biomart 0.1.0

data/History.txt

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+=== 0.1.0 2009-08-29
+
+* 1 major enhancement:
+  * Initial release:
+    * Basic gathering of information about a Biomart server.
+    * Counting functionality.
+    * Basic searching of a single dataset.

data/Manifest.txt

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+History.txt
+Manifest.txt
+README.rdoc
+Rakefile
+biomart.gemspec
+lib/biomart.rb
+lib/biomart/attribute.rb
+lib/biomart/database.rb
+lib/biomart/dataset.rb
+lib/biomart/filter.rb
+lib/biomart/server.rb
+script/console
+script/destroy
+script/generate
+tasks/shoulda.rake
+test/test_biomart.rb
+test/test_helper.rb

data/README.rdoc

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+= Biomart
+
+http://biomart.rubyforge.org
+
+http://github.com/dazoakley/biomart
+
+Biomart provides a simple interface for working with Biomart servers 
+(see http://www.biomart.org for more info on Biomart itself), so you 
+don't have to get down and dirty with the basic webservice calls yourself.
+
+== Install
+
+sudo gem install biomart
+
+== Usage
+
+Include the module in your code:
+
+  require "rubygems"
+  require "biomart"
+  
+To basically connect to a Biomart server and have access to all of its 
+information and meta data:
+  
+  biomart = Biomart::Server.new( "http://www.biomart.org/biomart" )
+
+  # List all of the available datasets on this Biomart server
+  # (be patient - this will take a while on this server as there's 
+  # a lot there...)
+  p biomart.list_datasets
+
+  # Grab the "kermits" dataset
+  kermits = biomart.datasets["kermits"]
+
+  # List it's filters and attributes
+  p kermits.list_filters
+  p kermits.list_attributes
+
+  # Count the total number of records in the dataset
+  p kermits.count()
+
+  # Do a count with a filter added
+  p kermits.count( :filters => { "sponsor" => "EUCOMM" } )
+
+  # Do a search using the default filters and attributes
+  # - this will return a hash with :headers (an array of the headers) 
+  #   and :data (an array of arrays of results)
+  #
+  # Doing a search like this is generally a BAD idea as biomarts tend 
+  # to hold a LOT of data... Unless you have time to kill...
+  p kermits.search()
+
+  # Do a search using some specific filters (but the default attributes)
+  p kermits.search( :filters => { "marker_symbol" => "Cbx1" } )
+
+  # Do a search with specific filters and attributes
+  p kermits.search( 
+      :filters => { "marker_symbol" => "Cbx1" }, 
+      :attributes => ["marker_symbol"] 
+    )
+  
+  # If you would like to retrieve a more useful results object - i.e. an 
+  # array of hashes, where each hash represents a row of results (keyed 
+  # by the attribute name), add the :process_results argument
+  p kermits.search( 
+      :filters => { "marker_symbol" => "Cbx1" }, 
+      :process_results => true 
+    )
+  
+Or if you know the dataset you wish to work with and would like to 
+just get on with things...
+  
+  htgt_targ = Biomart::Dataset.new( 
+    "http://www.sanger.ac.uk/htgt/biomart", 
+    { :name => "htgt_targ" } 
+  )
+  p htgt_targ.count( :filters => { "is_eucomm" => "1" } )
+  
+  # etc. etc.
+  
+See Biomart module and Class docs for more detail.
+  
+== Using a Proxy
+
+If you need to channel all of your requests via a proxy, specify your 
+proxy via Biomart.proxy:
+
+  Biomart.proxy = "http://proxy.example.com/"
+
+Now all requests made through Biomart will be proxied via proxy.example.com.
+
+Alternatively you can also set your proxy url in the environment variable 
+'http_proxy', and Biomart will automatically detect this.
+
+== Meta
+
+Written by Darren Oakley (daz dot oakley at gmail dot com)
+
+http://biomart.rubyforge.org
+
+http://github.com/dazoakley/biomart
+
+== License
+
+(The MIT License)
+
+Copyright (c) 2009 Darren Oakley
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+'Software'), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/Rakefile

