genomer-plugin-validate 0.0.1

data/spec/genomer-plugin-validate/validator_spec.rb

@@ -0,0 +1,107 @@
+require 'spec_helper'
+
+describe GenomerPluginValidate::Validator do
+
+  before do
+    @example = GenomerPluginValidate::Validator::ExampleValidator = Class.new
+    stub(described_class).require(anything)
+  end
+
+  after do
+    GenomerPluginValidate::Validator.send(:remove_const,'ExampleValidator')
+  end
+
+  describe "#validators" do
+
+    subject do
+      described_class.validators
+    end
+
+    its([:example_validator]){should ==  @example}
+
+  end
+
+  describe "#annotations_by_attribute" do
+
+    subject do
+       dummy_class = Class.new
+       dummy_class.send(:include, described_class)
+
+       dummy = dummy_class.new
+       stub(dummy).annotations{annotations}
+       dummy.annotations_by_attribute(attribute)
+    end
+
+    let(:attribute) do
+      'ID'
+    end
+
+    context "where there are no annotations" do
+
+      let(:annotations) do
+        []
+      end
+
+      it{ should == {}}
+
+    end
+
+    context "where there is one annotation using the ID attribute" do
+
+      let(:annotations) do
+        [annotation_with_id(1)]
+      end
+
+      its(['1']){ should == annotations }
+
+    end
+
+    context "where there is one annotation using the product attribute" do
+
+      let(:attribute) do
+        'product'
+      end
+
+      let(:annotations) do
+        [annotation(:attributes => {:product => '1'})]
+      end
+
+      its(['1']){ should == annotations }
+
+    end
+
+    context "where there is one annotation and one annotions with a missing ID" do
+
+      let(:annotations) do
+        [annotation_with_id(1), Annotation.new.to_gff3_record]
+      end
+
+      its(['1']){ should == annotations[0..0] }
+      its([nil]){ should == annotations[1..1] }
+
+    end
+
+    context "where there is two annotations with different attributes" do
+
+      let(:annotations) do
+        [annotation_with_id(1), annotation_with_id(2)]
+      end
+
+      its(['1']){ should == annotations[0..0] }
+      its(['2']){ should == annotations[1..1] }
+
+    end
+
+    context "where there is two annotations the same attribute" do
+
+      let(:annotations) do
+        [annotation_with_id(1), annotation_with_id(1)]
+      end
+
+      its(['1']){ should == annotations }
+
+    end
+
+  end
+
+end

data/spec/genomer-plugin-validate_spec.rb

@@ -0,0 +1,92 @@
+require 'spec_helper'
+
+describe GenomerPluginValidate do
+
+  describe "#run" do
+
+    after do
+      GenomerPluginValidate::Group.send(:remove_const,'Example')
+    end
+
+    before do
+      @example = GenomerPluginValidate::Group::Example = Class.new
+    end
+
+    subject do
+      described_class.new([arg].compact,{}).run
+    end
+
+    context "passed no arguments" do
+
+      let(:arg) do
+        nil
+      end
+
+      before do
+        def @example.description
+          "Some description"
+        end
+      end
+
+      it "should return the help message" do
+        msg = <<-EOS
+          USAGE: genomer validate <GROUP>
+          
+          Available validation groups:
+        EOS
+        subject.should include msg.unindent
+      end
+
+      it "should include the descriptions annotation groups" do
+        msg = '  example        Some description'
+        subject.should include msg
+      end
+
+    end
+
+    context "passed an unknown validation group name" do
+
+      let(:arg) do
+        "unknown"
+      end
+
+      it "should raise and Genomer::Error" do
+        lambda{subject.to_s}.should raise_error Genomer::Error,
+          "Unknown validation group 'unknown'"
+      end
+
+    end
+
+    context "passed a known validation group name" do
+
+      let(:validator) do
+        c = Class.new(Genomer::Plugin)
+        any_instance_of(c) do |instance|
+          mock(instance).run{ [['some_error_1', 'some_error_2'],['another_error_1']]}
+        end
+        c
+      end
+
+      before do
+        mock(GenomerPluginValidate::Group).groups{{'example' => @example}}
+        mock(@example).validators{ ['example'] }
+        mock(GenomerPluginValidate::Validator).validators{{'example' => validator}}
+      end
+
+      let(:arg) do
+        "example"
+      end
+
+      it "should return a string output of validation error array" do
+        subject.should ==<<-EOS.unindent.strip
+           some_error_1
+           some_error_2
+           another_error_1
+        EOS
+      end
+
+    end
+
+  end
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,35 @@
+current = File.dirname(__FILE__)
+$LOAD_PATH.unshift(File.join(current, '..', 'lib'), current)
+
+require 'rspec'
+require 'scaffolder/test/helpers'
+require 'heredoc_unindent'
+require 'genomer-plugin-validate'
+require 'validator_run_matcher'
+
+RSpec.configure do |config|
+  config.mock_with :rr
+
+  include Scaffolder::Test
+
+  def annotation(options = {})
+    attrs = options[:attributes] || {}
+    attrs[:ID].to_s ||= '1'
+
+    opts = {:start      => options[:start] || 1,
+            :end        => options[:end]   || 3,
+            :attributes => Hash[attrs.map{|(k,v)| [k.to_s,v]}]}
+
+    Annotation.new(opts).to_gff3_record
+  end
+
+  def annotation_with_id(id)
+    annotation(:attributes => {:ID => id})
+  end
+
+  def annotation_with_product(product)
+    annotation(:attributes => {'product' => product, 'ID' => 1})
+  end
+
+
+end

data/spec/validator_run_matcher.rb

@@ -0,0 +1,25 @@
+def errors_for(validator,annotations)
+  c = validator.new([],{})
+  stub(c).annotations{ annotations }
+  c.run
+end
+
+RSpec::Matchers.define :return_no_errors_for do |annotations|
+  match do
+    @actual   = errors_for(actual,annotations)
+    @expected = []
+    actual == expected
+  end
+
+  diffable
+end
+
+RSpec::Matchers.define :return_errors_for do |annotations,errors|
+  match do
+    @actual   = errors_for(actual,annotations)
+    @expected = errors
+    actual == expected
+  end
+
+  diffable
+end

metadata

@@ -0,0 +1,244 @@
+--- !ruby/object:Gem::Specification
+name: genomer-plugin-validate
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Michael Barton
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-05-28 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: genomer
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.4
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.4
+- !ruby/object:Gem::Dependency
+  name: heredoc_unindent
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.0
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.8.0
+- !ruby/object:Gem::Dependency
+  name: scaffolder-test-helpers
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.1
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.1.4
+- !ruby/object:Gem::Dependency
+  name: aruba
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.11
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.11
+- !ruby/object:Gem::Dependency
+  name: rr
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.4
+description: Test assembly files for common errors which may lead to incorrect assembly
+email:
+- mail@michaelbarton.me.uk
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- Rakefile
+- VERSION
+- features/annotations/bad-product-field.feature
+- features/annotations/command-line-interface.feature
+- features/annotations/duplicate_id.feature
+- features/annotations/identical_locations.feature
+- features/annotations/incorrect-attributes.feature
+- features/annotations/missing_attributes.feature
+- features/annotations/name.feature
+- features/command-line-interface.feature
+- features/support/env.rb
+- genomer-plugin-validate.gemspec
+- lib/extensions/string.rb
+- lib/genomer-plugin-validate.rb
+- lib/genomer-plugin-validate/group.rb
+- lib/genomer-plugin-validate/group/annotations.rb
+- lib/genomer-plugin-validate/validator.rb
+- lib/genomer-plugin-validate/validator/bad_product_field.rb
+- lib/genomer-plugin-validate/validator/duplicate_coordinates.rb
+- lib/genomer-plugin-validate/validator/duplicate_id.rb
+- lib/genomer-plugin-validate/validator/gff3_attributes.rb
+- lib/genomer-plugin-validate/validator/missing_id.rb
+- lib/genomer-plugin-validate/validator/no_name_or_product.rb
+- lib/genomer-plugin-validate/validator/uppercase_name.rb
+- lib/genomer-plugin-validate/validator/view_attributes.rb
+- man/genomer-validate.ronn
+- spec/genomer-plugin-validate/group/annotations_spec.rb
+- spec/genomer-plugin-validate/group_spec.rb
+- spec/genomer-plugin-validate/validator/bad_product_field_spec.rb
+- spec/genomer-plugin-validate/validator/duplicate_coordinates_spec.rb
+- spec/genomer-plugin-validate/validator/duplicate_id_spec.rb
+- spec/genomer-plugin-validate/validator/gff_attributes_spec.rb
+- spec/genomer-plugin-validate/validator/missing_id_spec.rb
+- spec/genomer-plugin-validate/validator/no_name_or_product_spec.rb
+- spec/genomer-plugin-validate/validator/uppercase_name_spec.rb
+- spec/genomer-plugin-validate/validator/view_attributes_spec.rb
+- spec/genomer-plugin-validate/validator_spec.rb
+- spec/genomer-plugin-validate_spec.rb
+- spec/spec_helper.rb
+- spec/validator_run_matcher.rb
+homepage: ''
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -1125290684225056222
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -1125290684225056222
+requirements: []
+rubyforge_project: genomer-plugin-validate
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Validate assembly files for errors
+test_files:
+- features/annotations/bad-product-field.feature
+- features/annotations/command-line-interface.feature
+- features/annotations/duplicate_id.feature
+- features/annotations/identical_locations.feature
+- features/annotations/incorrect-attributes.feature
+- features/annotations/missing_attributes.feature
+- features/annotations/name.feature
+- features/command-line-interface.feature
+- features/support/env.rb
+- spec/genomer-plugin-validate/group/annotations_spec.rb
+- spec/genomer-plugin-validate/group_spec.rb
+- spec/genomer-plugin-validate/validator/bad_product_field_spec.rb
+- spec/genomer-plugin-validate/validator/duplicate_coordinates_spec.rb
+- spec/genomer-plugin-validate/validator/duplicate_id_spec.rb
+- spec/genomer-plugin-validate/validator/gff_attributes_spec.rb
+- spec/genomer-plugin-validate/validator/missing_id_spec.rb
+- spec/genomer-plugin-validate/validator/no_name_or_product_spec.rb
+- spec/genomer-plugin-validate/validator/uppercase_name_spec.rb
+- spec/genomer-plugin-validate/validator/view_attributes_spec.rb
+- spec/genomer-plugin-validate/validator_spec.rb
+- spec/genomer-plugin-validate_spec.rb
+- spec/spec_helper.rb
+- spec/validator_run_matcher.rb