module MiGA::Common::Net

download_file_ftp(connection, file = nil, target = nil) { |transferred| ... } click to toggle source

Download a file via FTP using the connection (returned by .remote_connection) with remote name file into local target. If file is nil, it tries to guess the file from connection. If target is nil, it returns the read data instead

Alternatively, connection can simply be the host (String), a recognized Symbol (see .remote_connection), or a parsed URI object, in which case the function opens the connection automatically

Reports progress to the function block with two arguments: the currently transferred size and the total file size

# File lib/miga/common/net.rb, line 78
def download_file_ftp(connection, file = nil, target = nil)
  # Open connection unless passed
  close_conn = false
  if connection.is_a?(String) || connection.is_a?(Symbol) ||
        connection.is_a?(URI)
    connection = remote_connection(connection)
    file ||= remote_connection_uri.path
    close_conn = true
  end

  # Prepare download
  FileUtils.mkdir_p(File.dirname(target)) if target
  filesize = connection.size(file)
  transferred =
    target && connection.resume && File.exist?(target) ? File.size(target) : 0

  # Get in chunks of 1KiB
  ret = ''
  connection.getbinaryfile(file, target, 1024) do |data|
    yield(transferred += data.size, filesize) if block_given?
    ret += data unless target
  end

  # Close connection if automatically opened
  connection.close if close_conn
  ret unless target
end

http_request(method, url, *opts) click to toggle source

Submit an HTTP or HTTPS request using url, which should be a URL either as String or parsed URI. The request follows the method, which should be a Net::HTTP verb such as :get, :post, or :patch. All additional parameters for the corresponding method should be passed as opts.

# File lib/miga/common/net.rb, line 112
def http_request(method, url, *opts)
  doc = nil
  remote_connection(url).start do |http|
    res = http.send(method, remote_connection_uri.to_s, *opts)
    if %w[301 302].include?(res.code)
      DEBUG "REDIRECTION #{res.code}: #{res['location']}"
      return http_request(method, res['location'], *opts)
    end
    res.value # To force exception unless success
    doc = res.body
  end
  doc
end

Also aliased as: https_request

https_request(method, url, *opts)

Alias for: http_request

known_hosts(name) click to toggle source

Returns the URL of the host name (Symbol)

# File lib/miga/common/net.rb, line 18
def known_hosts(name)
  case name.to_sym
  when :miga_online_ftp
    "ftp://#{main_server}//" # <- // to simplify chdir in connection
  when :miga_db
    "ftp://#{main_server}/db"
  when :miga_dist
    "ftp://#{main_server}/dist"
  else
    raise "Unrecognized server name: #{name}"
  end
end

main_server() click to toggle source

Returns the address of the main MiGA server

# File lib/miga/common/net.rb, line 33
def main_server
  'gatech.microbial-genomes.org'
end

net_method(method, uri, *opts) click to toggle source

# File lib/miga/common/net.rb, line 126
def net_method(method, uri, *opts)
  attempts ||= 0
  uri = URI.parse(uri) if uri.is_a? String
  DEBUG "#{method.to_s.upcase}: #{uri} #{opts}"
  case method.to_sym
  when :ftp
    download_file_ftp(uri, *opts)
  else
    http_request(method, uri, *opts)
  end
rescue => e
  raise e if (attempts += 1) >= 3

  sleep 5 # <- For: 429 Too Many Requests
  DEBUG "RETRYING after: #{e}"
  retry
end

normalize_encoding(body) click to toggle source

Normalize the encoding of body to UTF-8 by attempting several common recodings. Code from github.com/seq-code/registry

# File lib/miga/common/net.rb, line 149
def normalize_encoding(body)
  # Test encodings
  body.force_encoding('utf-8')
  %w[iso8859-1 windows-1252 us-ascii ascii-8bit].each do |enc|
    break if body.valid_encoding?
    recode = body.force_encoding(enc).encode('utf-8')
    body = recode if recode.valid_encoding?
  end
  # If nothing works, replace offending characters with '?'
  unless body.valid_encoding?
    body = body.encode(
      'utf-8', invalid: :replace, undef: :replace, replace: '?'
    )
  end
  body
end

remote_connection(host) click to toggle source

Connect to an FTP host (String), a known host name (Symbol, see .known_hosts), or a parsed URI object

Sets the attribute remote_connection_uri to the parsed URI object silently

# File lib/miga/common/net.rb, line 43
def remote_connection(host)
  host = known_hosts(host) if host.is_a?(Symbol)
  uri = host.is_a?(URI) ? host : URI.parse(host)
  @remote_connection_uri = uri

  case uri.scheme
  when 'ftp'
    ftp = Net::FTP.new(uri.host)
    ftp.passive = true
    ftp.resume  = true
    ftp.login
    ftp.chdir(uri.path) unless host.is_a?(URI)
    ftp
  when 'http', 'https'
    http = Net::HTTP.new(uri.host, uri.port)
    http.read_timeout = 600
    http.use_ssl = uri.scheme == 'https'
    http
  else
    raise 'Only FTP, HTTP, and HTTPS are currently supported'
  end
end

Attributes

Public Instance Methods