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+require "rubygems"
+gem "hoe", ">= 2.1.0"
+require "hoe"
+require "fileutils"
+require "./lib/biomart"
+
+Hoe.plugin :newgem
+# Hoe.plugin :website
+# Hoe.plugin :cucumberfeatures
+
+# Generate all the Rake tasks
+# Run "rake -T" to see list of generated tasks (from gem root directory)
+$hoe = Hoe.spec "biomart" do
+  self.developer        "Darren Oakley", "daz.oakley@gmail.com"
+  self.rubyforge_name   = self.name
+  self.url              = "http://github.com/dazoakley/biomart"
+  self.summary          = "A ruby API for interacting with Biomart services."
+  self.description      = "A ruby API for interacting with Biomart services."
+  self.extra_deps       = [["builder",">= 0"]]
+  self.extra_dev_deps   = [["thoughtbot-shoulda",">=0"]]
+  self.extra_rdoc_files = ["README.rdoc"]
+end
+
+require "newgem/tasks"
+Dir["tasks/**/*.rake"].each { |t| load t }
+
+# TODO - want other tests/tasks run by default? Add them to the list
+# remove_task :default
+# task :default => [:spec, :features]

data/biomart.gemspec

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+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{biomart}
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Darren Oakley"]
+  s.date = %q{2009-08-29}
+  s.description = %q{A ruby API for interacting with Biomart services.}
+  s.email = ["daz.oakley@gmail.com"]
+  s.extra_rdoc_files = ["History.txt", "Manifest.txt", "README.rdoc"]
+  s.files = ["History.txt", "Manifest.txt", "README.rdoc", "Rakefile", "biomart.gemspec", "lib/biomart.rb", "lib/biomart/attribute.rb", "lib/biomart/database.rb", "lib/biomart/dataset.rb", "lib/biomart/filter.rb", "lib/biomart/server.rb", "script/console", "script/destroy", "script/generate", "tasks/shoulda.rake", "test/test_biomart.rb", "test/test_helper.rb"]
+  s.homepage = %q{http://github.com/dazoakley/biomart}
+  s.rdoc_options = ["--main", "README.rdoc"]
+  s.require_paths = ["lib"]
+  s.rubyforge_project = %q{biomart}
+  s.rubygems_version = %q{1.3.5}
+  s.summary = %q{A ruby API for interacting with Biomart services.}
+  s.test_files = ["test/test_biomart.rb", "test/test_helper.rb"]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<builder>, [">= 0"])
+      s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+      s.add_development_dependency(%q<hoe>, [">= 2.3.3"])
+    else
+      s.add_dependency(%q<builder>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<builder>, [">= 0"])
+  end
+end

data/lib/biomart.rb

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+require "uri"
+require "net/http"
+require "rexml/document"
+require "csv"
+
+require "rubygems"
+require "builder"
+
+module Biomart
+  VERSION = "0.1.0"
+  
+  # This is the base Biomart error/exception class. Rescue it if 
+  # you want to catch any exceptions that this code might raise.
+  class BiomartError < StandardError
+    attr_reader :data
+    
+    def initialize(data)
+      @data = data
+      super
+    end
+  end
+  
+  # Error class representing HTTP errors.
+  class HTTPError      < BiomartError; end
+  
+  # Error class representing biomart filter errors.  Usually raised 
+  # when a request is made for a incorrectly named (or non-existent) 
+  # filter.
+  class FilterError    < BiomartError; end
+  
+  # Error class representing biomart attribute errors.  Usually raised 
+  # when a request is made for a incorrectly named (or non-existent) 
+  # attribute.
+  class AttributeError < BiomartError; end
+  
+  # Error class representing biomart dataset errors.  Usually raised 
+  # when a request is made for a incorrectly named (or non-existent) 
+  # dataset.
+  class DatasetError   < BiomartError; end
+  
+  @@url    = 'http://www.biomart.org/biomart/martservice'
+  @@client = Net::HTTP
+  
+  # Centralised request function for handling all of the HTTP requests 
+  # to the biomart servers.
+  def request( params={} )
+    if Biomart.proxy or ENV['http_proxy']
+      proxy_uri = Biomart.proxy
+      proxy_uri ||= ENV['http_proxy']
+      proxy = URI.parse( proxy_uri )
+      @@client = Net::HTTP::Proxy( proxy.host, proxy.port )
+    end
+    
+    params[:url] = URI.escape(params[:url])
+    
+    if params[:method] === 'post'
+      res = @@client.post_form( URI.parse(params[:url]), { "query" => params[:query] } )
+    else
+      res = @@client.get_response( URI.parse(params[:url]) )
+    end
+    
+    # Process the response code/body to catch errors.
+    if res.code != "200"
+      raise HTTPError.new(res.code), "HTTP error #{res.code}, please check your biomart server and URL settings."
+    else
+      if res.body =~ /ERROR/
+        if res.body =~ /Filter (.+) NOT FOUND/
+          raise FilterError.new(res.body), "Biomart error. Filter #{$1} not found."
+        elsif res.body =~ /Attribute (.+) NOT FOUND/
+          raise AttributeError.new(res.body), "Biomart error. Attribute #{$1} not found."
+        elsif res.body =~ /Dataset (.+) NOT FOUND/
+          raise DatasetError.new(res.body), "Biomart error. Dataset #{$1} not found."
+        else
+          raise BiomartError.new(res.body), "Biomart error."
+        end
+      end
+    end
+    
+    return res.body
+  end
+  
+  class << self
+    attr_accessor :proxy
+  end
+  
+end
+
+directory = File.expand_path(File.dirname(__FILE__))
+
+require File.join(directory, 'biomart', 'server')
+require File.join(directory, 'biomart', 'database')
+require File.join(directory, 'biomart', 'dataset')
+require File.join(directory, 'biomart', 'filter')
+require File.join(directory, 'biomart', 'attribute')

