Merge pull request #309 from ncbo/refactor/rails-7-upgrade-continued

Rails 7.0.8 upgrade (part two)

.gitignore

@@ -42,3 +42,8 @@ node_modules
 /config/credentials/test.key
 /config/credentials/staging.key
 /config/credentials/production.key
+
+/app/assets/builds/*
+!/app/assets/builds/.keep
+
+/node_modules

Gemfile

@@ -5,27 +5,45 @@ source 'https://rubygems.org'
 # Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
 gem 'rails', '7.0.8'
 
-gem 'sass-rails', '~> 5.0'
-gem 'terser'
-# See https://github.com/rails/execjs#readme for more supported runtimes
-# gem 'therubyracer', platforms: :ruby
-# gem 'duktape'
+# The original asset pipeline for Rails [https://github.com/rails/sprockets-rails]
+gem 'sprockets-rails', require: 'sprockets/railtie'
+
+# Bundle and transpile JavaScript [https://github.com/rails/jsbundling-rails]
+gem 'jsbundling-rails', '~> 1.3'
+
+# Hotwire's SPA-like page accelerator [https://turbo.hotwired.dev]
+gem 'turbo-rails'
+
+# Hotwire's modest JavaScript framework [https://stimulus.hotwired.dev]
+gem 'stimulus-rails'
+
+# Build JSON APIs with ease [https://github.com/rails/jbuilder]
+# gem 'jbuilder'
+
+# Use Redis for Action Cable
+gem 'redis', '~> 4.0'
+
+# Use Kredis to get higher-level data types in Redis [https://github.com/rails/kredis]
+# gem 'kredis'
+
+# Use Active Model has_secure_password [https://guides.rubyonrails.org/active_model_basics.html#securepassword]
+# gem "bcrypt", "~> 3.1.7"
+
+# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
+gem 'tzinfo-data', platforms: %i[mingw mswin x64_mingw jruby]
+
+# Reduces boot times through caching; required in config/boot.rb
+gem 'bootsnap', require: false
+
+# Use Sass to process CSS
+gem 'sassc-rails'
 
 gem 'bootstrap', '~> 5.2.3'
 gem 'chart-js-rails'
 gem 'jquery-rails'
 gem 'jquery-ui-rails'
 gem 'select2-rails'
 
-# To use ActiveModel has_secure_password
-# gem 'bcrypt-ruby', '~> 3.0.0'
-
-# To use Jbuilder templates for JSON
-# gem 'jbuilder'
-
-# To use debugger
-# gem 'debugger'
-
 gem 'base64', '0.1.0'
 gem 'cube-ruby', require: 'cube'
 gem 'dalli'
@@ -39,6 +57,7 @@ gem 'iconv'
 gem 'multi_json'
 gem 'mysql2', '0.5.5'
 gem 'oj'
+gem 'ontologies_api_client', github: 'ncbo/ontologies_api_ruby_client', tag: 'v2.2.5'
 gem 'open_uri_redirections'
 gem 'pry'
 gem 'psych', '< 4'
@@ -49,39 +68,42 @@ gem 'recaptcha', '~> 5.9.0'
 gem 'rest-client'
 gem 'rexml', '~> 3'
 gem 'stackprof', require: false
+gem 'terser'
 gem 'thin'
 gem 'will_paginate', '~> 3.0'
 
-gem 'ontologies_api_client', github: 'ncbo/ontologies_api_ruby_client', tag: 'v2.2.5'
-
 group :staging, :production do
-  # application monitoring
+  # Application monitoring
   gem 'newrelic_rpm'
-  # logs in json format, useful for shipping logs to logstash
+  # Logs in json format, useful for shipping logs to logstash
   # gem 'rackstash', git: 'https://github.com/planio-gmbh/rackstash.git'
   # gem 'logstash-logger'
 end
 
 group :development do
-  # Capistrano Deployment
+  # Capistrano deployment
   gem 'bcrypt_pbkdf', '>= 1.0', '< 2.0', require: false # https://github.com/miloserdow/capistrano-deploy/issues/42
   gem 'capistrano', '~> 3.17', require: false
   gem 'capistrano-bundler', require: false
-  gem 'capistrano-rbenv', require: false
   gem 'capistrano-locally', require: false
   gem 'capistrano-passenger', require: false
   gem 'capistrano-rails', '~> 1.4', require: false
+  gem 'capistrano-rbenv', require: false
   gem 'capistrano-yarn', require: false
   gem 'ed25519', '>= 1.2', '< 2.0', require: false # https://github.com/miloserdow/capistrano-deploy/issues/42
   gem 'html2haml'
   gem 'listen'
-  # static code analysis
+
+  # Static code analysis
   gem 'brakeman', require: false
   gem 'rubocop', require: false
+
   # gem 'i18n-debug'
 end
 
-group :test, :development do
+group :development, :test do
+  # See https://guides.rubyonrails.org/debugging_rails_applications.html#debugging-with-the-debug-gem
+  gem 'debug', platforms: %i[mri mingw x64_mingw]
   gem 'rspec-rails'
 end
 

Gemfile.lock

@@ -92,6 +92,8 @@ GEM
       execjs (~> 2)
     base64 (0.1.0)
     bcrypt_pbkdf (1.1.0)
+    bootsnap (1.17.1)
+      msgpack (~> 1.2)
     bootstrap (5.2.3)
       autoprefixer-rails (>= 9.1.0)
       popper_js (>= 2.11.6, < 3)
@@ -129,12 +131,15 @@ GEM
     chart-js-rails (0.1.7)
       railties (> 3.1)
     coderay (1.1.3)
-    concurrent-ruby (1.2.2)
+    concurrent-ruby (1.2.3)
     crass (1.0.6)
     cube-ruby (0.0.3)
     daemons (1.4.1)
     dalli (3.2.6)
     date (3.3.4)
+    debug (1.9.1)
+      irb (~> 1.10)
+      reline (>= 0.3.8)
     diff-lcs (1.5.0)
     domain_name (0.6.20231109)
     ed25519 (1.3.0)
@@ -175,13 +180,19 @@ GEM
     i18n (1.14.1)
       concurrent-ruby (~> 1.0)
     iconv (1.0.8)
+    io-console (0.7.2)
+    irb (1.11.1)
+      rdoc
+      reline (>= 0.4.2)
     jquery-rails (4.6.0)
       rails-dom-testing (>= 1, < 3)
       railties (>= 4.2.0)
       thor (>= 0.14, < 2.0)
     jquery-ui-rails (6.0.1)
       railties (>= 3.2.16)
-    json (2.6.3)
+    jsbundling-rails (1.3.0)
+      railties (>= 6.0.0)
+    json (2.7.1)
     language_server-protocol (3.17.0.3)
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
@@ -202,7 +213,8 @@ GEM
       mime-types-data (~> 3.2015)
     mime-types-data (3.2023.1003)
     mini_mime (1.1.5)
-    minitest (5.20.0)
+    minitest (5.21.2)
+    msgpack (1.7.2)
     multi_json (1.15.0)
     multipart-post (2.3.0)
     mysql2 (0.5.5)
@@ -222,16 +234,16 @@ GEM
     newrelic_rpm (9.6.0)
       base64
     nio4r (2.6.1)
-    nokogiri (1.15.5-arm64-darwin)
+    nokogiri (1.16.0-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.15.5-x86_64-darwin)
+    nokogiri (1.16.0-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.15.5-x86_64-linux)
+    nokogiri (1.16.0-x86_64-linux)
       racc (~> 1.4)
     oj (3.16.1)
     open_uri_redirections (0.2.1)
-    parallel (1.23.0)
-    parser (3.2.2.4)
+    parallel (1.24.0)
+    parser (3.3.0.5)
       ast (~> 2.4.1)
       racc
     popper_js (2.11.8)
@@ -286,7 +298,10 @@ GEM
     rdoc (6.3.3)
     recaptcha (5.9.0)
       json
-    regexp_parser (2.8.2)
+    redis (4.8.1)
+    regexp_parser (2.9.0)
+    reline (0.4.2)
+      io-console (~> 0.5)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -310,15 +325,15 @@ GEM
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
     rspec-support (3.12.1)
-    rubocop (1.57.2)
+    rubocop (1.60.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.2.4)
+      parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.28.1, < 2.0)
+      rubocop-ast (>= 1.30.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
     rubocop-ast (1.30.0)
@@ -327,17 +342,6 @@ GEM
     ruby2_keywords (0.0.5)
     ruby_parser (3.20.3)
       sexp_processor (~> 4.16)
-    sass (3.7.4)
-      sass-listen (~> 4.0.0)
-    sass-listen (4.0.0)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
-    sass-rails (5.1.0)
-      railties (>= 5.2.0)
-      sass (~> 3.1)
-      sprockets (>= 2.8, < 4.0)
-      sprockets-rails (>= 2.0, < 4.0)
-      tilt (>= 1.1, < 3)
     sassc (2.4.0)
       ffi (~> 1.9)
     sassc-rails (2.1.2)
@@ -349,9 +353,9 @@ GEM
     select2-rails (4.0.13)
     sexp_processor (4.17.0)
     spawnling (2.1.5)
-    sprockets (3.7.2)
+    sprockets (4.2.1)
       concurrent-ruby (~> 1.0)
-      rack (> 1, < 3)
+      rack (>= 2.2.4, < 4)
     sprockets-rails (3.4.2)
       actionpack (>= 5.2)
       activesupport (>= 5.2)
@@ -360,6 +364,8 @@ GEM
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     stackprof (0.2.25)
+    stimulus-rails (1.3.3)
+      railties (>= 6.0.0)
     temple (0.10.3)
     terser (1.1.20)
       execjs (>= 0.3.0, < 3)
@@ -370,6 +376,10 @@ GEM
     thor (1.3.0)
     tilt (2.3.0)
     timeout (0.4.1)
+    turbo-rails (1.5.0)
+      actionpack (>= 6.0.0)
+      activejob (>= 6.0.0)
+      railties (>= 6.0.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     unicode-display_width (2.5.0)
@@ -389,6 +399,7 @@ PLATFORMS
 DEPENDENCIES
   base64 (= 0.1.0)
   bcrypt_pbkdf (>= 1.0, < 2.0)
+  bootsnap
   bootstrap (~> 5.2.3)
   brakeman
   capistrano (~> 3.17)
@@ -402,6 +413,7 @@ DEPENDENCIES
   chart-js-rails
   cube-ruby
   dalli
+  debug
   ed25519 (>= 1.2, < 2.0)
   flamegraph
   graphql (~> 2.0.27)
@@ -412,6 +424,7 @@ DEPENDENCIES
   iconv
   jquery-rails
   jquery-ui-rails
+  jsbundling-rails (~> 1.3)
   listen
   multi_json
   mysql2 (= 0.5.5)
@@ -426,15 +439,20 @@ DEPENDENCIES
   rails_autolink
   rdoc
   recaptcha (~> 5.9.0)
+  redis (~> 4.0)
   rest-client
   rexml (~> 3)
   rspec-rails
   rubocop
-  sass-rails (~> 5.0)
+  sassc-rails
   select2-rails
+  sprockets-rails
   stackprof
+  stimulus-rails
   terser
   thin
+  turbo-rails
+  tzinfo-data
   will_paginate (~> 3.0)
 
 BUNDLED WITH

Procfile.dev

@@ -0,0 +1,2 @@
+web: env RUBY_DEBUG_OPEN=true bin/rails server
+js: yarn build --watch

app/assets/config/manifest.js

@@ -0,0 +1,7 @@
+//= link_tree ../images
+//= link_tree ../builds
+//= link application.js
+//= link bp_annotator.js
+//= link bp_annotatorplus.js
+//= link vendor.js
+//= link_directory ../stylesheets .css

app/javascript/application-esbuild.js

@@ -0,0 +1,5 @@
+// Entry point for the build script in your package.json
+import '@hotwired/turbo-rails'
+import './controllers'
+
+Turbo.session.drive = false

app/javascript/controllers/application.js

@@ -0,0 +1,9 @@
+import { Application } from "@hotwired/stimulus"
+
+const application = Application.start()
+
+// Configure Stimulus development experience
+application.debug = false
+window.Stimulus   = application
+
+export { application }

app/javascript/controllers/index.js

@@ -0,0 +1,5 @@
+// This file is auto-generated by ./bin/rails stimulus:manifest:update
+// Run that command whenever you add a new controller or create them with
+// ./bin/rails generate stimulus controllerName
+
+import { application } from "./application"

app/views/layouts/_header.html.erb

@@ -26,6 +26,7 @@
   <%= stylesheet_link_tag "application" %>
 
   <!-- JavaScript -->
+  <%= javascript_include_tag "application-esbuild", "data-turbo-track": "reload", type: "module" %>
   <%= javascript_include_tag "vendor" %>
   <%= javascript_include_tag "//cdnjs.cloudflare.com/ajax/libs/handlebars.js/2.0.0/handlebars.min.js" %>
   <%= javascript_include_tag "//ajax.aspnetcdn.com/ajax/jquery.validate/1.11.1/jquery.validate.min.js" %>

app/views/layouts/angular.html.erb

@@ -33,6 +33,7 @@
   <%= stylesheet_link_tag "application" %>
 </head>
 <body class="<%= controller_name %> <%= action_name %> d-flex flex-column h-100">
+  <%=javascript_include_tag "application-esbuild", "data-turbo-track": "reload", type: "module" %>
   <%=javascript_include_tag "vendor"%>
   <%=javascript_include_tag "//cdnjs.cloudflare.com/ajax/libs/handlebars.js/2.0.0/handlebars.min.js"%>
   <%=javascript_include_tag "//cdnjs.cloudflare.com/ajax/libs/Chart.js/1.0.1/Chart.min.js"%>

app/views/layouts/appliance.html.haml

@@ -14,6 +14,7 @@
     = stylesheet_link_tag "https://use.fontawesome.com/releases/v5.2.0/css/all.css", integrity: "sha384-hWVjflwFxL6sNzntih27bfxkr27PmbbK/iSvJ+a4+0owXq79v+lsFkW54bOGbiDQ", crossorigin: "anonymous"
     = stylesheet_link_tag "application", media: "all"
 
+    = javascript_include_tag "application-esbuild", "data-turbo-track": "reload", type: "module"
     = javascript_include_tag "vendor"
     = javascript_include_tag "//cdnjs.cloudflare.com/ajax/libs/handlebars.js/2.0.0/handlebars.min.js"
     = javascript_include_tag "//ajax.aspnetcdn.com/ajax/jquery.validate/1.11.1/jquery.validate.min.js"

app/views/layouts/application.html.erb

@@ -3,6 +3,7 @@
 <head>
   <title>BioportalWebUi</title>
   <%= stylesheet_link_tag    "application", :media => "all" %>
+  <%= javascript_include_tag "application-esbuild", "data-turbo-track": "reload", type: "module" %>
   <%= javascript_include_tag "application"%>
   <%= csrf_meta_tags %>
 </head>