genomer 0.0.8 → 0.0.9

data/.gitignore

@@ -1,5 +1,6 @@
 tmp
 *.gem
+*.html
 
 # rcov generated
 coverage

data/CHANGELOG.mkd

@@ -0,0 +1,9 @@
+== 0.0.9 ==
+
+  * Genomer now has different behaviour dependent on whether inside or outside
+    a genomer project directory. These differences are as follows: 
+    * The 'init' command cannot be called inside an existing genomer project.
+    * All other commands cannot be when not inside a genomer project.
+    * Genomer no long throws an error when not inside a genomer project
+      directory, since a Gemfile is no longer attempted to be loaded.
+  * Version number can be shown using --version flag

data/README.mkd

@@ -1,4 +1,4 @@
-![Genomer: A swiss army knife for genome projects](http://genomer.s3.amazonaws.com/icon/genomer.png)
+![Genomer: A swiss army knife for genome projects](http://genomer.s3.amazonaws.com/icon/genomer/genomer.png)
 
 ## About
 
@@ -33,6 +33,12 @@ reproducible.
 [plasmid]: https://github.com/michaelbarton/chromosome-pfluorescens-r124-plasmid
 [genome]: https://github.com/michaelbarton/chromosome-pfluorescens-r124-genome
 
+## Screencasts
+
+  * [Installing Genomer](http://www.youtube.com/watch?v=bXws8RnBsUU)
+  * [Genomer example usage](http://www.youtube.com/watch?v=HfsdJOELFjs)
+  * [Generating Genbank upload files for a simple plasmid](http://www.youtube.com/watch?v=jVn62pMnIRA)
+
 ## Installing
 
 Ruby and RubyGems are required to use genomer and related plugins. Genomer is

data/features/cli/help.feature

@@ -3,7 +3,29 @@ Feature: Listing available commands
   A user can use the help command
   To list the available options to the console
 
-  Scenario: Running genomer with no commands
+  @disable-bundler
+  Scenario: Running genomer with no commands outside a project
+     When I run the genomer command with no arguments
+     Then the exit status should be 0
+      And the output should contain:
+      """
+      Use `genomer init NAME` to create a new genomer project called NAME
+
+      """
+
+  @disable-bundler
+  Scenario: Running genomer with the --version flag outside a project
+     When I run the genomer command with the arguments "--version"
+     Then the exit status should be 0
+      And the output should match:
+     """
+     Genomer version \d+.\d+.\d+
+     """
+
+  @disable-bundler
+  Scenario: Running genomer with no commands inside a project
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
      When I run the genomer command with no arguments
      Then the exit status should be 0
       And the output should contain:
@@ -13,7 +35,21 @@ Feature: Listing available commands
 
      """
 
-  Scenario: Running genomer with the help command
+  @disable-bundler
+  Scenario: Running genomer with the --version flag inside a project
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+     When I run the genomer command with the arguments "--version"
+     Then the exit status should be 0
+      And the output should match:
+     """
+     Genomer version \d+.\d+.\d+
+     """
+
+  @disable-bundler
+  Scenario: Running the genomer help command inside a genomer project
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
      When I run the genomer command with the arguments "help"
      Then the exit status should be 0
       And the output should contain:

data/features/cli/init.feature

@@ -57,23 +57,7 @@ Feature: Creating a new genomer project
 
     """
 
-  @disable-bundler
-  Scenario: Using the files generated in a new project
-    Given I run the genomer command with the arguments "init project"
-      And I cd to "project"
-      And I overwrite "Gemfile" with:
-      """
-      gem 'genomer',               :path => '../../../'
-      gem 'genomer-plugin-simple', :path => '../../../genomer-plugin-simple'
-      """
-     When I run the genomer command with the arguments "simple describe"
-     Then the exit status should be 0
-      And the output should contain:
-     """
-     The scaffold contains 1 entries
-     """
-
-   Scenario: Creating a new project where the directory already exists
+   Scenario: Creating a new project when the directory already exists
      Given a directory named "project"
      When I run the genomer command with the arguments "init project"
      Then the exit status should be 1
@@ -81,3 +65,13 @@ Feature: Creating a new genomer project
      """
      Error. Directory 'project' already exists.
      """
+
+  Scenario: Creating a new project when already inside a genomer project
+    Given I run the genomer command with the arguments "init project"
+      And I cd to "project"
+     When I run the genomer command with the arguments "init another_project"
+     Then the exit status should be 1
+     And the stderr should contain:
+      """
+      Error. This directory contains a 'Gemfile' and already appears to be a genomer project.
+      """