data/lib/biomart/attribute.rb

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+module Biomart
+  # Class representation for a biomart attribute. 
+  # Will belong to a Biomart::Dataset.
+  class Attribute
+    attr_reader :name, :display_name, :default
+    
+    def initialize(args)
+      @name         = args["internalName"]
+      @display_name = args["displayName"]
+      @default      = args["default"] ? true : false
+    end
+    
+  end
+end

data/lib/biomart/database.rb

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+module Biomart
+  # Class representation for a biomart database.
+  # Will contain many Biomart::Dataset objects, and belong to a Biomart::Server.
+  class Database
+    include Biomart
+    
+    attr_reader :name, :display_name, :visible
+    
+    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
+      @datasets     = {}
+    end
+    
+    # Returns an array of the dataset names (biomart 'name') 
+    # for this dataset.
+    def list_datasets
+      if @datasets.empty?
+        fetch_datasets
+      end
+      return @datasets.keys
+    end
+    
+    # Returns a hash (keyed by the biomart 'name' for the dataset) 
+    # of all of the Biomart::Dataset objects belonging to this server.
+    def datasets
+      if @datasets.empty?
+        fetch_datasets
+      end
+      return @datasets
+    end
+    
+    private
+    
+      # Utility method to do the webservice call to the biomart server 
+      # and collate/build the information about the datasets.
+      def fetch_datasets
+        url = @url + "?type=datasets&mart=#{@name}"
+        document = request( :url => url )
+        tsv_data = CSV.parse( document, "\t" )
+        tsv_data.each do |t|
+          if t[1] and ( t[3] === "1" )
+            dataset_attr = {
+              "name"         => t[1],
+              "displayName"  => t[2],
+              "visible"      => t[3]
+            }
+            @datasets[ dataset_attr["name"] ] = Dataset.new( @url, dataset_attr )
+          end
+        end
+      end
+    
+  end
+end

