lab_tech 0.1.0

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Files changed (65) hide show
  1. checksums.yaml +7 -0
  2. data/MIT-LICENSE +20 -0
  3. data/README.md +323 -0
  4. data/Rakefile +30 -0
  5. data/app/models/lab_tech/application_record.rb +5 -0
  6. data/app/models/lab_tech/default_cleaner.rb +87 -0
  7. data/app/models/lab_tech/experiment.rb +190 -0
  8. data/app/models/lab_tech/observation.rb +40 -0
  9. data/app/models/lab_tech/percentile.rb +41 -0
  10. data/app/models/lab_tech/result.rb +130 -0
  11. data/app/models/lab_tech/speedup.rb +65 -0
  12. data/app/models/lab_tech/summary.rb +183 -0
  13. data/config/routes.rb +2 -0
  14. data/db/migrate/20190815192130_create_experiment_tables.rb +50 -0
  15. data/lib/lab_tech.rb +176 -0
  16. data/lib/lab_tech/engine.rb +6 -0
  17. data/lib/lab_tech/version.rb +3 -0
  18. data/lib/tasks/lab_tech_tasks.rake +4 -0
  19. data/spec/dummy/Rakefile +6 -0
  20. data/spec/dummy/app/assets/config/manifest.js +1 -0
  21. data/spec/dummy/app/assets/javascripts/application.js +14 -0
  22. data/spec/dummy/app/assets/stylesheets/application.css +15 -0
  23. data/spec/dummy/app/controllers/application_controller.rb +2 -0
  24. data/spec/dummy/app/jobs/application_job.rb +2 -0
  25. data/spec/dummy/app/models/application_record.rb +3 -0
  26. data/spec/dummy/bin/bundle +3 -0
  27. data/spec/dummy/bin/rails +4 -0
  28. data/spec/dummy/bin/rake +4 -0
  29. data/spec/dummy/bin/setup +33 -0
  30. data/spec/dummy/bin/update +28 -0
  31. data/spec/dummy/config.ru +5 -0
  32. data/spec/dummy/config/application.rb +35 -0
  33. data/spec/dummy/config/boot.rb +5 -0
  34. data/spec/dummy/config/database.yml +25 -0
  35. data/spec/dummy/config/environment.rb +5 -0
  36. data/spec/dummy/config/environments/development.rb +46 -0
  37. data/spec/dummy/config/environments/production.rb +71 -0
  38. data/spec/dummy/config/environments/test.rb +36 -0
  39. data/spec/dummy/config/initializers/application_controller_renderer.rb +8 -0
  40. data/spec/dummy/config/initializers/backtrace_silencers.rb +7 -0
  41. data/spec/dummy/config/initializers/cors.rb +16 -0
  42. data/spec/dummy/config/initializers/filter_parameter_logging.rb +4 -0
  43. data/spec/dummy/config/initializers/inflections.rb +16 -0
  44. data/spec/dummy/config/initializers/mime_types.rb +4 -0
  45. data/spec/dummy/config/initializers/wrap_parameters.rb +14 -0
  46. data/spec/dummy/config/locales/en.yml +33 -0
  47. data/spec/dummy/config/puma.rb +34 -0
  48. data/spec/dummy/config/routes.rb +3 -0
  49. data/spec/dummy/config/spring.rb +6 -0
  50. data/spec/dummy/db/schema.rb +52 -0
  51. data/spec/dummy/db/test.sqlite3 +0 -0
  52. data/spec/dummy/log/development.log +0 -0
  53. data/spec/dummy/log/test.log +1519 -0
  54. data/spec/examples.txt +79 -0
  55. data/spec/models/lab_tech/default_cleaner_spec.rb +32 -0
  56. data/spec/models/lab_tech/experiment_spec.rb +110 -0
  57. data/spec/models/lab_tech/percentile_spec.rb +85 -0
  58. data/spec/models/lab_tech/result_spec.rb +198 -0
  59. data/spec/models/lab_tech/speedup_spec.rb +133 -0
  60. data/spec/models/lab_tech/summary_spec.rb +325 -0
  61. data/spec/models/lab_tech_spec.rb +23 -0
  62. data/spec/rails_helper.rb +62 -0
  63. data/spec/spec_helper.rb +98 -0
  64. data/spec/support/misc_helpers.rb +7 -0
  65. metadata +238 -0
@@ -0,0 +1,15 @@
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+ /*
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+ * This is a manifest file that'll be compiled into application.css, which will include all the files
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+ * listed below.
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+ *
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+ * Any CSS and SCSS file within this directory, lib/assets/stylesheets, vendor/assets/stylesheets,
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+ * or any plugin's vendor/assets/stylesheets directory can be referenced here using a relative path.
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+ *
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+ * You're free to add application-wide styles to this file and they'll appear at the bottom of the
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+ * compiled file so the styles you add here take precedence over styles defined in any other CSS/SCSS
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+ * files in this directory. Styles in this file should be added after the last require_* statement.
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+ * It is generally better to create a new file per style scope.
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+ *
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+ *= require_tree .
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+ *= require_self
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+ */
@@ -0,0 +1,2 @@
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+ class ApplicationController < ActionController::API
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+ end
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+ class ApplicationJob < ActiveJob::Base
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+ end
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+ class ApplicationRecord < ActiveRecord::Base
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+ self.abstract_class = true
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+ end
@@ -0,0 +1,3 @@
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+ #!/usr/bin/env ruby
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+ ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../Gemfile', __dir__)
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+ load Gem.bin_path('bundler', 'bundle')
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+ #!/usr/bin/env ruby
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+ APP_PATH = File.expand_path('../config/application', __dir__)
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+ require_relative '../config/boot'
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+ require 'rails/commands'
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+ #!/usr/bin/env ruby
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+ require_relative '../config/boot'
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+ require 'rake'
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+ Rake.application.run
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+ #!/usr/bin/env ruby
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+ require 'fileutils'
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+ include FileUtils
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+
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+ # path to your application root.
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+ APP_ROOT = File.expand_path('..', __dir__)
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+
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+ def system!(*args)
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+ system(*args) || abort("\n== Command #{args} failed ==")
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+ end
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+
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+ chdir APP_ROOT do
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+ # This script is a starting point to setup your application.
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+ # Add necessary setup steps to this file.
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+
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+ puts '== Installing dependencies =='
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+ system! 'gem install bundler --conservative'
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+ system('bundle check') || system!('bundle install')
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+
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+ # puts "\n== Copying sample files =="
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+ # unless File.exist?('config/database.yml')
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+ # cp 'config/database.yml.sample', 'config/database.yml'
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+ # end
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+
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+ puts "\n== Preparing database =="
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+ system! 'bin/rails db:setup'
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+
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+ puts "\n== Removing old logs and tempfiles =="
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+ system! 'bin/rails log:clear tmp:clear'
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+
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+ puts "\n== Restarting application server =="
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+ system! 'bin/rails restart'
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+ end
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+ #!/usr/bin/env ruby
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+ require 'fileutils'
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+ include FileUtils
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+
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+ # path to your application root.
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+ APP_ROOT = File.expand_path('..', __dir__)
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+
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+ def system!(*args)
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+ system(*args) || abort("\n== Command #{args} failed ==")
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+ end
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+
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+ chdir APP_ROOT do
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+ # This script is a way to update your development environment automatically.
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+ # Add necessary update steps to this file.
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+
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+ puts '== Installing dependencies =='
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+ system! 'gem install bundler --conservative'
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+ system('bundle check') || system!('bundle install')
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+
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+ puts "\n== Updating database =="
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+ system! 'bin/rails db:migrate'
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+
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+ puts "\n== Removing old logs and tempfiles =="
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+ system! 'bin/rails log:clear tmp:clear'
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+
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+ puts "\n== Restarting application server =="
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+ system! 'bin/rails restart'
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+ end
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+ # This file is used by Rack-based servers to start the application.
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+
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+ require_relative 'config/environment'
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+
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+ run Rails.application
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+ require_relative 'boot'
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+
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+ require "rails"
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+ # Pick the frameworks you want:
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+ require "active_model/railtie"
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+ # require "active_job/railtie"
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+ require "active_record/railtie"
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+ # require "active_storage/engine"
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+ # require "action_controller/railtie"
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+ # require "action_mailer/railtie"
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+ # require "action_view/railtie"
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+ # require "action_cable/engine"
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+ # require "sprockets/railtie"
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+ # require "rails/test_unit/railtie"
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+
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+ Bundler.require(*Rails.groups)
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+ require "lab_tech"
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+
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+ module Dummy
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+ class Application < Rails::Application
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+ # Initialize configuration defaults for [current] Rails version.
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+ config.load_defaults 5.1
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+
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+ # Settings in config/environments/* take precedence over those specified here.
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+ # Application configuration can go into files in config/initializers
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+ # -- all .rb files in that directory are automatically loaded after loading
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+ # the framework and any gems in your application.
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+
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+ # Only loads a smaller set of middleware suitable for API only apps.
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+ # Middleware like session, flash, cookies can be added back manually.
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+ # Skip views, helpers and assets when generating a new resource.
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+ config.api_only = true
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+ end
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+ end
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+
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+ # Set up gems listed in the Gemfile.
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+ ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../../Gemfile', __dir__)
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+
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+ require 'bundler/setup' if File.exist?(ENV['BUNDLE_GEMFILE'])
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+ $LOAD_PATH.unshift File.expand_path('../../../lib', __dir__)
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+ # SQLite version 3.x
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+ # gem install sqlite3
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+ #
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+ # Ensure the SQLite 3 gem is defined in your Gemfile
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+ # gem 'sqlite3'
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+ #
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+ default: &default
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+ adapter: sqlite3
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+ pool: <%= ENV.fetch("RAILS_MAX_THREADS") { 5 } %>
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+ timeout: 5000
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+
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+ development:
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+ <<: *default
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+ database: db/development.sqlite3
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+
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+ # Warning: The database defined as "test" will be erased and
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+ # re-generated from your development database when you run "rake".
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+ # Do not set this db to the same as development or production.
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+ test:
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+ <<: *default
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+ database: db/test.sqlite3
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+
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+ production:
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+ <<: *default
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+ database: db/production.sqlite3
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+ # Load the Rails application.
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+ require_relative 'application'
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+
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+ # Initialize the Rails application.
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+ Rails.application.initialize!
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+ Rails.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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+ # Do not eager load code on boot.
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+ config.eager_load = false
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+
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+ # Show full error reports.
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+ config.consider_all_requests_local = true
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+
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+ # Enable/disable caching. By default caching is disabled.
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+ # Run rails dev:cache to toggle caching.
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+ if Rails.root.join('tmp', 'caching-dev.txt').exist?
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+ config.action_controller.perform_caching = true
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+
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+ config.cache_store = :memory_store
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+ config.public_file_server.headers = {
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+ 'Cache-Control' => "public, max-age=#{2.days.to_i}"
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+ }
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+ else
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+ config.action_controller.perform_caching = false
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+
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+ config.cache_store = :null_store
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+ end
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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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+ # Raise an error on page load if there are pending migrations.
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+ config.active_record.migration_error = :page_load
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+
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+ # Highlight code that triggered database queries in logs.
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+ config.active_record.verbose_query_logs = true
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+
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+
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+ # Raises error for missing translations
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+ # config.action_view.raise_on_missing_translations = true
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+
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+ # Use an evented file watcher to asynchronously detect changes in source code,
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+ # routes, locales, etc. This feature depends on the listen gem.
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+ # config.file_watcher = ActiveSupport::EventedFileUpdateChecker
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+ end
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+ Rails.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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+ # Eager load code on boot. This eager loads most of Rails and
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+ # your application in memory, allowing both threaded web servers
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+ # and those relying on copy on write to perform better.
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+ # Rake tasks automatically ignore this option for performance.
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+ config.eager_load = 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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+ # Ensures that a master key has been made available in either ENV["RAILS_MASTER_KEY"]
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+ # or in config/master.key. This key is used to decrypt credentials (and other encrypted files).
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+ # config.require_master_key = true
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+
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+ # Disable serving static files from the `/public` folder by default since
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+ # Apache or NGINX already handles this.
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+ config.public_file_server.enabled = ENV['RAILS_SERVE_STATIC_FILES'].present?
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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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+ # 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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+ # Use the lowest log level to ensure availability of diagnostic information
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+ # when problems arise.
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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 = [ :request_id ]
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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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+ # Use a real queuing backend for Active Job (and separate queues per environment)
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+ # config.active_job.queue_adapter = :resque
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+ # config.active_job.queue_name_prefix = "dummy_#{Rails.env}"
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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 cannot 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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+ # Use default logging formatter so that PID and timestamp are not suppressed.
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+ config.log_formatter = ::Logger::Formatter.new
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+
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+ # Use a different logger for distributed setups.
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+ # require 'syslog/logger'
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+ # config.logger = ActiveSupport::TaggedLogging.new(Syslog::Logger.new 'app-name')
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+
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+ if ENV["RAILS_LOG_TO_STDOUT"].present?
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+ logger = ActiveSupport::Logger.new(STDOUT)
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+ logger.formatter = config.log_formatter
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+ config.logger = ActiveSupport::TaggedLogging.new(logger)
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+ end
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+
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+ # Do not dump schema after migrations.
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+ config.active_record.dump_schema_after_migration = false
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+ end
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+ Rails.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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+ # Do not eager load code on boot. This avoids loading your whole application
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+ # just for the purpose of running a single test. If you are using a tool that
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+ # preloads Rails for running tests, you may have to set it to true.
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+ config.eager_load = false
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+
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+ # Configure public file server for tests with Cache-Control for performance.
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+ config.public_file_server.enabled = true
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+ config.public_file_server.headers = {
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+ 'Cache-Control' => "public, max-age=#{1.hour.to_i}"
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+ }
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+
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+ # Show full error reports and disable caching.
22
+ 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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+ # Print deprecation notices to the stderr.
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+ config.active_support.deprecation = :stderr
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+
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+ # Raises error for missing translations
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+ # config.action_view.raise_on_missing_translations = true
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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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+ # ActiveSupport::Reloader.to_prepare do
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+ # ApplicationController.renderer.defaults.merge!(
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+ # http_host: 'example.org',
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+ # https: false
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+ # )
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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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+ # Avoid CORS issues when API is called from the frontend app.
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+ # Handle Cross-Origin Resource Sharing (CORS) in order to accept cross-origin AJAX requests.
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+
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+ # Read more: https://github.com/cyu/rack-cors
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+
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+ # Rails.application.config.middleware.insert_before 0, Rack::Cors do
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+ # allow do
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+ # origins 'example.com'
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+ #
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+ # resource '*',
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+ # headers: :any,
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+ # methods: [:get, :post, :put, :patch, :delete, :options, :head]
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+ # end
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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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+ # Configure sensitive parameters which will be filtered from the log file.
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+ Rails.application.config.filter_parameters += [:password]
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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. Inflections
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+ # are locale specific, and you may define rules for as many different
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+ # locales as you wish. All of these examples are active by default:
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+ # ActiveSupport::Inflector.inflections(:en) 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(:en) 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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+ # 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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+ # To enable root element in JSON for ActiveRecord objects.
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+ # ActiveSupport.on_load(:active_record) do
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+ # self.include_root_in_json = true
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+ # end
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+ # Files in the config/locales directory are used for internationalization
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+ # and are automatically loaded by Rails. If you want to use locales other
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+ # than English, add the necessary files in this directory.
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+ #
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+ # To use the locales, use `I18n.t`:
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+ #
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+ # I18n.t 'hello'
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+ #
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+ # In views, this is aliased to just `t`:
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+ #
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+ # <%= t('hello') %>
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+ #
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+ # To use a different locale, set it with `I18n.locale`:
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+ #
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+ # I18n.locale = :es
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+ #
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+ # This would use the information in config/locales/es.yml.
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+ #
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+ # The following keys must be escaped otherwise they will not be retrieved by
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+ # the default I18n backend:
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+ #
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+ # true, false, on, off, yes, no
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+ #
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+ # Instead, surround them with single quotes.
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+ #
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+ # en:
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+ # 'true': 'foo'
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+ #
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+ # To learn more, please read the Rails Internationalization guide
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+ # available at http://guides.rubyonrails.org/i18n.html.
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+
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+ en:
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+ hello: "Hello world"