data/features/cli/man.feature

@@ -8,8 +8,7 @@ Feature: Showing man pages for available commands
      Then the exit status should be 0
       And the output should contain:
       """
-      genomer man COMMAND
-      run `genomer help` for a list of available commands
+      Use `genomer init NAME` to create a new genomer project called NAME
 
       """
 
@@ -74,4 +73,8 @@ Feature: Showing man pages for available commands
   Scenario: Getting the man page for init
      When I run the genomer command with the arguments "man init"
      Then the exit status should be 0
-      And the output should contain "GENOMER-INIT(1)"
+      And the output should contain:
+      """
+      Use `genomer init NAME` to create a new genomer project called NAME
+
+      """

data/lib/genomer/runtime.rb

@@ -2,12 +2,37 @@ require 'unindent'
 require 'tempfile'
 require 'md2man'
 
+require 'genomer/version'
+
 class Genomer::Runtime
 
   attr :command
   attr :arguments
   attr :flags
 
+  MESSAGES = {
+    :error  => {
+      :init_again =>
+        "This directory contains a 'Gemfile' and already appears to be a genomer project."
+  },
+    :output => {
+      :version => "Genomer version #{Genomer::VERSION}",
+      :not_project =>
+        "Use `genomer init NAME` to create a new genomer project called NAME",
+      :simple_help =>
+        "genomer COMMAND [options]\nrun `genomer help` for a list of available commands",
+      :man =>
+        "genomer man COMMAND\nrun `genomer help` for a list of available commands"
+    }
+  }
+
+
+  def message(type,msg)
+    content = MESSAGES[type][msg]
+    type == :error ? raise(Genomer::Error, content) : content
+  end
+
+
   def initialize(settings)
     @command   = settings.rest.shift
     @arguments = settings.rest
@@ -15,23 +40,24 @@ class Genomer::Runtime
   end
 
   def execute!
-    case command
-    when nil    then short_help
-    when "help" then help
-    when "init" then init
-    when "man"  then man
-    else             run_plugin
+    return message :output, :version if flags[:version]
+
+    if genomer_project?
+      case command
+      when nil    then message :output, :simple_help
+      when "help" then help
+      when "init" then message :error, :init_again
+      when "man"  then man
+      else             run_plugin
+      end
+    else
+      case command
+      when "init" then init
+      else             message :output, :not_project
+      end
     end
   end
 
-  def short_help
-    msg =<<-EOF
-      genomer COMMAND [options]
-      run `genomer help` for a list of available commands
-    EOF
-    msg.unindent
-  end
-
   def help
     msg =<<-EOF
       genomer COMMAND [options]
@@ -42,11 +68,13 @@ class Genomer::Runtime
     EOF
     msg.unindent!
 
-    msg << Genomer::Plugin.plugins.inject(String.new) do |str,p|
-      str << '  '
-      str << p.name.gsub("genomer-plugin-","").ljust(12)
-      str << p.summary
-      str << "\n"
+    if File.exists?('Gemfile')
+      msg << Genomer::Plugin.plugins.inject(String.new) do |str,p|
+        str << '  '
+        str << p.name.gsub("genomer-plugin-","").ljust(12)
+        str << p.summary
+        str << "\n"
+      end
     end
     msg.strip
   end
@@ -65,12 +93,7 @@ class Genomer::Runtime
 
       Kernel.exec "man #{groffed_man_file(location).path}"
     else
-      msg =<<-EOF
-        genomer man COMMAND
-        run `genomer help` for a list of available commands
-      EOF
-      msg.unindent!
-      msg.strip
+      message :output, :man
     end
   end
 
@@ -110,11 +133,14 @@ class Genomer::Runtime
     end
 
     "Genomer project '#{project_name}' created.\n"
-
   end
 
   def run_plugin
     Genomer::Plugin[command].new(arguments,flags).run
   end
 
+  def genomer_project?
+    File.exists?('Gemfile')
+  end
+
 end

data/lib/genomer/version.rb

@@ -1,3 +1,3 @@
 module Genomer
-  VERSION = "0.0.8"
+  VERSION = "0.0.9"
 end

data/spec/genomer/runtime_spec.rb

@@ -1,7 +1,6 @@
 require 'spec_helper'
 
 describe Genomer::Runtime do
-  include FakeFS::SpecHelpers
 
   subject do
     Genomer::Runtime.new MockSettings.new arguments, flags
@@ -10,141 +9,62 @@ describe Genomer::Runtime do
   let(:flags){ {} }
   let(:arguments){ [] }
 
-  describe "with the command" do
+  describe "run" do
 
-    describe "none" do
+    context "inside a genomer project" 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
+      before do
+        stub.instance_of(described_class).genomer_project?{ true }
       end
 
-    end
+      describe "passed no arguments" do
 
-    describe "unknown" do
-
-      let(:arguments){ %w|unknown| }
-
-      it "should print an error message" do
-        error = <<-EOF
-          Unknown command or plugin 'unknown.'
+        it "should print the short help description" do
+          msg = <<-EOF
+          genomer COMMAND [options]
           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| }
+          EOF
+          subject.execute!.should == msg.unindent.strip
+        end
 
-      after do
-        FileUtils.rm_rf('project_name') if File.exists?('project_name')
       end
 
-      describe "with project name argument" do
+      describe "passed the --version flag" do
 
-        before do
-          @msg = subject.execute!
+        let(:flags) do
+          {:version => true}
         end
 
-        it "should print message that project has been created" do
-          @msg.should == "Genomer project 'project_name' created.\n"
+        it "should print the version information" do
+          msg = "Genomer version #{Genomer::VERSION}"
+          subject.execute!.should == msg.unindent
         end
 
-        it "should create a directory from the named argument" do
-          File.exists?('project_name').should be_true
-        end
+      end
 
-        it "should create an 'assembly' directory" do
-          File.exists?(File.join('project_name','assembly')).should be_true
-        end
+      describe "passed an unknown command" do
 
-        it "should create a 'scaffold.yml' file" do
-          file = File.join('project_name','assembly','scaffold.yml')
-          File.exists?(file).should be_true
-          File.read(file).should == <<-EOF.unindent
-            # Specify your genome scaffold in YAML format here. Reference nucleotide
-            # sequences in the 'sequences.fna' file using the first space delimited
-            # word of each fasta header.
-            #
-            # Go to http://next.gs/getting-started/ to start writing genome scaffold
-            # files.
-            #
-            # A simple one contig example is also provided below. Delete this as you
-            # start writing your own scaffold.
-            ---
-              -
-                sequence:
-                  source: "contig1"
-          EOF
-        end
+        let(:arguments){ %w|unknown| }
 
-        it "should create a 'sequence.fna' file" do
-          file = File.join('project_name','assembly','sequence.fna')
-          File.exists?(file).should be_true
-          File.read(file).should == <<-EOF.unindent
-            ; Add your assembled contigs and scaffolds sequences to this file.
-            ; These sequences can be referenced in the 'scaffold.yml' file
-            ; using the first space delimited word in each fasta header.
-            > contig1
-            ATGC
-          EOF
-        end
-
-        it "should create a 'annotations.gff' file" do
-          file = File.join('project_name','assembly','annotations.gff')
-
-          File.exists?(file).should be_true
-          File.read(file).should == <<-EOF.unindent
-            ##gff-version   3
-            ## Add your gff3 formatted annotations to this file
+        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
 