data/lib/biomart/dataset.rb

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+module Biomart
+  # Class represetation for a biomart dataset.
+  # Can belong to a Biomart::Database and a Biomart::Server.
+  class Dataset
+    include Biomart
+    
+    attr_reader :name, :display_name, :visible
+    
+    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
+    
+    # Returns a hash (keyed by the biomart 'internal_name' for the filter) 
+    # of all of the Biomart::Filter objects belonging to this dataset.
+    def filters
+      if @filters.empty?
+        fetch_configuration()
+      end
+      return @filters
+    end
+    
+    # Returns an array of the filter names (biomart 'internal_name') 
+    # for this dataset.
+    def list_filters
+      if @filters.empty?
+        fetch_configuration()
+      end
+      return @filters.keys
+    end
+    
+    # Returns a hash (keyed by the biomart 'internal_name' for the attribute) 
+    # of all of the Biomart::Attribute objects belonging to this dataset.
+    def attributes
+      if @attributes.empty?
+        fetch_configuration()
+      end
+      return @attributes
+    end
+    
+    # Returns an array of the attribute names (biomart 'internal_name') 
+    # for this dataset.
+    def list_attributes
+      if @attributes.empty?
+        fetch_configuration()
+      end
+      return @attributes.keys
+    end
+    
+    # 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)
+    def count( args={} )
+      args.merge!({ :count => "1" })
+      result = request( :method => 'post', :url => @url, :query => generate_xml(args) )
+      return result.to_i
+    end
+    
+    # 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).
+    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
+    
+    # Utility function to build the Biomart query XML
+    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
+    
+    private
+    
+      # Utility function to retrieve and process the configuration 
+      # xml for a dataset
+      def fetch_configuration
+        url = @url + "?type=configuration&dataset=#{@name}"
+        document = REXML::Document.new( request( :url => url ) )
+
+        # Top-Level filters...
+        REXML::XPath.each( document, '//FilterDescription' ) do |f|
+          unless f.attributes["displayType"].eql? "container"
+            @filters[ f.attributes["internalName"] ] = Filter.new( f.attributes )
+          end
+        end
+        
+        # Filters nested inside containers...
+        REXML::XPath.each( document, '//FilterDescription/Option' ) do |f|
+          if f.attributes["displayType"] != nil
+            @filters[ f.attributes["internalName"] ] = Filter.new( f.attributes )
+          end
+        end
+        
+        # Attributes are much simpler...
+        REXML::XPath.each( document, '//AttributeDescription' ) do |a|
+          @attributes[ a.attributes["internalName"] ] = Attribute.new( a.attributes )
+        end
+      end
+      
+      # Utility function to transform the tab-separated data retrieved 
+      # from the Biomart search query into a ruby object.
+      def process_tsv( args, tsv )
+        headers = []
+
+        if args[:attributes]
+          args[:attributes].each do |attribute|
+            headers.push(attribute)
+          end
+        else
+          self.attributes.each do |name,attribute|
+            if attribute.default
+              headers.push(name)
+            end
+          end
+        end
+
+        return {
+          :headers => headers,
+          :data    => CSV.parse( tsv, "\t" )
+        }
+      end
+
+      # Utility function to quickly convert a search result into an array of hashes
+      # (keyed by the attribute name) for easier processing - this is not done by 
+      # default on all searches as this can cause a large overhead on big data returns.
+      def conv_results_to_a_of_h( search_results )
+        result_objects = []
+
+        search_results[:data].each do |row|
+          tmp = {}
+          row.each_index do |index|
+            tmp[ search_results[:headers][index] ] = row[index]
+          end
+          result_objects.push(tmp)
+        end
+
+        return result_objects
+      end
+    
+  end
+end

data/lib/biomart/filter.rb

@@ -0,0 +1,15 @@
+module Biomart
+  # Class representation for a biomart filter. 
+  # Will belong to a Biomart::Dataset.
+  class Filter
+    attr_reader :name, :display_name, :default, :default_value
+    
+    def initialize(args)
+      @name          = args["internalName"]
+      @display_name  = args["displayName"]
+      @default       = args["defaultOn"] ? true : false
+      @default_value = args["defaultValue"]
+    end
+    
+  end
+end

