taxonomite 0.1.0

data/spec/dummy/app/views/taxonomite/index.html.erb

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+<h2>Select a node</h2>
+
+<% if @nodes %>
+    <% for node in @nodes %>
+        <p><%= link_to node.name, taxonomite_path(node) %> (<%= node.entity_type %>):  <%= node.description %></p>
+    <% end %>
+<% else %>
+    <p>No nodes defined.</p>
+<% end %>

data/spec/dummy/app/views/taxonomite/new.html.erb

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+<h1>Create a new node:</h1>
+
+<%= form_for @node, :url => { :action => :create } do |f| %>
+    <%= render 'shared/error_messages' %>
+
+    <p>
+        <%= f.label :name %><br />
+        <%= f.text_field :name %>
+    </p>
+    <p>
+        <%= f.label :description %><br />
+        <%= f.text_field :description %>
+    </p>
+
+    <%= f.submit "Create" %>
+<% end %>

data/spec/dummy/app/views/taxonomite/show.html.erb

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+<h2> Info on a node</h2>
+<% if @node %>
+    <ul>
+
+        <p>Name:        <%= link_to @node.typeifiedname, taxonomite_path(@node) %></p>
+        <p>Type:        <%= @node.entity_type %></p>
+        <p>Description: <%= @node.description %></p>
+        <p>Population:  <%= @node.aggregate_leaves("countme") %>
+
+        <% if @node.parent %>
+        <h3>Parent:</h3>
+            <li><%= link_to @node.parent.name, taxonomite_path(@node.parent) %></li>
+        <% end %>
+
+        <% if @node.has_children? %>
+            <h3>Children:</h3>
+            <%= render partial: 'node', collection: @node.children, as: :node %>
+        <% end %>
+
+    </ul>
+<% else %>
+    <p>Unable to find a Taxon.</p>
+<% end %>
+
+<br/>
+  <ul>
+  <li><%= link_to "Edit this node", edit_taxonomite_path(@node) %></li>
+  </ul>

data/spec/dummy/bin/bundle

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+#!/usr/bin/env ruby
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
+load Gem.bin_path('bundler', 'bundle')

data/spec/dummy/bin/rails

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+#!/usr/bin/env ruby
+APP_PATH = File.expand_path('../../config/application', __FILE__)
+require_relative '../config/boot'
+require 'rails/commands'

data/spec/dummy/bin/rake

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+#!/usr/bin/env ruby
+require_relative '../config/boot'
+require 'rake'
+Rake.application.run

data/spec/dummy/bin/setup

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+#!/usr/bin/env ruby
+require 'pathname'
+
+# path to your application root.
+APP_ROOT = Pathname.new File.expand_path('../../',  __FILE__)
+
+Dir.chdir APP_ROOT do
+  # This script is a starting point to setup your application.
+  # Add necessary setup steps to this file:
+
+  puts "== Installing dependencies =="
+  system "gem install bundler --conservative"
+  system "bundle check || bundle install"
+
+  # puts "\n== Copying sample files =="
+  # unless File.exist?("config/database.yml")
+  #   system "cp config/database.yml.sample config/database.yml"
+  # end
+
+  puts "\n== Preparing database =="
+  system "bin/rake db:setup"
+
+  puts "\n== Removing old logs and tempfiles =="
+  system "rm -f log/*"
+  system "rm -rf tmp/cache"
+
+  puts "\n== Restarting application server =="
+  system "touch tmp/restart.txt"
+end

data/spec/dummy/config.ru

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+# This file is used by Rack-based servers to start the application.
+
+require ::File.expand_path('../config/environment', __FILE__)
+run Rails.application

data/spec/dummy/config/application.rb

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+require File.expand_path('../boot', __FILE__)
+
+# Pick the frameworks you want:
+# require "active_record/railtie"
+require "active_model/railtie"
+require "active_job/railtie"
+require "action_controller/railtie"
+require "action_mailer/railtie"
+require "action_view/railtie"
+require "sprockets/railtie"
+require "mongoid"
+require "factory_girl_rails"
+# require "rails/test_unit/railtie"
+
+Bundler.require(*Rails.groups)
+require "taxonomite"
+
+# I hate this as its a specified path; get all the factories
+Dir["#{File.dirname(__FILE__)}/../../factories/*.rb"].each { |f| require f }
+
+module Dummy
+  class Application < Rails::Application
+    # Settings in config/environments/* take precedence over those specified here.
+    # Application configuration should go into files in config/initializers
+    # -- all .rb files in that directory are automatically loaded.
+
+    # Set Time.zone default to the specified zone and make Active Record auto-convert to this zone.
+    # Run "rake -D time" for a list of tasks for finding time zone names. Default is UTC.
+    # config.time_zone = 'Central Time (US & Canada)'
+
+    # The default locale is :en and all translations from config/locales/*.rb,yml are auto loaded.
+    # config.i18n.load_path += Dir[Rails.root.join('my', 'locales', '*.{rb,yml}').to_s]
+    # config.i18n.default_locale = :de
+  end
+end

data/spec/dummy/config/boot.rb

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+# Set up gems listed in the Gemfile.
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../../../Gemfile', __FILE__)
+
+require 'bundler/setup' if File.exist?(ENV['BUNDLE_GEMFILE'])
+$LOAD_PATH.unshift File.expand_path('../../../../lib', __FILE__)

data/spec/dummy/config/environment.rb

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+# Load the Rails application.
+require File.expand_path('../application', __FILE__)
+
+# Initialize the Rails application.
+Rails.application.initialize!

data/spec/dummy/config/environments/development.rb

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+Rails.application.configure do
+  # Settings specified here will take precedence over those in config/application.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 web server when you make code changes.
+  config.cache_classes = false
+
+  # Do not eager load code on boot.
+  config.eager_load = false
+
+  # Show full error reports and disable caching.
+  config.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
+
+  # Print deprecation notices to the Rails logger.
+  config.active_support.deprecation = :log
+
+  # Debug mode disables concatenation and preprocessing of assets.
+  # This option may cause significant delays in view rendering with a large
+  # number of complex assets.
+  config.assets.debug = true
+
+  # Asset digests allow you to set far-future HTTP expiration dates on all assets,
+  # yet still be able to expire them through the digest params.
+  config.assets.digest = true
+
+  # Adds additional error checking when serving assets at runtime.
+  # Checks for improperly declared sprockets dependencies.
+  # Raises helpful error messages.
+  config.assets.raise_runtime_errors = true
+
+  # Raises error for missing translations
+  # config.action_view.raise_on_missing_translations = true
+end

data/spec/dummy/config/environments/production.rb

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+Rails.application.configure do
+  # Settings specified here will take precedence over those in config/application.rb.
+
+  # Code is not reloaded between requests.
+  config.cache_classes = true
+
+  # Eager load code on boot. This eager loads most of Rails and
+  # your application in memory, allowing both threaded web servers
+  # and those relying on copy on write to perform better.
+  # Rake tasks automatically ignore this option for performance.
+  config.eager_load = true
+
+  # Full error reports are disabled and caching is turned on.
+  config.consider_all_requests_local       = false
+  config.action_controller.perform_caching = true
+
+  # Enable Rack::Cache to put a simple HTTP cache in front of your application
+  # Add `rack-cache` to your Gemfile before enabling this.
+  # For large-scale production use, consider using a caching reverse proxy like
+  # NGINX, varnish or squid.
+  # config.action_dispatch.rack_cache = true
+
+  # Disable serving static files from the `/public` folder by default since
+  # Apache or NGINX already handles this.
+  config.serve_static_files = ENV['RAILS_SERVE_STATIC_FILES'].present?
+
+  # Compress JavaScripts and CSS.
+  config.assets.js_compressor = :uglifier
+  # config.assets.css_compressor = :sass
+
+  # Do not fallback to assets pipeline if a precompiled asset is missed.
+  config.assets.compile = false
+
+  # Asset digests allow you to set far-future HTTP expiration dates on all assets,
+  # yet still be able to expire them through the digest params.
+  config.assets.digest = true
+
+  # `config.assets.precompile` and `config.assets.version` have moved to config/initializers/assets.rb
+
+  # Specifies the header that your server uses for sending files.
+  # config.action_dispatch.x_sendfile_header = 'X-Sendfile' # for Apache
+  # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for NGINX
+
+  # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
+  # config.force_ssl = true
+
+  # Use the lowest log level to ensure availability of diagnostic information
+  # when problems arise.
+  config.log_level = :debug
+
+  # Prepend all log lines with the following tags.
+  # config.log_tags = [ :subdomain, :uuid ]
+
+  # Use a different logger for distributed setups.
+  # config.logger = ActiveSupport::TaggedLogging.new(SyslogLogger.new)
+
+  # Use a different cache store in production.
+  # config.cache_store = :mem_cache_store
+
+  # Enable serving of images, stylesheets, and JavaScripts from an asset server.
+  # config.action_controller.asset_host = 'http://assets.example.com'
+
+  # Ignore bad email addresses and do not raise email delivery errors.
+  # Set this to true and configure the email server for immediate delivery to raise delivery errors.
+  # config.action_mailer.raise_delivery_errors = false
+
+  # Enable locale fallbacks for I18n (makes lookups for any locale fall back to
+  # the I18n.default_locale when a translation cannot be found).
+  config.i18n.fallbacks = true
+
+  # Send deprecation notices to registered listeners.
+  config.active_support.deprecation = :notify
+
+  # Use default logging formatter so that PID and timestamp are not suppressed.
+  config.log_formatter = ::Logger::Formatter.new
+end

data/spec/dummy/config/environments/test.rb

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+Rails.application.configure do
+  # Settings specified here will take precedence over those in config/application.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
+
+  # Do not eager load code on boot. This avoids loading your whole application
+  # just for the purpose of running a single test. If you are using a tool that
+  # preloads Rails for running tests, you may have to set it to true.
+  config.eager_load = false
+
+  # Configure static file server for tests with Cache-Control for performance.
+  config.serve_static_files   = true
+  config.static_cache_control = 'public, max-age=3600'
+
+  # Show full error reports and disable caching.
+  config.consider_all_requests_local       = true
+  config.action_controller.perform_caching = false
+
+  # Raise exceptions instead of rendering exception templates.
+  config.action_dispatch.show_exceptions = false
+
+  # Disable request forgery protection in test environment.
+  config.action_controller.allow_forgery_protection = false
+
+  # Tell Action Mailer 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
+
+  # Randomize the order test cases are executed.
+  config.active_support.test_order = :random
+
+  # Print deprecation notices to the stderr.
+  config.active_support.deprecation = :stderr
+
+  # Raises error for missing translations
+  # config.action_view.raise_on_missing_translations = true
+end

data/spec/dummy/config/initializers/assets.rb

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+# Be sure to restart your server when you modify this file.
+
+# Version of your assets, change this if you want to expire all your assets.
+Rails.application.config.assets.version = '1.0'
+
+# Add additional assets to the asset load path
+# Rails.application.config.assets.paths << Emoji.images_path
+
+# Precompile additional assets.
+# application.js, application.css, and all non-JS/CSS in app/assets folder are already added.
+# Rails.application.config.assets.precompile += %w( search.js )

data/spec/dummy/config/initializers/backtrace_silencers.rb

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+# Be sure to restart your server when you modify this file.
+
+# You can add backtrace silencers for libraries that you're using but don't wish to see in your backtraces.
+# Rails.backtrace_cleaner.add_silencer { |line| line =~ /my_noisy_library/ }
+
+# You can also remove all the silencers if you're trying to debug a problem that might stem from framework code.
+# Rails.backtrace_cleaner.remove_silencers!

data/spec/dummy/config/initializers/cookies_serializer.rb

@@ -0,0 +1,3 @@
+# Be sure to restart your server when you modify this file.
+
+Rails.application.config.action_dispatch.cookies_serializer = :json

data/spec/dummy/config/initializers/filter_parameter_logging.rb

@@ -0,0 +1,4 @@
+# Be sure to restart your server when you modify this file.
+
+# Configure sensitive parameters which will be filtered from the log file.
+Rails.application.config.filter_parameters += [:password]

data/spec/dummy/config/initializers/inflections.rb

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+# Be sure to restart your server when you modify this file.
+
+# Add new inflection rules using the following format. Inflections
+# are locale specific, and you may define rules for as many different
+# locales as you wish. All of these examples are active by default:
+# ActiveSupport::Inflector.inflections(:en) do |inflect|
+#   inflect.plural /^(ox)$/i, '\1en'
+#   inflect.singular /^(ox)en/i, '\1'
+#   inflect.irregular 'person', 'people'
+#   inflect.uncountable %w( fish sheep )
+# end
+
+# These inflection rules are supported but not enabled by default:
+# ActiveSupport::Inflector.inflections(:en) do |inflect|
+#   inflect.acronym 'RESTful'
+# end

data/spec/dummy/config/initializers/mime_types.rb

@@ -0,0 +1,4 @@
+# Be sure to restart your server when you modify this file.
+
+# Add new mime types for use in respond_to blocks:
+# Mime::Type.register "text/richtext", :rtf

data/spec/dummy/config/initializers/mongoid.rb

@@ -0,0 +1,8 @@
+# invoke Monkey patch for mongoid 4+ - to handle BSON-JSON ObjectId issues
+
+module ::BSON
+  class ObjectId
+      alias :to_json :to_s
+      alias :as_json :to_s
+  end
+end

data/spec/dummy/config/initializers/session_store.rb

@@ -0,0 +1,3 @@
+# Be sure to restart your server when you modify this file.
+
+Rails.application.config.session_store :cookie_store, key: '_dummy_session'

data/spec/dummy/config/initializers/wrap_parameters.rb

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+# Be sure to restart your server when you modify this file.
+
+# This file contains settings for ActionController::ParamsWrapper which
+# is enabled by default.
+
+# Enable parameter wrapping for JSON. You can disable this by setting :format to an empty array.
+ActiveSupport.on_load(:action_controller) do
+  wrap_parameters format: [:json] if respond_to?(:wrap_parameters)
+end
+

data/spec/dummy/config/locales/en.yml

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+# Files in the config/locales directory are used for internationalization
+# and are automatically loaded by Rails. If you want to use locales other
+# than English, add the necessary files in this directory.
+#
+# To use the locales, use `I18n.t`:
+#
+#     I18n.t 'hello'
+#
+# In views, this is aliased to just `t`:
+#
+#     <%= t('hello') %>
+#
+# To use a different locale, set it with `I18n.locale`:
+#
+#     I18n.locale = :es
+#
+# This would use the information in config/locales/es.yml.
+#
+# To learn more, please read the Rails Internationalization guide
+# available at http://guides.rubyonrails.org/i18n.html.
+
+en:
+  hello: "Hello world"

data/spec/dummy/config/mongoid.yml

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+development:
+  # Configure available database sessions. (required)
+  sessions:
+    # Defines the default session. (required)
+    default:
+      # Defines the name of the default database that Mongoid can connect to.
+      # (required).
+      database: dummy_development
+      # Provides the hosts the default session can connect to. Must be an array
+      # of host:port pairs. (required)
+      hosts:
+        - localhost:27017
+      options:
+        # Change the default write concern. (default = { w: 1 })
+        # write:
+        # w: 1
+
+        # Change the default consistency model to primary, secondary.
+        # 'secondary' will send reads to secondaries, 'primary' sends everything
+        # to master. (default: primary)
+        # read: secondary_preferred
+
+        # How many times Moped should attempt to retry an operation after
+        # failure. (default: The number of nodes in the cluster)
+        # max_retries: 20
+
+        # The time in seconds that Moped should wait before retrying an
+        # operation on failure. (default: 0.25)
+        # retry_interval: 0.25
+        
+        # The connection pool size per-node.  This should match or exceed the
+        # number of threads for a multi-threaded application. (default: 5)
+        # pool_size: 5
+        
+        # The time in seconds that Moped should wait for the pool to provide
+        # an available connection.  This number should probably remain at the 
+        # default, unless for some reason you absolutely need to limit the
+        # pool_size, as this wait is only used when the pool is saturated.
+        # (default: 0.5)
+        # pool_timeout: 0.5
+
+        # The time in seconds before Moped will timeout connection and node
+        # operations. (default: 5)
+        # timeout: 5
+        
+        # The amount of time in seconds between forced refreshes of node 
+        # information including the discovery of new peers. (default: 300)
+        # refresh_interval: 300
+        
+        # The amount of time in seconds that a node will be flagged as down.
+        # (default: 30) 
+        # down_interval: 30
+        
+        # Whether connections should use SSL. (default: nil/false)
+        # ssl: false
+        
+        # Whether Moped will use the existing seeds/nodes to find other peers.
+        # (default: true)
+        # auto_discover: true
+
+
+  # Configure Mongoid specific options. (optional)
+  options:
+    # Includes the root model name in json serialization. (default: false)
+    # include_root_in_json: false
+
+    # Include the _type field in serialization. (default: false)
+    # include_type_for_serialization: false
+
+    # Preload all models in development, needed when models use
+    # inheritance. (default: false)
+    # preload_models: false
+
+    # Protect id and type from mass assignment. (default: true)
+    # protect_sensitive_fields: true
+
+    # Raise an error when performing a #find and the document is not found.
+    # (default: true)
+    raise_not_found_error: false
+
+    # Raise an error when defining a scope with the same name as an
+    # existing method. (default: false)
+    # scope_overwrite_exception: false
+
+    # Use Active Support's time zone in conversions. (default: true)
+    # use_activesupport_time_zone: true
+
+    # Ensure all times are UTC in the app side. (default: false)
+    # use_utc: false
+test:
+  sessions:
+    default:
+      database: dummy_test
+      hosts:
+        - localhost:27017
+      options:
+        read: primary
+        # In the test environment we lower the retries and retry interval to
+        # low amounts for fast failures.
+        max_retries: 1
+        retry_interval: 0
+  options: 
+    raise_not_found_error: false