-        it "should create a 'Gemfile' file" do
-          file    = File.join('project_name','Gemfile')
-          version = Genomer::VERSION.split('.')[0..1] << '0'
-
-
-          File.exists?(file).should be_true
-          File.read(file).should == <<-EOF.unindent
-            source :rubygems
-
-            gem 'genomer',    '~> #{version.join('.')}'
-          EOF
-        end
       end
 
-      describe "when project already exists" do
+      describe "passed help command with no available plugins" do
 
-        before do
-          Dir.mkdir('project_name')
-        end
+        let(:arguments){ %w|help| }
 
-        it "should raise an error" do
-          lambda{ subject.execute! }.should raise_error(Genomer::Error,
-            "Directory 'project_name' already exists.")
+        before do
+          mock(Genomer::Plugin).plugins{ gems }
+          mock(File).exists?('Gemfile'){ true }
         end
 
-      end
-
-    end
-
-    describe "help" do
-
-      before do
-        mock(Genomer::Plugin).plugins{ gems }
-      end
-
-      let(:arguments){ %w|help| }
-
-      describe "with no available plugins" do
-
         let(:gems) do
           []
         end
@@ -165,9 +85,16 @@ describe Genomer::Runtime do
         it "should show the man command" do
           subject.execute!.should include "man         View man page for the specified plugin"
         end
-      end
+        end
+
+      describe "passed help command with one available plugin" do
+
+        let(:arguments){ %w|help| }
 
-      describe "with available genomer plugins" do
+        before do
+          mock(Genomer::Plugin).plugins{ gems }
+          mock(File).exists?('Gemfile'){ true }
+        end
 
         let(:gems) do
           [Gem::Specification.new do |s|
@@ -182,15 +109,7 @@ describe Genomer::Runtime do
 
       end
 
-    end
-
-    describe "man" do
-
-      before do
-        stub(Genomer::Plugin).plugins{ gems }
-      end
-
-      describe "and no command specified" do
+      describe "passed the man command with no arguments" do
 
         let(:arguments){ %w|man| }
 
@@ -202,9 +121,9 @@ describe Genomer::Runtime do
           subject.execute!.should include msg.unindent.strip
         end
 
-      end
+        end
 
-      describe "and a command specified" do
+      describe "passed the man command with an argument" do
 
         let(:arguments){ %w|man simple| }
         let(:man_file){ 'a' }
@@ -223,7 +142,7 @@ describe Genomer::Runtime do
 
       end
 
-      describe "and the init command specified" do
+      describe "passed the man command with the argument 'init'" do
 
         let(:arguments){ %w|man init| }
         let(:man_file){ File.expand_path File.dirname(__FILE__) + '/../../man/genomer-init.1.ronn' }
@@ -242,7 +161,7 @@ describe Genomer::Runtime do
 
       end
 
-      describe "with a subcommand specified" do
+      describe "passed the man command for a plugin" do
 
         let(:arguments){ %w|man simple subcommand| }
         let(:man_file){ 'a' }
@@ -261,23 +180,145 @@ describe Genomer::Runtime do
 
       end
 
-      describe "with an unknown subcommand specified" do
+        describe "passed the man command with an unknown plugin argument" do
 
-        let(:arguments){ %w|man simple subcommand| }
-        let(:man_file){ 'a' }
+          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 raise a genomer error" do
+            lambda{ subject.execute! }.
+              should raise_error(Genomer::Error,"No manual entry for command 'simple subcommand'")
+          end
+
+        end
+
+        describe "passed the init command" do
+
+          after do
+            FileUtils.rm_rf('project_name') if File.exists?('project_name')
+          end
+
+          let(:arguments){ %w|init project_name| }
+
+          it "should raise a genomer error" do
+            lambda{ subject.execute! }.
+              should raise_error(Genomer::Error,"This directory contains a 'Gemfile' and already appears to be a genomer project.")
+          end
+
+        end
+      end
+
+    context "outside a genomer project" do
+
+      before do
+        stub.instance_of(described_class).genomer_project?{ false }
+      end
+
+      describe "passed no arguments" do
+
+        it "should print the short help description" do
+          msg = <<-EOF
+          Use `genomer init NAME` to create a new genomer project called NAME
+          EOF
+          subject.execute!.should == msg.unindent.strip
+        end
+
+      end
+
+      describe "passed the init command with a project name argument" do
+
+        let(:arguments){ %w|init project_name| }
+
+        after do
+          FileUtils.rm_rf('project_name') if File.exists?('project_name')
+        end
 
         before do
-          mock(subject).man_file(['simple','subcommand']){ man_file }
-          mock(File).exists?(man_file){false}
+          @msg = subject.execute!
         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'")
+        it "should print message that project has been created" do
+          @msg.should == "Genomer project 'project_name' created.\n"
         end
 
