bio-gem 1.0.0 → 1.1.0

data/Gemfile

@@ -4,6 +4,7 @@ source "http://rubygems.org"
 #   gem "activesupport", ">= 2.3.5"
 gem "bundler", "~> 1.0.18"
 gem "jeweler", "~> 1.6.4"
+gem "rdoc"
 
 
 # Add dependencies to develop your gem here.
@@ -13,4 +14,5 @@ group :development do
   gem "bundler", "~> 1.0.18"
   gem "jeweler", "~> 1.6.4"
   gem "rcov", ">= 0"
+  gem "rdoc"
 end

data/Gemfile.lock

@@ -6,8 +6,11 @@ GEM
       bundler (~> 1.0)
       git (>= 1.2.5)
       rake
+    json (1.6.1)
     rake (0.9.2)
     rcov (0.9.10)
+    rdoc (3.11)
+      json (~> 1.4)
     shoulda (2.11.3)
 
 PLATFORMS
@@ -17,4 +20,5 @@ DEPENDENCIES
   bundler (~> 1.0.18)
   jeweler (~> 1.6.4)
   rcov
+  rdoc
   shoulda

data/VERSION

@@ -1 +1 @@
-1.0.0
+1.1.0

data/bio-gem.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-gem}
-  s.version = "1.0.0"
+  s.version = "1.1.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = [%q{Raoul J.P. Bonnal}]
-  s.date = %q{2011-09-26}
+  s.date = %q{2011-11-09}
   s.description = %q{BioGem is a scaffold generator for those Bioinformaticans who want to start coding an application or a library for using/extending BioRuby core library and sharing it through rubygems.org .
   The basic idea is to simplify and promote a modular approach to the BioRuby package.}
   s.email = %q{ilpuccio.febo@gmail.com}
@@ -35,9 +35,16 @@ Gem::Specification.new do |s|
     "lib/bio-gem/mod/jeweler/options.rb",
     "lib/bio-gem/templates/bin",
     "lib/bio-gem/templates/database",
+    "lib/bio-gem/templates/engine",
+    "lib/bio-gem/templates/foos_controller",
+    "lib/bio-gem/templates/foos_view_example",
+    "lib/bio-gem/templates/foos_view_index",
+    "lib/bio-gem/templates/foos_view_show",
     "lib/bio-gem/templates/lib",
+    "lib/bio-gem/templates/library",
     "lib/bio-gem/templates/migration",
     "lib/bio-gem/templates/rakefile",
+    "lib/bio-gem/templates/routes",
     "lib/bio-gem/templates/seeds",
     "test/helper.rb",
     "test/test_bio-gem.rb"
@@ -54,25 +61,31 @@ Gem::Specification.new do |s|
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<bundler>, ["~> 1.0.18"])
       s.add_runtime_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_runtime_dependency(%q<rdoc>, [">= 0"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<bundler>, ["~> 1.0.18"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
       s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<rdoc>, [">= 0"])
     else
       s.add_dependency(%q<bundler>, ["~> 1.0.18"])
       s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rdoc>, [">= 0"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<bundler>, ["~> 1.0.18"])
       s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
       s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<rdoc>, [">= 0"])
     end
   else
     s.add_dependency(%q<bundler>, ["~> 1.0.18"])
     s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rdoc>, [">= 0"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<bundler>, ["~> 1.0.18"])
     s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
     s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<rdoc>, [">= 0"])
   end
 end
 

data/lib/bio-gem/mod/jeweler.rb

@@ -3,6 +3,16 @@
 require 'bio-gem/mod/jeweler/options'
 require 'bio-gem/mod/jeweler/github_mixin'
 
+class String
+  def underscore
+       self.gsub(/::/, '/').
+         gsub(/([A-Z]+)([A-Z][a-z])/,'\1_\2').
+         gsub(/([a-z\d])([A-Z])/,'\1_\2').
+         tr("-", "_").
+         downcase
+     end
+end
+
 class Jeweler
   class Generator 
 
