Package org.biojava.nbio.core.util

Class FileDownloadUtils

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

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    static enum 
    FileDownloadUtils.Hash
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    FileDownloadUtils()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    createValidationFiles(URLConnection resourceUrlConnection, File localDestination, URL hashURL, FileDownloadUtils.Hash hash)
    Creates validation files beside a file to be downloaded.
    Whenever possible, for a file.ext file, it creates file.ext.size and file.hash_XXXX in the same folder where file.ext exists (XXXX may be DM5, SHA1, or SHA256).
    static void
    createValidationFiles(URL url, File localDestination, URL hashURL, FileDownloadUtils.Hash hash)
    Creates validation files beside a file to be downloaded.
    Whenever possible, for a file.ext file, it creates file.ext.size and file.hash for in the same folder where file.ext exists.
    static void
    deleteDirectory(String dir)
    Recursively delete a folder & contents
    static void
    deleteDirectory(Path dir)
    Recursively delete a folder & contents
    static void
    downloadFile(URL url, File destination)
    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.
    static String
    expandUserHome(String file)
    Expands ~ in paths to the user's home directory.
    static String
    getFileExtension(File f)
    Gets the file extension of a file, excluding '.'.
    static String
    getFilePrefix(File f)
    Gets the file name up to and excluding the first '.' character.
    static boolean
    ping(String url, int timeout)
    Pings a HTTP URL.
    static URLConnection
    prepareURLConnection(String url, int timeout)
    Prepare URLConnection with customised timeouts.
    static String
    toUnixPath(String path)
    Converts path to Unix convention and adds a terminating slash if it was omitted.
    static boolean
    validateFile(File localFile)
    Validate a local file based on pre-existing metadata files for size and hash.
    If the passed in localFile parameter is a file named file.ext, the function searches in the same folder for: file.ext.size: If found, it compares the size stored in it to the length of localFile (in bytes). file.ext.hash_XXXX (where XXXX is DM5, SHA1, or SHA256): If found, it compares the size stored in it to the hash code of localFile. If any of these comparisons fail, the function returns false. otherwise it returns true.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

  • Method Details

    • 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

    • createValidationFiles

      public static void createValidationFiles(URL url, File localDestination, URL hashURL, FileDownloadUtils.Hash hash)
      Creates validation files beside a file to be downloaded.
      Whenever possible, for a file.ext file, it creates file.ext.size and file.hash for in the same folder where file.ext exists. If the file connection size could not be deduced from the URL, no size file is created. If hashURL is null, no hash file is created.
      Parameters:
      url - the remote file URL to download
      localDestination - the local file to download into
      hashURL - the URL of the hash file to download. Can be null.
      hash - The Hashing algorithm. Ignored if hashURL is null.

    • createValidationFiles

      public static void createValidationFiles(URLConnection resourceUrlConnection, File localDestination, URL hashURL, FileDownloadUtils.Hash hash)
      Creates validation files beside a file to be downloaded.
      Whenever possible, for a file.ext file, it creates file.ext.size and file.hash_XXXX in the same folder where file.ext exists (XXXX may be DM5, SHA1, or SHA256). If the file connection size could not be deduced from the resourceUrlConnection URLConnection, no size file is created. If hashURL is null, no hash file is created.
      N.B. None of the hashing algorithms is implemented (yet), because we did not need any of them yet.
      Parameters:
      resourceUrlConnection - the remote file URLConnection to download
      localDestination - the local file to download into
      hashURL - the URL of the hash file to download. Can be null.
      hash - The Hashing algorithm. Ignored if hashURL is null.
      Since:
      7.0.0

    • validateFile

      public static boolean validateFile(File localFile)
      Validate a local file based on pre-existing metadata files for size and hash.
      If the passed in localFile parameter is a file named file.ext, the function searches in the same folder for:
      • file.ext.size: If found, it compares the size stored in it to the length of localFile (in bytes).
      • file.ext.hash_XXXX (where XXXX is DM5, SHA1, or SHA256): If found, it compares the size stored in it to the hash code of localFile.
      If any of these comparisons fail, the function returns false. otherwise it returns true.

      N.B. None of the 3 common verification hashing algorithms are implement yet.

      Parameters:
      localFile - The file to validate
      Returns:
      false if any of the size or hash code metadata files exists but its contents does not match the expected value in the file, true otherwise.
      Since:
      7.0.0

    • 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 & contents
      Parameters:
      dir - directory to delete
      Throws:
      IOException

    • deleteDirectory

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