genomer 0.0.5

data/spec/genomer/runtime_spec.rb

@@ -0,0 +1,262 @@
+require 'spec_helper'
+
+describe Genomer::Runtime do
+  include FakeFS::SpecHelpers
+
+  subject do
+    Genomer::Runtime.new MockSettings.new arguments, flags
+  end
+
+  let(:flags){ {} }
+  let(:arguments){ [] }
+
+  describe "with the command" do
+
+    describe "none" do
+
+      it "should print the short help description" do
+        msg = <<-EOF
+          genomer COMMAND [options]
+          run `genomer help` for a list of available commands
+        EOF
+        subject.execute!.should == msg.unindent
+      end
+
+    end
+
+    describe "unknown" do
+
+      let(:arguments){ %w|unknown| }
+
+      it "should print an error message" do
+        error = <<-EOF
+          Unknown command or plugin 'unknown.'
+          run `genomer help` for a list of available commands
+        EOF
+        lambda{ subject.execute! }.should raise_error(Genomer::Error,error.unindent)
+      end
+
+    end
+
+    describe "init" do
+
+      let(:arguments){ %w|init project_name| }
+
+      after do
+        FileUtils.rm_rf('project_name') if File.exists?('project_name')
+      end
+
+      describe "with project name argument" do
+
+        before do
+          subject.execute!
+        end
+
+        it "should create a directory from the named argument" do
+          File.exists?('project_name').should be_true
+        end
+
+        it "should create an 'assembly' directory" do
+          File.exists?(File.join('project_name','assembly')).should be_true
+        end
+
+      end
+
+      describe "when project already exists" do
+
+        before do
+          Dir.mkdir('project_name')
+        end
+
+        it "should raise an error" do
+          lambda{ subject.execute! }.should raise_error(Genomer::Error,
+            "Directory 'project_name' already exists.")
+        end
+
+      end
+
+    end
+
+    describe "help" do
+
+      let(:arguments){ %w|help| }
+
+      before do
+        mock(Genomer::Plugin).plugins{ gems }
+      end
+
+      describe "with no available plugins" do
+
+        let(:gems) do
+          []
+        end
+
+        it "should print the header description" do
+          msg = <<-EOF
+            genomer COMMAND [options]
+
+            Available commands:
+          EOF
+          subject.execute!.should include msg.unindent.strip
+        end
+
+        it "should show the init command" do
+          subject.execute!.should include "init        Create a new genomer project"
+        end
+
+        it "should show the man command" do
+          subject.execute!.should include "man         View man page for the specified plugin"
+        end
+      end
+
+      describe "with available genomer plugins" do
+
+        let(:gems) do
+          [Gem::Specification.new do |s|
+            s.name        = 'genomer-plugin-simple'
+            s.summary     = 'A simple scaffolder command'
+          end]
+        end
+
+        it "should print the plugin command description" do
+          subject.execute!.should include "simple      A simple scaffolder command"
+        end
+
+      end
+
+    end
+
+    describe "man" do
+
+      before do
+        stub(Genomer::Plugin).plugins{ gems }
+      end
+
+      describe "with no command specified" do
+
+        let(:arguments){ %w|man| }
+
+        it "should print the man help description" do
+          msg = <<-EOF
+            genomer man COMMAND
+            run `genomer help` for a list of available commands
+          EOF
+          subject.execute!.should include msg.unindent.strip
+        end
+
+      end
+
+      describe "with a command specified" do
+
+        let(:arguments){ %w|man simple| }
+        let(:man_file){ 'a' }
+        let(:groffed_man_file){ mock!.path{ 'b' } }
+
+        before do
+          mock(subject).man_file(['simple']){ man_file }
+          mock(subject).groffed_man_file(man_file){ groffed_man_file }
+          mock(File).exists?(man_file){true}
+        end
+
+        it "should call man for the groffed path" do
+          mock(Kernel).exec("man b")
+          subject.execute!
+        end
+
+      end
+
+      describe "with a subcommand specified" do
+
+        let(:arguments){ %w|man simple subcommand| }
+        let(:man_file){ 'a' }
+        let(:groffed_man_file){ mock!.path{ 'b' } }
+
+        before do
+          mock(subject).man_file(['simple','subcommand']){ man_file }
+          mock(subject).groffed_man_file(man_file){ groffed_man_file }
+          mock(File).exists?(man_file){true}
+        end
+
+        it "should call man for the groffed path" do
+          mock(Kernel).exec("man b")
+          subject.execute!
+        end
+
+      end
+
+      describe "with an unknown subcommand specified" do
+
+        let(:arguments){ %w|man simple subcommand| }
+        let(:man_file){ 'a' }
+
+        before do
+          mock(subject).man_file(['simple','subcommand']){ man_file }
+          mock(File).exists?(man_file){false}
+        end
+
+        it "should call man for the groffed path" do
+          lambda{ subject.execute! }.
+            should raise_error(Genomer::Error,"No manual entry for command 'simple subcommand'")
+        end
+
+      end
+
+    end
+
+  end
+
+  describe "#initialize" do
+
+    describe "with arguments and flags" do
+
+      let(:arguments){ %w|init project_name| }
+      let(:flags){ {:flag => 'something'} }
+
+      it "should set the runtime variables" do
+        subject.command.should   == 'init'
+        subject.arguments.should == ['project_name']
+        subject.flags[:flag]     == flags[:flag]
+      end
+
+    end
+
+  end
+
+  describe "#man_file" do
+
+    before do
+      mock(Genomer::Plugin).fetch('simple') do
+        mock!.full_gem_path{ '/tmp' }
+      end
+    end
+
+    it "should return the path to the man page for a command" do
+      subject.man_file(['simple']).should == '/tmp/man/genomer-simple.ronn'
+    end
+
+    it "should return the path to the man page for a subcommand" do
+      subject.man_file(['simple','subcommand']).should == '/tmp/man/genomer-simple-subcommand.ronn'
+    end
+
+  end
+
+  describe "#run_plugin" do
+
+    before do
+      mock(Genomer::Plugin).[]('plugin') do
+         mock!.new(anything,anything) do
+           mock!.run
+         end
+      end
+    end
+
+    let(:arguments){ %w|plugin arg1 arg2| }
+    let(:flags){ {:flag => 'arg3'} }
+
+    it "should fetch, initialize and run the required plugin" do
+      subject.run_plugin
+    end
+
+  end
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,45 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+
+require 'rspec'
+require 'fakefs/spec_helpers'
+require 'scaffolder/test/helpers'
+
+require 'genomer'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each do |f|
+  require File.expand_path(f)
+end
+
+RSpec.configure do |config|
+  config.mock_with :rr
+
+  include Scaffolder::Test
+  include Scaffolder::Test::Helpers
+
+  class MockSettings
+
+    attr :rest
+
+    def initialize(rest = [], command_args = {})
+      @rest = rest
+      @args = command_args
+    end
+
+    def [](arg)
+      @args[arg]
+    end
+
+    def flags
+      @args
+    end
+
+  end
+
+  config.after(:each) do
+    instance_variables.each do |ivar|
+      instance_variable_set(ivar, nil)
+    end
+  end
+end

