bio-gem 1.1.1 → 1.1.2

data/README.rdoc

@@ -7,7 +7,7 @@ listed at http://biogems.info
 
 The basic idea is to simplify and promote a modular approach to the BioRuby package.
 
-BioGem is not reinventing the wheel just putting together different tools like Jeweler and Bundler modifing their original behaviour when needed. Jeweler is used to create the initial scaffold, setting up git for versioning, releasing it to github.com and/or rubygems.org and packaging. Bundler is used used for setting up a predefined developing environment.
+BioGem is not reinventing the wheel just putting together different tools like Jeweler and Bundler modifying their original behavior when needed. Jeweler is used to create the initial scaffold, setting up git for versioning, releasing it to github.com and/or rubygems.org and packaging. Bundler is used used for setting up a predefined developing environment.
 
 Remind that
 * Jeweler is based on rake
@@ -18,8 +18,17 @@ Remind that
   are two different services and you need to create different accounts for them
   if you already use GitHub.com you are already all set for using BioGem
 
-== Contributing to bioruby-gem
- 
+== BioGems Official Plugin Archive
+
+* http://biogems.info/ 
+
+== Biogem Tutorial
+
+The latest version is on https://github.com/helios/bioruby-gem/blob/master/Tutorial.rdoc 
+
+./file.Tutorial.html
+
+== Contributing to bioruby-gem 
 * Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
 * Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
 * Fork the project
@@ -45,24 +54,24 @@ Some of these steps have been condensed:
   * pass just the simple name, it will add bioruby- for the first level directory and for the github repository
     BUT you'll require the library with bio-mystuff (and this will be the name used on rubygems)
   * creates a basic gem structure with a default dependencies for bioruby (bio) version 1.4.2
-	    |-- bin [optional = --with-bin]
-	    |   `-- biomystuff (executable)        
-	    |-- Gemfile
-	    |-- Gemfile.lock
-	    |-- LICENSE.txt
-	    |-- README.rdoc
-	    |-- Rakefile
-	    |-- lib
-	    |   `-- bio-mystuff.rb
-	    |-- conf[optional = --with-db]
-	    |   `-- database.yml put here the configuration of your database like in a rails app
-	    |-- db  [optional = --with-db] empty but put here your datasets or database(SQLite3?)
-	    |   |-- seeds.rb a file containing the preloaded datasets, they will be loaded during db setup process
-	    |   `-- migrate directory for migration, you must create migrations by hand, there is a template inside.
-	    `-- test
-	        |-- data [optional = --with-test-data]
-	        |-- helper.rb
-	        `-- test_bio-mystuff.rb
+        |-- bin [optional = --with-bin]
+        |   `-- biomystuff (executable)        
+        |-- Gemfile
+        |-- Gemfile.lock
+        |-- LICENSE.txt
+        |-- README.rdoc
+        |-- Rakefile
+        |-- lib
+        |   `-- bio-mystuff.rb
+        |-- conf[optional = --with-db]
+        |   `-- database.yml put here the configuration of your database like in a rails app
+        |-- db  [optional = --with-db] empty but put here your datasets or database(SQLite3?)
+        |   |-- seeds.rb a file containing the preloaded datasets, they will be loaded during db setup process
+        |   `-- migrate directory for migration, you must create migrations by hand, there is a template inside.
+        `-- test
+            |-- data [optional = --with-test-data]
+            |-- helper.rb
+            `-- test_bio-mystuff.rb
 
   * $ cd bioruby-mystuff
   * $ rake version:write (Initial Updated version: 0.0.0)
@@ -119,7 +128,7 @@ These options are for Jeweler
                                      GitHub token to use for interacting with the GitHub API
         --git-remote [GIT_REMOTE]    URI to set the git origin remote to
         --homepage [HOMEPAGE]        the homepage for your project (defaults to the GitHub repo)
-        --create-repo                create the repository on GitHub
+        --no-create-repo                create the repository on GitHub (repo is created by default)
 
         --yard                       use yard for documentation
         --rdoc                       use rdoc for documentation
@@ -146,7 +155,7 @@ These options are for Jeweler
     rake gemcutter:release   # Release gem to Gemcutter
     rake gemspec             # Generate and validate gemspec
     rake gemspec:debug       # Display the gemspec for debugging purposes, as jeweler knows it (not from the filesystem)
-    rake gemspec:generate    # Regenreate the gemspec on the filesystem
+    rake gemspec:generate    # Regenerate the gemspec on the filesystem
     rake gemspec:release     # Regenerate and validate gemspec, and then commits and pushes to git
     rake gemspec:validate    # Validates the gemspec on the filesystem
     rake git:release         # Tag and push release to git.
@@ -181,17 +190,17 @@ on your local directory you will see bioruby-mystuff but on rubygems you will pu
 Is a best practices, at least for me, to have a dummy class which establishes the connection with the database and inherit that class by the models. The benefit of this approach is to have multiple connections available at the same time in case you are developing/using multiple gems with different databases. This file is located in lib/bio/kb
 
     module Bio
-	  module KB
-	    class DummyMySpecialDB < ActiveRecord::Base
-	      self.abstract_class = true
-	      establish_connection(:adapter =>'sqlite3',:database =>"#{File.dirname(__FILE__)}/../../../db/yourdb.sqlite3")
-	    end
-	  end
-	end
-	
+      module KB
+        class DummyMySpecialDB < ActiveRecord::Base
+          self.abstract_class = true
+          establish_connection(:adapter =>'sqlite3',:database =>"#{File.dirname(__FILE__)}/../../../db/yourdb.sqlite3")
+        end
+      end
+    end
+    
 or you can use the configuration file db/database.yml and add this code to the module above. Note I don't like very much to add every time this code so in a future release I'll find out a way to add it automatically, probably overwriting the configurations call.
 
