setup sciNote for Rails 5.1

Gemfile

@@ -43,7 +43,7 @@ gem 'logging', '~> 2.0.0'
 gem 'aspector' # Aspect-oriented programming for Rails
 gem 'rgl' # Graph framework for project diagram calculations
 gem 'nested_form_fields'
-gem 'ajax-datatables-rails', '~> 0.4.0'
+gem 'ajax-datatables-rails', '~> 0.3.1'
 gem 'commit_param_routing' # Enables different submit actions in the same form to route to different actions in controller
 gem 'kaminari'
 gem "i18n-js", ">= 3.0.0.rc11" # Localization in javascript files
@@ -73,6 +73,7 @@ gem 'base62' # Used for smart annotations
 gem 'newrelic_rpm'
 
 group :development, :test do
+  gem 'listen', '~> 3.0'
   gem 'byebug'
   gem 'better_errors'
   gem 'binding_of_caller'

Gemfile.lock

@@ -52,8 +52,8 @@ GEM
       i18n (~> 0.7)
       minitest (~> 5.1)
       tzinfo (~> 1.1)
-    ajax-datatables-rails (0.4.0)
-      railties (>= 4.0)
+    ajax-datatables-rails (0.3.1)
+      railties (>= 3.1)
     ansi (1.5.0)
     arel (8.0.0)
     aspector (0.14.0)
@@ -139,6 +139,7 @@ GEM
     execjs (2.7.0)
     faker (1.7.3)
       i18n (~> 0.5)
+    ffi (1.9.18)
     figaro (1.1.1)
       thor (~> 0.14)
     font-awesome-rails (4.7.0.2)
@@ -178,6 +179,10 @@ GEM
       kaminari-core (= 1.0.1)
     kaminari-core (1.0.1)
     lazy_priority_queue (0.1.1)
+    listen (3.1.5)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+      ruby_dep (~> 1.2)
     little-plugger (1.1.4)
     logging (2.0.0)
       little-plugger (~> 1.1)
@@ -260,6 +265,9 @@ GEM
     rainbow (2.2.2)
       rake
     rake (12.0.0)
+    rb-fsevent (0.9.8)
+    rb-inotify (0.9.10)
+      ffi (>= 0.5.0, < 2)
     rdoc (4.3.0)
     recaptcha (4.3.1)
       json
@@ -283,6 +291,7 @@ GEM
       unicode-display_width (~> 1.0, >= 1.0.1)
     ruby-graphviz (1.2.3)
     ruby-progressbar (1.8.1)
+    ruby_dep (1.5.0)
     rubyzip (1.2.1)
     sanitize (4.5.0)
       crass (~> 1.0.2)
@@ -358,7 +367,7 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  ajax-datatables-rails (~> 0.4.0)
+  ajax-datatables-rails (~> 0.3.1)
   aspector
   auto_strip_attributes (~> 2.1)
   autosize-rails
@@ -393,6 +402,7 @@ DEPENDENCIES
   jquery-ui-rails
   js_cookie_rails
   kaminari
+  listen (~> 3.0)
   logging (~> 2.0.0)
   minitest-reporters (~> 1.1)
   momentjs-rails (~> 2.17.1)

app/controllers/application_controller.rb

@@ -5,7 +5,7 @@ class ApplicationController < ActionController::Base
   acts_as_token_authentication_handler_for User
   # Prevent CSRF attacks by raising an exception.
   # For APIs, you may want to use :null_session instead.
-  protect_from_forgery with: :exception
+  protect_from_forgery with: :exception, prepend: true
   before_action :authenticate_user!
   helper_method :current_team
   before_action :generate_intro_tutorial, if: :is_current_page_root?

app/models/activity.rb

@@ -1,4 +1,4 @@
-class Activity < ActiveRecord::Base
+class Activity < ApplicationRecord
   include InputSanitizeHelper
 
   after_create :generate_notification

app/models/application_record.rb

@@ -0,0 +1,3 @@
+class ApplicationRecord < ActiveRecord::Base
+  self.abstract_class = true
+end

app/models/asset.rb

@@ -1,4 +1,4 @@
-class Asset < ActiveRecord::Base
+class Asset < ApplicationRecord
   include SearchableModel
   include DatabaseHelper
   include Encryptor

app/models/asset_text_datum.rb

@@ -1,4 +1,4 @@
-class AssetTextDatum < ActiveRecord::Base
+class AssetTextDatum < ApplicationRecord
   include SearchableModel
 
   validates :data, presence: true

app/models/checklist.rb

@@ -1,4 +1,4 @@
-class Checklist < ActiveRecord::Base
+class Checklist < ApplicationRecord
   include SearchableModel
 
   auto_strip_attributes :name, nullify: false

app/models/checklist_item.rb

@@ -1,4 +1,4 @@
-class ChecklistItem < ActiveRecord::Base
+class ChecklistItem < ApplicationRecord
   auto_strip_attributes :text, nullify: false
   validates :text,
             presence: true,

app/models/comment.rb

@@ -1,4 +1,4 @@
-class Comment < ActiveRecord::Base
+class Comment < ApplicationRecord
   include SearchableModel
 
   auto_strip_attributes :message, nullify: false

app/models/connection.rb

@@ -1,4 +1,4 @@
-class Connection < ActiveRecord::Base
+class Connection < ApplicationRecord
   belongs_to :to, :class_name => 'MyModule', :foreign_key => 'input_id', inverse_of: :inputs
   belongs_to :from, :class_name => 'MyModule', :foreign_key => 'output_id', inverse_of: :outputs
 end

app/models/custom_field.rb

@@ -1,4 +1,4 @@
-class CustomField < ActiveRecord::Base
+class CustomField < ApplicationRecord
   auto_strip_attributes :name, nullify: false
   validates :name,
             presence: true,

app/models/experiment.rb

@@ -1,4 +1,4 @@
-class Experiment < ActiveRecord::Base
+class Experiment < ApplicationRecord
   include ArchivableModel
   include SearchableModel
 

app/models/my_module.rb

@@ -1,4 +1,4 @@
-class MyModule < ActiveRecord::Base
+class MyModule < ApplicationRecord
   include ArchivableModel, SearchableModel
 
   enum state: Extends::TASKS_STATES

app/models/my_module_group.rb

@@ -1,4 +1,4 @@
-class MyModuleGroup < ActiveRecord::Base
+class MyModuleGroup < ApplicationRecord
   include SearchableModel
 
   auto_strip_attributes :name, nullify: false

app/models/my_module_repository_row.rb

@@ -1,4 +1,4 @@
-class MyModuleRepositoryRow < ActiveRecord::Base
+class MyModuleRepositoryRow < ApplicationRecord
   belongs_to :assigned_by, foreign_key: 'assigned_by_id', class_name: 'User'
   belongs_to :repository_row
   belongs_to :my_module

app/models/my_module_tag.rb

@@ -1,4 +1,4 @@
-class MyModuleTag < ActiveRecord::Base
+class MyModuleTag < ApplicationRecord
   validates :my_module, :tag, presence: true
   validates :tag_id, uniqueness: { scope: :my_module_id }
 

app/models/notification.rb

@@ -1,4 +1,4 @@
-class Notification < ActiveRecord::Base
+class Notification < ApplicationRecord
   has_many :user_notifications, inverse_of: :notification, dependent: :destroy
   has_many :users, through: :user_notifications
   belongs_to :generator_user, class_name: 'User'

app/models/project.rb

@@ -1,4 +1,4 @@
-class Project < ActiveRecord::Base
+class Project < ApplicationRecord
   include ArchivableModel, SearchableModel
 
   enum visibility: { hidden: 0, visible: 1 }

app/models/protocol.rb

@@ -1,4 +1,4 @@
-class Protocol < ActiveRecord::Base
+class Protocol < ApplicationRecord
   include SearchableModel
   include RenamingUtil
 

app/models/protocol_keyword.rb

@@ -1,4 +1,4 @@
-class ProtocolKeyword < ActiveRecord::Base
+class ProtocolKeyword < ApplicationRecord
   auto_strip_attributes :name, nullify: false
   validates :name,
             length: { minimum: Constants::NAME_MIN_LENGTH,

app/models/protocol_protocol_keyword.rb

@@ -1,4 +1,4 @@
-class ProtocolProtocolKeyword < ActiveRecord::Base
+class ProtocolProtocolKeyword < ApplicationRecord
   after_create :increment_protocols_count
   after_destroy :decrement_protocols_count
 
@@ -20,4 +20,4 @@ class ProtocolProtocolKeyword < ActiveRecord::Base
       self.protocol_keyword.destroy
     end
   end
-end
+end

app/models/report.rb

@@ -1,4 +1,4 @@
-class Report < ActiveRecord::Base
+class Report < ApplicationRecord
   include SearchableModel
 
   auto_strip_attributes :name, :description, nullify: false

app/models/report_element.rb

@@ -1,4 +1,4 @@
-class ReportElement < ActiveRecord::Base
+class ReportElement < ApplicationRecord
   enum type_of: Extends::REPORT_ELEMENT_TYPES
 
   # This is only used by certain elements

app/models/repository.rb

@@ -1,4 +1,4 @@
-class Repository < ActiveRecord::Base
+class Repository < ApplicationRecord
   belongs_to :team
   belongs_to :created_by, foreign_key: :created_by_id, class_name: 'User'
   has_many :repository_columns

app/models/repository_cell.rb

@@ -1,4 +1,4 @@
-class RepositoryCell < ActiveRecord::Base
+class RepositoryCell < ApplicationRecord
   belongs_to :repository_row
   belongs_to :repository_column
   belongs_to :value, polymorphic: true, dependent: :destroy

app/models/repository_column.rb

@@ -1,4 +1,4 @@
-class RepositoryColumn < ActiveRecord::Base
+class RepositoryColumn < ApplicationRecord
   belongs_to :repository
   belongs_to :created_by, foreign_key: :created_by_id, class_name: 'User'
   has_many :repository_cells, dependent: :destroy

app/models/repository_date_value.rb

@@ -1,4 +1,4 @@
-class RepositoryDateValue < ActiveRecord::Base
+class RepositoryDateValue < ApplicationRecord
   belongs_to :created_by, foreign_key: :created_by_id, class_name: 'User'
   belongs_to :last_modified_by, foreign_key: :last_modified_by_id,
                                 class_name: 'User'

app/models/repository_row.rb

@@ -1,4 +1,4 @@
-class RepositoryRow < ActiveRecord::Base
+class RepositoryRow < ApplicationRecord
   belongs_to :repository
   belongs_to :created_by, foreign_key: :created_by_id, class_name: 'User'
   belongs_to :last_modified_by, foreign_key: :last_modified_by_id,

app/models/repository_table_state.rb

@@ -1,4 +1,4 @@
-class RepositoryTableState < ActiveRecord::Base
+class RepositoryTableState < ApplicationRecord
   belongs_to :user, inverse_of: :repository_table_states
   belongs_to :repository, inverse_of: :repository_table_states
 

app/models/repository_text_value.rb

@@ -1,4 +1,4 @@
-class RepositoryTextValue < ActiveRecord::Base
+class RepositoryTextValue < ApplicationRecord
   belongs_to :created_by, foreign_key: :created_by_id, class_name: 'User'
   belongs_to :last_modified_by, foreign_key: :last_modified_by_id,
                                 class_name: 'User'

app/models/result.rb

@@ -1,4 +1,4 @@
-class Result < ActiveRecord::Base
+class Result < ApplicationRecord
   include ArchivableModel, SearchableModel
 
   auto_strip_attributes :name, nullify: false

app/models/result_asset.rb

@@ -1,4 +1,4 @@
-class ResultAsset < ActiveRecord::Base
+class ResultAsset < ApplicationRecord
   validates :result, :asset, presence: true
 
   belongs_to :result, inverse_of: :result_asset

app/models/result_table.rb

@@ -1,4 +1,4 @@
-class ResultTable < ActiveRecord::Base
+class ResultTable < ApplicationRecord
   validates :result, :table, presence: true
 
   belongs_to :result, inverse_of: :result_table

app/models/result_text.rb

@@ -1,4 +1,4 @@
-class ResultText < ActiveRecord::Base
+class ResultText < ApplicationRecord
   auto_strip_attributes :text, nullify: false
   validates :text,
             presence: true,

app/models/sample.rb

@@ -1,4 +1,4 @@
-class Sample < ActiveRecord::Base
+class Sample < ApplicationRecord
   include SearchableModel
 
   auto_strip_attributes :name, nullify: false

app/models/sample_custom_field.rb

@@ -1,4 +1,4 @@
-class SampleCustomField < ActiveRecord::Base
+class SampleCustomField < ApplicationRecord
   include SearchableModel
 
   auto_strip_attributes :value, nullify: false

app/models/sample_group.rb

@@ -1,4 +1,4 @@
-class SampleGroup < ActiveRecord::Base
+class SampleGroup < ApplicationRecord
   include SearchableModel
 
   auto_strip_attributes :name, :color, nullify: false

app/models/sample_my_module.rb

@@ -1,4 +1,4 @@
-class SampleMyModule < ActiveRecord::Base
+class SampleMyModule < ApplicationRecord
   after_create :increment_nr_of_module_samples
   after_destroy :decrement_nr_of_module_samples
 

app/models/sample_type.rb

@@ -1,4 +1,4 @@
-class SampleType < ActiveRecord::Base
+class SampleType < ApplicationRecord
   include SearchableModel
 
   auto_strip_attributes :name, nullify: false

app/models/samples_table.rb

@@ -1,4 +1,4 @@
-class SamplesTable < ActiveRecord::Base
+class SamplesTable < ApplicationRecord
   validates :user, :team, presence: true
 
   belongs_to :user, inverse_of: :samples_tables

app/models/settings.rb

@@ -1,4 +1,4 @@
-class Settings < ActiveRecord::Base
+class Settings < ApplicationRecord
   def self.instance
     @instance ||= first
     @instance ||= new

app/models/step.rb

@@ -1,4 +1,4 @@
-class Step < ActiveRecord::Base
+class Step < ApplicationRecord
   include SearchableModel
 
   auto_strip_attributes :name, :description, nullify: false

app/models/step_asset.rb

@@ -1,4 +1,4 @@
-class StepAsset < ActiveRecord::Base
+class StepAsset < ApplicationRecord
   validates :step, :asset, presence: true
 
   belongs_to :step, inverse_of: :step_assets

app/models/step_table.rb

@@ -1,4 +1,4 @@
-class StepTable < ActiveRecord::Base
+class StepTable < ApplicationRecord
   validates :step, :table, presence: true
 
   belongs_to :step, inverse_of: :step_tables

app/models/table.rb

@@ -1,4 +1,4 @@
-class Table < ActiveRecord::Base
+class Table < ApplicationRecord
   include SearchableModel
 
   auto_strip_attributes :name, nullify: false

app/models/tag.rb

@@ -1,4 +1,4 @@
-class Tag < ActiveRecord::Base
+class Tag <ApplicationRecord
   include SearchableModel
 
   auto_strip_attributes :name, :color, nullify: false

app/models/team.rb

@@ -1,4 +1,4 @@
-class Team < ActiveRecord::Base
+class Team < ApplicationRecord
   include SearchableModel
 
   # Not really MVC-compliant, but we just use it for logger

app/models/temp_file.rb

@@ -1,4 +1,4 @@
-class TempFile < ActiveRecord::Base
+class TempFile < ApplicationRecord
   validates :session_id, presence: true
 
   has_attached_file :file

app/models/tiny_mce_asset.rb

@@ -1,4 +1,4 @@
-class TinyMceAsset < ActiveRecord::Base
+class TinyMceAsset < ApplicationRecord
   attr_accessor :reference
   before_create :set_reference
   after_create :update_estimated_size

app/models/token.rb

@@ -1,8 +1,8 @@
-class Token < ActiveRecord::Base
+class Token < ApplicationRecord
 
 	validates :token, presence: true
 	validates :ttl, presence: true
 
 	belongs_to :user, foreign_key: 'user_id', class_name: 'User', inverse_of: :tokens
 
-end
+end

app/models/user.rb

@@ -1,4 +1,4 @@
-class User < ActiveRecord::Base
+class User < ApplicationRecord
   include SearchableModel
 
   acts_as_token_authenticatable

app/models/user_my_module.rb

@@ -1,4 +1,4 @@
-class UserMyModule < ActiveRecord::Base
+class UserMyModule < ApplicationRecord
   validates :user, :my_module, presence: true
 
   belongs_to :user, inverse_of: :user_my_modules

app/models/user_notification.rb

@@ -1,4 +1,4 @@
-class UserNotification < ActiveRecord::Base
+class UserNotification < ApplicationRecord
   include NotificationsHelper
 
   belongs_to :user

app/models/user_project.rb

@@ -1,4 +1,4 @@
-class UserProject < ActiveRecord::Base
+class UserProject < ApplicationRecord
   enum role: { owner: 0, normal_user: 1, technician: 2, viewer: 3 }
 
   validates :role, presence: true

app/models/user_team.rb

@@ -1,4 +1,4 @@
-class UserTeam < ActiveRecord::Base
+class UserTeam < ApplicationRecord
   enum role: { guest: 0, normal_user: 1, admin: 2 }
 
   validates :role, presence: true

app/models/wopi_action.rb

@@ -1,4 +1,4 @@
-class WopiAction < ActiveRecord::Base
+class WopiAction < ApplicationRecord
   belongs_to :wopi_app, foreign_key: 'wopi_app_id', class_name: 'WopiApp'
   validates :action, :extension, :urlsrc, :wopi_app, presence: true
 

app/models/wopi_app.rb

@@ -1,4 +1,4 @@
-class WopiApp < ActiveRecord::Base
+class WopiApp < ApplicationRecord
   belongs_to :wopi_discovery,
              foreign_key: 'wopi_discovery_id',
              class_name: 'WopiDiscovery'

app/models/wopi_discovery.rb

@@ -1,4 +1,4 @@
-class WopiDiscovery < ActiveRecord::Base
+class WopiDiscovery < ApplicationRecord
   require 'base64'
 
   has_many :wopi_apps,

app/models/zip_export.rb

@@ -15,7 +15,7 @@ require 'fileutils'
 #     end
 #   end
 
-class ZipExport < ActiveRecord::Base
+class ZipExport < ApplicationRecord
   belongs_to :user
   has_attached_file :zip_file
   validates_attachment :zip_file,

bin/bundle

@@ -1,3 +1,3 @@
-#!/usr/bin/env ruby.exe
+#!/usr/bin/env ruby
 ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
 load Gem.bin_path('bundler', 'bundle')

bin/rails

@@ -1,4 +1,4 @@
-#!/usr/bin/env ruby.exe
-APP_PATH = File.expand_path('../../config/application', __FILE__)
+#!/usr/bin/env ruby
+APP_PATH = File.expand_path('../config/application', __dir__)
 require_relative '../config/boot'
 require 'rails/commands'

bin/rake

@@ -1,4 +1,4 @@
-#!/usr/bin/env ruby.exe
+#!/usr/bin/env ruby
 require_relative '../config/boot'
 require 'rake'
 Rake.application.run

bin/setup

@@ -1,29 +1,38 @@
-#!/usr/bin/env ruby.exe
+#!/usr/bin/env ruby
 require 'pathname'
+require 'fileutils'
+include FileUtils
 
 # path to your application root.
-APP_ROOT = Pathname.new File.expand_path('../../',  __FILE__)
+APP_ROOT = Pathname.new File.expand_path('../../', __FILE__)
 
-Dir.chdir APP_ROOT do
+def system!(*args)
+  system(*args) || abort("\n== Command #{args} failed ==")
+end
+
+chdir APP_ROOT do
   # This script is a starting point to setup your application.
-  # Add necessary setup steps to this file:
+  # Add necessary setup steps to this file.
+
+  puts '== Installing dependencies =='
+  system! 'gem install bundler --conservative'
+  system('bundle check') || system!('bundle install')
+
+  # Install JavaScript dependencies if using Yarn
+  # system('bin/yarn')
 
-  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"
+  # unless File.exist?('config/database.yml')
+  #   cp 'config/database.yml.sample', 'config/database.yml'
   # end
 
   puts "\n== Preparing database =="
-  system "bin/rake db:setup"
+  system! 'bin/rails db:setup'
 
   puts "\n== Removing old logs and tempfiles =="
-  system "rm -f log/*"
-  system "rm -rf tmp/cache"
+  system! 'bin/rails log:clear tmp:clear'
 
   puts "\n== Restarting application server =="
-  system "touch tmp/restart.txt"
+  system! 'bin/rails restart'
 end

bin/update

@@ -0,0 +1,29 @@
+#!/usr/bin/env ruby
+require 'pathname'
+require 'fileutils'
+include FileUtils
+
+# path to your application root.
+APP_ROOT = Pathname.new File.expand_path('../../', __FILE__)
+
+def system!(*args)
+  system(*args) || abort("\n== Command #{args} failed ==")
+end
+
+chdir APP_ROOT do
+  # This script is a way to update your development environment automatically.
+  # Add necessary update steps to this file.
+
+  puts '== Installing dependencies =='
+  system! 'gem install bundler --conservative'
+  system('bundle check') || system!('bundle install')
+
+  puts "\n== Updating database =="
+  system! 'bin/rails db:migrate'
+
+  puts "\n== Removing old logs and tempfiles =="
+  system! 'bin/rails log:clear tmp:clear'
+
+  puts "\n== Restarting application server =="
+  system! 'bin/rails restart'
+end

bin/yarn

@@ -0,0 +1,11 @@
+#!/usr/bin/env ruby
+VENDOR_PATH = File.expand_path('..', __dir__)
+Dir.chdir(VENDOR_PATH) do
+  begin
+    exec "yarnpkg #{ARGV.join(" ")}"
+  rescue Errno::ENOENT
+    $stderr.puts "Yarn executable was not detected in the system."
+    $stderr.puts "Download Yarn at https://yarnpkg.com/en/docs/install"
+    exit 1
+  end
+end

config/application.rb

@@ -1,4 +1,4 @@
-require File.expand_path('../boot', __FILE__)
+require_relative 'boot'
 
 require 'rails/all'
 
@@ -8,24 +8,19 @@ Bundler.require(*Rails.groups)
 
 module Scinote
   class Application < Rails::Application
+    # Initialize configuration defaults for originally generated Rails version.
+    config.load_defaults 5.1
+
     # 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
-
     config.encoding = 'utf-8'
 
     config.active_job.queue_adapter = :delayed_job
 
     # Do not swallow errors in after_commit/after_rollback callbacks.
-    config.active_record.raise_in_transactional_callbacks = true
+    #  config.active_record.raise_in_transactional_callbacks = true
 
     # Logging
     config.log_formatter = proc do |severity, datetime, progname, msg|

config/boot.rb

@@ -1,3 +1,3 @@
-ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../Gemfile', __dir__)
 
 require 'bundler/setup' # Set up gems listed in the Gemfile.

config/cable.yml

@@ -0,0 +1,10 @@
+development:
+  adapter: async
+
+test:
+  adapter: async
+
+production:
+  adapter: redis
+  url: redis://localhost:6379/1
+  channel_prefix: scinote_production

config/environment.rb

@@ -1,5 +1,5 @@
 # Load the Rails application.
-require File.expand_path('../application', __FILE__)
+require_relative 'application'
 
 # Set the encoding
 Encoding.default_external = Encoding::UTF_8

config/environments/development.rb

@@ -26,6 +26,8 @@ Rails.application.configure do
     reply_to: Rails.application.secrets.mailer_reply_to
   }
   config.action_mailer.raise_delivery_errors = true
+  config.action_mailer.perform_caching = false
+
   config.action_mailer.delivery_method = :smtp
 
   config.action_mailer.smtp_settings = {
@@ -86,4 +88,25 @@ Rails.application.configure do
   # Enable user registrations
   config.x.enable_user_registration =
     ENV['ENABLE_USER_REGISTRATION'] == 'false' ? false : true
+
+  # Use an evented file watcher to asynchronously detect changes in source code,
+  # routes, locales, etc. This feature depends on the listen gem.
+  config.file_watcher = ActiveSupport::EventedFileUpdateChecker
+
+  # Suppress logger output for asset requests.
+  config.assets.quiet = true
+
+  # Enable/disable caching. By default caching is disabled.
+  if Rails.root.join('tmp/caching-dev.txt').exist?
+    config.action_controller.perform_caching = true
+
+    config.cache_store = :memory_store
+    config.public_file_server.headers = {
+      'Cache-Control' => "public, max-age=#{2.days.seconds.to_i}"
+    }
+  else
+    config.action_controller.perform_caching = false
+
+    config.cache_store = :null_store
+  end
 end

config/environments/production.rb

@@ -48,7 +48,7 @@ Rails.application.configure do
 
   # 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?
+  # config.serve_static_files = ENV['RAILS_SERVE_STATIC_FILES'].present?
 
   # Compress JavaScripts and CSS.
   config.assets.js_compressor = :uglifier
@@ -119,4 +119,46 @@ Rails.application.configure do
   # Enable user registrations
   config.x.enable_user_registration =
     ENV['ENABLE_USER_REGISTRATION'] == 'false' ? false : true
+
+  # Use a different logger for distributed setups.
+  # require 'syslog/logger'
+  # config.logger = ActiveSupport::TaggedLogging.new(Syslog::Logger.new 'app-name')
+
+  if ENV["RAILS_LOG_TO_STDOUT"].present?
+    logger           = ActiveSupport::Logger.new(STDOUT)
+    logger.formatter = config.log_formatter
+    config.logger    = ActiveSupport::TaggedLogging.new(logger)
+  end
+
+  # Use a different cache store in production.
+  # config.cache_store = :mem_cache_store
+
+  # Use a real queuing backend for Active Job (and separate queues per environment)
+  # config.active_job.queue_adapter     = :resque
+  # config.active_job.queue_name_prefix = "scinote_#{Rails.env}"
+  config.action_mailer.perform_caching = false
+
+  # `config.assets.precompile` and `config.assets.version` have moved to config/initializers/assets.rb
+
+  # Enable serving of images, stylesheets, and JavaScripts from an asset server.
+  # config.action_controller.asset_host = 'http://assets.example.com'
+
+  # 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
+
+  # Mount Action Cable outside main process or domain
+  # config.action_cable.mount_path = nil
+  # config.action_cable.url = 'wss://example.com/cable'
+  # config.action_cable.allowed_request_origins = [ 'http://example.com', /http:\/\/example.*/ ]
+
+  # Disable serving static files from the `/public` folder by default since
+  # Apache or NGINX already handles this.
+  config.public_file_server.enabled = ENV['RAILS_SERVE_STATIC_FILES'].present?
+
+
+  # Attempt to read encrypted secrets from `config/secrets.yml.enc`.
+  # Requires an encryption key in `ENV["RAILS_MASTER_KEY"]` or
+  # `config/secrets.yml.key`.
+  config.read_encrypted_secrets = true
 end

config/environments/test.rb

@@ -1,6 +1,12 @@
 Rails.application.configure do
   # Settings specified here will take precedence over those in config/application.rb.
 
+  # Configure public file server for tests with Cache-Control for performance.
+  config.public_file_server.enabled = true
+  config.public_file_server.headers = {
+    'Cache-Control' => "public, max-age=#{1.hour.seconds.to_i}"
+  }
+
   # Enable this to be able to output stuff to STDOUT during tests
   # via Rails::logger.info "..."
   config.logger = Logger.new(STDOUT)

config/initializers/application_controller_renderer.rb

@@ -0,0 +1,6 @@
+# Be sure to restart your server when you modify this file.
+
+# ApplicationController.renderer.defaults.merge!(
+#   http_host: 'example.org',
+#   https: false
+# )

config/initializers/assets.rb

@@ -3,12 +3,16 @@
 # 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
+# Add additional assets to the asset load path.
 # Rails.application.config.assets.paths << Emoji.images_path
+# Add Yarn node_modules folder to the asset load path.
+Rails.application.config.assets.paths << Rails.root.join('node_modules')
 
 # Precompile additional assets.
-# application.js application.css, and all non-JS/CSS
-# in app/assets folder are already added.
+# application.js, application.css, and all non-JS/CSS in the app/assets
+# folder are already added.
+# Rails.application.config.assets.precompile += %w( admin.js admin.css )
+
 Rails.application.config.assets.precompile += %w(underscore.js)
 Rails.application.config.assets.precompile += %w(jsPlumb-2.0.4-min.js)
 Rails.application.config.assets.precompile += %w(jsnetworkx.js)

config/initializers/cookies_serializer.rb

@@ -1,3 +1,5 @@
 # Be sure to restart your server when you modify this file.
 
+# Specify a serializer for the signed and encrypted cookie jars.
+# Valid options are :json, :marshal, and :hybrid.
 Rails.application.config.action_dispatch.cookies_serializer = :json

config/initializers/devise_async.rb

@@ -1,4 +1,4 @@
 Devise::Async.enabled = true
 Devise::Async.backend = :delayed_job
 Devise::Async.queue = :devise_email
-Devise::Async.priority = 10
+#  Devise::Async.priority = 10

config/initializers/new_framework_defaults_5_1.rb

@@ -0,0 +1,14 @@
+# Be sure to restart your server when you modify this file.
+#
+# This file contains migration options to ease your Rails 5.1 upgrade.
+#
+# Once upgraded flip defaults one by one to migrate to the new default.
+#
+# Read the Guide for Upgrading Ruby on Rails for more info on each option.
+
+# Make `form_with` generate non-remote forms.
+Rails.application.config.action_view.form_with_generates_remote_forms = false
+
+# Unknown asset fallback will return the path passed in when the given
+# asset is not present in the asset pipeline.
+# Rails.application.config.assets.unknown_asset_fallback = false

config/initializers/wrap_parameters.rb

@@ -5,10 +5,10 @@
 
 # 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)
+  wrap_parameters format: [:json]
 end
 
 # To enable root element in JSON for ActiveRecord objects.
 # ActiveSupport.on_load(:active_record) do
-#  self.include_root_in_json = true
+#   self.include_root_in_json = true
 # end

config/locales/en.yml

@@ -910,8 +910,8 @@ en:
     column_create: "Create"
     columns_delete: "Delete"
     columns_visibility: "Visible columns"
-    view_all_records: "View all records"
-    view_assigned_records: "View assigned records"
+    view_all_records: "View all items"
+    view_assigned_records: "View assigned items"
     modal_delete_record:
       title: "Delete record"
       notice: "Are you sure you want to delete the selected records?"

config/puma.rb

@@ -13,3 +13,60 @@ on_worker_boot do
   # See: https://devcenter.heroku.com/articles/deploying-rails-applications-with-the-puma-web-server#on-worker-boot
   ActiveRecord::Base.establish_connection
 end
+
+# Puma can serve each request in a thread from an internal thread pool.
+# The `threads` method setting takes two numbers: a minimum and maximum.
+# Any libraries that use thread pools should be configured to match
+# the maximum value specified for Puma. Default is set to 5 threads for minimum
+# and maximum; this matches the default thread size of Active Record.
+#
+# threads_count = ENV.fetch("RAILS_MAX_THREADS") { 5 }
+# threads threads_count, threads_count
+#
+# Specifies the `port` that Puma will listen on to receive requests; default is 3000.
+#
+# port        ENV.fetch("PORT") { 3000 }
+#
+# Specifies the `environment` that Puma will run in.
+#
+# environment ENV.fetch("RAILS_ENV") { "development" }
+
+# Specifies the number of `workers` to boot in clustered mode.
+# Workers are forked webserver processes. If using threads and workers together
+# the concurrency of the application would be max `threads` * `workers`.
+# Workers do not work on JRuby or Windows (both of which do not support
+# processes).
+#
+# workers ENV.fetch("WEB_CONCURRENCY") { 2 }
+
+# Use the `preload_app!` method when specifying a `workers` number.
+# This directive tells Puma to first boot the application and load code
+# before forking the application. This takes advantage of Copy On Write
+# process behavior so workers use less memory. If you use this option
+# you need to make sure to reconnect any threads in the `on_worker_boot`
+# block.
+#
+# preload_app!
+
+# If you are preloading your application and using Active Record, it's
+# recommended that you close any connections to the database before workers
+# are forked to prevent connection leakage.
+#
+# before_fork do
+#   ActiveRecord::Base.connection_pool.disconnect! if defined?(ActiveRecord)
+# end
+
+# The code in the `on_worker_boot` will be called if you are using
+# clustered mode by specifying a number of `workers`. After each worker
+# process is booted, this block will be run. If you are using the `preload_app!`
+# option, you will want to use this block to reconnect to any threads
+# or connections that may have been created at application boot, as Ruby
+# cannot share connections between processes.
+#
+# on_worker_boot do
+#   ActiveRecord::Base.establish_connection if defined?(ActiveRecord)
+# end
+#
+
+# Allow puma to be restarted by `rails restart` command.
+#  plugin :tmp_restart

config/secrets.yml

@@ -1,5 +1,23 @@
 # Be sure to restart your server when you modify this file.
 
+# Your secret key is used for verifying the integrity of signed cookies.
+# If you change this key, all old signed cookies will become invalid!
+
+# Make sure the secret is at least 30 characters and all random,
+# no regular words or you'll be exposed to dictionary attacks.
+# You can use `rails secret` to generate a secure secret key.
+
+# Make sure the secrets in this file are kept private
+# if you're sharing your code publicly.
+
+# Shared secrets are available across all environments.
+
+# shared:
+#   api_key: a1B2c3D4e5F6
+
+# Environmental secrets are only available for that specific environment.
+# Be sure to restart your server when you modify this file.
+
 common: &common
 
 # ======================================================================
@@ -39,10 +57,13 @@ common: &common
 # ======================================================================
 
 development:
+  secret_key_base: 22f2adf8f5cb73351da28f2292daa840cc2a414ae00ae605b175a8d5c73932f7e5b8ff8ef8f1554a7f1064f9869b15347f7709f0daa6ccb24c50f3cace304f64
   <<: *common
 
 test:
+  secret_key_base: f3719934e04fa8871cf5d33d5c60f05e1b8995e0315265aef9f8b878da49bd2d386eb25ce35545b469a94ccf22f91e0052b93a15194b4f57b0c8d6ce8b150e1e
   <<: *common
 
 production:
-  <<: *common
+  secret_key_base: <%= ENV["SECRET_KEY_BASE"] %>
+  <<: *common

config/spring.rb

@@ -0,0 +1,6 @@
+%w(
+  .ruby-version
+  .rbenv-vars
+  tmp/restart.txt
+  tmp/caching-dev.txt
+).each { |path| Spring.watch(path) }