data/lib/biomart/server.rb

@@ -0,0 +1,78 @@
+module Biomart
+  # Class representation for a biomart server.
+  # Will contain many Biomart::Database and Biomart::Dataset objects.
+  class Server
+    include Biomart
+    
+    attr_reader :url
+    
+    def initialize( url )
+      @url = url or raise ArgumentError, "must pass :url"
+      unless @url =~ /martservice/
+        @url = @url + "/martservice"
+      end
+      
+      @databases = {}
+      @datasets  = {}
+    end
+    
+    # Returns an array of the database names (biomart 'name') 
+    # for this dataset.
+    def list_databases
+      if @databases.empty?
+        fetch_databases
+      end
+      return @databases.keys
+    end
+    
+    # Returns a hash (keyed by the biomart 'name' for the database) 
+    # of all of the Biomart::Database objects belonging to this server.
+    def databases
+      if @databases.empty?
+        fetch_databases
+      end
+      return @databases
+    end
+    
+    # Returns an array of the dataset names (biomart 'name') 
+    # for this dataset.
+    def list_datasets
+      if @datasets.empty?
+        fetch_datasets
+      end
+      return @datasets.keys
+    end
+    
+    # Returns a hash (keyed by the biomart 'name' for the dataset) 
+    # of all of the Biomart::Dataset objects belonging to this server.
+    def datasets
+      if @datasets.empty?
+        fetch_datasets
+      end
+      return @datasets
+    end
+    
+    private
+    
+      # Utility method to do the webservice call to the biomart server 
+      # and collate/build the information about the databases.
+      def fetch_databases
+        url = @url + '?type=registry'
+        document = REXML::Document.new( request( :url => url ) )
+        REXML::XPath.each( document, "//MartURLLocation" ) do |d|
+          if d.attributes["visible"] === "1"
+            @databases[ d.attributes["name"] ] = Database.new( @url, d.attributes )
+          end
+        end
+      end
+      
+      # Utility function to collate all of the Biomart::Dataset objects 
+      # contained within the Biomart::Database objects.
+      def fetch_datasets
+        self.databases.each do |name,database|
+          @datasets.merge!( database.datasets )
+        end
+      end
+    
+  end
+end

data/script/console

@@ -0,0 +1,10 @@
+#!/usr/bin/env ruby
+# File: script/console
+irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
+
+libs =  " -r irb/completion"
+# Perhaps use a console_lib to store any extra methods I may want available in the cosole
+# libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
+libs <<  " -r #{File.dirname(__FILE__) + '/../lib/biomart.rb'}"
+puts "Loading biomart gem"
+exec "#{irb} #{libs} --simple-prompt"

data/script/destroy

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/destroy'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Destroy.new.run(ARGV)

data/script/generate

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/generate'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Generate.new.run(ARGV)

data/tasks/shoulda.rake

@@ -0,0 +1,15 @@
+begin
+  require 'shoulda'
+rescue LoadError
+  require 'rubygems' unless ENV['NO_RUBYGEMS']
+  require 'shoulda'
+end
+
+require 'rake/testtask'
+
+desc "Run the shoulda test under /spec"
+Rake::TestTask.new do |t|
+   t.libs << "test"
+   t.test_files = FileList['spec/*_spec.rb']
+   t.verbose = true
+end