@@ -55,7 +65,31 @@ class Jeweler
     def bin_name
       "bio#{original_project_name}"
     end
-
+    
+    def engine_dirs
+      %w{app app/controllers app/views app/helpers config app/views/foos}
+    end
+    
+    def engine_name
+      "#{project_name}-engine"
+    end
+    
+    def engine_filename
+      "#{engine_name}.rb"
+    end
+    
+    def engine_module_name
+      project_name.split('-').map{|module_sub_name| module_sub_name.capitalize}.join      
+    end
+    
+    def engine_name_prefix
+      project_name.split('-').gsub(/-/,'_')<<'_'
+    end
+    
+    def engine_namespace
+      "/#{options[:biogem_engine]}"
+    end
+    
     def render_template_generic(source, template_dir = template_dir_biogem)
       template_contents = File.read(File.join(template_dir, source))
       template          = ERB.new(template_contents, nil, '<>')
@@ -75,6 +109,15 @@ class Jeweler
       end
       $stdout.puts "\t#{status}\t#{destination}"
     end
+    
+    def output_template_in_target_generic_update(source, destination = source, template_dir = template_dir_biogem)
+      final_destination = File.join(target_dir, destination)
+      template_result   = render_template_generic(source, template_dir)
+
+      File.open(final_destination, 'a') {|file| file.write(template_result)}
+
+      $stdout.puts "\tcreate\t#{destination}"
+    end    
 
     def template_dir_biogem
       File.join(File.dirname(__FILE__),'..', 'templates')
@@ -128,6 +171,20 @@ class Jeweler
         
         # Fill lib/bio-plugin.rb with some default comments
         output_template_in_target_generic 'lib', File.join(lib_dir, lib_filename)
+                
+        #creates the strutures and files needed to have a ready to go Rails' engine
+        if namespace=options[:biogem_engine]
+          engine_dirs.each do |dir|
+            mkdir_in_target dir
+          end
+          output_template_in_target_generic 'engine', File.join('lib', engine_filename )
+          output_template_in_target_generic_update 'library', File.join('lib', lib_filename)
+          output_template_in_target_generic 'routes', File.join('config', "routes.rb" )
+          output_template_in_target_generic 'foos_controller', File.join('app',"controllers", "foos_controller.rb" )
+          output_template_in_target_generic 'foos_view_index', File.join('app',"views","foos", "inedx.html.erb" )
+          output_template_in_target_generic 'foos_view_show', File.join('app',"views","foos", "show.html.erb" )
+          output_template_in_target_generic 'foos_view_example', File.join('app',"views","foos", "example.html.erb" )          
+        end
       end #not_bio_gem_meta
     end
 
@@ -137,8 +194,22 @@ class Jeweler
       'token' => github_token,
       'description' => summary,
       'name' => github_repo_name
+      # BY DEFAULT THE REPO IS CREATED
+      # DO NOT PUSH THE REPO BECAUSE USER MUST ADD INFO TO CONFIGURATION FILES
       # TODO do a HEAD request to see when it's ready?
-      @repo.push('origin')
+      #@repo.push('origin')
+    end
+    
+    
+    def puts_template_message(message, length=70, padding=4)
+      puts "*"*(length+padding*2+2)
+      puts "*"+" "*(length+padding*2)+"*"
+      message=message.join("\n") if message.kind_of? Array
+      message.scan(/.{1,70}/).map do |sub_message|
+        puts "*"+" "*padding+sub_message+" "*(length-sub_message.size+padding)+"*"
+      end
+      puts "*"+" "*(length+padding*2)+"*"
+      puts "*"*(length+padding*2+2)
     end
   end #Generator
 end #Jeweler

data/lib/bio-gem/mod/jeweler/options.rb

@@ -10,6 +10,7 @@ class Jeweler
         self[:testing_framework]       = :shoulda
         self[:documentation_framework] = :rdoc
         self[:use_bundler]             = true
+        self[:create_repo]             = true
 
         git_config =  if Pathname.new("~/.gitconfig").expand_path.exist?
           Git.global_config
@@ -44,14 +45,19 @@ class Jeweler
             self[:biogem_bin] = true
           end
 
