Class: Biomart::Dataset

Inherits:
Object
  • Object
show all
Includes:
Biomart
Defined in:
lib/biomart/dataset.rb

Overview

Class represetation for a biomart dataset. Can belong to a Biomart::Database and a Biomart::Server.

Constant Summary

Constants included from Biomart

VERSION

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Biomart

#request

Constructor Details

#initialize(url, args) ⇒ Dataset

Returns a new instance of Dataset.



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# File 'lib/biomart/dataset.rb', line 9

def initialize( url, args )
  @url = url or raise ArgumentError, "must pass :url"
  unless @url =~ /martservice/
    @url = @url + "/martservice"
  end
  
  @name         = args["name"] || args[:name]
  @display_name = args["displayName"] || args[:display_name]
  @visible      = ( args["visible"] || args[:visible] ) ? true : false
  
  @filters      = {}
  @attributes   = {}
  @importables  = {}
  @exportables  = {}
end

Instance Attribute Details

#display_name ⇒ Object (readonly)

Returns the value of attribute display_name.



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# File 'lib/biomart/dataset.rb', line 7

def display_name
  @display_name
end

#name ⇒ Object (readonly)

Returns the value of attribute name.



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# File 'lib/biomart/dataset.rb', line 7

def name
  @name
end

#visible ⇒ Object (readonly)

Returns the value of attribute visible.



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# File 'lib/biomart/dataset.rb', line 7

def visible
  @visible
end

Instance Method Details

#attributes ⇒ Object

Returns a hash (keyed by the biomart ‘internal_name’ for the attribute) of all of the Biomart::Attribute objects belonging to this dataset.



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# File 'lib/biomart/dataset.rb', line 45

def attributes
  if @attributes.empty?
    fetch_configuration()
  end
  return @attributes
end

#count(args = {}) ⇒ Object

Function to perform a Biomart count. Returns an integer value for the result of the count query.

optional arguments:

:filters

hash of key-value pairs (filter => search term)



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# File 'lib/biomart/dataset.rb', line 67

def count( args={} )
  args.merge!({ :count => "1" })
  result = request( :method => 'post', :url => @url, :query => generate_xml(args) )
  return result.to_i
end

#filters ⇒ Object

Returns a hash (keyed by the biomart ‘internal_name’ for the filter) of all of the Biomart::Filter objects belonging to this dataset.



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# File 'lib/biomart/dataset.rb', line 27

def filters
  if @filters.empty?
    fetch_configuration()
  end
  return @filters
end

#generate_xml(args = {}) ⇒ Object

Utility function to build the Biomart query XML



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# File 'lib/biomart/dataset.rb', line 96

def generate_xml( args={} )
  biomart_xml = ""
  xml = Builder::XmlMarkup.new( :target => biomart_xml, :indent => 2 )
  
  xml.instruct!
  xml.declare!( :DOCTYPE, :Query )
  xml.Query( :virtualSchemaName => "default", :formatter => "TSV", :header => "0", :uniqueRows => "1", :count => args[:count], :datasetConfigVersion => "0.6" ) {
    xml.Dataset( :name => @name, :interface => "default" ) {
      
      if args[:filters]
        args[:filters].each do |name,value|
          if value.is_a? Array
            value = value.join(",")
          end
          xml.Filter( :name => name, :value => value )
        end
      else
        self.filters.each do |name,filter|
          if filter.default
            xml.Filter( :name => name, :value => filter.default_value )
          end
        end
      end
      
      unless args[:count]
        if args[:attributes]
          args[:attributes].each do |name|
            xml.Attribute( :name => name )
          end
        else
          self.attributes.each do |name,attribute|
            if attribute.default
              xml.Attribute( :name => name )
            end
          end
        end
      end
      
    }
  }
  
  return biomart_xml
end

#list_attributes ⇒ Object

Returns an array of the attribute names (biomart ‘internal_name’) for this dataset.



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# File 'lib/biomart/dataset.rb', line 54

def list_attributes
  if @attributes.empty?
    fetch_configuration()
  end
  return @attributes.keys
end

#list_filters ⇒ Object

Returns an array of the filter names (biomart ‘internal_name’) for this dataset.



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# File 'lib/biomart/dataset.rb', line 36

def list_filters
  if @filters.empty?
    fetch_configuration()
  end
  return @filters.keys
end

#search(args = {}) ⇒ Object

Function to perform a Biomart search.

optional arguments:

:filters

hash of key-value pairs (filter => search term)

:attributes

array of attributes to retrieve

:process_results

true/false - convert search results to object

By default will return a hash with the following:

:headers

array of headers

:data

array of arrays containing search results

But with the :process_results option will return an array of hashes, where each hash represents a row of results (keyed by the attribute name).



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# File 'lib/biomart/dataset.rb', line 88

def search( args={} )
  response = request( :method => 'post', :url => @url, :query => generate_xml(args) )
  result   = process_tsv( args, response )
  result   = conv_results_to_a_of_h( result ) if args[:process_results]
  return result
end