return number1.compareTo(number2);
                } catch (NumberFormatException nfe) {
                    // alpha-numerical sorting
                    return filename1.compareToIgnoreCase(filename2);
                }
            }
        });

        generateManifest(imageDirectory.getFileName().toString(), files);
    } else {
        // automatically generate the help statement
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("ManifestGenerator", options);
    }
}

From source file:GIST.IzbirkomExtractor.IzbirkomExtractor.java

/**
 * @param args// w ww . j a v  a  2  s .  c o m
 */
public static void main(String[] args) {

    // process command-line options
    Options options = new Options();
    options.addOption("n", "noaddr", false, "do not do any address matching (for testing)");
    options.addOption("i", "info", false, "create and populate address information table");
    options.addOption("h", "help", false, "this message");

    // database connection
    options.addOption("s", "server", true, "database server to connect to");
    options.addOption("d", "database", true, "OSM database name");
    options.addOption("u", "user", true, "OSM database user name");
    options.addOption("p", "pass", true, "OSM database password");

    // logging options
    options.addOption("l", "logdir", true, "log file directory (default './logs')");
    options.addOption("e", "loglevel", true, "log level (default 'FINEST')");

    // automatically generate the help statement
    HelpFormatter help_formatter = new HelpFormatter();

    // database URI for connection
    String dburi = null;

    // Information message for help screen
    String info_msg = "IzbirkomExtractor [options] <html_directory>";

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

        if (cmd.hasOption('h') || cmd.getArgs().length != 1) {
            help_formatter.printHelp(info_msg, options);
            System.exit(1);
        }

        /* prohibit n and i together */
        if (cmd.hasOption('n') && cmd.hasOption('i')) {
            System.err.println("Options 'n' and 'i' cannot be used together.");
            System.exit(1);
        }

        /* require database arguments without -n */
        if (cmd.hasOption('n')
                && (cmd.hasOption('s') || cmd.hasOption('d') || cmd.hasOption('u') || cmd.hasOption('p'))) {
            System.err.println("Options 'n' and does not need any databse parameters.");
            System.exit(1);
        }

        /* require all 4 database options to be used together */
        if (!cmd.hasOption('n')
                && !(cmd.hasOption('s') && cmd.hasOption('d') && cmd.hasOption('u') && cmd.hasOption('p'))) {
            System.err.println(
                    "For database access all of the following arguments have to be specified: server, database, user, pass");
            System.exit(1);
        }

        /* useful variables */
        SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd'T'kk:mm");
        String dateString = formatter.format(new Date());

        /* setup logging */
        File logdir = new File(cmd.hasOption('l') ? cmd.getOptionValue('l') : "logs");
        FileUtils.forceMkdir(logdir);
        File log_file_name = new File(
                logdir + "/" + IzbirkomExtractor.class.getName() + "-" + formatter.format(new Date()) + ".log");
        FileHandler log_file = new FileHandler(log_file_name.getPath());

        /* create "latest" link to currently created log file */
        Path latest_log_link = Paths.get(logdir + "/latest");
        Files.deleteIfExists(latest_log_link);
        Files.createSymbolicLink(latest_log_link, Paths.get(log_file_name.getName()));

        log_file.setFormatter(new SimpleFormatter());
        LogManager.getLogManager().reset(); // prevents logging to console
        logger.addHandler(log_file);
        logger.setLevel(cmd.hasOption('e') ? Level.parse(cmd.getOptionValue('e')) : Level.FINEST);

        // open directory with HTML files and create file list
        File dir = new File(cmd.getArgs()[0]);
        if (!dir.isDirectory()) {
            System.err.println("Unable to find directory '" + cmd.getArgs()[0] + "', exiting");
            System.exit(1);
        }
        PathMatcher pmatcher = FileSystems.getDefault()
                .getPathMatcher("glob:?  * ?*.html");
        ArrayList<File> html_files = new ArrayList<>();
        for (Path file : Files.newDirectoryStream(dir.toPath()))
            if (pmatcher.matches(file.getFileName()))
                html_files.add(file.toFile());
        if (html_files.size() == 0) {
            System.err.println("No matching HTML files found in '" + dir.getAbsolutePath() + "', exiting");
            System.exit(1);
        }

        // create csvResultSink
        FileOutputStream csvout_file = new FileOutputStream("parsed_addresses-" + dateString + ".csv");
        OutputStreamWriter csvout = new OutputStreamWriter(csvout_file, "UTF-8");
        ResultSink csvResultSink = new CSVResultSink(csvout, new CSVStrategy('|', '"', '#'));

        // Connect to DB and osmAddressMatcher
        AddressMatcher osmAddressMatcher;
        DBSink dbSink = null;
        DBInfoSink dbInfoSink = null;
        if (cmd.hasOption('n')) {
            osmAddressMatcher = new DummyAddressMatcher();
        } else {
            dburi = "jdbc:postgresql://" + cmd.getOptionValue('s') + "/" + cmd.getOptionValue('d');
            Connection con = DriverManager.getConnection(dburi, cmd.getOptionValue('u'),
                    cmd.getOptionValue('p'));
            osmAddressMatcher = new OsmAddressMatcher(con);
            dbSink = new DBSink(con);
            if (cmd.hasOption('i'))
                dbInfoSink = new DBInfoSink(con);
        }

        /* create resultsinks */
        SinkMultiplexor sm = SinkMultiplexor.newSinkMultiplexor();
        sm.addResultSink(csvResultSink);
        if (dbSink != null) {
            sm.addResultSink(dbSink);
            if (dbInfoSink != null)
                sm.addResultSink(dbInfoSink);
        }

        // create tableExtractor
        TableExtractor te = new TableExtractor(osmAddressMatcher, sm);

        // TODO: printout summary of options: processing date/time, host, directory of HTML files, jdbc uri, command line with parameters

        // iterate through files
        logger.info("Start processing " + html_files.size() + " files in " + dir);
        for (int i = 0; i < html_files.size(); i++) {
            System.err.println("Parsing #" + i + ": " + html_files.get(i));
            te.processHTMLfile(html_files.get(i));
        }

        System.err.println("Processed " + html_files.size() + " HTML files");
        logger.info("Finished processing " + html_files.size() + " files in " + dir);

    } catch (ParseException e1) {
        System.err.println("Failed to parse CLI: " + e1.getMessage());
        help_formatter.printHelp(info_msg, options);
        System.exit(1);
    } catch (IOException e) {
        System.err.println("I/O Exception: " + e.getMessage());
        e.printStackTrace();
        System.exit(1);
    } catch (SQLException e) {
        System.err.println("Database '" + dburi + "': " + e.getMessage());
        System.exit(1);
    } catch (ResultSinkException e) {
        System.err.println("Failed to initialize ResultSink: " + e.getMessage());
        System.exit(1);
    } catch (TableExtractorException e) {
        System.err.println("Failed to initialize Table Extractor: " + e.getMessage());
        System.exit(1);
    } catch (CloneNotSupportedException | IllegalAccessException | InstantiationException e) {
        System.err.println("Something really odd happened: " + e.getMessage());
        e.printStackTrace();
        System.exit(1);
    }
}

From source file:com.textocat.textokit.postagger.opennlp.PackageModelZipAsArtifact.java

public static void main(String[] args) throws IOException {
    PackageModelZipAsArtifact cli = new PackageModelZipAsArtifact();
    new JCommander(cli, args);
    Path inputZipPath = Paths.get(cli.inputZipPathStr);
    if (!Files.isRegularFile(inputZipPath)) {
        System.err.println(inputZipPath + " is not an existing file.");
        System.exit(1);//from  w w  w  .  j  a v a  2  s.  c o m
    }
    POSModelJarManifestBean manifestBean = new POSModelJarManifestBean(cli.languageCode, cli.modelVariant);
    Path outputJarPath = inputZipPath
            .resolveSibling(FilenameUtils.getBaseName(inputZipPath.getFileName().toString()) + ".jar");
    try (OutputStream out = new BufferedOutputStream(Files.newOutputStream(outputJarPath))) {
        JarOutputStream jout = new JarOutputStream(out, manifestBean.toManifest());
        jout.putNextEntry(new ZipEntry(ClasspathPOSModelHolder.getClassPath(manifestBean.getLanguageCode(),
                manifestBean.getModelVariant())));
        FileUtils.copyFile(inputZipPath.toFile(), jout);
        jout.closeEntry();
        jout.close();
    }
}