-          o.on("--with-db", 'create the database directory for a db application-library') do
+          o.on('--with-db', 'create the database directory for a db application-library.') do
             self[:biogem_db] = true
           end
 
-          o.on("--with-test-data",'create the data directory inside the test directory if the user need to set up a test with its own dataset') do
+          o.on('--with-test-data','create the data directory inside the test directory if the user need to set up a test with its own dataset') do
             self[:biogem_test_data] = true
           end
           
+          o.on('--with-engine [NAMESPACE]', 'create a Rails engine with the namespace given in input. Set default database creation') do |namespace|
+            self[:biogem_engine] = namespace
+            self[:biogem_db] = true
+          end
+          
           o.separator ""
           
           o.separator "These options are for Jeweler"

data/lib/bio-gem/templates/engine

@@ -0,0 +1,43 @@
+require '<%= require_name %>'
+require 'rails'
+
+module <%= engine_module_name %>
+  class Engine < Rails::Engine
+
+    # Config defaults
+# DEPRECATED
+    config.widget_factory_name = "default factory name"
+    config.mount_at = '/'
+    
+    # # Load rake tasks
+    # rake_tasks do
+    #   load File.join(File.dirname(__FILE__), 'rails/railties/tasks.rake')
+    # end
+    
+    # Check the gem config
+    initializer "check config" do |app|
+      # make sure mount_at ends with trailing slash
+      config.mount_at += '/'  unless config.mount_at.last == '/'
+    end
+    
+    initializer "static assets" do |app|
+      app.middleware.use ::ActionDispatch::Static, "#{root}/public"
+    end
+    
+    # consider the possibility to keep the modules in the lib directory, which is more compatible
+    # with a normal gem/package
+    paths["app/models"]           << "lib"
+  end
+end
+
+# #In your Rails application into 
+# # config/initializers
+# # create a file called <%= require_name %>.rb
+# # you can change the mount point of you engine, using option
+# # --with_engine=namespace like http://YourDomain:port/YourMountPoint
+# # Otherwise, if you want your RailsEngine to be called at root level, leave everything as it now, without that file.
+# module <%= engine_module_name %>
+#    class Engine < Rails::Engine
+#      engine_name = '<%= engine_namespace %>'
+#    end
+# end

data/lib/bio-gem/templates/foos_controller

@@ -0,0 +1,13 @@
+class FoosController < ApplicationController
+  def example
+    @shuttle =  "TEST CASE"
+  end
+
+  def index
+    @index = "Something relevant"
+  end
+
+  def show
+    @item = "It's me"
+  end
+end

data/lib/bio-gem/templates/foos_view_example

@@ -0,0 +1 @@
+This is just an example of a call from a controller <%%= @shuttle %>

data/lib/bio-gem/templates/foos_view_index

@@ -0,0 +1 @@
+This could be a list of item but for now I just read from a fake index <%%= @index %>

data/lib/bio-gem/templates/foos_view_show

@@ -0,0 +1,3 @@
+<H1>
+Who is the item ? <%%= @item %>
+<H1>

data/lib/bio-gem/templates/library

@@ -0,0 +1,6 @@
+
+if (defined?(Rails) && Rails::VERSION::MAJOR == 3)
+  require '<%= engine_name %>'
+else
+  #require the usual dependencies here
+end

