Module: Bioroebe::Biomart

Included in:
Database, Dataset, Server
Defined in:
lib/bioroebe/biomart/filter.rb,
lib/bioroebe/biomart/server.rb,
lib/bioroebe/biomart/biomart.rb,
lib/bioroebe/biomart/dataset.rb,
lib/bioroebe/biomart/database.rb,
lib/bioroebe/biomart/attribute.rb

Defined Under Namespace

Classes: ArgumentError, Attribute, AttributeError, BiomartError, Database, Dataset, DatasetError, Filter, FilterError, HTTPError, Server

Class Attribute Summary collapse

Instance Method Summary collapse

Class Attribute Details

.proxy ⇒ Object

Bioroebe::Biomart.proxy = “proxy.example.com/”



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# File 'lib/bioroebe/biomart/biomart.rb', line 208

def proxy
  @proxy
end

.timeout ⇒ Object

Returns the value of attribute timeout.



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# File 'lib/bioroebe/biomart/biomart.rb', line 209

def timeout
  @timeout
end

Instance Method Details

#request(params) ⇒ String

#

request

Centralised request function for handling all of the HTTP requests to the biomart servers.

#

Examples:

request({
  :url     => 'http://www.example.com',   # the url
  :method  => 'get',                      # get/post
  :query   => 'a string',                 # when using post, send this as 'query' (i.e. the biomart query xml)
  :timeout => 60                          # override the default timeout
})

Parameters:

  • params (Hash) —

    Parameters to be passed to the request method.

Returns:

  • (String) —

    The response body

Raises:

  • Biomart::ArgumentError Raised if a params hash is not passed (or it is empty)

  • Biomart::HTTPError Raised if a HTTP error was encountered

  • Biomart::FilterError Raised when a filter is not found

  • Biomart::AttributeError Raised when an attribute is not found

  • Biomart::DatasetError Raised when a dataset is not found

  • Biomart::BiomartError Raised for any other unhandled error



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# File 'lib/bioroebe/biomart/biomart.rb', line 166

def request(params)
  raise ArgumentError if !params.is_a?(Hash) || params.empty?

  require 'uri'

  if params[:url] =~ / /
    params[:url].gsub!(' ','+')
  end

  uri      = URI.parse( params[:url] )
  client   = net_http_client()
  req      = nil
  response = nil

  case params[:method]
  when 'post'
    req           = Net::HTTP::Post.new(uri.path)
    req.form_data = { 'query' => params[:query] }
  else
    req           = Net::HTTP::Get.new(uri.request_uri)
  end

  client.start(uri.host, uri.port) { |http|
    if Biomart.timeout or params[:timeout]
      http.read_timeout = params[:timeout] ? params[:timeout] : Biomart.timeout
      http.open_timeout = params[:timeout] ? params[:timeout] : Biomart.timeout
    end
    response = http.request(req)
  }
  response_code = response.code
  response_body = response.body
  if defined? Encoding && response_body.encoding == Encoding::ASCII_8BIT
    response_body = response_body.force_encoding(Encoding::UTF_8).encode
  end
  check_response(response_body, response_code)
  return response_body
end