Package org.biojava.nbio.core.util

Class FileDownloadUtils

java.lang.Object
org.biojava.nbio.core.util.FileDownloadUtils
public class FileDownloadUtils extends Object

  • Constructor Details

    • FileDownloadUtils

      public FileDownloadUtils()

  • Method Details

    • copy

      public static void copy(File src, File dst) throws IOException
      Copy the content of file src to dst TODO since java 1.7 this is provided in java.nio.file.Files
      Parameters:
      src -
      dst -
      Throws:
      IOException

    • getFileExtension

      public static String getFileExtension(File f)
      Gets the file extension of a file, excluding '.'. If the file name has no extension the file name is returned.
      Parameters:
      f - a File
      Returns:
      The extension

    • getFilePrefix

      public static String getFilePrefix(File f)
      Gets the file name up to and excluding the first '.' character. If there is no extension, the full filename is returned.
      Parameters:
      f - A file
      Returns:
      A possibly empty but non-null String.

    • downloadFile

      public static void downloadFile(URL url, File destination) throws IOException
      Download the content provided at URL url and store the result to a local file, using a temp file to cache the content in case something goes wrong in download. A timeout of 60 seconds is hard-coded and 10 retries are attempted.
      Parameters:
      url -
      destination -
      Throws:
      IOException

    • toUnixPath

      public static String toUnixPath(String path)
      Converts path to Unix convention and adds a terminating slash if it was omitted.
      Parameters:
      path - original platform dependent path
      Returns:
      path in Unix convention
      Since:
      3.2

    • expandUserHome

      public static String expandUserHome(String file)
      Expands ~ in paths to the user's home directory.

      This does not work for some special cases for paths: Other users' homes (~user/...), and Tilde expansion within the path (/.../~/...). In these cases the original argument is returned.

      Parameters:
      file - A filepath starting with a tilde
      Returns:
      An absolute path

    • ping

      public static boolean ping(String url, int timeout)
      Pings a HTTP URL. This effectively sends a HEAD request and returns true if the response code is in the 200-399 range.
      Parameters:
      url - The HTTP URL to be pinged.
      timeout - The timeout in millis for both the connection timeout and the response read timeout. Note that the total timeout is effectively two times the given timeout.
      Returns:
      true if the given HTTP URL has returned response code 200-399 on a HEAD request within the given timeout, otherwise false.

    • prepareURLConnection

      public static URLConnection prepareURLConnection(String url, int timeout) throws IOException
      Prepare URLConnection with customised timeouts.
      Parameters:
      url - The URL
      timeout - The timeout in millis for both the connection timeout and the response read timeout. Note that the total timeout is effectively two times the given timeout.

      Example of code. UrlConnection conn = prepareURLConnection("http://www.google.com/", 20000); conn.connect(); conn.getInputStream();

      NB. User should execute connect() method before getting input stream.

      Returns:
      Throws:
      IOException

    • deleteDirectory

      public static void deleteDirectory(Path dir) throws IOException
      Recursively delete a folder invalid input: '&' contents
      Parameters:
      dir - directory to delete
      Throws:
      IOException

    • deleteDirectory

      public static void deleteDirectory(String dir) throws IOException
      Recursively delete a folder invalid input: '&' contents
      Parameters:
      dir - directory to delete
      Throws:
      IOException