bio 0.7.1 → 1.0.0

data/lib/bio/shell/rails/config/database.yml

@@ -0,0 +1,85 @@
+# MySQL (default setup).  Versions 4.1 and 5.0 are recommended.
+#
+# Get the fast C bindings:
+#   gem install mysql
+#   (on OS X: gem install mysql -- --include=/usr/local/lib)
+# And be sure to use new-style password hashing:
+#   http://dev.mysql.com/doc/refman/5.0/en/old-client.html
+development:
+  adapter: mysql
+  database: kumamushi_development
+  username: root
+  password:
+  socket: /tmp/mysql.sock
+
+  # Connect on a TCP socket.  If omitted, the adapter will connect on the
+  # domain socket given by socket instead.
+  #host: localhost
+  #port: 3306
+  
+# Warning: The database defined as 'test' will be erased and
+# re-generated from your development database when you run 'rake'.
+# Do not set this db to the same as development or production.
+test:
+  adapter: mysql
+  database: kumamushi_test
+  username: root
+  password:
+  socket: /tmp/mysql.sock
+
+production:
+  adapter: mysql
+  database: kumamushi_production
+  username: root
+  password: 
+  socket: /tmp/mysql.sock
+
+
+# PostgreSQL versions 7.4 - 8.1
+#
+# Get the C bindings:
+#   gem install postgres
+# or use the pure-Ruby bindings on Windows:
+#   gem install postgres-pr
+postgresql_example:
+  adapter: postgresql
+  database: kumamushi_development
+  username: kumamushi
+  password:
+
+  # Connect on a TCP socket.  Omitted by default since the client uses a
+  # domain socket that doesn't need configuration.
+  #host: remote-database
+  #port: 5432
+
+  # Schema search path.  The server defaults to $user,public
+  #schema_search_path: myapp,sharedapp,public
+
+  # Character set encoding.  The server defaults to sql_ascii.
+  #encoding: UTF8
+
+  # Minimum log levels, in increasing order:
+  #   debug5, debug4, debug3, debug2, debug1,
+  #   info, notice, warning, error, log, fatal, or panic
+  # The server defaults to notice.
+  #min_messages: warning
+
+
+# SQLite version 2.x
+#   gem install sqlite-ruby
+sqlite_example:
+  adapter: sqlite
+  database: db/development.sqlite2
+
+
+# SQLite version 3.x
+#   gem install sqlite3-ruby
+sqlite3_example:
+  adapter: sqlite3
+  database: db/development.sqlite3
+
+
+# In-memory SQLite 3 database.  Useful for tests.
+sqlite3_in_memory_example:
+  adapter: sqlite3
+  database: ":memory:"

data/lib/bio/shell/rails/config/environment.rb

@@ -0,0 +1,53 @@
+# Be sure to restart your web server when you modify this file.
+
+# Uncomment below to force Rails into production mode when 
+# you don't control web/app server and can't set it the proper way
+# ENV['RAILS_ENV'] ||= 'production'
+
+# Bootstrap the Rails environment, frameworks, and default configuration
+require File.join(File.dirname(__FILE__), 'boot')
+
+Rails::Initializer.run do |config|
+  # Settings in config/environments/* take precedence those specified here
+  
+  # Skip frameworks you're not going to use
+  # config.frameworks -= [ :action_web_service, :action_mailer ]
+
+  # Add additional load paths for your own custom dirs
+  # config.load_paths += %W( #{RAILS_ROOT}/extras )
+
+  # Force all environments to use the same logger level 
+  # (by default production uses :info, the others :debug)
+  # config.log_level = :debug
+
+  # Use the database for sessions instead of the file system
+  # (create the session table with 'rake create_sessions_table')
+  # config.action_controller.session_store = :active_record_store
+
+  # Enable page/fragment caching by setting a file-based store
+  # (remember to create the caching directory and make it readable to the application)
+  # config.action_controller.fragment_cache_store = :file_store, "#{RAILS_ROOT}/cache"
+
+  # Activate observers that should always be running
+  # config.active_record.observers = :cacher, :garbage_collector
+
+  # Make Active Record use UTC-base instead of local time
+  # config.active_record.default_timezone = :utc
+  
+  # Use Active Record's schema dumper instead of SQL when creating the test database
+  # (enables use of different database adapters for development and test environments)
+  # config.active_record.schema_format = :ruby
+
+  # See Rails::Configuration for more options
+end
+
+# Add new inflection rules using the following format 
+# (all these examples are active by default):
+# Inflector.inflections do |inflect|
+#   inflect.plural /^(ox)$/i, '\1en'
+#   inflect.singular /^(ox)en/i, '\1'
+#   inflect.irregular 'person', 'people'
+#   inflect.uncountable %w( fish sheep )
+# end
+
+# Include your application configuration below

data/lib/bio/shell/rails/config/environments/development.rb

@@ -0,0 +1,19 @@
+# Settings specified here will take precedence over those in config/environment.rb
+
+# In the development environment your application's code is reloaded on
+# every request.  This slows down response time but is perfect for development
+# since you don't have to restart the webserver when you make code changes.
+config.cache_classes     = false
+
+# Log error messages when you accidentally call methods on nil.
+config.whiny_nils        = true
+
+# Enable the breakpoint server that script/breakpointer connects to
+config.breakpoint_server = true
+
+# Show full error reports and disable caching
+config.action_controller.consider_all_requests_local = true
+config.action_controller.perform_caching             = false
+
+# Don't care if the mailer can't send
+config.action_mailer.raise_delivery_errors = false

data/lib/bio/shell/rails/config/environments/production.rb

@@ -0,0 +1,19 @@
+# Settings specified here will take precedence over those in config/environment.rb
+
+# The production environment is meant for finished, "live" apps.
+# Code is not reloaded between requests
+config.cache_classes = true
+
+# Use a different logger for distributed setups
+# config.logger        = SyslogLogger.new
+
+
+# Full error reports are disabled and caching is turned on
+config.action_controller.consider_all_requests_local = false
+config.action_controller.perform_caching             = true
+
+# Enable serving of images, stylesheets, and javascripts from an asset server
+# config.action_controller.asset_host                  = "http://assets.example.com"
+
+# Disable delivery errors if you bad email addresses should just be ignored
+# config.action_mailer.raise_delivery_errors = false

data/lib/bio/shell/rails/config/environments/test.rb

@@ -0,0 +1,19 @@
+# Settings specified here will take precedence over those in config/environment.rb
+
+# The test environment is used exclusively to run your application's
+# test suite.  You never need to work with it otherwise.  Remember that
+# your test database is "scratch space" for the test suite and is wiped
+# and recreated between test runs.  Don't rely on the data there!
+config.cache_classes = true
+
+# Log error messages when you accidentally call methods on nil.
+config.whiny_nils    = true
+
+# Show full error reports and disable caching
+config.action_controller.consider_all_requests_local = true
+config.action_controller.perform_caching             = false
+
+# Tell ActionMailer not to deliver emails to the real world.
+# The :test delivery method accumulates sent emails in the
+# ActionMailer::Base.deliveries array.
+config.action_mailer.delivery_method = :test

data/lib/bio/shell/rails/config/routes.rb

@@ -0,0 +1,19 @@
+ActionController::Routing::Routes.draw do |map|
+  # Add your own custom routes here.
+  # The priority is based upon order of creation: first created -> highest priority.
+  
+  # Here's a sample route:
+  # map.connect 'products/:id', :controller => 'catalog', :action => 'view'
+  # Keep in mind you can assign values other than :controller and :action
+
+  # You can have the root of your site routed by hooking up '' 
+  # -- just remember to delete public/index.html.
+  # map.connect '', :controller => "welcome"
+
+  # Allow downloading Web Service WSDL as a file with an extension
+  # instead of a file named 'wsdl'
+  map.connect ':controller/service.wsdl', :action => 'wsdl'
+
+  # Install the default route as the lowest priority.
+  map.connect ':controller/:action/:id'
+end

data/lib/bio/shell/rails/doc/README_FOR_APP

@@ -0,0 +1,2 @@
+Use this README file to introduce your application and point to useful places in the API for learning more.
+Run "rake appdoc" to generate API documentation for your models and controllers.

data/lib/bio/shell/rails/public/404.html

@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+   "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<body>
+  <h1>File not found</h1>
+  <p>Change this error message for pages not found in public/404.html</p>
+</body>
+</html>

data/lib/bio/shell/rails/public/500.html

@@ -0,0 +1,8 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+   "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<body>
+  <h1>Application error (Apache)</h1>
+  <p>Change this error message for exceptions thrown outside of an action (like in Dispatcher setups or broken Ruby code) in public/500.html</p>
+</body>
+</html>

data/lib/bio/shell/rails/public/dispatch.cgi

@@ -0,0 +1,10 @@
+#!/usr/bin/env ruby
+
+require File.dirname(__FILE__) + "/../config/environment" unless defined?(RAILS_ROOT)
+
+# If you're using RubyGems and mod_ruby, this require should be changed to an absolute path one, like:
+# "/usr/local/lib/ruby/gems/1.8/gems/rails-0.8.0/lib/dispatcher" -- otherwise performance is severely impaired
+require "dispatcher"
+
+ADDITIONAL_LOAD_PATHS.reverse.each { |dir| $:.unshift(dir) if File.directory?(dir) } if defined?(Apache::RubyRun)
+Dispatcher.dispatch

data/lib/bio/shell/rails/public/dispatch.fcgi

@@ -0,0 +1,24 @@
+#!/usr/bin/env ruby
+#
+# You may specify the path to the FastCGI crash log (a log of unhandled
+# exceptions which forced the FastCGI instance to exit, great for debugging)
+# and the number of requests to process before running garbage collection.
+#
+# By default, the FastCGI crash log is RAILS_ROOT/log/fastcgi.crash.log
+# and the GC period is nil (turned off).  A reasonable number of requests
+# could range from 10-100 depending on the memory footprint of your app.
+#
+# Example:
+#   # Default log path, normal GC behavior.
+#   RailsFCGIHandler.process!
+#
+#   # Default log path, 50 requests between GC.
+#   RailsFCGIHandler.process! nil, 50
+#
+#   # Custom log path, normal GC behavior.
+#   RailsFCGIHandler.process! '/var/log/myapp_fcgi_crash.log'
+#
+require File.dirname(__FILE__) + "/../config/environment"
+require 'fcgi_handler'
+
+RailsFCGIHandler.process!

data/lib/bio/shell/rails/public/dispatch.rb

@@ -0,0 +1,10 @@
+#!/usr/bin/env ruby
+
+require File.dirname(__FILE__) + "/../config/environment" unless defined?(RAILS_ROOT)
+
+# If you're using RubyGems and mod_ruby, this require should be changed to an absolute path one, like:
+# "/usr/local/lib/ruby/gems/1.8/gems/rails-0.8.0/lib/dispatcher" -- otherwise performance is severely impaired
+require "dispatcher"
+
+ADDITIONAL_LOAD_PATHS.reverse.each { |dir| $:.unshift(dir) if File.directory?(dir) } if defined?(Apache::RubyRun)
+Dispatcher.dispatch

data/lib/bio/shell/rails/public/index.html

@@ -0,0 +1,277 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+        "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html>
+  <head>
+    <meta http-equiv="Content-type" content="text/html; charset=utf-8" />
+    <title>Ruby on Rails: Welcome aboard</title>
+    <style type="text/css" media="screen">
+      body {
+        margin: 0;
+        margin-bottom: 25px;
+        padding: 0;
+        background-color: #f0f0f0;
+        font-family: "Lucida Grande", "Bitstream Vera Sans", "Verdana";
+        font-size: 13px;
+        color: #333;
+      }
+      
+      h1 {
+        font-size: 28px;
+        color: #000;
+      }
+      
+      a  {color: #03c}
+      a:hover {
+        background-color: #03c;
+        color: white;
+        text-decoration: none;
+      }
+      
+      
+      #page {
+        background-color: #f0f0f0;
+        width: 750px;
+        margin: 0;
+        margin-left: auto;
+        margin-right: auto;
+      }
+      
+      #content {
+        float: left;
+        background-color: white;
+        border: 3px solid #aaa;
+        border-top: none;
+        padding: 25px;
+        width: 500px;
+      }
+      
+      #sidebar {
+        float: right;
+        width: 175px;
+      }
+
+      #footer {
+        clear: both;
+      }
+      
+
+      #header, #about, #getting-started {
+        padding-left: 75px;
+        padding-right: 30px;
+      }
+
+
+      #header {
+        background-image: url("images/rails.png");
+        background-repeat: no-repeat;
+        background-position: top left;
+        height: 64px;
+      }
+      #header h1, #header h2 {margin: 0}
+      #header h2 {
+        color: #888;
+        font-weight: normal;
+        font-size: 16px;
+      }
+      
+      
+      #about h3 {
+        margin: 0;
+        margin-bottom: 10px;
+        font-size: 14px;
+      }
+      
+      #about-content {
+        background-color: #ffd;
+        border: 1px solid #fc0;
+        margin-left: -11px;
+      }
+      #about-content table {
+        margin-top: 10px;
+        margin-bottom: 10px;
+        font-size: 11px;
+        border-collapse: collapse;
+      }
+      #about-content td {
+        padding: 10px;
+        padding-top: 3px;
+        padding-bottom: 3px;
+      }
+      #about-content td.name  {color: #555}
+      #about-content td.value {color: #000}
+      
+      #about-content.failure {
+        background-color: #fcc;
+        border: 1px solid #f00;
+      }
+      #about-content.failure p {
+        margin: 0;
+        padding: 10px;
+      }
+      
+      
+      #getting-started {
+        border-top: 1px solid #ccc;
+        margin-top: 25px;
+        padding-top: 15px;
+      }
+      #getting-started h1 {
+        margin: 0;
+        font-size: 20px;
+      }
+      #getting-started h2 {
+        margin: 0;
+        font-size: 14px;
+        font-weight: normal;
+        color: #333;
+        margin-bottom: 25px;
+      }
+      #getting-started ol {
+        margin-left: 0;
+        padding-left: 0;
+      }
+      #getting-started li {
+        font-size: 18px;
+        color: #888;
+        margin-bottom: 25px;
+      }
+      #getting-started li h2 {
+        margin: 0;
+        font-weight: normal;
+        font-size: 18px;
+        color: #333;
+      }
+      #getting-started li p {
+        color: #555;
+        font-size: 13px;
+      }
+      
+      
+      #search {
+        margin: 0;
+        padding-top: 10px;
+        padding-bottom: 10px;
+        font-size: 11px;
+      }
+      #search input {
+        font-size: 11px;
+        margin: 2px;
+      }
+      #search-text {width: 170px}
+      
+      
+      #sidebar ul {
+        margin-left: 0;
+        padding-left: 0;
+      }
+      #sidebar ul h3 {
+        margin-top: 25px;
+        font-size: 16px;
+        padding-bottom: 10px;
+        border-bottom: 1px solid #ccc;
+      }
+      #sidebar li {
+        list-style-type: none;
+      }
+      #sidebar ul.links li {
+        margin-bottom: 5px;
+      }
+      
+    </style>
+    <script type="text/javascript" src="javascripts/prototype.js"></script>
+    <script type="text/javascript" src="javascripts/effects.js"></script>
+    <script type="text/javascript">
+      function about() {
+        if (Element.empty('about-content')) {
+          new Ajax.Updater('about-content', 'rails_info/properties', {
+            method:     'get',
+            onFailure:  function() {Element.classNames('about-content').add('failure')},
+            onComplete: function() {new Effect.BlindDown('about-content', {duration: 0.25})}
+          });
+        } else {
+          new Effect[Element.visible('about-content') ? 
+            'BlindUp' : 'BlindDown']('about-content', {duration: 0.25});
+        }
+      }
+      
+      window.onload = function() {
+        $('search-text').value = '';
+        $('search').onsubmit = function() {
+          $('search-text').value = 'site:rubyonrails.org ' + $F('search-text');
+        }
+      }
+    </script>
+  </head>
+  <body>
+    <div id="page">
+      <div id="sidebar">
+        <ul id="sidebar-items">
+          <li>
+            <form id="search" action="http://www.google.com/search" method="get">
+              <input type="hidden" name="hl" value="en" />
+              <input type="text" id="search-text" name="q" value="site:rubyonrails.org " />
+              <input type="submit" value="Search" /> the Rails site
+            </form>
+          </li>
+        
+          <li>
+            <h3>Join the community</h3>
+            <ul class="links">
+              <li><a href="http://www.rubyonrails.org/">Ruby on Rails</a></li>
+              <li><a href="http://weblog.rubyonrails.org/">Official weblog</a></li>
+              <li><a href="http://lists.rubyonrails.org/">Mailing lists</a></li>
+              <li><a href="http://wiki.rubyonrails.org/rails/pages/IRC">IRC channel</a></li>
+              <li><a href="http://wiki.rubyonrails.org/">Wiki</a></li>
+              <li><a href="http://dev.rubyonrails.org/">Bug tracker</a></li>
+            </ul>
+          </li>
+          
+          <li>
+            <h3>Browse the documentation</h3>
+            <ul class="links">
+              <li><a href="http://api.rubyonrails.org/">Rails API</a></li>
+              <li><a href="http://www.ruby-doc.org/stdlib/">Ruby standard library</a></li>
+              <li><a href="http://www.ruby-doc.org/core/">Ruby core</a></li>
+            </ul>
+          </li>
+        </ul>
+      </div>
+
+      <div id="content">
+        <div id="header">
+          <h1>Welcome aboard</h1>
+          <h2>You&rsquo;re riding the Rails!</h2>
+        </div>
+
+        <div id="about">
+          <h3><a href="rails_info/properties" onclick="about(); return false">About your application&rsquo;s environment</a></h3>
+          <div id="about-content" style="display: none"></div>
+        </div>
+        
+        <div id="getting-started">
+          <h1>Getting started</h1>
+          <h2>Here&rsquo;s how to get rolling:</h2>
+          
+          <ol>
+            <li>
+              <h2>Create your databases and edit <tt>config/database.yml</tt></h2>
+              <p>Rails needs to know your login and password.</p>
+            </li>
+          
+            <li>
+              <h2>Use <tt>script/generate</tt> to create your models and controllers</h2>
+              <p>To see all available options, run it without parameters.</p>
+            </li>
+            
+            <li>
+              <h2>Set up a default route and remove or rename this file</h2>
+              <p>Routes are setup in config/routes.rb.</p>
+            </li>
+          </ol>
+        </div>
+      </div>
+      
+      <div id="footer">&nbsp;</div>
+    </div>
+  </body>
+</html>