metadata

@@ -0,0 +1,290 @@
+--- !ruby/object:Gem::Specification
+name: genomer
+version: !ruby/object:Gem::Version
+  version: 0.0.5
+  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: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.9.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.9.0
+- !ruby/object:Gem::Dependency
+  name: bundler
+  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: configliere
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.8
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.8
+- !ruby/object:Gem::Dependency
+  name: scaffolder
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+- !ruby/object:Gem::Dependency
+  name: scaffolder-annotation-locator
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.2
+- !ruby/object:Gem::Dependency
+  name: unindent
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+- !ruby/object:Gem::Dependency
+  name: ronn
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.7.3
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.7.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.7.0
+- !ruby/object:Gem::Dependency
+  name: fakefs
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+- !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
+- !ruby/object:Gem::Dependency
+  name: scaffolder-test-helpers
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.4.0
+- !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
+description: Turns scaffolded contigs and annotations into a genome.
+email:
+- mail@michaelbarton.me.uk
+executables:
+- genomer
+extensions: []
+extra_rdoc_files: []
+files:
+- .document
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- bin/genomer
+- cucumber.yml
+- features/api/annotation_ids.feature
+- features/api/annotation_location.feature
+- features/api/scaffold.feature
+- features/cli/create.feature
+- features/cli/error.feature
+- features/cli/help.feature
+- features/cli/man.feature
+- features/cli/plugins.feature
+- features/step_definitions/genomer_steps.rb
+- features/support/env.rb
+- genomer-plugin-simple/genomer-plugin-simple.gemspec
+- genomer-plugin-simple/lib/genomer-plugin-simple.rb
+- genomer-plugin-simple/man/genomer-simple-subcommand.ronn
+- genomer-plugin-simple/man/genomer-simple.ronn
+- genomer.gemspec
+- lib/genomer.rb
+- lib/genomer/error.rb
+- lib/genomer/plugin.rb
+- lib/genomer/runtime.rb
+- lib/genomer/version.rb
+- man/genomer-init.1.ronn
+- spec/genomer/plugin_spec.rb
+- spec/genomer/runtime_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/michaelbarton/genomer
+licenses:
+- MIT
+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: 4331820328226072819
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: 1.8.0
+requirements: []
+rubyforge_project: genomer
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Build genome output files
+test_files: []