data/test/test_biomart.rb

@@ -0,0 +1,145 @@
+require File.dirname(__FILE__) + '/test_helper.rb'
+
+class BiomartTest < Test::Unit::TestCase
+  def setup
+    @htgt     = Biomart::Server.new('http://www.sanger.ac.uk/htgt/biomart')
+    @htgt_alt = Biomart::Server.new('http://www.sanger.ac.uk/htgt/biomart')
+  end
+  
+  context "A Biomart::Server instance" do
+    should "have databases" do
+      assert( @htgt_alt.list_databases.is_a?( Array ), "Biomart::Server.list_databases is not returning an array." )
+      assert( @htgt_alt.list_databases.include?( "htgt" ), "Biomart::Server datbase parsing is off - htgt is not in htgt!" )
+      assert( @htgt.databases["htgt"].is_a?( Biomart::Database ), "Biomart::Server is not creating Biomart::Database objects." )
+    end
+    
+    should "have datasets" do
+      assert( @htgt_alt.list_datasets.is_a?( Array ), "Biomart::Server.list_datasets is not returning an array." )
+      assert( @htgt_alt.list_datasets.include?( "htgt_targ" ), "Biomart::Server dataset parsing is off - htgt_targ is not in htgt!" )
+      assert( @htgt.datasets["htgt_targ"].is_a?( Biomart::Dataset ), "Biomart::Server is not creating Biomart::Dataset objects." )
+    end
+  end
+  
+  context "A Biomart::Database instance" do
+    setup do
+      @htgt_database = @htgt.databases["htgt"]
+    end
+    
+    should "have basic metadata" do
+      assert( @htgt_database.display_name, "Biomart::Database does not have a 'display name'." )
+      assert( @htgt_database.name, "Biomart::Database does not have a 'name'." )
+      assert( @htgt_database.visible != nil, "Biomart::Database does not have a 'visible' flag." )
+    end
+    
+    should "have datasets" do
+      assert( @htgt_database.list_datasets.is_a?( Array ), "Biomart::Database.list_datasets is not returning an array." )
+      assert( @htgt_database.list_datasets.include?( "htgt_targ" ), "Biomart::Database dataset parsing is off - htgt_targ is not in htgt!" )
+      assert( @htgt_database.datasets["htgt_targ"].is_a?( Biomart::Dataset ), "Biomart::Database is not creating Biomart::Dataset objects." )
+    end
+  end
+  
+  context "A Biomart::Dataset instance" do
+    setup do
+      @htgt_targ = @htgt.datasets["htgt_targ"]
+      @htgt_trap = @htgt.datasets["htgt_trap"]
+      @kermits = @htgt.datasets["kermits"]
+    end
+    
+    should "have basic metadata" do
+      assert( @htgt_targ.display_name, "Biomart::Dataset does not have a 'display name'." )
+      assert( @htgt_targ.name, "Biomart::Dataset does not have a 'name'." )
+      assert( @htgt_targ.visible != nil, "Biomart::Dataset does not have a 'visible' flag." )
+    end
+    
+    should "have filters" do
+      assert( @htgt_targ.list_filters.is_a?( Array ), "Biomart::Dataset.list_filters is not returning an array." )
+      assert( @htgt_targ.list_filters.include?( "ensembl_gene_id" ), "Biomart::Dataset filter parsing is off - ensembl_gene_id is not in htgt_targ!" )
+      assert( @kermits.filters["ensembl_gene_id"].is_a?( Biomart::Filter ), "Biomart::Dataset is not creating Biomart::Filter objects." )
+    end
+    
+    should "have attributes" do
+      assert( @htgt_targ.list_attributes.is_a?( Array ), "Biomart::Dataset.list_attributes is not returning an array." )
+      assert( @htgt_targ.list_attributes.include?( "ensembl_gene_id" ), "Biomart::Dataset attribute parsing is off - ensembl_gene_id is not in htgt_targ!" )
+      assert( @kermits.attributes["ensembl_gene_id"].is_a?( Biomart::Attribute ), "Biomart::Dataset is not creating Biomart::Attribute objects." )
+    end
+    
+    should "perform count queries" do
+      htgt_count = @htgt_targ.count()
+      assert( htgt_count.is_a?( Integer ), "Biomart::Dataset.count is not returning integers." )
+      assert( htgt_count > 0, "Biomart::Dataset.count is returning zero - this is wrong!" )
+      
+      htgt_count_single_filter = @htgt_targ.count( :filters => { "is_eucomm" => "1" } )
+      assert( htgt_count_single_filter.is_a?( Integer ), "Biomart::Dataset.count (with single filter) is not returning integers." )
+      assert( htgt_count_single_filter > 0, "Biomart::Dataset.count (with single filter) is returning zero - this is wrong!" )
+      
+      htgt_count_single_filter_group_value = @htgt_targ.count( :filters => { "marker_symbol" => ["Cbx1","Cbx7","Art4"] } )
+      assert( htgt_count_single_filter_group_value.is_a?( Integer ), "Biomart::Dataset.count (with single filter, group value) is not returning integers." )
+      assert( htgt_count_single_filter_group_value > 0, "Biomart::Dataset.count (with single filter, group value) is returning zero - this is wrong!" )
+    end
+    
+    should "perform search queries" do
+      search = @htgt_trap.search()
+      assert( search.is_a?( Hash ), "Biomart::Dataset.search (no options) is not returning a hash." )
+      assert( search[:data].is_a?( Array ), "Biomart::Dataset.search[:data] (no options) is not returning an array." )
+      
+      search1 = @htgt_targ.search( :filters => { "marker_symbol" => "Cbx1" }, :process_results => true )
+      assert( search1.is_a?( Array ), "Biomart::Dataset.search (filters defined with processing) is not returning an array." )
+      assert( search1.first.is_a?( Hash ), "Biomart::Dataset.search (filters defined with processing) is not returning an array of hashes." )
+      assert( search1.first["marker_symbol"] == "Cbx1", "Biomart::Dataset.search (filters defined with processing) is not returning the correct info." )
+      
+      search2 = @htgt_targ.search( :filters => { "marker_symbol" => "Cbx1" }, :attributes => ["marker_symbol","ensembl_gene_id"], :process_results => true )
+      assert( search2.is_a?( Array ), "Biomart::Dataset.search (filters and attributes defined with processing) is not returning an array." )
+      assert( search2.first.is_a?( Hash ), "Biomart::Dataset.search (filters and attributes defined with processing) is not returning an array of hashes." )
+      assert( search2.first["marker_symbol"] == "Cbx1", "Biomart::Dataset.search (filters and attributes defined with processing) is not returning the correct info." )
+    end
+  end
+  
+  context "The Biomart module" do
+    setup do
+      @not_biomart = Biomart::Server.new('http://www.sanger.ac.uk')
+      @htgt_targ   = @htgt.datasets["htgt_targ"]
+      @bad_dataset = Biomart::Dataset.new( "http://www.sanger.ac.uk/htgt/biomart", { :name => "wibble" } )
+    end
+    
+    should "handle user/configuration errors (i.e. incorrect URLs etc)" do
+      begin
+        @not_biomart.list_databases
+      rescue Biomart::HTTPError => e
+        http_error = e
+      end
+      
+      assert( http_error.is_a?( Biomart::HTTPError ), "Biomart.request is not processing HTTP errors correctly." )
+    end
+    
+    should "handle biomart server errors gracefully" do
+      begin
+        @htgt_targ.count( :filters => { "wibbleblibbleblip" => "1" } )
+      rescue Biomart::FilterError => e
+        filter_error = e
+      end
+      
+      begin
+        @htgt_targ.search( :attributes => ["wibbleblibbleblip"] )
+      rescue Biomart::AttributeError => e
+        attribute_error = e
+      end
+      
+      begin
+        @bad_dataset.count()
+      rescue Biomart::DatasetError => e
+        dataset_error = e
+      end
+      
+      begin
+        @bad_dataset.count()
+      rescue Biomart::BiomartError => e
+        general_error = e
+      end
+      
+      assert( filter_error.is_a?( Biomart::FilterError ), "Biomart.request is not handling Biomart filter errors correctly." )
+      assert( attribute_error.is_a?( Biomart::AttributeError ), "Biomart.request is not handling Biomart attribute errors correctly." )
+      assert( dataset_error.is_a?( Biomart::DatasetError ), "Biomart.request is not handling Biomart dataset errors correctly." )
+      assert( general_error.is_a?( Biomart::BiomartError ), "Biomart.request is not handling general Biomart errors correctly." )
+    end
+  end
+end