From source file:com.ignorelist.kassandra.steam.scraper.TaggerCli.java

/**
 * @param args the command line arguments
 * @throws java.io.IOException/* w w  w.j av a  2s.c  o  m*/
 * @throws org.antlr.runtime.RecognitionException
 * @throws org.apache.commons.cli.ParseException
 */
public static void main(String[] args) throws IOException, RecognitionException, ParseException {
    Options options = buildOptions();
    CommandLineParser parser = new DefaultParser();
    CommandLine commandLine;
    try {
        commandLine = parser.parse(options, args);
    } catch (ParseException pe) {
        System.out.println(pe.getMessage());
        System.out.println();
        printHelp(options);
        System.exit(0);
        return;
    }
    if (commandLine.hasOption("h")) {
        printHelp(options);
        System.exit(0);
    }
    final PathResolver pathResolver = new PathResolver();

    Configuration configuration;
    Path configurationFile = pathResolver.findConfiguration();
    if (Files.isRegularFile(configurationFile)) {
        configuration = Configuration.fromPropertiesFile(configurationFile);
    } else {
        configuration = new Configuration();
    }
    configuration = toConfiguration(configuration, commandLine);
    //configuration.toProperties().store(System.err, null);

    if (!Files.isRegularFile(configurationFile)) {
        configuration.writeProperties(configurationFile);
        System.err.println(
                "no configuration file present, write based on CLI options: " + configurationFile.toString());
        configuration.toProperties().store(System.err, null);
    }

    Set<Path> sharedConfigPaths = configuration.getSharedConfigPaths();
    if (sharedConfigPaths.size() > 1 && !commandLine.hasOption("w")) {
        System.err.println("multiple sharedconfig.vdf available:\n" + Joiner.on("\n").join(sharedConfigPaths)
                + "\n, can not write to stdout. Need to specify -w or -f with a single sharedconfig.vdf");
        System.exit(1);
    }

    Tagger.Options taggerOptions = Tagger.Options.fromConfiguration(configuration);

    final String[] removeTagsValues = commandLine.getOptionValues("remove");
    if (null != removeTagsValues) {
        taggerOptions.setRemoveTags(Sets.newHashSet(removeTagsValues));
    }

    Set<TagType> tagTypes = configuration.getTagTypes();
    if (null == tagTypes) {
        System.err.println("no tag types!");
        System.exit(1);
    }

    final boolean printTags = commandLine.hasOption("p");

    final HtmlTagLoader htmlTagLoader = new HtmlTagLoader(pathResolver.findCachePath("html"),
            null == configuration.getCacheExpiryDays() ? 7 : configuration.getCacheExpiryDays());
    final BatchTagLoader tagLoader = new BatchTagLoader(htmlTagLoader, configuration.getDownloadThreads());
    if (true || commandLine.hasOption("v")) {
        tagLoader.registerEventListener(new CliEventLoggerLoaded());
    }
    Tagger tagger = new Tagger(tagLoader);

    if (printTags) {
        Set<String> availableTags = tagger.getAvailableTags(sharedConfigPaths, taggerOptions);
        Joiner.on("\n").appendTo(System.out, availableTags);
    } else {
        for (Path path : sharedConfigPaths) {
            VdfNode tagged = tagger.tag(path, taggerOptions);
            if (commandLine.hasOption("w")) {
                Path backup = path.getParent()
                        .resolve(path.getFileName().toString() + ".bak" + new Date().getTime());
                Files.copy(path, backup, StandardCopyOption.REPLACE_EXISTING);
                System.err.println("backup up " + path + " to " + backup);
                Files.copy(new ByteArrayInputStream(tagged.toPrettyString().getBytes(StandardCharsets.UTF_8)),
                        path, StandardCopyOption.REPLACE_EXISTING);
                try {
                    Files.setPosixFilePermissions(path, SHARED_CONFIG_POSIX_PERMS);
                } catch (Exception e) {
                    System.err.println(e);
                }
                System.err.println("wrote " + path);
            } else {
                System.out.println(tagged.toPrettyString());
                System.err.println("pipe to file and copy to: " + path.toString());
            }
        }
    }
}

From source file:com.github.houbin217jz.thumbnail.Thumbnail.java

public static void main(String[] args) {

    Options options = new Options();
    options.addOption("s", "src", true,
            "????????????");
    options.addOption("d", "dst", true, "");
    options.addOption("r", "ratio", true, "/??, 30%???0.3????????");
    options.addOption("w", "width", true, "(px)");
    options.addOption("h", "height", true, "?(px)");
    options.addOption("R", "recursive", false, "???????");

    HelpFormatter formatter = new HelpFormatter();
    String formatstr = "java -jar thumbnail.jar " + "[-s/--src <path>] " + "[-d/--dst <path>] "
            + "[-r/--ratio double] " + "[-w/--width integer] " + "[-h/--height integer] " + "[-R/--recursive] ";

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;/*from   www  .  j a  v a2s .co m*/
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e1) {
        formatter.printHelp(formatstr, options);
        return;
    }

    final Path srcDir, dstDir;
    final Integer width, height;
    final Double ratio;

    //
    if (cmd.hasOption("s")) {
        srcDir = Paths.get(cmd.getOptionValue("s")).toAbsolutePath();
    } else {
        srcDir = Paths.get("").toAbsolutePath(); //??
    }

    //
    if (cmd.hasOption("d")) {
        dstDir = Paths.get(cmd.getOptionValue("d")).toAbsolutePath();
    } else {
        formatter.printHelp(formatstr, options);
        return;
    }

    if (!Files.exists(srcDir, LinkOption.NOFOLLOW_LINKS)
            || !Files.isDirectory(srcDir, LinkOption.NOFOLLOW_LINKS)) {
        System.out.println("[" + srcDir.toAbsolutePath() + "]??????");
        return;
    }

    if (Files.exists(dstDir, LinkOption.NOFOLLOW_LINKS)) {
        if (!Files.isDirectory(dstDir, LinkOption.NOFOLLOW_LINKS)) {
            //????????
            System.out.println("????????");
            return;
        }
    } else {
        //????????
        try {
            Files.createDirectories(dstDir);
        } catch (IOException e) {
            e.printStackTrace();
            return;
        }
    }

    //??
    if (cmd.hasOption("w") && cmd.hasOption("h")) {
        try {
            width = Integer.valueOf(cmd.getOptionValue("width"));
            height = Integer.valueOf(cmd.getOptionValue("height"));
        } catch (NumberFormatException e) {
            System.out.println("??????");
            return;
        }
    } else {
        width = null;
        height = null;
    }

    //?
    if (cmd.hasOption("r")) {
        try {
            ratio = Double.valueOf(cmd.getOptionValue("r"));
        } catch (NumberFormatException e) {
            System.out.println("?????");
            return;
        }
    } else {
        ratio = null;
    }

    if (width != null && ratio != null) {
        System.out.println("??????????????");
        return;
    }

    if (width == null && ratio == null) {
        System.out.println("????????????");
        return;
    }

    //
    int maxDepth = 1;
    if (cmd.hasOption("R")) {
        maxDepth = Integer.MAX_VALUE;
    }

    try {
        //Java 7 ??@see http://docs.oracle.com/javase/jp/7/api/java/nio/file/Files.html
        Files.walkFileTree(srcDir, EnumSet.of(FileVisitOption.FOLLOW_LINKS), maxDepth,
                new SimpleFileVisitor<Path>() {
                    @Override
                    public FileVisitResult visitFile(Path path, BasicFileAttributes basicFileAttributes)
                            throws IOException {

                        //???&???
                        String filename = path.getFileName().toString().toLowerCase();

                        if (filename.endsWith(".jpg") || filename.endsWith(".jpeg")) {
                            //Jpeg??

