scaffolder-test-helpers 0.1.0 → 0.2.0

data/Rakefile

@@ -21,8 +21,8 @@ Jeweler::Tasks.new do |gem|
   gem.name = "scaffolder-test-helpers"
   gem.homepage = "http://github.com/michaelbarton/scaffolder-test-helpers"
   gem.license = "MIT"
-  gem.summary = %Q{Common methods for testing scaffolder.}
-  gem.description = %Q{Helper methods and cucumber steps for testing scaffolder.}
+  gem.summary = %Q{Methods and classes for testing scaffolder.}
+  gem.description = %Q{Useful Helper methods and classes for testing scaffolder.}
   gem.email = "mail@michaelbarton.me.uk"
   gem.authors = ["Michael Barton"]
 end

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/lib/scaffolder/test/helpers.rb

@@ -2,36 +2,32 @@ require 'tempfile'
 require 'bio'
 require 'scaffolder'
 
+require 'scaffolder/test/sequence'
+require 'scaffolder/test/unresolved'
+
 module Scaffolder::Test
   module Helpers
 
-    def write_sequence_file(entries,file = Tempfile.new("sequence").path)
-      File.open(file,'w') do |tmp|
-        make_sequence(entries).each do |entry|
-          seq = Bio::Sequence.new(entry[:sequence])
-          tmp.print(seq.output(:fasta,:header => entry[:name]))
-        end
-      end
-      file
+    def generate_scaffold_files(entries)
+      [write_scaffold_file(entries),write_sequence_file(entries)]
     end
 
     def write_scaffold_file(entries,file = Tempfile.new("scaffold").path)
-      File.open(file,'w'){|tmp| tmp.print(YAML.dump(make_scaffold(entries)))}
+      File.open(file,'w') do |tmp|
+        tmp.print(YAML.dump(entries.map{|e| e.to_hash }))
+      end
       file
     end
 
-    def make_scaffold(entries)
-      entries.map do |entry|
-        {'sequence' => {'source' => (entry['name'] || entry[:name]) }}
+    def write_sequence_file(entries,file = Tempfile.new("sequence").path)
+      File.open(file,'w') do |tmp|
+        entries.each do |entry|
+          tmp.puts(entry.to_fasta) if entry.respond_to? :to_fasta
+        end
       end
+      file
     end
 
-    def make_sequence(entries)
-      entries.map do |entry|
-        {:name => (entry['name'] || entry[:name]),
-          :sequence => (entry['nucleotides'] || entry[:nucleotides]) }
-      end.flatten
-    end
 
   end
 end

data/lib/scaffolder/test/sequence.rb

@@ -0,0 +1,33 @@
+require 'scaffolder'
+
+module Scaffolder::Test
+  class Sequence
+
+    def initialize(options = {})
+      @options = options
+    end
+
+    [:name,:sequence,:reverse,:start,:stop].each do |attribute|
+      define_method(attribute) do |*arg|
+        unless arg.first
+          return @options[attribute]
+        end
+        @options[attribute] = arg.first
+        return self
+      end
+    end
+
+    def to_hash
+      hash = {'source' => name}
+      [:start,:stop,:reverse].each do |attribute|
+        hash[attribute.to_s] = @options[attribute] if @options[attribute]
+      end
+      {'sequence' => hash}
+    end
+
+    def to_fasta
+      Bio::Sequence.new(sequence).output(:fasta,:header => name).strip
+    end
+
+  end
+end

data/lib/scaffolder/test/unresolved.rb

@@ -0,0 +1,17 @@
+require 'scaffolder'
+
+module Scaffolder::Test
+  class Unresolved
+
+    attr_reader :length
+
+    def initialize(options = {})
+      @length = options[:length]
+    end
+
+    def to_hash
+      {'unresolved' => {'length' => length}}
+    end
+
+  end
+end

data/scaffolder-test-helpers.gemspec

@@ -5,12 +5,12 @@
 
 Gem::Specification.new do |s|
   s.name = %q{scaffolder-test-helpers}
-  s.version = "0.1.0"
+  s.version = "0.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Michael Barton"]
-  s.date = %q{2011-01-04}
-  s.description = %q{Helper methods and cucumber steps for testing scaffolder.}
+  s.date = %q{2011-04-03}
+  s.description = %q{Useful Helper methods and classes for testing scaffolder.}
   s.email = %q{mail@michaelbarton.me.uk}
   s.extra_rdoc_files = [
     "LICENSE.txt",
@@ -18,25 +18,29 @@ Gem::Specification.new do |s|
   ]
   s.files = [
     ".document",
-    ".rspec",
     "Gemfile",
     "LICENSE.txt",
     "README.rdoc",
     "Rakefile",
     "VERSION",
-    "lib/scaffolder/test/cucumber_steps.rb",
     "lib/scaffolder/test/helpers.rb",
+    "lib/scaffolder/test/sequence.rb",
+    "lib/scaffolder/test/unresolved.rb",
     "scaffolder-test-helpers.gemspec",
     "spec/scaffolder/test/helpers_spec.rb",
+    "spec/scaffolder/test/sequence_spec.rb",
+    "spec/scaffolder/test/unresolved_spec.rb",
     "spec/spec_helper.rb"
   ]
   s.homepage = %q{http://github.com/michaelbarton/scaffolder-test-helpers}
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
   s.rubygems_version = %q{1.3.7}
-  s.summary = %q{Common methods for testing scaffolder.}
+  s.summary = %q{Methods and classes for testing scaffolder.}
   s.test_files = [
     "spec/scaffolder/test/helpers_spec.rb",
+    "spec/scaffolder/test/sequence_spec.rb",
+    "spec/scaffolder/test/unresolved_spec.rb",
     "spec/spec_helper.rb"
   ]
 

data/spec/scaffolder/test/helpers_spec.rb

@@ -1,14 +1,71 @@
 require File.join(File.dirname(__FILE__),'..','..','spec_helper')
 
-describe Scaffolder::Test::Helpers do
+describe Scaffolder::Test::Helpers, "#generate_scaffold_files method" do
 
-  it{ described_class.class.should == Module }
+  describe "pass an array with a single sequence" do
 
-  describe "namespace loading" do
+    before(:all) do
+      entries = [Sequence.new(:name => 'c1',:sequence => 'ATG')]
+      @scaf_file, @seq_file = described_class.generate_scaffold_files(entries)
+    end
 
-    it{ Scaffolder.class.should == Class }
-    it{ Scaffolder.methods.should include("update_with_sequence") }
+    it "should create the corresponding scaffold file" do
+      File.exists?(@scaf_file).should be_true
+      scaffold = YAML.load(File.read(@scaf_file))
+      scaffold.should == [{'sequence' => {'source' => 'c1'}}]
+    end
+
+    it "should create the corresponding sequence file" do
+      File.exists?(@seq_file).should be_true
+      sequence = File.read(@seq_file)
+      sequence.should == ">c1\nATG\n"
+    end
+
+  end
+
+  describe "pass an array with two sequences" do
+
+    before(:all) do
+      entries = [Sequence.new(:name => 'c1',:sequence => 'ATG'),
+                 Sequence.new(:name => 'c2',:sequence => 'ATG')]
+      @scaf_file, @seq_file = described_class.generate_scaffold_files(entries)
+    end
+
+    it "should create the corresponding scaffold file" do
+      File.exists?(@scaf_file).should be_true
+      scaffold = YAML.load(File.read(@scaf_file))
+      scaffold.should == [{'sequence' => {'source' => 'c1'}},
+        {'sequence' => {'source' => 'c2'}}]
+    end
+
+    it "should create the corresponding sequence file" do
+      File.exists?(@seq_file).should be_true
+      sequence = File.read(@seq_file)
+      sequence.should == ">c1\nATG\n>c2\nATG\n"
+    end
 
   end
 
+  describe "pass an array with a sequence and an unresolved region" do
+
+    before(:all) do
+      entries = [Sequence.new(:name => 'c1',:sequence => 'ATG'),
+                 Unresolved.new(:length => 5)]
+      @scaf_file, @seq_file = generate_scaffold_files(entries)
+    end
+
+    it "should create the corresponding scaffold file" do
+      File.exists?(@scaf_file).should be_true
+      scaffold = YAML.load(File.read(@scaf_file))
+      scaffold.should == [{'sequence' => {'source' => 'c1'}},
+        {'unresolved' => {'length' => 5}}]
+    end
+
+    it "should create the corresponding sequence file" do
+      File.exists?(@seq_file).should be_true
+      sequence = File.read(@seq_file)
+      sequence.should == ">c1\nATG\n"
+    end
+
+  end
 end

data/spec/scaffolder/test/sequence_spec.rb

@@ -0,0 +1,52 @@
+require File.join(File.dirname(__FILE__),'..','..','spec_helper')
+
+describe Scaffolder::Test::Sequence do
+
+  describe "basic instance" do
+    subject do
+      described_class.new(:name => 'contig1',:sequence => 'ATGCCC')
+    end
+
+    its(:name)    {should == 'contig1'}
+    its(:sequence){should == 'ATGCCC'}
+
+    its(:to_fasta){should == ">contig1\nATGCCC"}
+    its(:to_hash) {should == {'sequence' => {'source' => 'contig1'}} }
+  end
+
+  [:start,:stop,:reverse].each do |attribute|
+
+    describe "instance with #{attribute} attribute" do
+
+      let(:value){:value}
+      subject do
+        described_class.new(:name => 'contig1',:sequence => 'ATGCCC',
+                            attribute => value)
+      end
+
+      its(:name)    {should == 'contig1'}
+      its(:sequence){should == 'ATGCCC'}
+      its(attribute){should == value}
+
+      its(:to_fasta){should == ">contig1\nATGCCC"}
+      its(:to_hash) do
+        should == {'sequence' => {'source' => 'contig1', attribute.to_s => value}}
+      end
+
+    end
+
+    describe "chaining instance attributes" do
+
+      let(:value){:value}
+      subject do
+        instance = described_class.new(:name => 'contig1',:sequence => 'ATGCCC')
+        instance.send(attribute,value)
+      end
+
+      its(attribute){should == value}
+
+    end
+
+  end
+
+end

data/spec/scaffolder/test/unresolved_spec.rb

@@ -0,0 +1,14 @@
+require File.join(File.dirname(__FILE__),'..','..','spec_helper')
+
+describe Scaffolder::Test::Unresolved do
+
+  describe "basic instance" do
+    subject do
+      described_class.new(:length => 5)
+    end
+
+    its(:length) {should == 5}
+    its(:to_hash){should == {'unresolved' => {'length' => 5}} }
+  end
+
+end

data/spec/spec_helper.rb

@@ -1,12 +1,10 @@
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
-require 'rspec'
 
+require 'rspec'
 require 'scaffolder/test/helpers'
 
-# Requires supporting files with custom matchers and macros, etc,
-# in ./support/ and its subdirectories.
-Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
-
-RSpec.configure do |config|
+RSpec.configure do
+  include Scaffolder::Test
+  include Scaffolder::Test::Helpers
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: scaffolder-test-helpers
 version: !ruby/object:Gem::Version 
-  hash: 27
+  hash: 23
   prerelease: false
   segments: 
   - 0
-  - 1
+  - 2
   - 0
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors: 
 - Michael Barton
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-01-04 00:00:00 -05:00
+date: 2011-04-03 00:00:00 -04:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -123,7 +123,7 @@ dependencies:
   name: yard
   prerelease: false
   version_requirements: *id007
-description: Helper methods and cucumber steps for testing scaffolder.
+description: Useful Helper methods and classes for testing scaffolder.
 email: mail@michaelbarton.me.uk
 executables: []
 
@@ -134,16 +134,18 @@ extra_rdoc_files:
 - README.rdoc
 files: 
 - .document
-- .rspec
 - Gemfile
 - LICENSE.txt
 - README.rdoc
 - Rakefile
 - VERSION
-- lib/scaffolder/test/cucumber_steps.rb
 - lib/scaffolder/test/helpers.rb
+- lib/scaffolder/test/sequence.rb
+- lib/scaffolder/test/unresolved.rb
 - scaffolder-test-helpers.gemspec
 - spec/scaffolder/test/helpers_spec.rb
+- spec/scaffolder/test/sequence_spec.rb
+- spec/scaffolder/test/unresolved_spec.rb
 - spec/spec_helper.rb
 has_rdoc: true
 homepage: http://github.com/michaelbarton/scaffolder-test-helpers
@@ -178,7 +180,9 @@ rubyforge_project:
 rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
-summary: Common methods for testing scaffolder.
+summary: Methods and classes for testing scaffolder.
 test_files: 
 - spec/scaffolder/test/helpers_spec.rb
+- spec/scaffolder/test/sequence_spec.rb
+- spec/scaffolder/test/unresolved_spec.rb
 - spec/spec_helper.rb

data/.rspec

@@ -1 +0,0 @@
---color

data/lib/scaffolder/test/cucumber_steps.rb

@@ -1,24 +0,0 @@
-require 'scaffolder/test/helpers'
-require 'cucumber'
-
-World(Scaffolder::Test::Helpers)
-
-Given /^the scaffold is composed of the sequences:$/ do |sequences|
-  @entries = sequences.hashes.map do |seq|
-    {'sequence' => {'source' => seq['name']}}
-  end
-  @sequences = sequences.hashes.map do |seq|
-    {:name => seq['name'], :sequence => seq['nucleotides']}
-  end
-
-  @sequence_file = write_sequence_file(@sequences)
-  @scaffold_file = write_scaffold_file(@entries)
-end
-
-Given /^the scaffold file is called "([^"]*)"$/ do |file|
-  FileUtils.mv(@scaffold_file,file)
-end
-
-Given /^the sequence file is called "([^"]*)"$/ do |file|
-  FileUtils.mv(@sequence_file,file)
-end