data/test/test_helper.rb

@@ -0,0 +1,9 @@
+begin
+  require 'shoulda'
+rescue LoadError
+  require 'rubygems' unless ENV['NO_RUBYGEMS']
+  require 'shoulda'
+end
+
+$:.unshift(File.dirname(__FILE__) + '/../lib')
+require 'Biomart'

metadata

@@ -0,0 +1,105 @@
+--- !ruby/object:Gem::Specification 
+name: biomart
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+platform: ruby
+authors: 
+- Darren Oakley
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-08-29 00:00:00 +01:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: builder
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: thoughtbot-shoulda
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: hoe
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.3.3
+    version: 
+description: A ruby API for interacting with Biomart services.
+email: 
+- daz.oakley@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- History.txt
+- Manifest.txt
+- README.rdoc
+files: 
+- History.txt
+- Manifest.txt
+- README.rdoc
+- Rakefile
+- biomart.gemspec
+- lib/biomart.rb
+- lib/biomart/attribute.rb
+- lib/biomart/database.rb
+- lib/biomart/dataset.rb
+- lib/biomart/filter.rb
+- lib/biomart/server.rb
+- script/console
+- script/destroy
+- script/generate
+- tasks/shoulda.rake
+- test/test_biomart.rb
+- test/test_helper.rb
+has_rdoc: true
+homepage: http://github.com/dazoakley/biomart
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --main
+- README.rdoc
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: biomart
+rubygems_version: 1.3.5
+signing_key: 
+specification_version: 3
+summary: A ruby API for interacting with Biomart services.
+test_files: 
+- test/test_biomart.rb
+- test/test_helper.rb