biomart 0.2.0 → 0.2.1

data/.gitignore

@@ -0,0 +1,4 @@
+coverage*
+simplecov*
+tmp/metric_fu*
+tmp/*.json

data/Gemfile

@@ -0,0 +1,4 @@
+source "http://rubygems.org"
+
+# Specify your gem's dependencies in lorem.gemspec
+gemspec

data/Gemfile.lock

@@ -0,0 +1,22 @@
+PATH
+  remote: .
+  specs:
+    biomart (0.2.1)
+      builder
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    builder (2.1.2)
+    shoulda (2.11.3)
+    simplecov (0.4.0)
+      simplecov-html (~> 0.4.0)
+    simplecov-html (0.4.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  biomart!
+  shoulda (>= 2.10)
+  simplecov

data/History.txt

@@ -1,3 +1,11 @@
+=== 0.2.1 2011-02-16
+
+* 1 minor bugfix:
+  * Force retrieved ASCII_8BIT text encoding to UTF-8 when running in 
+    Ruby 1.9+.
+* 1 minor enhancement:
+  * Added support for boolean filters.
+
 === 0.2.0 2010-06-10
 
 * 2 major enhancements:

data/{Manifest.txt → Manifest}

@@ -9,10 +9,11 @@ lib/biomart/database.rb
 lib/biomart/dataset.rb
 lib/biomart/filter.rb
 lib/biomart/server.rb
-script/console
-script/destroy
-script/generate
+lib/biomart/version.rb
 tasks/metrics.rake
+tasks/rcov.rake
 tasks/shoulda.rake
+tasks/yard.rake
 test/test_biomart.rb
 test/test_helper.rb
+Manifest

data/README.rdoc

@@ -10,7 +10,7 @@ don't have to get down and dirty with the basic webservice calls yourself.
 
 == Install
 
-sudo gem install biomart
+  gem install biomart
 
 == Usage
 
@@ -80,6 +80,39 @@ just get on with things...
   
 See Biomart module and Class docs for more detail.
 
+== Advanced Filtering
+
+Most filters in biomart are just pure textual filters, i.e.
+
+  kermits.search( :filters => { "marker_symbol" => "Cbx1" } )
+
+To filter on more than one term, simply pass a comma concatenated string, 
+or an array (the following two searches are equivalent):
+
+  kermits.search( :filters => { "marker_symbol" => "Cbx1,Mysm1" } )
+  kermits.search( :filters => { "marker_symbol" => ["Cbx1","Mysm1"] } )
+
+Finally, there are also boolean filters (shown in the standard MartView 
+interface as a filter name and then two radio buttons: 'Only' or 
+'Excluded').  These filers can only accept the following:
+
+- 'Only': true / 'only' / 'included'
+- 'Excluded': false / 'excluded'
+
+Here's some example usage:
+
+  snp_mart = Biomart::Dataset.new( "http://www.ensembl.org/biomart", { :name => "hsapiens_snp" } )
+  
+  # These are equivalent to selecting 'Only' in MartView
+  snp_mart.search( :filters => { 'with_variation_annotation' => true,       'ensembl_gene' => 'ENSG00000244734' } )
+  snp_mart.search( :filters => { 'with_variation_annotation' => 'only',     'ensembl_gene' => 'ENSG00000244734' } )
+  snp_mart.search( :filters => { 'with_variation_annotation' => 'included', 'ensembl_gene' => 'ENSG00000244734' } )
+  
+  # These are equivalent to selecting 'Excluded' in MartView
+  snp_mart.search( :filters => { 'with_variation_annotation' => false,      'ensembl_gene' => 'ENSG00000244734' } )
+  snp_mart.search( :filters => { 'with_variation_annotation' => 'excluded', 'ensembl_gene' => 'ENSG00000244734' } )
+  
+
 == Federated Searches
 
 To perform a federated search across two datasets...
@@ -130,6 +163,36 @@ possible to federate across more than two datasets in biomart itself.
 
 Count queries are only allowed on single datasets.
 
+== Required Attributes
+
+As biomarts are generally big de-normalised data stores, a common task 
+after receiving a set of results is to filter out rows that don't have 
+information for a given attribute or set of attributes.  A facility for 
+doing this has been built into the gem.
+
+  htgt = Biomart::Server.new( "http://www.sanger.ac.uk/htgt/biomart" )
+  
+  res = htgt.datasets["mmusculus_gene_ensembl"].search(
+    :filters => {
+      "chromosome_name" => "1",
+      "start"           => "1",
+      "end"             => "10000000"
+    },
+    :attributes => [
+      "ensembl_gene_id", "ensembl_transcript_id",
+      "mouse_paralog_ensembl_gene", "mouse_paralog_chromosome"
+    ],
+    :required_attributes => ["mouse_paralog_ensembl_gene"]
+  )
+
+The above will perform a basic search and then automatically remove 
+any result row that does not have a value for the "mouse_paralog_ensembl_gene" 
+attribute.
+
+Note: You can specify more than one required attribute.  If more than one 
+required attribute is specified, ALL of these attributes must be present 
+for a data row to be returned (it is using AND logic).
+
 == Using a Proxy
 
 If you need to channel all of your requests via a proxy, specify your 

data/Rakefile

@@ -1,32 +1,6 @@
-require "rubygems"
+require 'bundler'
 
-gem "flog", "= 2.2.0"
-gem "hoe", ">= 2.1.0"
+Bundler::GemHelper.install_tasks
 
-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 XML based webservices."
-  self.extra_deps       = [["builder",">= 0"]]
-  self.extra_dev_deps   = [["shoulda",">= 2.10"]]
-  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]
+Dir['tasks/*.rake'].each { |t| load t }
+task :default => [:test]

data/biomart.gemspec

@@ -1,40 +1,25 @@
 # -*- encoding: utf-8 -*-
+$:.push File.expand_path("../lib", __FILE__)
+require "biomart/version"
 
 Gem::Specification.new do |s|
-  s.name = %q{biomart}
-  s.version = "0.2.0"
+  s.name        = "biomart"
+  s.version     = Biomart::VERSION
+  s.platform    = Gem::Platform::RUBY
+  s.authors     = ["Darren Oakley"]
+  s.email       = ["daz.oakley@gmail.com"]
+  s.homepage    = "http://github.com/dazoakley/biomart"
+  s.summary     = "A ruby API for interacting with Biomart services."
+  s.description = "A ruby API for interacting with Biomart XML based webservices."
 
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Darren Oakley"]
-  s.date = %q{2010-06-10}
-  s.description = %q{A ruby API for interacting with Biomart XML based webservices.}
-  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/metrics.task", "tasks/shoulda.task", "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{1.3.7}
-  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
+  s.rubyforge_project = "biomart"
 
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<builder>, [">= 0"])
-      s.add_development_dependency(%q<shoulda>, [">= 2.10"])
-      s.add_development_dependency(%q<hoe>, [">= 2.6.1"])
-    else
-      s.add_dependency(%q<builder>, [">= 0"])
-      s.add_dependency(%q<shoulda>, [">= 2.10"])
-      s.add_dependency(%q<hoe>, [">= 2.6.1"])
-    end
-  else
-    s.add_dependency(%q<builder>, [">= 0"])
-    s.add_dependency(%q<shoulda>, [">= 2.10"])
-    s.add_dependency(%q<hoe>, [">= 2.6.1"])
-  end
+  s.files         = `git ls-files`.split("\n")
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  s.require_paths = ["lib"]
+  
+  s.add_runtime_dependency("builder", [">= 0"])
+  s.add_development_dependency("shoulda", [">= 2.10"])
+  s.add_development_dependency("simplecov", [">= 0"])
 end

data/lib/biomart.rb

@@ -8,8 +8,6 @@ require "rubygems"
 require "builder"
 
 module Biomart
-  VERSION = "0.2.0"
-  
   # 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
@@ -71,9 +69,16 @@ module Biomart
       response = http.request(req)
     end
     
-    check_response( response.body, response.code )
+    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
+    return response_body
   end
   
   class << self
@@ -133,6 +138,7 @@ end
 
 directory = File.expand_path(File.dirname(__FILE__))
 
+require File.join(directory, 'biomart', 'version')
 require File.join(directory, 'biomart', 'server')
 require File.join(directory, 'biomart', 'database')
 require File.join(directory, 'biomart', 'dataset')

data/lib/biomart/dataset.rb

@@ -6,6 +6,19 @@ module Biomart
     
     attr_reader :name, :display_name, :visible
     
+    # Creates a new Biomart::Dataset object.
+    #
+    # @param [String] url The URL location of the biomart server.
+    # @param [Hash] args An arguments hash giving details of the dataset.
+    #
+    # arguments hash:
+    #
+    #   {
+    #     :name         => String,     #
+    #     "name"        => String,     #
+    #     :display_name => {}          #
+    #     
+    #   }
     def initialize( url, args )
       @url = url or raise ArgumentError, "must pass :url"
       unless @url =~ /martservice/
@@ -235,15 +248,30 @@ module Biomart
 
           if args[:filters]
             args[:filters].each do |name,value|
-              if value.is_a? Array
-                value = value.join(",")
+              raise Biomart::ArgumentError, "The filter '#{name}' does not exist" if dataset.filters[name].nil?
+              
+              if dataset.filters[name].type == 'boolean'
+                value = value.downcase if value.is_a? String
+                if [true,'included','only'].include?(value)
+                  xml.Filter( :name => name, :excluded => '0' )
+                elsif [false,'excluded'].include?(value)
+                  xml.Filter( :name => name, :excluded => '1' )
+                else
+                  raise Biomart::ArgumentError, "The boolean filter '#{name}' can only accept 'true/included/only' or 'false/excluded' arguments."
+                end
+              else
+                value = value.join(",") if value.is_a? Array
+                xml.Filter( :name => name, :value => value )
               end
-              xml.Filter( :name => name, :value => value )
             end
           else
             dataset.filters.each do |name,filter|
               if filter.default?
-                xml.Filter( :name => name, :value => filter.default_value )
+                if filter.type == 'boolean'
+                  xml.Filter( :name => name, :excluded => filter.default_value )
+                else
+                  xml.Filter( :name => name, :value => filter.default_value )
+                end
               end
             end
           end

data/lib/biomart/filter.rb

@@ -13,6 +13,8 @@ module Biomart
       @qualifier       = args["qualifier"]
       @type            = args["type"]
       @multiple_values = args["multipleValues"] ? true : false
+      
+      @type.downcase! unless @type.nil?
     end
     
     # Convenience method to see if this filter is hidden from 

data/lib/biomart/version.rb

@@ -0,0 +1,3 @@
+module Biomart
+  VERSION = "0.2.1"
+end

data/tasks/rcov.rake

@@ -0,0 +1,16 @@
+begin
+  require "rcov/rcovtask"
+
+  desc "Analyze code coverage with tests"
+  Rcov::RcovTask.new do |t|
+    t.libs << "test"
+    t.test_files = FileList["test/test*.rb"]
+    t.verbose = true
+    t.rcov_opts << "--exclude /gems/,/Library/,spec,features"
+  end
+rescue LoadError
+  if /^1\.8/ === RUBY_VERSION
+    puts "[ERROR] Unable to load 'rcov' tasks - please install rcov"
+  end
+end
+

data/tasks/shoulda.rake

@@ -1,15 +1,13 @@
 begin
-  require 'shoulda'
-rescue LoadError
-  require 'rubygems' unless ENV['NO_RUBYGEMS']
-  require 'shoulda'
-end
+  require "shoulda"
+  require "rake/testtask"
 
-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
+  desc "Run the test suite under /test"
+  Rake::TestTask.new do |t|
+     t.libs << "test"
+     t.test_files = FileList["test/test*.rb"]
+     t.verbose = true
+  end
+rescue LoadError
+  puts "[ERROR] Unable to load 'test' task - please install shoulda"
 end

data/tasks/yard.rake

@@ -0,0 +1,9 @@
+begin
+  require "yard"
+  
+  YARD::Rake::YardocTask.new do |t|
+    t.files   = ['lib/**/*.rb']
+  end
+rescue LoadError
+  puts "[ERROR] Unable to load 'yard' tasks - please install yard"
+end

data/test/test_biomart.rb

@@ -1,4 +1,4 @@
-require File.dirname(__FILE__) + '/test_helper.rb'
+require 'test_helper'
 
 class BiomartTest < Test::Unit::TestCase
   def setup
@@ -42,12 +42,13 @@ class BiomartTest < Test::Unit::TestCase
   
   context "A Biomart::Dataset instance" do
     setup do
-      @htgt_targ = @htgt.datasets["htgt_targ"]
-      @htgt_trap = @htgt.datasets["htgt_trap"]
-      @kermits   = @htgt.datasets["kermits"]
-      @ensembl   = @htgt.datasets["mmusculus_gene_ensembl"]
-      @emma      = Biomart::Dataset.new( "http://www.emmanet.org/biomart", { :name => "strains" } )
-      @dcc       = Biomart::Dataset.new( "http://www.i-dcc.org/biomart", { :name => "dcc" } )
+      @htgt_targ   = @htgt.datasets["htgt_targ"]
+      @htgt_trap   = @htgt.datasets["htgt_trap"]
+      @kermits     = @htgt.datasets["kermits"]
+      @ensembl     = @htgt.datasets["mmusculus_gene_ensembl"]
+      @ensembl_var = Biomart::Dataset.new( "http://www.ensembl.org/biomart", { :name => "hsapiens_snp" } )
+      @emma        = Biomart::Dataset.new( "http://www.emmanet.org/biomart", { :name => "strains" } )
+      @dcc         = Biomart::Dataset.new( "http://www.knockoutmouse.org/biomart", { :name => "dcc" } )
     end
     
     should "have basic metadata" do
@@ -252,6 +253,47 @@ class BiomartTest < Test::Unit::TestCase
         assert_equal( false, data_row["ikmc_project_id"].nil?, "The required_attributes search has not filtered out nil values." )
       end
     end
+    
+    should "perform searches that involve boolean filters" do
+      search_opts = {
+        :filters         => { 'with_variation_annotation' => true, 'ensembl_gene' => 'ENSG00000244734' },
+        :attributes      => [ 'refsnp_id','chr_name','chrom_start' ],
+        :process_results => true
+      }
+      
+      true_results = {}
+      assert_nothing_raised( Biomart::BiomartError ) { true_results = @ensembl_var.search( search_opts ) }
+      assert( !true_results.empty?, "The search using a boolean filter is empty." )
+      
+      search_opts[:filters].merge!({ 'with_variation_annotation' => 'included' })
+      true_results2 = {}
+      assert_nothing_raised( Biomart::BiomartError ) { true_results2 = @ensembl_var.search( search_opts ) }
+      assert( !true_results2.empty?, "The search using a boolean filter is empty." )
+      assert_equal( true_results, true_results2, "Using 'included' for a boolean filter does not give the same result as 'true'." )
+      
+      search_opts[:filters].merge!({ 'with_variation_annotation' => 'only' })
+      true_results3 = {}
+      assert_nothing_raised( Biomart::BiomartError ) { true_results3 = @ensembl_var.search( search_opts ) }
+      assert( !true_results3.empty?, "The search using a boolean filter is empty." )
+      assert_equal( true_results, true_results3, "Using 'only' for a boolean filter does not give the same result as 'true'." )
+      
+      search_opts[:filters].merge!({ 'with_variation_annotation' => false })
+      false_results = {}
+      assert_nothing_raised( Biomart::BiomartError ) { false_results = @ensembl_var.search( search_opts ) }
+      assert( !false_results.empty?, "The search using a boolean filter is empty." )
+      
+      search_opts[:filters].merge!({ 'with_variation_annotation' => 'excluded' })
+      false_results2 = {}
+      assert_nothing_raised( Biomart::BiomartError ) { false_results2 = @ensembl_var.search( search_opts ) }
+      assert( !false_results2.empty?, "The search using a boolean filter is empty." )
+      assert_equal( false_results, false_results2, "Using 'excluded' for a boolean filter does not give the same result as 'false'." )
+      
+      search_opts[:filters].merge!({ 'with_variation_annotation' => 'flibble' })
+      assert_raise( Biomart::ArgumentError ) { @ensembl_var.search( search_opts ) }
+      
+      search_opts[:filters].merge!({ 'with_variation_annot' => true })
+      assert_raise( Biomart::ArgumentError ) { @ensembl_var.search( search_opts ) }
+    end
   end
   
   context "A Biomart::Attribute instance" do
@@ -282,6 +324,7 @@ class BiomartTest < Test::Unit::TestCase
       
       assert( !ens_gene_id.name.nil?, "Biomart::Filter.name is nil." )
       assert( !ens_gene_id.display_name.nil?, "Biomart::Filter.display_name is nil." )
+      assert( !ens_gene_id.type.nil?, "Biomart::Filter.type is nil." )
       
       assert( true_false.include?( ens_gene_id.hidden? ), "Biomart::Filter.hidden? is not returning true/false." )
       assert( true_false.include?( ens_gene_id.default? ), "Biomart::Filter.default? is not returning true/false." )
@@ -294,7 +337,7 @@ class BiomartTest < Test::Unit::TestCase
       @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" } )
-      @good_biomart = Biomart::Server.new( "http://www.i-dcc.org/biomart" )
+      @good_biomart = Biomart::Server.new( "http://www.knockoutmouse.org/biomart" )
     end
     
     should "allow you to ping a server" do
@@ -308,7 +351,7 @@ class BiomartTest < Test::Unit::TestCase
     end
     
     should "handle biomart server errors gracefully" do
-      assert_raise( Biomart::FilterError )    { @htgt_targ.count( :filters => { "wibbleblibbleblip" => "1" } ) }
+      assert_raise( Biomart::ArgumentError )  { @htgt_targ.count( :filters => { "wibbleblibbleblip" => "1" } ) }
       assert_raise( Biomart::AttributeError ) { @htgt_targ.search( :attributes => ["wibbleblibbleblip"] ) }
       assert_raise( Biomart::DatasetError )   { @bad_dataset.count() }
       

data/test/test_helper.rb

@@ -1,9 +1,16 @@
-begin
-  require 'shoulda'
-rescue LoadError
-  require 'rubygems' unless ENV['NO_RUBYGEMS']
-  require 'shoulda'
+
+$:.unshift( "#{File.expand_path(File.dirname(__FILE__))}/../lib" )
+
+require 'rubygems'
+require 'bundler/setup'
+require 'shoulda'
+
+# Set-up SimpleCov (code coverage tool for Ruby 1.9)
+if /^1.9/ === RUBY_VERSION
+  require 'simplecov'
+  SimpleCov.start do
+    coverage_dir 'simplecov'
+  end
 end
 
-$:.unshift(File.dirname(__FILE__) + '/../lib')
 require 'biomart'

metadata

@@ -1,13 +1,12 @@
 --- !ruby/object:Gem::Specification 
 name: biomart
 version: !ruby/object:Gem::Version 
-  hash: 23
   prerelease: false
   segments: 
   - 0
   - 2
-  - 0
-  version: 0.2.0
+  - 1
+  version: 0.2.1
 platform: ruby
 authors: 
 - Darren Oakley
@@ -15,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-06-10 00:00:00 +01:00
+date: 2011-02-16 00:00:00 +00:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -26,7 +25,6 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 3
         segments: 
         - 0
         version: "0"
@@ -40,7 +38,6 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 23
         segments: 
         - 2
         - 10
@@ -48,19 +45,16 @@ dependencies:
   type: :development
   version_requirements: *id002
 - !ruby/object:Gem::Dependency 
-  name: hoe
+  name: simplecov
   prerelease: false
   requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 21
         segments: 
-        - 2
-        - 6
-        - 1
-        version: 2.6.1
+        - 0
+        version: "0"
   type: :development
   version_requirements: *id003
 description: A ruby API for interacting with Biomart XML based webservices.
@@ -70,13 +64,14 @@ executables: []
 
 extensions: []
 
-extra_rdoc_files: 
-- History.txt
-- Manifest.txt
-- README.rdoc
+extra_rdoc_files: []
+
 files: 
+- .gitignore
+- Gemfile
+- Gemfile.lock
 - History.txt
-- Manifest.txt
+- Manifest
 - README.rdoc
 - Rakefile
 - biomart.gemspec
@@ -86,11 +81,12 @@ files:
 - lib/biomart/dataset.rb
 - lib/biomart/filter.rb
 - lib/biomart/server.rb
+- lib/biomart/version.rb
 - script/console
-- script/destroy
-- script/generate
 - tasks/metrics.rake
+- tasks/rcov.rake
 - tasks/shoulda.rake
+- tasks/yard.rake
 - test/test_biomart.rb
 - test/test_helper.rb
 has_rdoc: true
@@ -98,9 +94,8 @@ homepage: http://github.com/dazoakley/biomart
 licenses: []
 
 post_install_message: 
-rdoc_options: 
-- --main
-- README.rdoc
+rdoc_options: []
+
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
@@ -108,7 +103,6 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 3
       segments: 
       - 0
       version: "0"
@@ -117,7 +111,6 @@ required_rubygems_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 3
       segments: 
       - 0
       version: "0"

data/script/destroy

@@ -1,14 +0,0 @@
-#!/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

@@ -1,14 +0,0 @@
-#!/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)