data/lib/bio-gem/templates/routes

@@ -0,0 +1,40 @@
+Rails.application.routes.draw do
+
+ #DEPRECATED 
+ mount_at = <%= engine_module_name %>::Engine.engine_name== "<%= engine_module_name.underscore %>_engine" ? "" : <%= engine_module_name %>::Engine.engine_name
+
+
+#ROUTES from code below:
+# YourPathToTheControllerFiles = bio/kb/gex
+# OtherControllerName = slice
+# 
+#               gex     /gex(.:format)                        {:controller=>"bio/kb/gex/populations", :action=>"index"}
+# filter_population GET /gex/populations/:id/filter(.:format) {:action=>"filter", :controller=>"bio/kb/gex/populations"}
+#       populations GET /gex/populations(.:format)            {:action=>"index", :controller=>"bio/kb/gex/populations"}
+#        population GET /gex/populations/:id(.:format)        {:action=>"show", :controller=>"bio/kb/gex/populations"}
+#           samples GET /gex/samples(.:format)                {:action=>"index", :controller=>"bio/kb/gex/samples"}
+#            sample GET /gex/samples/:id(.:format)            {:action=>"show", :controller=>"bio/kb/gex/samples"}
+#            slices GET /gex/slices(.:format)                 {:action=>"index", :controller=>"bio/kb/gex/slices"}
+#             slice GET /gex/slices/:id(.:format)             {:action=>"show", :controller=>"bio/kb/gex/slices"}
+#  
+# Uncomment to activate the resources
+## or you can reconfigure mount_at 
+## mount <%= engine_module_name %>::Engine=>"your_mount_point", :as=>'your_personal_engine_name' # but is better to redefine the mount point in the Rails application.
+# yourPathToTheControllerFiles = 'foopath'
+# controllerName = :foos
+# otherControllerName = :sampels
+# ---
+# scope mount_at, yourPathToTheControllerFiles do    
+#   resources controllerName, :only => [ :index, :show] do
+#     member do
+#       get :example
+#     end
+#   end
+#   resources otherControllerName, :only =>[:index, :show]
+# end #scope
+
+<% puts_template_message ["Remember to require this library in the Gemfile of your Rails application.",
+                          "Please take a look at #{target_dir}/lib/#{require_name}-engine.rb file for an example of how integrate your engine into a rails application.",
+                          "Thanks!"] %> 
+
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gem
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.1.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-09-26 00:00:00.000000000Z
+date: 2011-11-09 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2164719420 !ruby/object:Gem::Requirement
+  requirement: &2161194560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: 1.0.18
   type: :runtime
   prerelease: false
-  version_requirements: *2164719420
+  version_requirements: *2161194560
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2164717980 !ruby/object:Gem::Requirement
+  requirement: &2161193880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,21 @@ dependencies:
         version: 1.6.4
   type: :runtime
   prerelease: false
-  version_requirements: *2164717980
+  version_requirements: *2161193880
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &2161193260 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *2161193260
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2164716880 !ruby/object:Gem::Requirement
+  requirement: &2161192420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2164716880
+  version_requirements: *2161192420
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2164716080 !ruby/object:Gem::Requirement
+  requirement: &2161191600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +65,10 @@ dependencies:
         version: 1.0.18
   type: :development
   prerelease: false
-  version_requirements: *2164716080
+  version_requirements: *2161191600
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2164714920 !ruby/object:Gem::Requirement
+  requirement: &2161190920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +76,21 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2164714920
+  version_requirements: *2161190920
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2164713220 !ruby/object:Gem::Requirement
+  requirement: &2161190240 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2161190240
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &2161189240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,7 +98,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2164713220
+  version_requirements: *2161189240
 description: ! "BioGem is a scaffold generator for those Bioinformaticans who want
   to start coding an application or a library for using/extending BioRuby core library
   and sharing it through rubygems.org .\n  The basic idea is to simplify and promote
@@ -105,9 +127,16 @@ files:
 - lib/bio-gem/mod/jeweler/options.rb
 - lib/bio-gem/templates/bin
 - lib/bio-gem/templates/database
+- lib/bio-gem/templates/engine
+- lib/bio-gem/templates/foos_controller
+- lib/bio-gem/templates/foos_view_example
+- lib/bio-gem/templates/foos_view_index
+- lib/bio-gem/templates/foos_view_show
 - lib/bio-gem/templates/lib
+- lib/bio-gem/templates/library
 - lib/bio-gem/templates/migration
 - lib/bio-gem/templates/rakefile
+- lib/bio-gem/templates/routes
 - lib/bio-gem/templates/seeds
 - test/helper.rb
 - test/test_bio-gem.rb
@@ -126,7 +155,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -913022692014142837
+      hash: 2864487456249026807
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: