Dependencies: Rails 7.2 (#701)

* chore: upgrade rails to 7.2

* chore: remove raising exception on missing callback actions

* chore: update active_job config to not use good_job for tests

* chore: fix enum deprecations

* chore: fix action mailer config in test

* chore: update asserts for no jobs to ignore turbo jobs

* chore: run migrations and revert change in ruby github action that wasn't running all the tests

* chore: fix flakey test due to Turbo::Streams::BroadcastStreamJob being enqueued

* chore: update cuprite and remove addition to ruby github action

* chore: disable cuprite inspector

* chore: increase capybara timeout

* chore: more attempts at test issues in github actions

* chore: update capybara and cuprite setup

* chore: fix flaky group links test

* chore: use precompiled assets in testing when CI=true

* chore: increase ferrum page load timeout to 75 from 60

* chore: add in FERRUM_GOTO_WAIT in ruby github actions setup and set it to 0.2 default is 0.1

* chore: increase ferrum timeout to 0.5 seconds

* chore: revert changes in axe_helper.rb, modify cuprite timeout to default of 5 seconds, and increase capybara max wait time to 20 seconds

* chore: fix flakey project groups link test

* chore: ran bin/rails app:update and added missing files

* chore: increase cuprite page load timeout to 15 seconds from 5 seconds

* chore: fix flaky groups groups link test

* chore: increase cuprite page load timeout to 30 seconds

* chore: change assert order in test to fix random flakes

.github/workflows/linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1
       - name: rubocop

.github/workflows/ruby.yml

@@ -19,6 +19,7 @@ jobs:
           POSTGRES_PASSWORD: test
           POSTGRES_USER: test
           POSTGRES_HOST: postgres
+          FERRUM_GOTO_WAIT: 0.5 # wait 0.5 seconds before checking is network traffic is still pending
         ports:
           - 5432:5432
         # Set health checks to wait until postgres has started
@@ -29,8 +30,10 @@ jobs:
           --health-retries 5
 
     steps:
+      - name: Install packages
+        run: sudo apt-get update && sudo apt-get install --no-install-recommends -y curl libjemalloc2 libvips
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1
         with:
@@ -46,9 +49,19 @@ jobs:
           cache: "pnpm"
       - name: Install dependencies
         run: pnpm install
+      - name: Precompile assets
+        run: |
+          bin/rails assets:precompile
       - name: Run tests
         run: |
           bin/rails test:all
+      - name: Keep screenshots from failed system tests
+        uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: screenshots
+          path: ${{ github.workspace }}/tmp/screenshots
+          if-no-files-found: ignore
       - name: Report coverage
         if: github.event_name == 'pull_request'
         uses: aki77/simplecov-report-action@v1

.github/workflows/sapporo.yml

@@ -30,7 +30,7 @@ jobs:
 
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1
         with:

Dockerfile

@@ -1,14 +1,22 @@
 # syntax = docker/dockerfile:1
 
+# docker build -t my-app .
+# docker run -d -p 80:80 -p 443:443 --name irida-next -e RAILS_MASTER_KEY=<value from config/master.key> irida-next
+
 # Make sure RUBY_VERSION matches the Ruby version in .ruby-version and Gemfile
 ARG RUBY_VERSION=3.3.1
-FROM registry.docker.com/library/ruby:$RUBY_VERSION-slim as base
+FROM docker.io/library/ruby:$RUBY_VERSION-slim as base
 
 # Rails app lives here
 WORKDIR /rails
 
+# Install base packages
+RUN apt-get update -qq && \
+    apt-get install --no-install-recommends -y curl libjemalloc2 libvips postgresql-client && \
+    rm -rf /var/lib/apt/lists /var/cache/apt/archives
+
 # Set production environment
-ENV RAILS_ENV=production \
+ENV RAILS_ENV="production" \
     BUNDLE_DEPLOYMENT="1" \
     BUNDLE_PATH="/usr/local/bundle" \
     BUNDLE_WITHOUT="development"
@@ -19,15 +27,8 @@ FROM base as build
 
 # Install packages needed to build gems and node modules
 RUN apt-get update -qq && \
-    apt-get install --no-install-recommends -y \
-    build-essential \
-    curl \
-    git \
-    libpq-dev \
-    libvips \
-    node-gyp \
-    pkg-config \
-    python-is-python3
+    apt-get install --no-install-recommends -y build-essential git libpq-dev node-gyp pkg-config python-is-python3 && \
+    rm -rf /var/lib/apt/lists /var/cache/apt/archives
 
 # Install JavaScript dependencies
 ARG NODE_VERSION=20.14.0
@@ -55,31 +56,22 @@ COPY . .
 RUN bundle exec bootsnap precompile app/ lib/
 
 # Precompiling assets for production without requiring secret RAILS_MASTER_KEY
-RUN SECRET_KEY_BASE=fakekeyforassets ./bin/rails assets:precompile
+RUN SECRET_KEY_BASE_DUMMY=1 ./bin/rails assets:precompile
+
+RUN rm -rf node_modules
 
 # Final stage for app image
 FROM base
 
-# Install packages needed for deployment
-RUN apt-get update -qq && \
-    apt-get install --no-install-recommends -y \
-    libvips \
-    postgresql-client \
-    && rm -rf /var/lib/apt/lists /var/cache/apt/archives
-
-# Upgrade all packages
-RUN apt-get update -qq && \
-    apt-get upgrade -y \
-    && rm -rf /var/lib/apt/lists /var/cache/apt/archives
-
 # Copy built artifacts: gems, application
-COPY --from=build /usr/local/bundle /usr/local/bundle
+COPY --from=build "${BUNDLE_PATH}" "${BUNDLE_PATH}"
 COPY --from=build /rails /rails
 
 # Run and own only the runtime files as a non-root user for security
-RUN useradd rails --home /rails --shell /bin/bash && \
-    chown -R rails:rails db log storage tmp private private/pipelines
-USER rails:rails
+RUN groupadd --system --gid 1000 rails && \
+    useradd rails --uid 1000 --gid 1000 --create-home --shell /bin/bash && \
+    chown -R rails:rails db log storage tmp
+USER 1000:1000
 
 # Entrypoint prepares the database.
 ENTRYPOINT ["/rails/bin/docker-entrypoint"]

Gemfile

@@ -6,7 +6,7 @@ git_source(:github) { |repo| "https://github.com/#{repo}.git" }
 ruby '3.3.1'
 
 # Bundle edge Rails instead: gem "rails", github: "rails/rails", branch: "main"
-gem 'rails', '~> 7.1.3'
+gem 'rails', '~> 7.2.0'
 
 # The original asset pipeline for Rails [https://github.com/rails/sprockets-rails]
 gem 'sprockets-rails'
@@ -36,7 +36,7 @@ gem 'jbuilder'
 # 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]
+gem 'tzinfo-data', platforms: %i[windows jruby]
 
 # Reduces boot times through caching; required in config/boot.rb
 gem 'bootsnap', require: false
@@ -66,7 +66,7 @@ gem 'view_component', '~> 3.12'
 gem 'pagy', '~> 6.1' # omit patch digit
 
 # Ransack
-gem 'ransack', '~> 4.1', '>= 4.1.1'
+gem 'ransack', '~> 4.2.1'
 
 # Use Active Storage variants [https://guides.rubyonrails.org/active_storage_overview.html#transforming-images]
 # gem "image_processing", "~> 1.2"
@@ -128,7 +128,10 @@ gem 'local_time', '~> 3.0', '>= 3.0.2'
 
 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 'debug', platforms: %i[mri windows], require: 'debug/prelude'
+
+  # Static analysis for security vulnerabilities [https://brakemanscanner.org/]
+  gem 'brakeman', require: false
 end
 
 group :development do