                            /*
                             * relative??:
                             * rootPath: /a/b/c/d
                             * filePath: /a/b/c/d/e/f.jpg
                             * rootPath.relativize(filePath) = e/f.jpg
                             */

                            /*
                             * resolve??
                             * rootPath: /a/b/c/output
                             * relativePath: e/f.jpg
                             * rootPath.resolve(relativePath) = /a/b/c/output/e/f.jpg
                             */

                            Path dst = dstDir.resolve(srcDir.relativize(path));

                            if (!Files.exists(dst.getParent(), LinkOption.NOFOLLOW_LINKS)) {
                                Files.createDirectories(dst.getParent());
                            }
                            doResize(path.toFile(), dst.toFile(), width, height, ratio);
                        }
                        return FileVisitResult.CONTINUE;
                    }
                });
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:edu.harvard.hul.ois.drs.pdfaconvert.PdfaConvert.java

public static void main(String[] args) throws IOException {
    if (logger == null) {
        System.out.println("About to initialize Log4j");
        logger = LogManager.getLogger();
        System.out.println("Finished initializing Log4j");
    }//from   ww  w  . j  a v a 2  s  .co m

    logger.debug("Entering main()");

    // WIP: the following command line code was pulled from FITS
    Options options = new Options();
    Option inputFileOption = new Option(PARAM_I, true, "input file");
    options.addOption(inputFileOption);
    options.addOption(PARAM_V, false, "print version information");
    options.addOption(PARAM_H, false, "help information");
    options.addOption(PARAM_O, true, "output sub-directory");

    CommandLineParser parser = new DefaultParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args, true);
    } catch (ParseException e) {
        System.err.println(e.getMessage());
        System.exit(1);
    }

    // print version info
    if (cmd.hasOption(PARAM_V)) {
        if (StringUtils.isEmpty(applicationVersion)) {
            applicationVersion = "<not set>";
            System.exit(1);
        }
        System.out.println("Version: " + applicationVersion);
        System.exit(0);
    }

    // print help info
    if (cmd.hasOption(PARAM_H)) {
        displayHelp();
        System.exit(0);
    }

    // input parameter
    if (cmd.hasOption(PARAM_I)) {
        String input = cmd.getOptionValue(PARAM_I);
        boolean hasValue = cmd.hasOption(PARAM_I);
        logger.debug("Has option {} value: [{}]", PARAM_I, hasValue);
        String paramVal = cmd.getOptionValue(PARAM_I);
        logger.debug("value of option: [{}] ****", paramVal);

        File inputFile = new File(input);
        if (!inputFile.exists()) {
            logger.warn("{} does not exist or is not readable.", input);
            System.exit(1);
        }

        String subDir = cmd.getOptionValue(PARAM_O);
        PdfaConvert convert;
        if (!StringUtils.isEmpty(subDir)) {
            convert = new PdfaConvert(subDir);
        } else {
            convert = new PdfaConvert();
        }
        if (inputFile.isDirectory()) {
            if (inputFile.listFiles() == null || inputFile.listFiles().length < 1) {
                logger.warn("Input directory is empty, nothing to process.");
                System.exit(1);
            } else {
                logger.debug("Have directory: [{}] with file count: {}", inputFile.getAbsolutePath(),
                        inputFile.listFiles().length);
                DirectoryStream<Path> dirStream = null;
                dirStream = Files.newDirectoryStream(inputFile.toPath());
                for (Path filePath : dirStream) {
                    logger.debug("Have file name: {}", filePath.toString());
                    // Note: only handling files, not recursively going into sub-directories
                    if (filePath.toFile().isFile()) {
                        // Catch possible exception for each file so can handle other files in directory.
                        try {
                            convert.examine(filePath.toFile());
                        } catch (Exception e) {
                            logger.error("Problem processing file: {} -- Error message: {}",
                                    filePath.getFileName(), e.getMessage());
                        }
                    } else {
                        logger.warn("Not a file so not processing: {}", filePath.toString()); // could be a directory but not recursing
                    }
                }
                dirStream.close();
            }
        } else {
            logger.debug("About to process file: {}", inputFile.getPath());
            try {
                convert.examine(inputFile);
            } catch (Exception e) {
                logger.error("Problem processing file: {} -- Error message: {}", inputFile.getName(),
                        e.getMessage());
                logger.debug("Problem processing file: {} -- Error message: {}", inputFile.getName(),
                        e.getMessage(), e);
            }
        }
    } else {
        System.err.println("Missing required option: " + PARAM_I);
        displayHelp();
        System.exit(-1);
    }

    System.exit(0);
}

From source file:fr.afcepf.atod.wine.data.parser.XmlParser.java

public static void main(String[] args) {
    log.info("\t ### debut du test ###");
    /*URL url;/*from  w  w  w  . ja v  a 2 s . c  o m*/
    try {
     url = new URL(apiBaseUrl+"/categorymap?filter=categories(490)&apikey="+apikey); 
       if(Files.exists(Paths.get(getResourcePath() + "FilesXML/ategoryMap.xml"))==false){
      File file = new File(getResourcePath() + "FilesXML/categoryMap.xml");
     FileUtils.copyURLToFile(url, file);
       }
       //100 vins rouges fr au dela de 100  
       url = new URL(apiBaseUrl+"/catalog?filter=categories(490+124)+price(100)&size=100&search=France&apikey="+apikey);
       if(Files.exists(Paths.get(getResourcePath() + "FilesXML/Wines/RedWines100.xml"))==false){
      File file = new File(getResourcePath() + "FilesXML/Wines/RedWines100.xml");
     FileUtils.copyURLToFile(url, file);
       }
       //100 vins rouges fr entre 50 et 100
       url = new URL(apiBaseUrl+"/catalog?filter=categories(490+124)+price(50|100)&size=100&search=France&apikey="+apikey);
       if(Files.exists(Paths.get(getResourcePath() + "FilesXML/Wines/RedWines50-100.xml"))==false){
      File file = new File(getResourcePath() + "FilesXML/Wines/RedWines50-100.xml");
     FileUtils.copyURLToFile(url, file);
       }
       //100 vins rouges fr entre 10 et 50
       url = new URL(apiBaseUrl+"/catalog?filter=categories(490+124)+price(10|50)&size=100&search=France&apikey="+apikey);
       if(Files.exists(Paths.get(getResourcePath() + "FilesXML/Wines/RedWines10-50.xml"))==false){
      File file = new File(getResourcePath() + "FilesXML/Wines/RedWines10-50.xml");
     FileUtils.copyURLToFile(url, file);
       }
       //100 vins blancs fr au dela de 100  
       url = new URL(apiBaseUrl+"/catalog?filter=categories(490+125)+price(100)&size=100&search=France&apikey="+apikey);
       if(Files.exists(Paths.get(getResourcePath() + "FilesXML/Wines/WhiteWines100.xml"))==false){
      File file = new File(getResourcePath() + "FilesXML/Wines/WhiteWines100.xml");
     FileUtils.copyURLToFile(url, file);
       }
       //100 vins blancs fr entre 50 et 100
       url = new URL(apiBaseUrl+"/catalog?filter=categories(490+125)+price(50|100)&size=100&search=France&apikey="+apikey);
       if(Files.exists(Paths.get(getResourcePath() + "FilesXML/Wines/WhiteWines50-100.xml"))==false){
      File file = new File(getResourcePath() + "FilesXML/Wines/WhiteWines50-100.xml");
     FileUtils.copyURLToFile(url, file);
       }
       //100 vins blancs fr entre 10 et 50
       url = new URL(apiBaseUrl+"/catalog?filter=categories(490+125)+price(10|50)&size=100&search=France&apikey="+apikey);
       if(Files.exists(Paths.get(getResourcePath() + "FilesXML/Wines/WhiteWines10-50.xml"))==false){
      File file = new File(getResourcePath() + "FilesXML/Wines/WhiteWines10-50.xml");
     FileUtils.copyURLToFile(url, file);
       }
       //100 champagnes fr au dela de 100  
       url = new URL(apiBaseUrl+"/catalog?filter=categories(490+123)+price(100)&size=100&search=France&apikey="+apikey);
       if(Files.exists(Paths.get(getResourcePath() + "FilesXML/Wines/ChampagneWines100.xml"))==false){
      File file = new File(getResourcePath() + "FilesXML/Wines/ChampagneWines100.xml");
     FileUtils.copyURLToFile(url, file);
       }
       //100 champagnes fr entre 50 et 100 
       url = new URL(apiBaseUrl+"/catalog?filter=categories(490+123)+price(50|100)&size=100&search=France&apikey="+apikey);
       if(Files.exists(Paths.get(getResourcePath() + "FilesXML/Wines/ChampagneWines50-100.xml"))==false){
      File file = new File(getResourcePath() + "FilesXML/Wines/ChampagneWines50-100.xml");
     FileUtils.copyURLToFile(url, file);
       }
       //100 vins ross fr
       url = new URL(apiBaseUrl+"/catalog?filter=categories(490+126)&size=100&search=France&apikey="+apikey);
       if(Files.exists(Paths.get(getResourcePath() + "FilesXML/Wines/RoseWines10-50.xml"))==false){
      File file = new File(getResourcePath() + "FilesXML/Wines/RoseWines10-50.xml");
     FileUtils.copyURLToFile(url, file);
       }                       
    } catch (IOException e) {
     // TODO Auto-generated catch block
     e.printStackTrace();
    }*/
    Locale.setDefault(Locale.US);
    BeanFactory bf2 = new AnnotationConfigApplicationContext(ElasticsearchConfiguration.class);
    WineService esRepository = (WineService) bf2.getBean(WineService.class);
    esRepository.deleteIdx();
    BeanFactory bf = new ClassPathXmlApplicationContext("classpath:springData.xml");
    IDaoProduct daoVin = (IDaoProduct) bf.getBean(IDaoProduct.class);
    IDaoSupplier daoSupplier = (IDaoSupplier) bf.getBean(IDaoSupplier.class);
    IDaoAdmin daoAdmin = bf.getBean(IDaoAdmin.class);
    IDaoSpecialEvent daoEvent = bf.getBean(IDaoSpecialEvent.class);
    IDaoCountry daoCountry = bf.getBean(IDaoCountry.class);
    IDaoCustomer daoCustomer = bf.getBean(IDaoCustomer.class);
    IDaoShippingMethode daoShippingMethod = bf.getBean(IDaoShippingMethode.class);
    IDaoPaymentInfo daoPayment = bf.getBean(IDaoPaymentInfo.class);
    IDaoProductFeature daoFeature = (IDaoProductFeature) bf.getBean(IDaoProductFeature.class);
    try {
        daoCountry
                .insertObj(new Country(null, "AT", "Autriche", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry
                .insertObj(new Country(null, "BE", "Belgique", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry
                .insertObj(new Country(null, "BG", "Bulgarie", "BGN", "Lev Bulgare", "flaticon-bulgaria-lev"));
        daoCountry.insertObj(new Country(null, "CY", "Chypre", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry.insertObj(new Country(null, "CZ", "Rpublique Tchque", "CZK", "Couronne tchque",
                "flaticon-czech-republic-koruna-currency-symbol"));
        daoCountry.insertObj(
                new Country(null, "DE", "Allemagne", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry.insertObj(new Country(null, "DK", "Danemark", "DKK", "Couronne danoise",
                "flaticon-denmark-krone-currency-symbol"));
        daoCountry.insertObj(new Country(null, "EE", "Estonie", "EEK", "Couronne estonienne",
                "flaticon-estonia-kroon-currency-symbol"));
        daoCountry
                .insertObj(new Country(null, "ES", "Espagne", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry
                .insertObj(new Country(null, "FI", "Finlande", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry.insertObj(new Country(null, "GB", "Royaume-Uni", "GBP", "Livre sterling",
                "flaticon-pound-symbol-variant"));
        daoCountry.insertObj(new Country(null, "GR", "Grce", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry.insertObj(new Country(null, "HU", "Hongrie", "HUF", "Forint hongrois",
                "flaticon-hungary-forint-currency-symbol"));
        daoCountry
                .insertObj(new Country(null, "IE", "Irlande", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry.insertObj(new Country(null, "IT", "Italie", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry.insertObj(
                new Country(null, "JP", "Japon", "JPY", "Yen japonais", "flaticon-yen-currency-symbol"));
        daoCountry.insertObj(new Country(null, "LT", "Lituanie", "LTL", "Litas lituanien",
                "flaticon-lithuania-litas-currency-symbol"));
        daoCountry.insertObj(
                new Country(null, "LU", "Luxembourg", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry.insertObj(new Country(null, "LV", "Lettonie", "LVL", "Lats letton", "flaticon-latvia-lat"));
        daoCountry.insertObj(new Country(null, "MT", "Malte", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry
                .insertObj(new Country(null, "NL", "Pays-Bas", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry.insertObj(new Country(null, "PL", "Pologne", "PLN", "Zloty polonais",
                "flaticon-poland-zloty-currency-symbol"));
        daoCountry
                .insertObj(new Country(null, "PT", "Portugal", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry
                .insertObj(new Country(null, "RO", "Roumanie", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry.insertObj(new Country(null, "SE", "Sude", "SEK", "Couronne sudoise",
                "flaticon-sweden-krona-currency-symbol"));
        daoCountry.insertObj(
                new Country(null, "SI", "Slovnie", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry.insertObj(
                new Country(null, "SK", "Slovaquie", "EUR", "Euro", "flaticon-euro-currency-symbol"));
        daoCountry.insertObj(new Country(null, "US", "Etats-Unis", "USD", "Dollar U.S.",
                "flaticon-dollar-currency-symbol-2"));
        daoCountry.insertObj(new Country(null, "FR", "France", "EUR", "Euro", "flaticon-euro-currency-symbol"));
    } catch (WineException e2) {
        // TODO Auto-generated catch block
        e2.printStackTrace();
    }

    Admin admin = null;
    Customer customer1 = null;
    Customer customer2 = null;
    Customer customer3 = null;

    try {
        admin = new Admin(null, "strateur", "admini", new Date(), "nicolastorero@gmail.com",
                "nicolastorero@gmail.com", "test1234", "0680413240", new Date(), new Date(), Civility.MR);
        customer1 = new Customer(null, "Wang", "Fen", new Date(), "fenwang@hotmail.com", "fenwang@hotmail.com",
                "test1234", "0666666666", new Date(), new Date(), Civility.MISS, true);
        customer2 = new Customer(null, "Anes", "Zouheir", new Date(), "zouheir.anes@gmail.com",
                "zouheir.anes@gmail.com", "test1234", "0666666666", new Date(), new Date(), Civility.MR, true);
        customer3 = new Customer(null, "Storero", "Nicolas", new Date(), "nicolastorero@gmail.com",
                "nicolastorero@gmail.com", "test1234", "0666666666", new Date(), new Date(), Civility.MR, true);
        daoAdmin.insertObj(admin);
        daoShippingMethod.insertObj(new ShippingMethod(null, "Colissimo"));
        daoPayment.insertObj(new PaymentInfo(null, "Visa"));
        daoCustomer.insertObj(customer1);
        daoCustomer.insertObj(customer2);
        Country c = daoCountry.findObj(29);
        customer3.addAdress(new Adress(null, "rue de rivoli", "18", "75001", "Paris", c, false));
        customer3.addAdress(new Adress(null, "rue de rivoli", "18", "75001", "Paris", c, true));
        daoCustomer.updateObj(customer3);
    } catch (WineException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    Product productRand = new Product(null, "pre", 500.0, "un produit");
    SpecialEvent se = new SpecialEvent(null, "Promotest", new Date(), new Date(), new Date(),
            "10% sur une slection de produits", true, admin, 10);
    Product productAccessorie = new ProductAccessories(null, "un mug", 25.0, "un beau mug", new Date());
    Supplier supplier1 = new Supplier(null, "Aux bon vins de Bourgogne", "05 85 74 85 69",
            "vinsbourgogne@gmail.com", new Date());
    Supplier supplier2 = new Supplier(null, "Aux bon vins de Bordeaux", "04 85 74 85 69",
            "vinsbordeaux@gmail.com", new Date());
    Supplier supplier3 = new Supplier(null, "Aux bon vins de l'Aude", "07 85 74 85 69", "vinsaude@gmail.com",
            new Date());
    try {
        //Les Set sont particulirement adapts pour manipuler une grande
        //quantit de donnes. Cependant, les performances de ceux-ci peuvent
        //tre amoindries en insertion. Gnralement, on opte pour un HashSet,
        //car il est plus performant en temps d'accs 
        ProductSupplier productSuppliers1 = new ProductSupplier();
        ProductSupplier productSuppliers2 = new ProductSupplier();
        productSuppliers1.setProduct(productRand);
        productSuppliers1.setSupplier(daoSupplier.insertObj(supplier1));
        productSuppliers1.setQuantity(30);
        productSuppliers2.setProduct(productRand);
        productSuppliers2.setSupplier(daoSupplier.insertObj(supplier2));
        productSuppliers2.setQuantity(15);
        productRand.getProductSuppliers().add(productSuppliers1);
        productRand.getProductSuppliers().add(productSuppliers2);
        daoVin.insertObj(productRand);
        ProductSupplier productSuppliers3 = new ProductSupplier();
        productSuppliers3.setProduct(productAccessorie);
        productSuppliers3.setSupplier(daoSupplier.insertObj(supplier3));
        productSuppliers3.setQuantity(20);
        productAccessorie.getProductSuppliers().add(productSuppliers3);
        daoVin.insertObj(productAccessorie);
        for (Path filepath : Files.newDirectoryStream(Paths.get(getResourcePath() + "FilesXML/Wines/"))) {
            if (filepath.getFileName().toString().contains("xml")) {
                list.add(parseSampleXml("FilesXML/Wines/" + filepath.getFileName()));
            }
        }
    } catch (WineException ex) {
        java.util.logging.Logger.getLogger(XmlParser.class.getName()).log(Level.SEVERE, null, ex);
    } catch (IOException e) {
        java.util.logging.Logger.getLogger(XmlParser.class.getName()).log(Level.SEVERE, null, e);
    }
    try {
        daoEvent.insertObj(se);
        if (features.isEmpty() == false) {
            for (ProductFeature pf : features.values()) {
                daoFeature.insertObj(pf);
            }
        }
        Integer cpt = 0;
        for (ArrayList<ProductWine> subList : list) {
            for (ProductWine productWine : subList) {
                ProductSupplier ps = new ProductSupplier();
                ps.setProduct(productWine);
                ps.setSupplier(supplier1);
                ps.setQuantity(randomWithRange(1, 50));
                productWine.getProductSuppliers().add(ps);
                if (cpt % 2 == 0) {
                    ProductSupplier ps2 = new ProductSupplier();
                    ps2.setProduct(productWine);
                    ps2.setSupplier(supplier2);
                    ps2.setQuantity(randomWithRange(1, 50));
                    productWine.getProductSuppliers().add(ps2);
                } else if (cpt % 3 == 0) {
                    ProductSupplier ps3 = new ProductSupplier();
                    ps3.setProduct(productWine);
                    ps3.setSupplier(supplier3);
                    ps3.setQuantity(randomWithRange(1, 50));
                    productWine.getProductSuppliers().add(ps3);
                }
                if (cpt < 11) {
                    productWine.setSpeEvent(se);
                }
                daoVin.insertObj(productWine);
                Wine esWine = new Wine(productWine.getId(), productWine.getName(), productWine.getAppellation(),
                        productWine.getPrice(), productWine.getApiId(),
                        new WineType(productWine.getProductType().getId(),
                                productWine.getProductType().getType()),
                        new WineVintage(((productWine.getProductVintage() != null)
                                ? productWine.getProductVintage().getYear().toString()
                                : "")),
                        new WineVarietal(productWine.getProductVarietal().getId(),
                                productWine.getProductVarietal().getDescription()));
                for (ProductFeature feat : productWine.getFeatures()) {
                    esWine.addFeature(new WineFeature(feat.getId(), feat.getLabel()));
                }
                esRepository.save(esWine);
                cpt++;
            }
        }
    } catch (WineException paramE) {
        // TODO Auto-generated catch block
        paramE.printStackTrace();
    }

    /*BeanFactory bf = new ClassPathXmlApplicationContext("classpath:springData.xml");
    IDaoProduct daoVin = (IDaoProduct) bf.getBean(IDaoProduct.class);
    try {
     BeanFactory bf = new ClassPathXmlApplicationContext("classpath:springData.xml");
       IDaoProduct daoVin = (IDaoProduct) bf.getBean(IDaoProduct.class);
       List<Product> list = daoVin.findAllObj();
       for (Product product : list) {
      String imagesUrl = ((ProductWine)product).getImagesUrl();
      String xmlId = ((ProductWine)product).getApiId().toString();
      String [] urls = imagesUrl.split("\\|");
      for (int i = 0; i < urls.length; i++) {
       if(urls[i].trim()!=""){
          URL url = new URL(urls[i].trim());
          String filename = FilenameUtils.getBaseName(url.toString())+"."+FilenameUtils.getExtension(url.toString());
          if(Files.exists(Paths.get(getResourcePath() + "wine_pictures/"+xmlId+"/"+filename))==false){
              File file = new File(getResourcePath() + "wine_pictures/"+xmlId+"/"+filename);
              try {
                FileUtils.copyURLToFile(url, file);
             } catch (FileNotFoundException e) {
                        
             }
           }
          if(filename==xmlId+"m.jpg"){
             if(Files.exists(Paths.get(getResourcePath() + "wine_pictures/"+xmlId+"/"+xmlId+"l.jpg"))==false){
                 File file = new File(getResourcePath() + "wine_pictures/"+xmlId+"/"+xmlId+"l.jpg");
                 URL url2 = new URL(urls[i].trim().replace("m.jpg", "l.jpg"));
                 try {
                   FileUtils.copyURLToFile(url2, file);
                } catch (FileNotFoundException e) {
                           
                }
              }
          }
       }
    }
             
      if(xmlId.length()==6){
       URL url = new URL("http://cdn.fluidretail.net/customers/c1477/"+xmlId.substring(0, 2)+"/"+xmlId.substring(2,4)+"/"+xmlId.substring(4)+"/_s/pi/n/"+xmlId+"_spin_spin2/main_variation_na_view_01_204x400.jpg");
        if(Files.exists(Paths.get(getResourcePath() + "wine_pictures/"+xmlId+"/"+xmlId+"_front.jpg"))==false){
           File file = new File(getResourcePath() + "wine_pictures/"+xmlId+"/"+xmlId+"_front.jpg");
           try {
             FileUtils.copyURLToFile(url, file);
          } catch (FileNotFoundException e) {
                     
          }
        }
        URL url2 = new URL("http://cdn.fluidretail.net/customers/c1477/"+xmlId.substring(0, 2)+"/"+xmlId.substring(2,4)+"/"+xmlId.substring(4)+"/_s/pi/n/"+xmlId+"_spin_spin2/main_variation_na_view_07_204x400.jpg");
        if(Files.exists(Paths.get(getResourcePath() + "wine_pictures/"+xmlId+"/"+xmlId+"_back.jpg"))==false){
           File file = new File(getResourcePath() + "wine_pictures/"+xmlId+"/"+xmlId+"_back.jpg");
           try {
              FileUtils.copyURLToFile(url2, file);
           } catch (FileNotFoundException e) {
                     
          }
        }
    }
       }
    } catch (MalformedURLException e) {
     // TODO Auto-generated catch block
     e.printStackTrace();
    } catch (IOException e) {
     // TODO Auto-generated catch block
     e.printStackTrace();
    } catch (WineException e) {
     // TODO Auto-generated catch block
     e.printStackTrace();
    } 
    //http://cdn.fluidretail.net/customers/c1477/13/68/80/_s/pi/n/136880_spin_spin2/main_variation_na_view_01_204x400.jpg*/
    insert_translations(bf, bf2);
    log.info("\t ### Fin du test ###");
}

From source file:tuit.java

@SuppressWarnings("ConstantConditions")
public static void main(String[] args) {
    System.out.println(licence);//  ww  w  .  ja  v a  2s.c o m
    //Declare variables
    File inputFile;
    File outputFile;
    File tmpDir;
    File blastnExecutable;
    File properties;
    File blastOutputFile = null;
    //
    TUITPropertiesLoader tuitPropertiesLoader;
    TUITProperties tuitProperties;
    //
    String[] parameters = null;
    //
    Connection connection = null;
    MySQL_Connector mySQL_connector;
    //
    Map<Ranks, TUITCutoffSet> cutoffMap;
    //
    BLASTIdentifier blastIdentifier = null;
    //
    RamDb ramDb = null;

    CommandLineParser parser = new GnuParser();
    Options options = new Options();

    options.addOption(tuit.IN, "input<file>", true, "Input file (currently fasta-formatted only)");
    options.addOption(tuit.OUT, "output<file>", true, "Output file (in " + tuit.TUIT_EXT + " format)");
    options.addOption(tuit.P, "prop<file>", true, "Properties file (XML formatted)");
    options.addOption(tuit.V, "verbose", false, "Enable verbose output");
    options.addOption(tuit.B, "blast_output<file>", true, "Perform on a pre-BLASTed output");
    options.addOption(tuit.DEPLOY, "deploy", false, "Deploy the taxonomic databases");
    options.addOption(tuit.UPDATE, "update", false, "Update the taxonomic databases");
    options.addOption(tuit.USE_DB, "usedb", false, "Use RDBMS instead of RAM-based taxonomy");

    Option option = new Option(tuit.REDUCE, "reduce", true,
            "Pack identical (100% similar sequences) records in the given sample file");
    option.setArgs(Option.UNLIMITED_VALUES);
    options.addOption(option);
    option = new Option(tuit.COMBINE, "combine", true,
            "Combine a set of given reduction files into an HMP Tree-compatible taxonomy");
    option.setArgs(Option.UNLIMITED_VALUES);
    options.addOption(option);
    options.addOption(tuit.NORMALIZE, "normalize", false,
            "If used in combination with -combine ensures that the values are normalized by the root value");

    HelpFormatter formatter = new HelpFormatter();

    try {

        //Get TUIT directory
        final File tuitDir = new File(
                new File(tuit.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath())
                        .getParent());
        final File ramDbFile = new File(tuitDir, tuit.RAM_DB);

        //Setup logger
        Log.getInstance().setLogName("tuit.log");

        //Read command line
        final CommandLine commandLine = parser.parse(options, args, true);

        //Check if the REDUCE option is on
        if (commandLine.hasOption(tuit.REDUCE)) {

            final String[] fileList = commandLine.getOptionValues(tuit.REDUCE);
            for (String s : fileList) {
                final Path path = Paths.get(s);
                Log.getInstance().log(Level.INFO, "Processing " + path.toString() + "...");
                final NucleotideFastaSequenceReductor nucleotideFastaSequenceReductor = NucleotideFastaSequenceReductor
                        .fromPath(path);
                ReductorFileOperator.save(nucleotideFastaSequenceReductor,
                        path.resolveSibling(path.getFileName().toString() + ".rdc"));
            }

            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }

        //Check if COMBINE is on
        if (commandLine.hasOption(tuit.COMBINE)) {
            final boolean normalize = commandLine.hasOption(tuit.NORMALIZE);
            final String[] fileList = commandLine.getOptionValues(tuit.COMBINE);
            //TODO: implement a test for format here

            final List<TreeFormatter.TreeFormatterFormat.HMPTreesOutput> hmpTreesOutputs = new ArrayList<>();
            final TreeFormatter treeFormatter = TreeFormatter
                    .newInstance(new TreeFormatter.TuitLineTreeFormatterFormat());
            for (String s : fileList) {
                final Path path = Paths.get(s);
                Log.getInstance().log(Level.INFO, "Merging " + path.toString() + "...");
                treeFormatter.loadFromPath(path);
                final TreeFormatter.TreeFormatterFormat.HMPTreesOutput output = TreeFormatter.TreeFormatterFormat.HMPTreesOutput
                        .newInstance(treeFormatter.toHMPTree(normalize), s.substring(0, s.indexOf(".")));
                hmpTreesOutputs.add(output);
                treeFormatter.erase();
            }
            final Path destination;
            if (commandLine.hasOption(OUT)) {
                destination = Paths.get(commandLine.getOptionValue(tuit.OUT));
            } else {
                destination = Paths.get("merge.tcf");
            }
            CombinatorFileOperator.save(hmpTreesOutputs, treeFormatter, destination);
            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }

        if (!commandLine.hasOption(tuit.P)) {
            throw new ParseException("No properties file option found, exiting.");
        } else {
            properties = new File(commandLine.getOptionValue(tuit.P));
        }

        //Load properties
        tuitPropertiesLoader = TUITPropertiesLoader.newInstanceFromFile(properties);
        tuitProperties = tuitPropertiesLoader.getTuitProperties();

        //Create tmp directory and blastn executable
        tmpDir = new File(tuitProperties.getTMPDir().getPath());
        blastnExecutable = new File(tuitProperties.getBLASTNPath().getPath());

        //Check for deploy
        if (commandLine.hasOption(tuit.DEPLOY)) {
            if (commandLine.hasOption(tuit.USE_DB)) {
                NCBITablesDeployer.fastDeployNCBIDatabasesFromNCBI(connection, tmpDir);
            } else {
                NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile);
            }

            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }
        //Check for update
        if (commandLine.hasOption(tuit.UPDATE)) {
            if (commandLine.hasOption(tuit.USE_DB)) {
                NCBITablesDeployer.updateDatabasesFromNCBI(connection, tmpDir);
            } else {
                //No need to specify a different way to update the database other than just deploy in case of the RAM database
                NCBITablesDeployer.fastDeployNCBIRamDatabaseFromNCBI(tmpDir, ramDbFile);
            }
            Log.getInstance().log(Level.FINE, "Task done, exiting...");
            return;
        }

        //Connect to the database
        if (commandLine.hasOption(tuit.USE_DB)) {
            mySQL_connector = MySQL_Connector.newDefaultInstance(
                    "jdbc:mysql://" + tuitProperties.getDBConnection().getUrl().trim() + "/",
                    tuitProperties.getDBConnection().getLogin().trim(),
                    tuitProperties.getDBConnection().getPassword().trim());
            mySQL_connector.connectToDatabase();
            connection = mySQL_connector.getConnection();
        } else {
            //Probe for ram database

            if (ramDbFile.exists() && ramDbFile.canRead()) {
                Log.getInstance().log(Level.INFO, "Loading RAM taxonomic map...");
                try {
                    ramDb = RamDb.loadSelfFromFile(ramDbFile);
                } catch (IOException ie) {
                    if (ie instanceof java.io.InvalidClassException)
                        throw new IOException("The RAM-based taxonomic database needs to be updated.");
                }

            } else {
                Log.getInstance().log(Level.SEVERE,
                        "The RAM database either has not been deployed, or is not accessible."
                                + "Please use the --deploy option and check permissions on the TUIT directory. "
                                + "If you were looking to use the RDBMS as a taxonomic reference, plese use the -usedb option.");
                return;
            }
        }

        if (commandLine.hasOption(tuit.B)) {
            blastOutputFile = new File(commandLine.getOptionValue(tuit.B));
            if (!blastOutputFile.exists() || !blastOutputFile.canRead()) {
                throw new Exception("BLAST output file either does not exist, or is not readable.");
            } else if (blastOutputFile.isDirectory()) {
                throw new Exception("BLAST output file points to a directory.");
            }
        }
        //Check vital parameters
        if (!commandLine.hasOption(tuit.IN)) {
            throw new ParseException("No input file option found, exiting.");
        } else {
            inputFile = new File(commandLine.getOptionValue(tuit.IN));
            Log.getInstance().setLogName(inputFile.getName().split("\\.")[0] + ".tuit.log");
        }
        //Correct the output file option if needed
        if (!commandLine.hasOption(tuit.OUT)) {
            outputFile = new File((inputFile.getPath()).split("\\.")[0] + tuit.TUIT_EXT);
        } else {
            outputFile = new File(commandLine.getOptionValue(tuit.OUT));
        }

        //Adjust the output level
        if (commandLine.hasOption(tuit.V)) {
            Log.getInstance().setLevel(Level.FINE);
            Log.getInstance().log(Level.INFO, "Using verbose output for the log");
        } else {
            Log.getInstance().setLevel(Level.INFO);
        }
        //Try all files
        if (inputFile != null) {
            if (!inputFile.exists() || !inputFile.canRead()) {
                throw new Exception("Input file either does not exist, or is not readable.");
            } else if (inputFile.isDirectory()) {
                throw new Exception("Input file points to a directory.");
            }
        }

        if (!properties.exists() || !properties.canRead()) {
            throw new Exception("Properties file either does not exist, or is not readable.");
        } else if (properties.isDirectory()) {
            throw new Exception("Properties file points to a directory.");
        }

        //Create blast parameters
        final StringBuilder stringBuilder = new StringBuilder();
        for (Database database : tuitProperties.getBLASTNParameters().getDatabase()) {
            stringBuilder.append(database.getUse());
            stringBuilder.append(" ");//Gonna insert an extra space for the last database
        }
        String remote;
        String entrez_query;
        if (tuitProperties.getBLASTNParameters().getRemote().getDelegate().equals("yes")) {
            remote = "-remote";
            entrez_query = "-entrez_query";
            parameters = new String[] { "-db", stringBuilder.toString(), remote, entrez_query,
                    tuitProperties.getBLASTNParameters().getEntrezQuery().getValue(), "-evalue",
                    tuitProperties.getBLASTNParameters().getExpect().getValue() };
        } else {
            if (!commandLine.hasOption(tuit.B)) {
                if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase()
                        .startsWith("NOT")
                        || tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase()
                                .startsWith("ALL")) {
                    parameters = new String[] { "-db", stringBuilder.toString(), "-evalue",
                            tuitProperties.getBLASTNParameters().getExpect().getValue(), "-negative_gilist",
                            TUITFileOperatorHelper.restrictToEntrez(tmpDir,
                                    tuitProperties.getBLASTNParameters().getEntrezQuery().getValue()
                                            .toUpperCase().replace("NOT", "OR"))
                                    .getAbsolutePath(),
                            "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() };
                } else if (tuitProperties.getBLASTNParameters().getEntrezQuery().getValue().toUpperCase()
                        .equals("")) {
                    parameters = new String[] { "-db", stringBuilder.toString(), "-evalue",
                            tuitProperties.getBLASTNParameters().getExpect().getValue(), "-num_threads",
                            tuitProperties.getBLASTNParameters().getNumThreads().getValue() };
                } else {
                    parameters = new String[] { "-db", stringBuilder.toString(), "-evalue",
                            tuitProperties.getBLASTNParameters().getExpect().getValue(),
                            /*"-gilist", TUITFileOperatorHelper.restrictToEntrez(
                            tmpDir, tuitProperties.getBLASTNParameters().getEntrezQuery().getValue()).getAbsolutePath(),*/ //TODO remove comment!!!!!
                            "-num_threads", tuitProperties.getBLASTNParameters().getNumThreads().getValue() };
                }
            }
        }
        //Prepare a cutoff Map
        if (tuitProperties.getSpecificationParameters() != null
                && tuitProperties.getSpecificationParameters().size() > 0) {
            cutoffMap = new HashMap<Ranks, TUITCutoffSet>(tuitProperties.getSpecificationParameters().size());
            for (SpecificationParameters specificationParameters : tuitProperties
                    .getSpecificationParameters()) {
                cutoffMap.put(Ranks.valueOf(specificationParameters.getCutoffSet().getRank()),
                        TUITCutoffSet.newDefaultInstance(
                                Double.parseDouble(
                                        specificationParameters.getCutoffSet().getPIdentCutoff().getValue()),
                                Double.parseDouble(specificationParameters.getCutoffSet()
                                        .getQueryCoverageCutoff().getValue()),
                                Double.parseDouble(
                                        specificationParameters.getCutoffSet().getAlpha().getValue())));
            }
        } else {
            cutoffMap = new HashMap<Ranks, TUITCutoffSet>();
        }
        final TUITFileOperatorHelper.OutputFormat format;
        if (tuitProperties.getBLASTNParameters().getOutputFormat().getFormat().equals("rdp")) {
            format = TUITFileOperatorHelper.OutputFormat.RDP_FIXRANK;
        } else {
            format = TUITFileOperatorHelper.OutputFormat.TUIT;
        }

        try (TUITFileOperator<NucleotideFasta> nucleotideFastaTUITFileOperator = NucleotideFastaTUITFileOperator
                .newInstance(format, cutoffMap);) {
            nucleotideFastaTUITFileOperator.setInputFile(inputFile);
            nucleotideFastaTUITFileOperator.setOutputFile(outputFile);
            final String cleanupString = tuitProperties.getBLASTNParameters().getKeepBLASTOuts().getKeep();
            final boolean cleanup;
            if (cleanupString.equals("no")) {
                Log.getInstance().log(Level.INFO, "Temporary BLAST files will be deleted.");
                cleanup = true;
            } else {
                Log.getInstance().log(Level.INFO, "Temporary BLAST files will be kept.");
                cleanup = false;
            }
            //Create blast identifier
            ExecutorService executorService = Executors.newSingleThreadExecutor();
            if (commandLine.hasOption(tuit.USE_DB)) {

                if (blastOutputFile == null) {
                    blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromFileOperator(tmpDir,
                            blastnExecutable, parameters, nucleotideFastaTUITFileOperator, connection,
                            cutoffMap,
                            Integer.parseInt(
                                    tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                            cleanup);

                } else {
                    try {
                        blastIdentifier = TUITBLASTIdentifierDB.newInstanceFromBLASTOutput(
                                nucleotideFastaTUITFileOperator, connection, cutoffMap, blastOutputFile,
                                Integer.parseInt(
                                        tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                                cleanup);

                    } catch (JAXBException e) {
                        Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName()
                                + ", please check input. The file must be XML formatted.");
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }

            } else {
                if (blastOutputFile == null) {
                    blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromFileOperator(tmpDir,
                            blastnExecutable, parameters, nucleotideFastaTUITFileOperator, cutoffMap,
                            Integer.parseInt(
                                    tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                            cleanup, ramDb);

                } else {
                    try {
                        blastIdentifier = TUITBLASTIdentifierRAM.newInstanceFromBLASTOutput(
                                nucleotideFastaTUITFileOperator, cutoffMap, blastOutputFile,
                                Integer.parseInt(
                                        tuitProperties.getBLASTNParameters().getMaxFilesInBatch().getValue()),
                                cleanup, ramDb);

                    } catch (JAXBException e) {
                        Log.getInstance().log(Level.SEVERE, "Error reading " + blastOutputFile.getName()
                                + ", please check input. The file must be XML formatted.");
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
            }
            Future<?> runnableFuture = executorService.submit(blastIdentifier);
            runnableFuture.get();
            executorService.shutdown();
        }
    } catch (ParseException pe) {
        Log.getInstance().log(Level.SEVERE, (pe.getMessage()));
        formatter.printHelp("tuit", options);
    } catch (SAXException saxe) {
        Log.getInstance().log(Level.SEVERE, saxe.getMessage());
    } catch (FileNotFoundException fnfe) {
        Log.getInstance().log(Level.SEVERE, fnfe.getMessage());
    } catch (TUITPropertyBadFormatException tpbfe) {
        Log.getInstance().log(Level.SEVERE, tpbfe.getMessage());
    } catch (ClassCastException cce) {
        Log.getInstance().log(Level.SEVERE, cce.getMessage());
    } catch (JAXBException jaxbee) {
        Log.getInstance().log(Level.SEVERE,
                "The properties file is not well formatted. Please ensure that the XML is consistent with the io.properties.dtd schema.");
    } catch (ClassNotFoundException cnfe) {
        //Probably won't happen unless the library deleted from the .jar
        Log.getInstance().log(Level.SEVERE, cnfe.getMessage());
        //cnfe.printStackTrace();
    } catch (SQLException sqle) {
        Log.getInstance().log(Level.SEVERE,
                "A database communication error occurred with the following message:\n" + sqle.getMessage());
        //sqle.printStackTrace();
        if (sqle.getMessage().contains("Access denied for user")) {
            Log.getInstance().log(Level.SEVERE, "Please use standard database login: "
                    + NCBITablesDeployer.login + " and password: " + NCBITablesDeployer.password);
        }
    } catch (Exception e) {
        Log.getInstance().log(Level.SEVERE, e.getMessage());
        e.printStackTrace();
    } finally {
        if (connection != null) {
            try {
                connection.close();
            } catch (SQLException sqle) {
                Log.getInstance().log(Level.SEVERE, "Problem closing the database connection: " + sqle);
            }
        }
        Log.getInstance().log(Level.FINE, "Task done, exiting...");
    }
}

From source file:edu.cmu.tetrad.cli.search.FgsCli.java

/**
 * @param args the command line arguments
 *///from w w w.j a  va 2 s  .c  o  m
public static void main(String[] args) {
    if (args == null || args.length == 0 || Args.hasLongOption(args, "help")) {
        Args.showHelp("fgs", MAIN_OPTIONS);
        return;
    }

    parseArgs(args);

    System.out.println("================================================================================");
    System.out.printf("FGS Discrete (%s)%n", DateTime.printNow());
    System.out.println("================================================================================");

    String argInfo = createArgsInfo();
    System.out.println(argInfo);
    LOGGER.info("=== Starting FGS Discrete: " + Args.toString(args, ' '));
    LOGGER.info(argInfo.trim().replaceAll("\n", ",").replaceAll(" = ", "="));

    Set<String> excludedVariables = (excludedVariableFile == null) ? Collections.EMPTY_SET
            : getExcludedVariables();

    runPreDataValidations(excludedVariables, System.err);
    DataSet dataSet = readInDataSet(excludedVariables);
    runOptionalDataValidations(dataSet, System.err);

    Path outputFile = Paths.get(dirOut.toString(), outputPrefix + ".txt");
    try (PrintStream writer = new PrintStream(
            new BufferedOutputStream(Files.newOutputStream(outputFile, StandardOpenOption.CREATE)))) {
        String runInfo = createOutputRunInfo(excludedVariables, dataSet);
        writer.println(runInfo);
        String[] infos = runInfo.trim().replaceAll("\n\n", ";").split(";");
        for (String s : infos) {
            LOGGER.info(s.trim().replaceAll("\n", ",").replaceAll(":,", ":").replaceAll(" = ", "="));
        }

        Graph graph = runFgs(dataSet, writer);

        writer.println();
        writer.println(graph.toString());
    } catch (IOException exception) {
        LOGGER.error("FGS failed.", exception);
        System.err.printf("%s: FGS failed.%n", DateTime.printNow());
        System.out.println("Please see log file for more information.");
        System.exit(-128);
    }
    System.out.printf("%s: FGS finished!  Please see %s for details.%n", DateTime.printNow(),
            outputFile.getFileName().toString());
    LOGGER.info(
            String.format("FGS finished!  Please see %s for details.", outputFile.getFileName().toString()));
}

From source file:edu.cmu.tetrad.cli.search.FgsDiscrete.java

/**
 * @param args the command line arguments
 *///from  ww w . j a  va  2 s  .co m
public static void main(String[] args) {
    if (args == null || args.length == 0 || Args.hasLongOption(args, "help")) {
        Args.showHelp("fgs-discrete", MAIN_OPTIONS);
        return;
    }

    parseArgs(args);

    System.out.println("================================================================================");
    System.out.printf("FGS Discrete (%s)%n", DateTime.printNow());
    System.out.println("================================================================================");

    String argInfo = createArgsInfo();
    System.out.println(argInfo);
    LOGGER.info("=== Starting FGS Discrete: " + Args.toString(args, ' '));
    LOGGER.info(argInfo.trim().replaceAll("\n", ",").replaceAll(" = ", "="));

    Set<String> excludedVariables = (excludedVariableFile == null) ? Collections.EMPTY_SET
            : getExcludedVariables();

    runPreDataValidations(excludedVariables, System.err);

    DataSet dataSet = readInDataSet(excludedVariables);

    runOptionalDataValidations(dataSet, System.err);

    Path outputFile = Paths.get(dirOut.toString(), outputPrefix + ".txt");
    try (PrintStream writer = new PrintStream(
            new BufferedOutputStream(Files.newOutputStream(outputFile, StandardOpenOption.CREATE)))) {
        String runInfo = createOutputRunInfo(excludedVariables, dataSet);
        writer.println(runInfo);
        String[] infos = runInfo.trim().replaceAll("\n\n", ";").split(";");
        for (String s : infos) {
            LOGGER.info(s.trim().replaceAll("\n", ",").replaceAll(":,", ":").replaceAll(" = ", "="));
        }

        Graph graph = runFgsDiscrete(dataSet, writer);

        writer.println();
        writer.println(graph.toString());

        if (graphML) {
            writeOutGraphML(graph, Paths.get(dirOut.toString(), outputPrefix + "_graph.txt"));
        }
    } catch (IOException exception) {
        LOGGER.error("FGS Discrete failed.", exception);
        System.err.printf("%s: FGS Discrete failed.%n", DateTime.printNow());
        System.out.println("Please see log file for more information.");
        System.exit(-128);
    }
    System.out.printf("%s: FGS Discrete finished!  Please see %s for details.%n", DateTime.printNow(),
            outputFile.getFileName().toString());
    LOGGER.info(String.format("FGS Discrete finished!  Please see %s for details.",
            outputFile.getFileName().toString()));
}