Beispiel #1
1
  private void unzipPlugin(Path zip, Path target) throws IOException {
    Files.createDirectories(target);

    try (ZipInputStream zipInput = new ZipInputStream(Files.newInputStream(zip))) {
      ZipEntry entry;
      byte[] buffer = new byte[8192];
      while ((entry = zipInput.getNextEntry()) != null) {
        Path targetFile = target.resolve(entry.getName());

        // be on the safe side: do not rely on that directories are always extracted
        // before their children (although this makes sense, but is it guaranteed?)
        Files.createDirectories(targetFile.getParent());
        if (entry.isDirectory() == false) {
          try (OutputStream out = Files.newOutputStream(targetFile)) {
            int len;
            while ((len = zipInput.read(buffer)) >= 0) {
              out.write(buffer, 0, len);
            }
          }
        }
        zipInput.closeEntry();
      }
    }
  }
Beispiel #2
0
  public static void main(String[] args) throws MessagingException, IOException {
    Properties props = new Properties();
    try (InputStream in = Files.newInputStream(Paths.get("mail", "mail.properties"))) {
      props.load(in);
    }
    List<String> lines = Files.readAllLines(Paths.get(args[0]), Charset.forName("UTF-8"));

    String from = lines.get(0);
    String to = lines.get(1);
    String subject = lines.get(2);

    StringBuilder builder = new StringBuilder();
    for (int i = 3; i < lines.size(); i++) {
      builder.append(lines.get(i));
      builder.append("\n");
    }

    Console console = System.console();
    String password = new String(console.readPassword("Password: "));

    Session mailSession = Session.getDefaultInstance(props);
    // mailSession.setDebug(true);
    MimeMessage message = new MimeMessage(mailSession);
    message.setFrom(new InternetAddress(from));
    message.addRecipient(RecipientType.TO, new InternetAddress(to));
    message.setSubject(subject);
    message.setText(builder.toString());
    Transport tr = mailSession.getTransport();
    try {
      tr.connect(null, password);
      tr.sendMessage(message, message.getAllRecipients());
    } finally {
      tr.close();
    }
  }
Beispiel #3
0
 public static void main(String[] args) throws IOException {
   Properties props = new Properties();
   try (InputStream in = Files.newInputStream(Paths.get(args[0]))) {
     props.load(in);
   }
   String url = props.remove("url").toString();
   String result = doPost(url, props);
   System.out.println(result);
 }
Beispiel #4
0
  /**
   * Gets a connection from the properties specified in the file database.properties
   *
   * @return the database connection
   */
  public static Connection getConnection() throws SQLException, IOException {
    Properties props = new Properties();
    try (InputStream in = Files.newInputStream(Paths.get("database.properties"))) {
      props.load(in);
    }

    String drivers = props.getProperty("jdbc.drivers");
    if (drivers != null) System.setProperty("jdbc.drivers", drivers);

    String url = props.getProperty("jdbc.url");
    String username = props.getProperty("jdbc.username");
    String password = props.getProperty("jdbc.password");

    return DriverManager.getConnection(url, username, password);
  }
  private void processFile(Path inGzPath, String conservedType) throws IOException {

    BufferedReader br =
        new BufferedReader(
            new InputStreamReader(new GZIPInputStream(Files.newInputStream(inGzPath))));

    String line = null;
    String chromosome = "";
    int start = 0, end = 0;
    float value;
    Map<String, String> attributes = new HashMap<>();
    //        ConservedRegion conservedRegion =  null;
    List<Float> values = new ArrayList<>();

    ConservedRegionChunk conservedRegion = null;

    while ((line = br.readLine()) != null) {
      if (line.startsWith("fixedStep")) {
        // new group, save last
        if (conservedRegion != null) {
          conservedRegion.setEnd(end);
          conservedRegion =
              new ConservedRegionChunk(
                  chromosome, start, end, conservedType, start / CHUNKSIZE, values);
          fileSerializer.serialize(conservedRegion, getOutputFileName(chromosome));
        }

        //                offset = 0;
        attributes.clear();
        String[] attrFields = line.split(" ");
        String[] attrKeyValue;
        for (String attrField : attrFields) {
          if (!attrField.equalsIgnoreCase("fixedStep")) {
            attrKeyValue = attrField.split("=");
            attributes.put(attrKeyValue[0].toLowerCase(), attrKeyValue[1]);
          }
        }
        chromosome = attributes.get("chrom").replace("chr", "");
        start = Integer.parseInt(attributes.get("start"));
        end = Integer.parseInt(attributes.get("start"));

        values = new ArrayList<>(2000);
      } else {
        int startChunk = start / CHUNKSIZE;
        end++;
        int endChunk = end / CHUNKSIZE;

        if (startChunk != endChunk) {
          conservedRegion =
              new ConservedRegionChunk(
                  chromosome, start, end - 1, conservedType, startChunk, values);
          fileSerializer.serialize(conservedRegion, getOutputFileName(chromosome));
          values.clear();
          start = end;
        }

        value = Float.parseFloat(line.trim());
        values.add(value);
      }
    }
    // write last
    conservedRegion =
        new ConservedRegionChunk(chromosome, start, end, conservedType, start / CHUNKSIZE, values);
    fileSerializer.serialize(conservedRegion, getOutputFileName(chromosome));
    br.close();
  }