-	root_path = File.join(File.dirname(__FILE__),"../../../")
+    root_path = File.join(File.dirname(__FILE__),"../../../")
     configurations = YAML.load_file(File.join(root_path,"conf/database.yml"))
     configurations.each_pair do |key, db_info|
       db_info["database"] = File.join(root_path, db_info["database"]) if db_info["adapter"]=='sqlite3'
@@ -203,21 +212,21 @@ This code is necessary because the db is inside the gem and you can't know where
 The model must be located in a directory structure like lib/bio/kb/yourclass this is important because ActiveRecord can map the namespace with the directory tree.
 
     module Bio
-	  module KB
-	      module MySpecialDB
-	         class Mytable < Bio::KB::DummyMySpecialDB
-	         end
-	      end
-	  end
-	end
+      module KB
+        module MySpecialDB
+          class Mytable < Bio::KB::DummyMySpecialDB
+          end
+        end
+     end
+    end
 
 === Seeds
 Before populate you seeds.rb file you must declare a model. The model is declared in the usual Rails' way, see above.
 
-	 #Use this file to load a default dataset into your database
-	 %w(Raoul Toshiaki Francesco).each do |coder|
-	   Bio::KB::MySpecialDB::Example.create(:name=>coder, :tag=>"bioruby", :type=>"developer")
-	 end
+     #Use this file to load a default dataset into your database
+     %w(Raoul Toshiaki Francesco).each do |coder|
+       Bio::KB::MySpecialDB::Example.create(:name=>coder, :tag=>"bioruby", :type=>"developer")
+     end
 
 === StepByStep
 Toshiaki Katayama wrote a step by step guide for a bio-foobar plugin @ http://bioruby.open-bio.org/wiki/BiogemInstallation.

data/Rakefile

@@ -49,5 +49,6 @@ Rake::RDocTask.new do |rdoc|
   rdoc.rdoc_dir = 'rdoc'
   rdoc.title = "bio-gem #{version}"
   rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('Tutorial.rdoc')
   rdoc.rdoc_files.include('lib/**/*.rb')
 end

data/Tutorial.rdoc

@@ -0,0 +1,436 @@
+= Biogem Tutorial
+
+The latest version is on https://github.com/helios/bioruby-gem/blob/master/Tutorial.rdoc 
+
+== Installation
+=== Pre-requisites
+* Ruby: at least 1.9.x, current tested version is 1.9.2
+* [RVM]: RVM is optional but kindly suggested. RVM allows multiple ruby interpreters in your home directory in a very straightforward way
+* GitHub & RubyGems: In order to use Biogem to its fullest potential, you must create a regular GitHub  http://github.com and  RubyGems http://rubygems.org account. Why? Because for sharing and keeping track of source code we (currenlty) use github and for distributing the plugin we rely on RubyGems, the reference Ruby gem repository. To configure github and automate most of Biogem's tasks:
+   $ git config --global user.name "Firstname Lastname" Sets the name of the user for all git instances on the system
+   $ git config --global user.email "your_email@youremail.com"
+   $ git config --global github.user "user_id"
+   $ git config --global github.token "TOKEN ASSIGNED BY GITHUB"
+
+Note: another Ruby version management system used in BioRuby community is https://github.com/sstephenson/rbenv but for now we can not provide support for it.
+
+=== Download
+
+Install the biogem toolset with
+
+   $ gem install bio-gem
+
+all the required dependencies will be downloaded and installed automatically.
+
+== Create your first BioRuby Plugin
+=== Standard
+
+To create a BioRuby plugin named bio-foo in the bioruby-foo directory
+
+   $ Biogem foo
+
+   create	.gitignore
+   create	Rakefile
+   create	Gemfile
+   create	LICENSE.txt
+   create	README.rdoc
+   create	.document
+   create	lib
+   create	lib/bio-foo.rb
+   create	test
+   create	test/helper.rb
+   create	test/test_bio-foo.rb
+   create	lib/bio-foo.rb
+   Jeweler has prepared your gem in bioruby-foo
+   Jeweler has pushed your repo to http://github.com/helios/bioruby-foo
+   Fetching source index for http://rubygems.org/
+   Using rake (0.9.2.2)
+   Using bio (1.4.2) 
+   Using bundler (1.0.21) 
+   Using git (1.2.5) 
+   Using jeweler (1.6.4) 
+   Using rcov (0.9.11) 
+   Using shoulda (2.11.3) 
+   Your bundle is complete! Use `bundle show [gemname]` to see where a bundled gem is installed.
+   rake version:write
+   Generated: bio-foo.gemspec
+   bio-foo.gemspec is valid.
+	
+In case you are not connected to internet the following message will appear:
+
+   Seems you are not connected to Internet, can't create a remote repository.
+   Do not forget to create it by hand, from GitHub, and sync it with this project.
+
+Note the name of the plugin is important. Plugins are published as Ruby gems on http://rubygems.org/. All plugins that start with the name bio dash (bio-) are automatically listed on the Biogems website http://biogems.info/ !
+
+The first step is to open Rakefile and modify the gem.summary and gem.description. These parameters are necessary, because they describe your gem and its importance. If you let them as default the gem, will not publish. Examples of summary and description can be found on http://biogems.info/
+
+
+=== With a DataBase
+If you want to distribute a library which uses a local database Biogem creates for you a database template and add features coming from Ruby on Rails to manage the database. You can define Models, Fixtures and Migrations like a regular Rails application. SQLite3 is the default database engine in order to have a portable library, is also possible to configure the library to use different RDBMS like PostgreSQL, MySQL; please refer to ActiveRecord for further details.
+
+   $ Biogem --with-db foo      
+     create	.gitignore
+     create	Rakefile
+     create	Gemfile
+     create	LICENSE.txt
+     create	README.rdoc
+     create	.document
+     create	lib
+     create	lib/bio-foo.rb
+     create	test
+     create	test/helper.rb
+     create	test/test_bio-foo.rb
+   + create	db
+   + create	db/migrate
+   + create	config
+   + create	config/database.yml
+   + create	db/migrate/001_create_example.rb
+   + create	db/seeds.rb
+     update	Rakefile
+   + create	lib/foo/connect.rb
+   + create	lib/foo/example.rb
+     create	lib/bio-foo.rb
+     Jeweler has prepared your gem in bioruby-foo
+     Jeweler has pushed your repo to http://github.com/helios/bioruby-foo
+     Fetching source index for http://rubygems.org/
+     Using rake (0.9.2.2) 
+   + Using multi_json (1.0.3) 
+   + Using activesupport (3.1.1) 
+   + Using builder (3.0.0) 
+   + Using i18n (0.6.0) 
+   + Using activemodel (3.1.1) 
+   + Using arel (2.2.1) 
+   + Using tzinfo (0.3.31) 
+   + Using activerecord (3.1.1) 
+     Using bio (1.4.2) 
+     Using bundler (1.0.21) 
+     Using git (1.2.5) 
+     Using jeweler (1.6.4) 
+     Using rcov (0.9.11) 
+     Using shoulda (2.11.3) 
+   + Using sqlite3 (1.3.4)
+
+Rows with symbol + are differences between the standard command
+
+
+==== DataBaseConnection
+Is a best practice, at least for me, to have a dummy class which establishes the connection with the database and then inherit that class by models. The benefit of this approach is to have multiple connections available at the same time, just in case you are developing/using multiple gems with different databases. This file is located in lib/bio/your_module/connect.rb
+
+    module Bio
+      module YourModule
+        class DummyMySpecialDB < ActiveRecord::Base
+          self.abstract_class = true
+          establish_connection(:adapter =>'sqlite3',:database =>"#{File.dirname(__FILE__)}/../../../db/yourdb.sqlite3")
+        end
+      end
+    end
+	
+or you can use configuration file located in config/database.yml and add the following code to the module above:
+
+   root_path = File.join(File.dirname(__FILE__),"../../../")
+   configurations = YAML.load_file(File.join(root_path,"conf/database.yml"))
+   configurations.each_pair do |key, db_info|
+      db_info["database"] = File.join(root_path, db_info["database"]) if db_info["adapter"]=='sqlite3'
+   end
+   establish_connection(configurations["default"])
+
+Note: The latter is the default method.
+
+===== DBConfiguration
+In file config/database.yml
+
+   # SQLite version 3.x
+   # gem install sqlite3
+   default:
+     adapter: sqlite3
+     database: db/bio-foo.sqlite3
+     pool: 5
+     timeout: 5000
+
+===== Create the database
+   bundle exec rake db:create 
+Create the database from config/database.yml for the current default (use db:create:all to create all dbs in the config
+
+==== Create A Table Using Migration
+In file db/migrate/001_create_example.rb
+
+The code below create a table name example. As best practice name this file with a prefix index like 001_create_example.rb and the next migration 002.... and so on, this will help you to keep track over the time.
+Please refer to Rails' documentation
+   
+   class CreateExample < ActiveRecord::Migration
+     def self.up
+       #primary key id is created automatically by ActiveRecord::Migration
+       create_table :example do |t|
+         t.string :name
+         t.string :tag
+         t.string :type
+       end
+   
+       add_index :example, :name
+     end
+   
+     def self.down
+       drop_table :example
+     end
+   end
+
+Once you have defined the table you can create it
+   $ bundle exec rake db:migrate
+Migrate the database (options: VERSION=x, VERBOSE=false)
+
+===== Defining a Model
+The model must be located in a directory structure like lib/bio/your_module/your_class this is important because ActiveRecord map the namespace with the directory tree.
+
+    module Bio
+      module YourModule
+        class Mytable < Bio::YourModule::DummyMySpecialDB
+        end
+      end
+    end
+Then using the 
+
+===== Seeds
+Before populate your databse file you must declare a model. The model is declared in the usual Rails' way, see above.
+Use file db/seeds.rb to load a default dataset into your database
+
+   %w(Raoul Toshiaki Francesco).each do |coder|
+     Bio::YourModule::Example.create(:name=>coder, :tag=>"bioruby", :type=>"developer")
+   end
+
+=== Rails Engine With Database a BioPlugin
+Biogem is intended to help you also in advanced task like create a gem that can be reused in multiple rails applications, serving for instance a database, libraries and/or controllers,models,views.
+==== Why Rails Engine
+In bioinformatics is very common to presents data using a web application, and often you find are re using the same libraries and database for the same purpose, with a just a small difference in applications or your need to put together different functionalities which are spread along multiple database and libraries.
+==== HowToEngines
+To example this Biogem's features we want to create a Rails application which provides a form to users. Data submitted are submitted to TogoWS and the result is returned in a web page. In the mean time we want to store suers queries and return them in the page of TogoWS' result. We'll create a Rails application and a separated Biogem to store queries and provide connection to TogoWS, following "man in the middle" pattern.
+
+    $ biogem --with-engine Foo foo
+Note: a database is automatically configure for the newly created gem
+
+    $ rails new Webfoo
+
+You can test your application just inserting into Rails application Gemfile the newly created gem:
+    gem 'bio-foo', :path=>'path_gem_dir'
+
+update the installation running:
+     cd Webfoo
+     bundle install
+
+Enable the route for the added gem (in biouby-foo/config/routes.rb) uncomment:
+    yourPathToTheControllerFiles = 'foopath'
+    controllerName = :foos
+    otherControllerName = :samples
+    #---
+    scope mount_at, yourPathToTheControllerFiles do    
+      resources controllerName do
+        member do
+          get :example
+        end
+      end
+      resources otherControllerName, :only =>[:index, :show]
+    end #scope
+
+In bioruby-foo/lib/bio/foo/example.rb be sure the example class is uncommented:
+    module Bio
+      module Foo
+        class Example < DummyConn
+        end
+      end
+    end
+
+Create and migrate bioruby-foo database:
+    cd bioruby-foo
+    bundle exec rake db:create
+    bundle exec rake db:migrate
+
+Run your Rails server and load the web page
+    cd Webfoo
+    rails s
+
+open your browser to http://localhost:3000/foos/new
+
+Controller,Views and Module are located in bioruby-foo:
+* app/controllers
+* app/views
+* app/helpers
+* lib/bio/your_module/your_table.rb
+
+The latter path has modified by purpose from standard Rails configuration to keep a consistency with a normal ruby/gem library, in case developer wants to use a database but not a rails engine.
+
+=== A Meta Plugin
+A meta package or plugin is a very simple gem, essentially a configuration's gem. This particular plugin is used to aggregate other plugins or gems taking advantage of RubyGems dependencies. An example of this feature are: bio-core, bio-ext, bio-biollinux plugins which have different purposes and they can contain the same plugins but in different versions.
+
+   $ Biogem --meta foo                            
+
+   create	.gitignore
+   create	Rakefile
+   create	Gemfile
+   create	LICENSE.txt
+   create	README.rdoc
+   create	.document
+
+Those are the only files created by Biogem and are the only required to work as a meta-package. The user can add its libraries to the Gemfile and update information in Rakefile
+
+===== Gemfile
+This is Gemfile's content
+   source "http://rubygems.org"
+   # Add dependencies required to use your gem here.
+   # Example:
+   #   gem "activesupport", ">= 2.3.5"
+
+   # Add dependencies to develop your gem here.
+   # Include everything needed to run rake, tests, features, etc.
+   group :development do
+     gem "shoulda", ">= 0"
+     gem "bundler", "~> 1.0.0"
+     gem "jeweler", "~> 1.6.4"
+     gem "rcov", ">= 0"
+     gem "bio", ">= 1.4.2"
+   end
+
+In general if you add gems to the development section that gems will be installed only if you want to contribute the the original plugin source code. Otherwise you must add your gem requirements outside development group.
+Note: because this file is used by bundler as well, you can specify multiple source. For development purposes is also possible to specify different location than rubygems, local or github:
+   gem "the_perfect_gem", :path=>"your_local_path_on_your_hard_drive"
+   gem "JohnDoe_perfect_gem", :git=>"http://github.com/johndow/the_perfect_gem"
+
+== Manage Plugin Versions
+   $ rake version:bump:(major | minor | patch)
+will increase the level of your actual version by 1. A version is composed by X.Y.Z where X = major, Y = minor, Z = patch and we suggest the following approach for bumping the version:
+* major: new features or modifications which introduce incompatibilities with older version
+* minor: new features which keep backward compatibility
+* patch: fix a bug keeping backward compatibility
+Note: every time you want to publish your plugin on RubyGems the version must be bumped by 1 in at least one of the X.Y.Z otherwise RubyGems will give your an error. If you want to remove a specific version from RubyGems you must yank it but remember that version number, will not be available anymore
+   gem yank GEM -v VERSION [-p PLATFORM] [--undo] [options]
+=== Bumping Minor Version
+   $ bundle exec rake version:bump:minor
+   Current version: 0.0.0
+   Updated version: 0.1.0
+
+== Releasing the Plugin
+After hack, git add and commit you may be ready to distribute the plugin and now you have two ways
+* Only GitHub
+* GitHub and RubyGems
+===  Only on GitHub
+   $ bundle exec rake git:release
+=== GitHub and Rubygems at the same time
+   $ bundle exec rake release
+
+
+== Options
+These are the available options, they come from Biogem and from jeweler. I don't know if in the future I'll keep all of them.
+
+Usage: Biogem [options] reponame, e.g.
+   $ Biogem the-perfect-gem
+
+
+        --directory [DIRECTORY]      specify the directory to generate into
+These options are for Biogem
+        --meta                       create a meta package, just the Rakefile, Gemfile, Licence, Readme. This options takes the precedence over every other option.
+        --with-bin                   create the bin directory and an executable template script called bioreponame
+        --with-db                    create the database directory for a db application-library
+        --with-test-data             create the data directory inside the test directory if the user need to set up a test with its own dataset
+        --with-engine [NAMESPACE]    create a Rails engine with the namespace given in input. Dy default set up the environment to use an SQLite3 database
+These options are for Jeweler
+        --rspec                      generate rspec code examples
+        --shoulda                    generate shoulda tests
+        --testunit                   generate test/unit tests
+        --bacon                      generate bacon specifications
+        --testspec                   generate test/spec tests
+        --minitest                   generate minitest tests
+        --micronaut                  generate micronaut examples
+        --riot                       generate riot tests
+        --shindo                     generate shindo tests
+
+        --[no-]bundler               use bundler for managing dependencies
+        --cucumber                   generate cucumber stories in addition to the other tests
+
+        --reek                       generate rake task for reek
+        --roodi                      generate rake task for roodi
+
+        --summary [SUMMARY]          specify the summary of the project
+        --description [DESCRIPTION]  specify a description of the project
+
+        --user-name [USER_NAME]      the user's name, ie that is credited in the LICENSE
+        --user-email [USER_EMAIL]    the user's email, ie that is credited in the Gem specification
+
+        --github-username [GITHUB_USERNAME]
+                                     name of the user on GitHub to set the project up under
+        --github-token [GITHUB_TOKEN]
+                                     GitHub token to use for interacting with the GitHub API
+        --git-remote [GIT_REMOTE]    URI to set the git origin remote to
+        --homepage [HOMEPAGE]        the homepage for your project (defaults to the GitHub repo)
+        --no-create-repo                create the repository on GitHub (repo is created by default)
+
+        --yard                       use yard for documentation
+        --rdoc                       use rdoc for documentation
+    -h, --help                       display this help and exit
+
+== Tasks
+Biogems, like other frameworks, offers a bunch of predefined and common operations for the developers. These are so called tasks and can be listed simply typing:
+   $ rake -T 
+but because we are in a "development environment" is strongly suggested to use a very similar command 
+   $ bundle exec rake -T
+which guarantees that all the called programs/tasks will be executed inside the current development environment (bound to specific libraries versions). Follows the list of all available tasks for Biogem
+
+    rake build               # Build gem into pkg/
+    rake clobber_rcov        # Remove rcov products for rcov
+    rake clobber_rdoc        # Remove rdoc products
+    rake console[script]     # Start IRB with all runtime dependencies loaded
+    rake db:create           # Create the database from config/database.yml for the current default (use db:create:all to create all dbs in the config)
+    rake db:drop             # Drops the database for the current default (use db:drop:all to drop all databases)
+    rake db:fixtures:load    # Load fixtures into the current environment's database.
+    rake db:migrate          # Migrate the database (options: VERSION=x, VERBOSE=false).
+    rake db:migrate:status   # Display status of migrations
+    rake db:rollback         # Rolls the schema back to the previous version (specify steps w/ STEP=n).
+    rake db:schema:dump      # Create a db/schema.rb file that can be portably used against any DB supported by AR
+    rake db:schema:load      # Load a schema.rb file into the database
+    rake db:seed             # Load the seed data from db/seeds.rb
+    rake db:setup            # Create the database, load the schema, and initialize with the seed data (use db:reset to also drop the db first)
+    rake db:structure:dump   # Dump the database structure to an SQL file
+    rake db:version          # Retrieves the current schema version number
+    rake gemcutter:release   # Release gem to Gemcutter
+    rake gemspec             # Generate and validate gemspec
+    rake gemspec:debug       # Display the gemspec for debugging purposes, as jeweler knows it (not from the filesystem)
+    rake gemspec:generate    # Regenreate the gemspec on the filesystem
+    rake gemspec:release     # Regenerate and validate gemspec, and then commits and pushes to git
+    rake gemspec:validate    # Validates the gemspec on the filesystem
+    rake git:release         # Tag and push release to git.
+    rake install             # Build and install gem using `gem install`
+    rake rcov                # Analyze code coverage with tests
+    rake rdoc                # Build the rdoc HTML Files
+    rake release             # Release gem
+    rake rerdoc              # Force a rebuild of the RDOC files
+    rake test                # Run tests
+    rake version             # Displays the current version
+    rake version:bump:major  # Bump the major version by 1
+    rake version:bump:minor  # Bump the a minor version by 1
+    rake version:bump:patch  # Bump the patch version by 1
+    rake version:write       # Writes out an explicit version.
+
+
+==  Advanced Developers
+
+* Remember to modify .gitignore to exclude unwanted files.
+
+== BioRuby's Wiki Official Documentation
+
+* http://bioruby.open-bio.org/wiki/Plugins
+=== StepByStep
+Toshiaki Katayama wrote a step by step guide for a bio-foobar plugin @ http://bioruby.open-bio.org/wiki/BiogemInstallation; note this information could be older than this.
+
+
+== Biogems Official Plugin Archive
+
+* http://Biogems.info/ 
+
+
+== TODO
+* better command line, wrap or re-implement some of the funcionalities provided by Bundler and Jeweler
+* use YAML for database configuration
+
+== Copyright
+
+Copyright (c) 2010 Raoul J.P. Bonnal, Toshiaki Katayama, and Pjotr Prins. See LICENSE.txt for
+further details.
+

data/VERSION

@@ -1 +1 @@
-1.1.1
+1.1.2

data/bio-gem.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-gem}
-  s.version = "1.1.1"
+  s.version = "1.1.2"
 
   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{2011-11-09}
+  s.date = %q{2011-11-29}
   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}
@@ -25,6 +25,7 @@ Gem::Specification.new do |s|
     "LICENSE.txt",
     "README.rdoc",
     "Rakefile",
+    "Tutorial.rdoc",
     "VERSION",
     "bin/biogem",
     "bio-gem.gemspec",
@@ -35,10 +36,13 @@ 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/db_connection",
+    "lib/bio-gem/templates/db_model",
     "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_new",
     "lib/bio-gem/templates/foos_view_show",
     "lib/bio-gem/templates/lib",
     "lib/bio-gem/templates/library",

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

@@ -5,12 +5,12 @@ 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
+    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
@@ -27,7 +27,7 @@ class Jeweler
       end
     end
 
-     alias original_project_name project_name  
+    alias original_project_name project_name  
     def project_name
       prj_name = original_project_name=~/^bio-/ ? original_project_name : "bio-#{original_project_name}" 
       prj_name
@@ -65,31 +65,43 @@ 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 sub_module
+      project_name.split('-')[1..-1].map{|x| x.capitalize}.join
+    end
+    
+    def lib_sub_module
+      File.join(lib_dir,"bio",sub_module.downcase)
+    end
+    
+    def exists_dir?(dir)
+      Dir.exists?(File.join(target_dir,dir))
+    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, '<>')
@@ -109,7 +121,7 @@ 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)
@@ -128,11 +140,16 @@ class Jeweler
       migrate_dir = File.join(db_dir, "migrate")
       mkdir_in_target(db_dir)
       mkdir_in_target(migrate_dir)
-      mkdir_in_target("conf")
-      output_template_in_target_generic 'database', File.join("conf", "database.yml")
+      mkdir_in_target("config") unless exists_dir?("config")
+      mkdir_in_target("lib/bio")
+      mkdir_in_target(lib_sub_module)
+      output_template_in_target_generic 'database', File.join("config", "database.yml")
       output_template_in_target_generic 'migration', File.join(migrate_dir, "001_create_example.rb" )
       output_template_in_target_generic 'seeds', File.join(db_dir, "seeds.rb")
       output_template_in_target_generic 'rakefile', 'Rakefile', template_dir_biogem, 'a' #need to spec all the option to enable the append option
+      #TODO I'd like to have a parameter from command like with defines the Namespace of the created bio-gem to automatically costruct directory structure
+      output_template_in_target_generic 'db_connection', File.join(lib_sub_module,"connect.rb")
+      output_template_in_target_generic 'db_model', File.join(lib_sub_module,"example.rb")
     end
 
     alias original_create_files create_files
@@ -147,7 +164,7 @@ class Jeweler
         else
           raise FileInTheWay, "The directory #{target_dir} already exists, aborting. Maybe move it out of the way before continuing?"
         end
-        
+
         output_template_in_target '.gitignore'
         output_template_in_target 'Rakefile'
         output_template_in_target 'Gemfile'  if should_use_bundler
@@ -156,7 +173,7 @@ class Jeweler
         output_template_in_target '.document'
       else
         original_create_files
-        
+
         if options[:biogem_test_data]
           mkdir_in_target("test") unless File.exists? "#{target_dir}/test"
           mkdir_in_target test_data_dir  
@@ -168,39 +185,44 @@ class Jeweler
           # TODO: set the file as executable
           File.chmod 0655, File.join(target_dir, bin_dir, bin_name)
         end
-        
+
         # 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
+            mkdir_in_target(dir) unless exists_dir?(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_index', File.join('app',"views","foos", "index.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" )          
+          output_template_in_target_generic 'foos_view_example', File.join('app',"views","foos", "example.html.erb" )
+          output_template_in_target_generic 'foos_view_new', File.join('app',"views","foos", "new.html.erb" )
         end
       end #not_bio_gem_meta
     end
 
     def create_and_push_repo
-      Net::HTTP.post_form URI.parse('http://github.com/api/v2/yaml/repos/create'),
-      'login' => github_username,
-      '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')
+      begin 
+        Net::HTTP.post_form URI.parse('http://github.com/api/v2/yaml/repos/create'),
+        'login' => github_username,
+        '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')
+      rescue  SocketError => se
+        puts_template_message("Seems you are not connected to Internet, can't create a remote repository. Do not forget to create it by hand, from GitHub, and sync it with this project.")
+      end
     end
-    
-    
+
+
     def puts_template_message(message, length=70, padding=4)
       puts "*"*(length+padding*2+2)
       puts "*"+" "*(length+padding*2)+"*"

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

@@ -10,7 +10,7 @@ class Jeweler
         self[:testing_framework]       = :shoulda
         self[:documentation_framework] = :rdoc
         self[:use_bundler]             = true
-        self[:create_repo]             = true
+        self[:create_repo]             = self[:create_repo] || true
 
         git_config =  if Pathname.new("~/.gitconfig").expand_path.exist?
           Git.global_config
@@ -156,8 +156,8 @@ class Jeweler
             self[:homepage] = homepage
           end
 
-          o.on('--create-repo', 'create the repository on GitHub') do
-            self[:create_repo] = true
+          o.on('--no-create-repo', 'create the repository on GitHub') do
+            self[:create_repo] = false
           end
 
 

data/lib/bio-gem/templates/db_connection

@@ -0,0 +1,13 @@
+module Bio
+  module <%= sub_module.capitalize %>
+    class DummyConn < ActiveRecord::Base
+        self.abstract_class = true
+        root_path = File.join(File.dirname(__FILE__),"../../../")
+        configurations =  YAML.load_file(File.join(root_path,"config/database.yml"))
+        configurations.each_pair do |key, db_info|
+          db_info["database"] = File.join(root_path, db_info["database"]) if db_info["adapter"]=='sqlite3'
+        end
+        establish_connection(configurations["default"])
+    end
+  end
+end

data/lib/bio-gem/templates/db_model

@@ -0,0 +1,6 @@
+module Bio
+  module <%= sub_module.capitalize %>
+    class Example < DummyConn
+    end
+  end
+end

data/lib/bio-gem/templates/foos_controller

@@ -1,5 +1,8 @@
 class FoosController < ApplicationController
   def example
+    @example = Bio::Foo::Example.find(params["id"])
+    @examples = Bio::Foo:Example.all
+    @togo=TOGOWS.entry('genbank', @example.gene_name)
     @shuttle =  "TEST CASE"
   end
 
@@ -10,4 +13,19 @@ class FoosController < ApplicationController
   def show
     @item = "It's me"
   end
+
+  def new
+    @example =  Bio::Foo::Example.new
+  end
+
+  def create
+    @example = Bio::Foo::Example.new(params[:example])
+    if @example.save
+      redirect_to example_url(@example)
+    else
+      # This line overrides the default rendering behavior, which
+      # would have been to render the "create" view.
+      render :action => "new"
+    end
+  end
 end

data/lib/bio-gem/templates/foos_view_example

@@ -1 +1,13 @@
-This is just an example of a call from a controller <%%= @shuttle %>
+<p>This is just an example of a call from a controller <%%= @shuttle %></p>
+
+<p>Your query was <%%= @example.gene_name %></p>
+
+<p>I found on TOGOWS this answer: <%%= @togo %></p>
+
+<p>In the past you asked for all this things</p>
+<table>
+	<tr><th>Questions</th></tr>
+	<%% @examples.each do |example|%>
+	<tr><td><%%= example.gene_name%></td></tr>
+	<%% end %>
+</table>

data/lib/bio-gem/templates/foos_view_new

@@ -0,0 +1,4 @@
+<%%= form_for @example, :url => { :action => "create" }, :html => {:class => "nifty_form"} do |f| %>
+  <%%= f.text_field :gene_name %>
+  <%%= f.submit "Create" %>
+<%% end %>

data/lib/bio-gem/templates/lib

@@ -8,3 +8,10 @@
 # and put your plugin's code there. It is bad practice to write other code 
 # directly into this file, because doing so causes confusion if this biogem 
 # was ever to get merged into the main bioruby tree.
+
+<% if options[:biogem_db] %>
+require '<%= File.join("bio",sub_module.downcase,"connect") %>'
+  <% unless options[:biogem_engine] %>
+require '<%= File.join("bio",sub_module.downcase,"example") %>'
+  <% end %>
+<% end %>

data/lib/bio-gem/templates/library

@@ -3,4 +3,7 @@ if (defined?(Rails) && Rails::VERSION::MAJOR == 3)
   require '<%= engine_name %>'
 else
   #require the usual dependencies here
+  <% if options[:biogem_db] %>
+    require '<%= File.join("bio",sub_module.downcase,"example") %>'
+  <% end %>
 end

data/lib/bio-gem/templates/migration

@@ -5,16 +5,16 @@
 # class CreateExample < ActiveRecord::Migration
 #   def self.up
 #     #primary key id is created automatically by ActiveRecord::Migration
-#     create_table :example do |t|
-#       t.string :name
+#     create_table :examples do |t|
+#       t.string :gene_name
 #       t.string :tag
 #       t.string :type
 #     end
 # 
-#     add_index :example, :name
+#     add_index :examples, :gene_name
 #   end
 # 
 #   def self.down
-#     drop_table :example
+#     drop_table :examples
 #   end
 # end

data/lib/bio-gem/templates/rakefile

@@ -1,3 +1,6 @@
+# encoding: utf-8
+Encoding.default_external = Encoding::UTF_8
+Encoding.default_internal = Encoding::UTF_8
 
 $LOAD_PATH.unshift File.join(File.dirname(__FILE__),'lib')
 require 'active_support'
@@ -9,7 +12,7 @@ require 'active_record'
 namespace :db do
   task :load_config do
     require 'active_record'
-    ActiveRecord::Base.configurations = YAML.load_file("conf/database.yml")
+    ActiveRecord::Base.configurations = YAML.load_file("config/database.yml")
   end
 
   task :environment => :load_config do
@@ -303,7 +306,7 @@ namespace :db do
       fixtures_dir = ENV['FIXTURES_DIR'] ? File.join(base_dir, ENV['FIXTURES_DIR']) : base_dir
 
       (ENV['FIXTURES'] ? ENV['FIXTURES'].split(/,/).map {|f| File.join(fixtures_dir, f) } : Dir["#{fixtures_dir}/**/*.{yml,csv}"]).each do |fixture_file|
-        Fixtures.create_fixtures(fixtures_dir, fixture_file[(fixtures_dir.size + 1)..-5])
+        ActiveRecord::Fixtures.create_fixtures(fixtures_dir, fixture_file[(fixtures_dir.size + 1)..-5])
       end
     end
 

data/lib/bio-gem/templates/routes

@@ -22,10 +22,10 @@ Rails.application.routes.draw do
 ## 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
-# ---
+# otherControllerName = :samples
+## ---
 # scope mount_at, yourPathToTheControllerFiles do    
-#   resources controllerName, :only => [ :index, :show] do
+#   resources controllerName do #, :only => [ :index, :show, :new] do
 #     member do
 #       get :example
 #     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gem
 version: !ruby/object:Gem::Version
-  version: 1.1.1
+  version: 1.1.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-11-09 00:00:00.000000000Z
+date: 2011-11-29 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2153443100 !ruby/object:Gem::Requirement
+  requirement: &2154015700 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: 1.0.18
   type: :runtime
   prerelease: false
-  version_requirements: *2153443100
+  version_requirements: *2154015700
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2153441480 !ruby/object:Gem::Requirement
+  requirement: &2154015180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: 1.6.4
   type: :runtime
   prerelease: false
-  version_requirements: *2153441480
+  version_requirements: *2154015180
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &2153434540 !ruby/object:Gem::Requirement
+  requirement: &2154014540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2153434540
+  version_requirements: *2154014540
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2153433620 !ruby/object:Gem::Requirement
+  requirement: &2154013740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153433620
+  version_requirements: *2154013740
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2153432960 !ruby/object:Gem::Requirement
+  requirement: &2154012940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 1.0.18
   type: :development
   prerelease: false
-  version_requirements: *2153432960
+  version_requirements: *2154012940
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2153432380 !ruby/object:Gem::Requirement
+  requirement: &2154012100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +76,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2153432380
+  version_requirements: *2154012100
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2153431780 !ruby/object:Gem::Requirement
+  requirement: &2154011320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153431780
+  version_requirements: *2154011320
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &2153430520 !ruby/object:Gem::Requirement
+  requirement: &2154003500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,7 +98,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153430520
+  version_requirements: *2154003500
 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
@@ -117,6 +117,7 @@ files:
 - LICENSE.txt
 - README.rdoc
 - Rakefile
+- Tutorial.rdoc
 - VERSION
 - bin/biogem
 - bio-gem.gemspec
@@ -127,10 +128,13 @@ files:
 - lib/bio-gem/mod/jeweler/options.rb
 - lib/bio-gem/templates/bin
 - lib/bio-gem/templates/database
+- lib/bio-gem/templates/db_connection
+- lib/bio-gem/templates/db_model
 - 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_new
 - lib/bio-gem/templates/foos_view_show
 - lib/bio-gem/templates/lib
 - lib/bio-gem/templates/library
@@ -155,7 +159,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1020591000777977995
+      hash: 823213589522284135
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: