aqueduct-i2b2 0.1.0

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Files changed (43) hide show
  1. data/CHANGELOG.rdoc +8 -0
  2. data/LICENSE +112 -0
  3. data/README.rdoc +17 -0
  4. data/Rakefile +41 -0
  5. data/aqueduct-i2b2.gemspec +31 -0
  6. data/lib/aqueduct-i2b2.rb +7 -0
  7. data/lib/aqueduct-i2b2/version.rb +12 -0
  8. data/lib/aqueduct/wrappers/i2b2.rb +715 -0
  9. data/lib/tasks/aqueduct-i2b2_tasks.rake +4 -0
  10. data/test/aqueduct-i2b2_test.rb +7 -0
  11. data/test/dummy/README.rdoc +261 -0
  12. data/test/dummy/Rakefile +7 -0
  13. data/test/dummy/app/assets/javascripts/application.js +15 -0
  14. data/test/dummy/app/assets/stylesheets/application.css +13 -0
  15. data/test/dummy/app/controllers/application_controller.rb +3 -0
  16. data/test/dummy/app/helpers/application_helper.rb +2 -0
  17. data/test/dummy/app/views/layouts/application.html.erb +14 -0
  18. data/test/dummy/config.ru +4 -0
  19. data/test/dummy/config/application.rb +56 -0
  20. data/test/dummy/config/boot.rb +10 -0
  21. data/test/dummy/config/database.yml +25 -0
  22. data/test/dummy/config/environment.rb +5 -0
  23. data/test/dummy/config/environments/development.rb +37 -0
  24. data/test/dummy/config/environments/production.rb +67 -0
  25. data/test/dummy/config/environments/test.rb +37 -0
  26. data/test/dummy/config/initializers/backtrace_silencers.rb +7 -0
  27. data/test/dummy/config/initializers/inflections.rb +15 -0
  28. data/test/dummy/config/initializers/mime_types.rb +5 -0
  29. data/test/dummy/config/initializers/secret_token.rb +7 -0
  30. data/test/dummy/config/initializers/session_store.rb +8 -0
  31. data/test/dummy/config/initializers/wrap_parameters.rb +14 -0
  32. data/test/dummy/config/locales/en.yml +5 -0
  33. data/test/dummy/config/routes.rb +58 -0
  34. data/test/dummy/db/schema.rb +16 -0
  35. data/test/dummy/db/test.sqlite3 +0 -0
  36. data/test/dummy/log/test.log +8 -0
  37. data/test/dummy/public/404.html +26 -0
  38. data/test/dummy/public/422.html +26 -0
  39. data/test/dummy/public/500.html +25 -0
  40. data/test/dummy/public/favicon.ico +0 -0
  41. data/test/dummy/script/rails +6 -0
  42. data/test/test_helper.rb +10 -0
  43. metadata +153 -0
@@ -0,0 +1,37 @@
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+ Dummy::Application.configure do
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+ # Settings specified here will take precedence over those in config/application.rb
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+
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+ # In the development environment your application's code is reloaded on
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+ # every request. This slows down response time but is perfect for development
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+ # since you don't have to restart the web server when you make code changes.
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+ config.cache_classes = false
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+
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+ # Log error messages when you accidentally call methods on nil.
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+ config.whiny_nils = true
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+
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+ # Show full error reports and disable caching
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+ config.consider_all_requests_local = true
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+ config.action_controller.perform_caching = false
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+
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+ # Don't care if the mailer can't send
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+ config.action_mailer.raise_delivery_errors = false
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+
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+ # Print deprecation notices to the Rails logger
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+ config.active_support.deprecation = :log
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+
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+ # Only use best-standards-support built into browsers
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+ config.action_dispatch.best_standards_support = :builtin
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+
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+ # Raise exception on mass assignment protection for Active Record models
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+ config.active_record.mass_assignment_sanitizer = :strict
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+
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+ # Log the query plan for queries taking more than this (works
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+ # with SQLite, MySQL, and PostgreSQL)
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+ config.active_record.auto_explain_threshold_in_seconds = 0.5
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+
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+ # Do not compress assets
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+ config.assets.compress = false
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+
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+ # Expands the lines which load the assets
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+ config.assets.debug = true
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+ end
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+ Dummy::Application.configure do
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+ # Settings specified here will take precedence over those in config/application.rb
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+
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+ # Code is not reloaded between requests
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+ config.cache_classes = true
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+
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+ # Full error reports are disabled and caching is turned on
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+ config.consider_all_requests_local = false
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+ config.action_controller.perform_caching = true
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+
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+ # Disable Rails's static asset server (Apache or nginx will already do this)
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+ config.serve_static_assets = false
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+
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+ # Compress JavaScripts and CSS
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+ config.assets.compress = true
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+
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+ # Don't fallback to assets pipeline if a precompiled asset is missed
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+ config.assets.compile = false
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+
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+ # Generate digests for assets URLs
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+ config.assets.digest = true
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+
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+ # Defaults to Rails.root.join("public/assets")
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+ # config.assets.manifest = YOUR_PATH
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+
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+ # Specifies the header that your server uses for sending files
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+ # config.action_dispatch.x_sendfile_header = "X-Sendfile" # for apache
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+ # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for nginx
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+
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+ # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
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+ # config.force_ssl = true
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+
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+ # See everything in the log (default is :info)
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+ # config.log_level = :debug
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+
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+ # Prepend all log lines with the following tags
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+ # config.log_tags = [ :subdomain, :uuid ]
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+
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+ # Use a different logger for distributed setups
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+ # config.logger = ActiveSupport::TaggedLogging.new(SyslogLogger.new)
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+
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+ # Use a different cache store in production
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+ # config.cache_store = :mem_cache_store
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+
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+ # Enable serving of images, stylesheets, and JavaScripts from an asset server
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+ # config.action_controller.asset_host = "http://assets.example.com"
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+
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+ # Precompile additional assets (application.js, application.css, and all non-JS/CSS are already added)
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+ # config.assets.precompile += %w( search.js )
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+
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+ # Disable delivery errors, bad email addresses will be ignored
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+ # config.action_mailer.raise_delivery_errors = false
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+
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+ # Enable threaded mode
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+ # config.threadsafe!
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+
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+ # Enable locale fallbacks for I18n (makes lookups for any locale fall back to
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+ # the I18n.default_locale when a translation can not be found)
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+ config.i18n.fallbacks = true
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+
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+ # Send deprecation notices to registered listeners
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+ config.active_support.deprecation = :notify
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+
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+ # Log the query plan for queries taking more than this (works
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+ # with SQLite, MySQL, and PostgreSQL)
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+ # config.active_record.auto_explain_threshold_in_seconds = 0.5
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+ end
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+ Dummy::Application.configure do
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+ # Settings specified here will take precedence over those in config/application.rb
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+
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+ # The test environment is used exclusively to run your application's
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+ # test suite. You never need to work with it otherwise. Remember that
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+ # your test database is "scratch space" for the test suite and is wiped
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+ # and recreated between test runs. Don't rely on the data there!
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+ config.cache_classes = true
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+
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+ # Configure static asset server for tests with Cache-Control for performance
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+ config.serve_static_assets = true
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+ config.static_cache_control = "public, max-age=3600"
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+
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+ # Log error messages when you accidentally call methods on nil
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+ config.whiny_nils = true
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+
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+ # Show full error reports and disable caching
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+ config.consider_all_requests_local = true
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+ config.action_controller.perform_caching = false
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+
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+ # Raise exceptions instead of rendering exception templates
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+ config.action_dispatch.show_exceptions = false
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+
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+ # Disable request forgery protection in test environment
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+ config.action_controller.allow_forgery_protection = false
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+
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+ # Tell Action Mailer not to deliver emails to the real world.
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+ # The :test delivery method accumulates sent emails in the
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+ # ActionMailer::Base.deliveries array.
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+ config.action_mailer.delivery_method = :test
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+
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+ # Raise exception on mass assignment protection for Active Record models
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+ config.active_record.mass_assignment_sanitizer = :strict
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+
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+ # Print deprecation notices to the stderr
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+ config.active_support.deprecation = :stderr
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+ end
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+ # Be sure to restart your server when you modify this file.
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+
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+ # You can add backtrace silencers for libraries that you're using but don't wish to see in your backtraces.
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+ # Rails.backtrace_cleaner.add_silencer { |line| line =~ /my_noisy_library/ }
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+
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+ # You can also remove all the silencers if you're trying to debug a problem that might stem from framework code.
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+ # Rails.backtrace_cleaner.remove_silencers!
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+ # Be sure to restart your server when you modify this file.
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+
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+ # Add new inflection rules using the following format
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+ # (all these examples are active by default):
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+ # ActiveSupport::Inflector.inflections do |inflect|
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+ # inflect.plural /^(ox)$/i, '\1en'
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+ # inflect.singular /^(ox)en/i, '\1'
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+ # inflect.irregular 'person', 'people'
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+ # inflect.uncountable %w( fish sheep )
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+ # end
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+ #
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+ # These inflection rules are supported but not enabled by default:
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+ # ActiveSupport::Inflector.inflections do |inflect|
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+ # inflect.acronym 'RESTful'
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+ # end
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+ # Be sure to restart your server when you modify this file.
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+
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+ # Add new mime types for use in respond_to blocks:
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+ # Mime::Type.register "text/richtext", :rtf
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+ # Mime::Type.register_alias "text/html", :iphone
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+ # Be sure to restart your server when you modify this file.
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+
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+ # Your secret key for verifying the integrity of signed cookies.
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+ # If you change this key, all old signed cookies will become invalid!
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+ # Make sure the secret is at least 30 characters and all random,
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+ # no regular words or you'll be exposed to dictionary attacks.
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+ Dummy::Application.config.secret_token = '6232881d30c4dedb755c7639701379d2c5084a66e5e7c03be119c790693737ae9ebbb1eb3d5cb0415d4c93790c7461144adbc6b358ab0300d94ebfbcdf02122b'
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+ # Be sure to restart your server when you modify this file.
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+
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+ Dummy::Application.config.session_store :cookie_store, key: '_dummy_session'
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+
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+ # Use the database for sessions instead of the cookie-based default,
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+ # which shouldn't be used to store highly confidential information
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+ # (create the session table with "rails generate session_migration")
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+ # Dummy::Application.config.session_store :active_record_store
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+ # Be sure to restart your server when you modify this file.
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+ #
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+ # This file contains settings for ActionController::ParamsWrapper which
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+ # is enabled by default.
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+
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+ # Enable parameter wrapping for JSON. You can disable this by setting :format to an empty array.
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+ ActiveSupport.on_load(:action_controller) do
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+ wrap_parameters format: [:json]
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+ end
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+
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+ # Disable root element in JSON by default.
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+ ActiveSupport.on_load(:active_record) do
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+ self.include_root_in_json = false
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+ end
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+ # Sample localization file for English. Add more files in this directory for other locales.
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+ # See https://github.com/svenfuchs/rails-i18n/tree/master/rails%2Flocale for starting points.
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+
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+ en:
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+ hello: "Hello world"
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+ Dummy::Application.routes.draw do
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+ # The priority is based upon order of creation:
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+ # first created -> highest priority.
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+
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+ # Sample of regular route:
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+ # match 'products/:id' => 'catalog#view'
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+ # Keep in mind you can assign values other than :controller and :action
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+
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+ # Sample of named route:
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+ # match 'products/:id/purchase' => 'catalog#purchase', :as => :purchase
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+ # This route can be invoked with purchase_url(:id => product.id)
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+
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+ # Sample resource route (maps HTTP verbs to controller actions automatically):
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+ # resources :products
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+
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+ # Sample resource route with options:
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+ # resources :products do
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+ # member do
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+ # get 'short'
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+ # post 'toggle'
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+ # end
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+ #
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+ # collection do
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+ # get 'sold'
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+ # end
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+ # end
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+
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+ # Sample resource route with sub-resources:
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+ # resources :products do
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+ # resources :comments, :sales
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+ # resource :seller
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+ # end
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+
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+ # Sample resource route with more complex sub-resources
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+ # resources :products do
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+ # resources :comments
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+ # resources :sales do
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+ # get 'recent', :on => :collection
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+ # end
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+ # end
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+
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+ # Sample resource route within a namespace:
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+ # namespace :admin do
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+ # # Directs /admin/products/* to Admin::ProductsController
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+ # # (app/controllers/admin/products_controller.rb)
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+ # resources :products
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+ # end
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+
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+ # You can have the root of your site routed with "root"
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+ # just remember to delete public/index.html.
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+ # root :to => 'welcome#index'
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+
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+ # See how all your routes lay out with "rake routes"
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+
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+ # This is a legacy wild controller route that's not recommended for RESTful applications.
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+ # Note: This route will make all actions in every controller accessible via GET requests.
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+ # match ':controller(/:action(/:id))(.:format)'
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+ end
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+ # encoding: UTF-8
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+ # This file is auto-generated from the current state of the database. Instead
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+ # of editing this file, please use the migrations feature of Active Record to
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+ # incrementally modify your database, and then regenerate this schema definition.
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+ #
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+ # Note that this schema.rb definition is the authoritative source for your
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+ # database schema. If you need to create the application database on another
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+ # system, you should be using db:schema:load, not running all the migrations
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+ # from scratch. The latter is a flawed and unsustainable approach (the more migrations
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+ # you'll amass, the slower it'll run and the greater likelihood for issues).
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+ #
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+ # It's strongly recommended to check this file into your version control system.
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+
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+ ActiveRecord::Schema.define(:version => 0) do
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+
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+ end
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+  (0.1ms) select sqlite_version(*)
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+  (2.6ms) CREATE TABLE "schema_migrations" ("version" varchar(255) NOT NULL)
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+  (0.0ms) PRAGMA index_list("schema_migrations")
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+  (1.5ms) CREATE UNIQUE INDEX "unique_schema_migrations" ON "schema_migrations" ("version")
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+  (0.2ms) select sqlite_version(*)
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+  (0.1ms) SELECT "schema_migrations"."version" FROM "schema_migrations"
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+  (0.2ms) begin transaction
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+  (0.0ms) rollback transaction
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <title>The page you were looking for doesn't exist (404)</title>
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+ <style type="text/css">
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+ body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
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+ div.dialog {
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+ width: 25em;
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+ padding: 0 4em;
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+ margin: 4em auto 0 auto;
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+ border: 1px solid #ccc;
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+ border-right-color: #999;
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+ border-bottom-color: #999;
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+ }
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+ h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
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+ </style>
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+ </head>
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+
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+ <body>
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+ <!-- This file lives in public/404.html -->
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+ <div class="dialog">
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+ <h1>The page you were looking for doesn't exist.</h1>
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+ <p>You may have mistyped the address or the page may have moved.</p>
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+ </div>
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+ </body>
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+ </html>
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <title>The change you wanted was rejected (422)</title>
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+ <style type="text/css">
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+ body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
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+ div.dialog {
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+ width: 25em;
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+ padding: 0 4em;
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+ margin: 4em auto 0 auto;
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+ border: 1px solid #ccc;
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+ border-right-color: #999;
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+ border-bottom-color: #999;
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+ }
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+ h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
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+ </style>
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+ </head>
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+
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+ <body>
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+ <!-- This file lives in public/422.html -->
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+ <div class="dialog">
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+ <h1>The change you wanted was rejected.</h1>
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+ <p>Maybe you tried to change something you didn't have access to.</p>
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+ </div>
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+ </body>
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+ </html>
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <title>We're sorry, but something went wrong (500)</title>
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+ <style type="text/css">
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+ body { background-color: #fff; color: #666; text-align: center; font-family: arial, sans-serif; }
7
+ div.dialog {
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+ width: 25em;
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+ padding: 0 4em;
10
+ margin: 4em auto 0 auto;
11
+ border: 1px solid #ccc;
12
+ border-right-color: #999;
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+ border-bottom-color: #999;
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+ }
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+ h1 { font-size: 100%; color: #f00; line-height: 1.5em; }
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+ </style>
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+ </head>
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+
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+ <body>
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+ <!-- This file lives in public/500.html -->
21
+ <div class="dialog">
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+ <h1>We're sorry, but something went wrong.</h1>
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+ </div>
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+ </body>
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+ </html>
File without changes
@@ -0,0 +1,6 @@
1
+ #!/usr/bin/env ruby
2
+ # This command will automatically be run when you run "rails" with Rails 3 gems installed from the root of your application.
3
+
4
+ APP_PATH = File.expand_path('../../config/application', __FILE__)
5
+ require File.expand_path('../../config/boot', __FILE__)
6
+ require 'rails/commands'
@@ -0,0 +1,10 @@
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+ # Configure Rails Environment
2
+ ENV["RAILS_ENV"] = "test"
3
+
4
+ require File.expand_path("../dummy/config/environment.rb", __FILE__)
5
+ require "rails/test_help"
6
+
7
+ Rails.backtrace_cleaner.remove_silencers!
8
+
9
+ # Load support files
10
+ Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each { |f| require f }
metadata ADDED
@@ -0,0 +1,153 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: aqueduct-i2b2
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.1.0
5
+ prerelease:
6
+ platform: ruby
7
+ authors:
8
+ - Remo Mueller
9
+ autorequire:
10
+ bindir: bin
11
+ cert_chain: []
12
+ date: 2012-01-31 00:00:00.000000000 Z
13
+ dependencies:
14
+ - !ruby/object:Gem::Dependency
15
+ name: rails
16
+ requirement: &70210129730760 !ruby/object:Gem::Requirement
17
+ none: false
18
+ requirements:
19
+ - - ~>
20
+ - !ruby/object:Gem::Version
21
+ version: 3.2.1
22
+ type: :runtime
23
+ prerelease: false
24
+ version_requirements: *70210129730760
25
+ - !ruby/object:Gem::Dependency
26
+ name: aqueduct
27
+ requirement: &70210129729220 !ruby/object:Gem::Requirement
28
+ none: false
29
+ requirements:
30
+ - - ~>
31
+ - !ruby/object:Gem::Version
32
+ version: 0.1.0
33
+ type: :runtime
34
+ prerelease: false
35
+ version_requirements: *70210129729220
36
+ - !ruby/object:Gem::Dependency
37
+ name: sqlite3
38
+ requirement: &70210129728740 !ruby/object:Gem::Requirement
39
+ none: false
40
+ requirements:
41
+ - - ! '>='
42
+ - !ruby/object:Gem::Version
43
+ version: '0'
44
+ type: :development
45
+ prerelease: false
46
+ version_requirements: *70210129728740
47
+ description: Connects to an instance of i2b2 through Aqueduct interface
48
+ email:
49
+ - remosm@gmail.com
50
+ executables: []
51
+ extensions: []
52
+ extra_rdoc_files: []
53
+ files:
54
+ - lib/aqueduct/wrappers/i2b2.rb
55
+ - lib/aqueduct-i2b2/version.rb
56
+ - lib/aqueduct-i2b2.rb
57
+ - lib/tasks/aqueduct-i2b2_tasks.rake
58
+ - aqueduct-i2b2.gemspec
59
+ - CHANGELOG.rdoc
60
+ - LICENSE
61
+ - Rakefile
62
+ - README.rdoc
63
+ - test/aqueduct-i2b2_test.rb
64
+ - test/dummy/app/assets/javascripts/application.js
65
+ - test/dummy/app/assets/stylesheets/application.css
66
+ - test/dummy/app/controllers/application_controller.rb
67
+ - test/dummy/app/helpers/application_helper.rb
68
+ - test/dummy/app/views/layouts/application.html.erb
69
+ - test/dummy/config/application.rb
70
+ - test/dummy/config/boot.rb
71
+ - test/dummy/config/database.yml
72
+ - test/dummy/config/environment.rb
73
+ - test/dummy/config/environments/development.rb
74
+ - test/dummy/config/environments/production.rb
75
+ - test/dummy/config/environments/test.rb
76
+ - test/dummy/config/initializers/backtrace_silencers.rb
77
+ - test/dummy/config/initializers/inflections.rb
78
+ - test/dummy/config/initializers/mime_types.rb
79
+ - test/dummy/config/initializers/secret_token.rb
80
+ - test/dummy/config/initializers/session_store.rb
81
+ - test/dummy/config/initializers/wrap_parameters.rb
82
+ - test/dummy/config/locales/en.yml
83
+ - test/dummy/config/routes.rb
84
+ - test/dummy/config.ru
85
+ - test/dummy/db/schema.rb
86
+ - test/dummy/db/test.sqlite3
87
+ - test/dummy/log/test.log
88
+ - test/dummy/public/404.html
89
+ - test/dummy/public/422.html
90
+ - test/dummy/public/500.html
91
+ - test/dummy/public/favicon.ico
92
+ - test/dummy/Rakefile
93
+ - test/dummy/README.rdoc
94
+ - test/dummy/script/rails
95
+ - test/test_helper.rb
96
+ homepage: https://github.com/remomueller
97
+ licenses: []
98
+ post_install_message:
99
+ rdoc_options: []
100
+ require_paths:
101
+ - lib
102
+ required_ruby_version: !ruby/object:Gem::Requirement
103
+ none: false
104
+ requirements:
105
+ - - ! '>='
106
+ - !ruby/object:Gem::Version
107
+ version: '0'
108
+ required_rubygems_version: !ruby/object:Gem::Requirement
109
+ none: false
110
+ requirements:
111
+ - - ! '>='
112
+ - !ruby/object:Gem::Version
113
+ version: '0'
114
+ requirements: []
115
+ rubyforge_project:
116
+ rubygems_version: 1.8.11
117
+ signing_key:
118
+ specification_version: 3
119
+ summary: Connect to an instance of i2b2 through Aqueduct
120
+ test_files:
121
+ - test/aqueduct-i2b2_test.rb
122
+ - test/dummy/app/assets/javascripts/application.js
123
+ - test/dummy/app/assets/stylesheets/application.css
124
+ - test/dummy/app/controllers/application_controller.rb
125
+ - test/dummy/app/helpers/application_helper.rb
126
+ - test/dummy/app/views/layouts/application.html.erb
127
+ - test/dummy/config/application.rb
128
+ - test/dummy/config/boot.rb
129
+ - test/dummy/config/database.yml
130
+ - test/dummy/config/environment.rb
131
+ - test/dummy/config/environments/development.rb
132
+ - test/dummy/config/environments/production.rb
133
+ - test/dummy/config/environments/test.rb
134
+ - test/dummy/config/initializers/backtrace_silencers.rb
135
+ - test/dummy/config/initializers/inflections.rb
136
+ - test/dummy/config/initializers/mime_types.rb
137
+ - test/dummy/config/initializers/secret_token.rb
138
+ - test/dummy/config/initializers/session_store.rb
139
+ - test/dummy/config/initializers/wrap_parameters.rb
140
+ - test/dummy/config/locales/en.yml
141
+ - test/dummy/config/routes.rb
142
+ - test/dummy/config.ru
143
+ - test/dummy/db/schema.rb
144
+ - test/dummy/db/test.sqlite3
145
+ - test/dummy/log/test.log
146
+ - test/dummy/public/404.html
147
+ - test/dummy/public/422.html
148
+ - test/dummy/public/500.html
149
+ - test/dummy/public/favicon.ico
150
+ - test/dummy/Rakefile
151
+ - test/dummy/README.rdoc
152
+ - test/dummy/script/rails
153
+ - test/test_helper.rb