Upgraded default to Rails 5.2 and use encrypted credentials now

.gitignore

@@ -1,19 +1,24 @@
 /coverage
-.idea/
+.idea
 .bundle
 tmp/
+log/
+public/assets/
+public/system/
+
 config/database.yml
 config/secrets.yml
 config/application.yml
-log/
+# Ignore master key for decrypting credentials and more.
+config/master.key
+
 .DS_Store
-rails_best_practices_output.html
+
 dump.rdb
+latest.dump
 specimens.xls
 species.xls
-public/assets/
-public/system/
-latest.dump
 spec/examples.txt
+
 .rbenv-vars
-.env
+.env

Gemfile

@@ -45,6 +45,7 @@ gem 'select2-rails' # Integrate Select2 Javascript library
 gem 'ancestry' # Self-related models
 gem 'bcrypt', platforms: :ruby
 gem 'bio' # BioRuby
+gem 'bootsnap'
 gem 'bootstrap-sass'
 gem 'bootstrap_progressbar'
 gem 'builder'
@@ -56,7 +57,6 @@ gem 'net-ssh'
 gem 'roo-xls' # Handle excel files
 gem 'rubyzip' # Handle zip files
 gem 'simple_form'
-gem 'slim' # TODO: Used anywhere?
 gem 'sprockets-rails', require: 'sprockets/railtie'
 # gem 'turbolinks' # Turbolinks makes navigating your web application faster TODO: Does not work unless first changes to js code, in particular data-tables (see http://guides.rubyonrails.org/working_with_javascript_in_rails.html#turbolinks)
 gem 'whenever', require: false # Runs scheduled jobs via cron
@@ -77,8 +77,7 @@ group :development do
   gem 'bullet' # Checks for n+1 queries
   gem 'binding_of_caller' # Extends features of better_errors
   gem 'meta_request' # Supporting gem for Google Chrome Rails Panel
-  # gem 'spring' # Spring speeds up development by keeping your application running in the background
-  # gem 'spring-watcher-listen'
+  gem 'spring' # Spring speeds up development by keeping your application running in the background
   gem 'yard' # Documentation generation tool
 end
 

Gemfile.lock

@@ -980,6 +980,8 @@ GEM
     binding_of_caller (0.8.0)
       debug_inspector (>= 0.0.1)
     bio (2.0.1)
+    bootsnap (1.4.6)
+      msgpack (~> 1.0)
     bootstrap-multiselect_rails (0.9.5)
     bootstrap-sass (3.4.1)
       autoprefixer-rails (>= 5.2.1)
@@ -1117,6 +1119,8 @@ GEM
     mini_mime (1.0.2)
     mini_portile2 (2.4.0)
     minitest (5.14.0)
+    msgpack (1.3.3)
+    msgpack (1.3.3-x86-mingw32)
     mustermann (1.1.1)
       ruby2_keywords (~> 0.0.1)
     nenv (0.3.0)
@@ -1268,11 +1272,9 @@ GEM
       rack (~> 2.0)
       rack-protection (= 2.0.8.1)
       tilt (~> 2.0)
-    slim (4.1.0)
-      temple (>= 0.7.6, < 0.9)
-      tilt (>= 2.0.6, < 2.1)
     spreadsheet (1.2.6)
       ruby-ole (>= 1.0)
+    spring (2.1.0)
     sprockets (4.0.0)
       concurrent-ruby (~> 1.0)
       rack (> 1, < 3)
@@ -1283,7 +1285,6 @@ GEM
     sshkit (1.21.0)
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
-    temple (0.8.2)
     terrapin (0.6.0)
       climate_control (>= 0.0.3, < 1.0)
     thor (0.20.3)
@@ -1328,6 +1329,7 @@ DEPENDENCIES
   better_errors
   binding_of_caller
   bio
+  bootsnap
   bootstrap-multiselect_rails
   bootstrap-sass
   bootstrap_progressbar
@@ -1381,7 +1383,7 @@ DEPENDENCIES
   simple_form
   simplecov
   sinatra
-  slim
+  spring
   sprockets-rails
   tzinfo-data
   uglifier

app/controllers/contigs_controller.rb

@@ -5,7 +5,7 @@ class ContigsController < ApplicationController
 
   load_and_authorize_resource
 
-  http_basic_authenticate_with name: ENV['API_USER_NAME'], password: ENV['API_PASSWORD'], only: [:as_fasq, :change_via_script, :compare_contigs]
+  http_basic_authenticate_with name: ENV['API_USER_NAME'], password: Rails.application.credentials.api_password, only: [:as_fasq, :change_via_script, :compare_contigs]
 
   skip_before_action :verify_authenticity_token, only: [:as_fasq, :change_via_script, :compare_contigs]
 

app/controllers/mislabel_analyses_controller.rb

@@ -5,7 +5,7 @@ class MislabelAnalysesController < ApplicationController
 
   before_action :set_mislabel_analysis, only: %i[show destroy import download_results]
 
-  http_basic_authenticate_with name: ENV['API_USER_NAME'], password: ENV['API_PASSWORD'], only: :download_results
+  http_basic_authenticate_with name: ENV['API_USER_NAME'], password: Rails.application.credentials.api_password, only: :download_results
   skip_before_action :verify_authenticity_token, only: :download_results
 
   def index

app/controllers/ngs_runs_controller.rb

@@ -3,7 +3,7 @@ class NgsRunsController < ApplicationController
 
   load_and_authorize_resource
 
-  http_basic_authenticate_with name: ENV['API_USER_NAME'], password: ENV['API_PASSWORD'], only: [:import, :revised_tpm]
+  http_basic_authenticate_with name: ENV['API_USER_NAME'], password: Rails.application.credentials.api_password, only: [:import, :revised_tpm]
   skip_before_action :verify_authenticity_token, only: [:import, :revised_tpm]
 
   before_action :set_ngs_run, only: [:show, :edit, :update, :destroy, :import, :analysis_results]

app/models/contig_search.rb

@@ -15,7 +15,7 @@ class ContigSearch < ApplicationRecord
   validates_attachment_content_type :search_result_archive, :content_type => /\Aapplication\/zip/
 
   # Validate filename
-  validates_attachment_file_name :search_result_archive, :matches => [/zip\Z/]
+  validates_attachment_file_name :search_result_archive, :matches => %r{\.zip\Z}i
 
   def contigs
     @contigs ||= find_contigs

bin/rails

@@ -1,4 +1,9 @@
 #!/usr/bin/env ruby
+begin
+  load File.expand_path('../spring', __FILE__)
+rescue LoadError => e
+  raise unless e.message.include?('spring')
+end
 APP_PATH = File.expand_path('../config/application', __dir__)
 require_relative '../config/boot'
 require 'rails/commands'

bin/rake

@@ -1,4 +1,9 @@
 #!/usr/bin/env ruby
+begin
+  load File.expand_path('../spring', __FILE__)
+rescue LoadError => e
+  raise unless e.message.include?('spring')
+end
 require_relative '../config/boot'
 require 'rake'
 Rake.application.run

bin/spring

@@ -1,19 +1,17 @@
 #!/usr/bin/env ruby
-# frozen_string_literal: true
 
-# This file loads spring without using Bundler, in order to be fast
-# It gets overwritten when you run the `spring binstub` command
+# This file loads Spring without using Bundler, in order to be fast.
+# It gets overwritten when you run the `spring binstub` command.
 
 unless defined?(Spring)
   require 'rubygems'
   require 'bundler'
 
-  if match = Bundler.default_lockfile.read.match(/^GEM$.*?^    spring \((.*?)\)$.*?^$/m)
-    ENV['GEM_PATH'] = ([Bundler.bundle_path.to_s] + Gem.path).join(File::PATH_SEPARATOR)
-    ENV['GEM_HOME'] = ''
-    Gem.paths = ENV
-
-    gem 'spring', match[1]
+  lockfile = Bundler::LockfileParser.new(Bundler.default_lockfile.read)
+  spring = lockfile.specs.detect { |spec| spec.name == 'spring' }
+  if spring
+    Gem.use_paths Gem.dir, Bundler.bundle_path.to_s, *Gem.path
+    gem 'spring', spring.version
     require 'spring/binstub'
   end
 end

config/application.rb

@@ -11,6 +11,9 @@ module GBOLapp
   class Application < Rails::Application
     config.load_defaults 5.2
 
+    # Keep old default of not requiring belongs to associations
+    Rails.application.config.active_record.belongs_to_required_by_default = false
+
     # 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.

config/credentials.yml.enc

@@ -0,0 +1 @@
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--sRwDJlZGIJ0mrctd--ivcbdsXY8cEXtCuu0fssZA==

config/environments/development.rb

@@ -28,7 +28,7 @@
   end
 
   # Store uploaded files on the local file system (see config/storage.yml for options)
-  config.active_storage.service = :local
+  # config.active_storage.service = :local
 
   # Don't care if the mailer can't send.
   config.action_mailer.raise_delivery_errors = false

config/environments/production.rb

@@ -16,7 +16,7 @@
 
   # Ensures that a master key has been made available in either ENV["RAILS_MASTER_KEY"]
   # or in config/master.key. This key is used to decrypt credentials (and other encrypted files).
-  # config.require_master_key = true
+  config.require_master_key = true
 
   # Disable serving static files from the `/public` folder by default since
   # Apache or NGINX already handles this.
@@ -39,7 +39,7 @@
   # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for NGINX
 
   # Store uploaded files on the local file system (see config/storage.yml for options)
-  config.active_storage.service = :local
+  # config.active_storage.service = :local
 
   # Mount Action Cable outside main process or domain
   # config.action_cable.mount_path = nil
@@ -109,8 +109,8 @@
       path: '/:class/:attachment/:id_partition/:style/:filename',
       s3_credentials: {
           bucket: ENV['S3_BUCKET_NAME'],
-          access_key_id: ENV['AWS_ACCESS_KEY_ID'],
-          secret_access_key: ENV['AWS_SECRET_ACCESS_KEY'],
+          access_key_id: Rails.application.credentials.aws[:access_key_id],
+          secret_access_key: Rails.application.credentials.aws[:secret_access_key],
           s3_region: ENV['S3_REGION'],
           preserve_files: true
       }

config/environments/test.rb

@@ -29,7 +29,7 @@
   config.action_controller.allow_forgery_protection = false
 
   # Store uploaded files on the local file system in a temporary directory
-  config.active_storage.service = :test
+  # config.active_storage.service = :test
 
   config.action_mailer.perform_caching = false
 

config/initializers/assets.rb

@@ -13,5 +13,5 @@
 # folder are already added.
 # Rails.application.config.assets.precompile += %w( admin.js admin.css )
 
-config.assets.paths << "#{Rails}/app/assets/fonts"
-config.assets.paths << "#{Rails}/vendor/assets/fonts"
+Rails.application.config.assets.paths << Rails.root.join('/app/assets/fonts')
+Rails.application.config.assets.paths << Rails.root.join('/vendor/assets/fonts')

config/spring.rb

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