+        it "should create the expected directories" do
+          File.exists?('project_name').should be_true
+          File.exists?(File.join('project_name','assembly')).should be_true
+        end
+
+        it "should create a 'scaffold.yml' file" do
+          file = File.join('project_name','assembly','scaffold.yml')
+          File.exists?(file).should be_true
+          File.read(file).should == <<-EOF.unindent
+            # Specify your genome scaffold in YAML format here. Reference nucleotide
+            # sequences in the 'sequences.fna' file using the first space delimited
+            # word of each fasta header.
+            #
+            # Go to http://next.gs/getting-started/ to start writing genome scaffold
+            # files.
+            #
+            # A simple one contig example is also provided below. Delete this as you
+            # start writing your own scaffold.
+            ---
+              -
+                sequence:
+                  source: "contig1"
+          EOF
+        end
+
+        it "should create a 'sequence.fna' file" do
+          file = File.join('project_name','assembly','sequence.fna')
+          File.exists?(file).should be_true
+          File.read(file).should == <<-EOF.unindent
+            ; Add your assembled contigs and scaffolds sequences to this file.
+            ; These sequences can be referenced in the 'scaffold.yml' file
+            ; using the first space delimited word in each fasta header.
+            > contig1
+            ATGC
+          EOF
+        end
+
+        it "should create a 'annotations.gff' file" do
+          file = File.join('project_name','assembly','annotations.gff')
+
+          File.exists?(file).should be_true
+          File.read(file).should == <<-EOF.unindent
+            ##gff-version   3
+            ## Add your gff3 formatted annotations to this file
+          EOF
+        end
+
+        it "should create a 'Gemfile' file" do
+          file    = File.join('project_name','Gemfile')
+          version = Genomer::VERSION.split('.')[0..1] << '0'
+
+
+          File.exists?(file).should be_true
+          File.read(file).should == <<-EOF.unindent
+            source :rubygems
+
+            gem 'genomer',    '~> #{version.join('.')}'
+          EOF
+        end
       end
 
+      describe "passed the --version flag" do
+
+        let(:flags) do
+          {:version => true}
+        end
+
+        it "should print the version information" do
+          msg = "Genomer version #{Genomer::VERSION}"
+          subject.execute!.should == msg.unindent
+        end
+
+      end
     end
 
   end

data/spec/spec_helper.rb

@@ -5,6 +5,7 @@ require 'fakefs/spec_helpers'
 require 'scaffolder/test/helpers'
 
 require 'genomer'
+require 'genomer/version'
 
 # Requires supporting files with custom matchers and macros, etc,
 # in ./support/ and its subdirectories.
@@ -22,17 +23,13 @@ RSpec.configure do |config|
 
     attr :rest
 
-    def initialize(rest = [], command_args = {})
+    def initialize(rest = [], args = {})
       @rest = rest
-      @args = command_args
+      @args = args
     end
 
-    def [](arg)
-      @args[arg]
-    end
-
-    def flags
-      @args
+    def method_missing(method, *args, &block)
+      @args.send(method, *args, &block)
     end
 
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genomer
 version: !ruby/object:Gem::Version
-  version: 0.0.8
+  version: 0.0.9
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-01-17 00:00:00.000000000 Z
+date: 2013-02-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -230,6 +230,7 @@ files:
 - .document
 - .gitignore
 - .travis.yml
+- CHANGELOG.mkd
 - Gemfile
 - LICENSE.txt
 - README.mkd
@@ -274,7 +275,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1310621877616390557
+      hash: -2610476547918174305
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: