[release] Merge Develop into Master for 1.19.0

.rubocop.yml

@@ -9,6 +9,9 @@ AllCops:
     - vendor/**/*
   NewCops: enable
 
+Layout/IndentationWidth:
+  EnforcedStyleAlignWith: relative_to_receiver
+
 Rails/InverseOf:
   Enabled: false
 

.rubocop_todo.yml

@@ -1,6 +1,6 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config --no-exclude-limit`
-# on 2025-08-27 14:16:51 UTC using RuboCop version 1.79.2.
+# on 2026-03-23 09:57:06 UTC using RuboCop version 1.85.1.
 # The point is for the user to remove these configuration records
 # one by one as the offenses are removed from the code base.
 # Note that changes in the inspected code, or installation of new
@@ -21,7 +21,7 @@ Layout/ExtraSpacing:
   Exclude:
     - 'test/controllers/users_controller_test.rb'
 
-# Offense count: 31
+# Offense count: 32
 # This cop supports safe autocorrection (--autocorrect).
 # Configuration parameters: EnforcedStyle, IndentationWidth.
 # SupportedStyles: special_inside_parentheses, consistent, align_braces
@@ -49,13 +49,6 @@ Lint/EmptyBlock:
     - 'Gemfile'
     - 'config/routes.rb'
 
-# Offense count: 2
-# Configuration parameters: AllowComments.
-Lint/EmptyClass:
-  Exclude:
-    - 'app/models/presenter.rb'
-    - 'test/test_helper.rb'
-
 # Offense count: 3
 # Configuration parameters: AllowedParentClasses.
 Lint/MissingSuper:
@@ -71,7 +64,7 @@ Lint/ParenthesesAsGroupedExpression:
 
 # Offense count: 5
 # This cop supports safe autocorrection (--autocorrect).
-# Configuration parameters: AutoCorrect, IgnoreEmptyBlocks, AllowUnusedKeywordArguments.
+# Configuration parameters: IgnoreEmptyBlocks, AllowUnusedKeywordArguments.
 Lint/UnusedBlockArgument:
   Exclude:
     - 'app/controllers/qc_assets_controller.rb'
@@ -81,22 +74,20 @@ Lint/UnusedBlockArgument:
 
 # Offense count: 3
 # This cop supports safe autocorrection (--autocorrect).
-# Configuration parameters: AutoCorrect, AllowUnusedKeywordArguments, IgnoreEmptyMethods, IgnoreNotImplementedMethods, NotImplementedExceptions.
+# Configuration parameters: AllowUnusedKeywordArguments, IgnoreEmptyMethods, IgnoreNotImplementedMethods, NotImplementedExceptions.
 # NotImplementedExceptions: NotImplementedError
 Lint/UnusedMethodArgument:
   Exclude:
     - 'app/helpers/application_helper.rb'
     - 'app/models/gatekeeper/robot.rb'
     - 'app/models/presenter/lot.rb'
 
-# Offense count: 4
+# Offense count: 3
 # This cop supports safe autocorrection (--autocorrect).
-# Configuration parameters: AutoCorrect.
 Lint/UselessAssignment:
   Exclude:
     - 'app/helpers/application_helper.rb'
     - 'app/models/gatekeeper/robot.rb'
-    - 'lib/tasks/config.rake'
 
 # Offense count: 21
 # Configuration parameters: AllowedMethods, AllowedPatterns, CountRepeatedAttributes, Max.
@@ -214,8 +205,6 @@ Rails/Delegate:
     - 'test/mock_api.rb'
 
 # Offense count: 5
-# Configuration parameters: Include.
-# Include: **/app/controllers/**/*.rb, **/app/mailers/**/*.rb
 Rails/LexicallyScopedActionFilter:
   Exclude:
     - 'app/controllers/assets_controller.rb'
@@ -271,21 +260,6 @@ Style/IfUnlessModifier:
     - 'lib/tasks/config.rake'
     - 'test/mock_api.rb'
 
-# Offense count: 1
-# This cop supports safe autocorrection (--autocorrect).
-# Configuration parameters: EnforcedStyle.
-# SupportedStyles: line_count_dependent, lambda, literal
-Style/Lambda:
-  Exclude:
-    - 'lib/tasks/config.rake'
-
-# Offense count: 1
-# This cop supports safe autocorrection (--autocorrect).
-# Configuration parameters: .
-# SupportedStyles: call, braces
-Style/LambdaCall:
-  EnforcedStyle: braces
-
 # Offense count: 5
 Style/MissingRespondToMissing:
   Exclude:
@@ -344,6 +318,12 @@ Style/PreferredHashMethods:
     - 'app/models/qc_asset_creator/plate_conversion.rb'
     - 'test/mock_api.rb'
 
+# Offense count: 1
+# This cop supports unsafe autocorrection (--autocorrect-all).
+Style/ReduceToHash:
+  Exclude:
+    - 'app/models/qc_asset_creator/multiple_tag2_conversion.rb'
+
 # Offense count: 4
 # This cop supports safe autocorrection (--autocorrect).
 Style/StderrPuts:
@@ -391,9 +371,9 @@ Style/ZeroLengthPredicate:
     - 'app/models/gatekeeper/plate.rb'
     - 'app/models/gatekeeper/tube.rb'
 
-# Offense count: 78
+# Offense count: 76
 # This cop supports safe autocorrection (--autocorrect).
-# Configuration parameters: Max, AllowHeredoc, AllowURI, AllowQualifiedName, URISchemes, IgnoreCopDirectives, AllowedPatterns, SplitStrings.
+# Configuration parameters: Max, AllowHeredoc, AllowURI, AllowQualifiedName, URISchemes, AllowRBSInlineAnnotation, AllowCopDirectives, AllowedPatterns, SplitStrings.
 # URISchemes: http, https
 Layout/LineLength:
   Exclude:

.ruby-version

@@ -1 +1 @@
-3.4.8
+3.4.9

Gemfile.lock

@@ -88,14 +88,14 @@ GEM
       mutex_m
       securerandom (>= 0.3)
       tzinfo (~> 2.0)
-    addressable (2.8.7)
-      public_suffix (>= 2.0.2, < 7.0)
+    addressable (2.8.9)
+      public_suffix (>= 2.0.2, < 8.0)
     ast (2.4.3)
     autoprefixer-rails (10.4.7.0)
       execjs (~> 2)
     base64 (0.3.0)
     benchmark (0.5.0)
-    bigdecimal (4.0.1)
+    bigdecimal (4.1.0)
     bootsnap (1.23.0)
       msgpack (~> 1.2)
     bootstrap-datepicker-rails (1.10.0.1)
@@ -152,7 +152,7 @@ GEM
       rails-dom-testing (>= 1, < 3)
       railties (>= 4.2.0)
       thor (>= 0.14, < 2.0)
-    json (2.18.1)
+    json (2.19.3)
     json_api_client (1.23.0)
       activemodel (>= 6.0.0)
       activesupport (>= 6.0.0)
@@ -191,7 +191,7 @@ GEM
     minitest-rails-capybara (0.0.2)
       capybara
       minitest-rails
-    mocha (3.0.2)
+    mocha (3.1.0)
       ruby2_keywords (>= 0.0.5)
     msgpack (1.8.0)
     multi_json (1.15.0)
@@ -214,12 +214,12 @@ GEM
       racc (~> 1.4)
     nokogiri (1.19.1-x86_64-linux-gnu)
       racc (~> 1.4)
-    oj (3.16.15)
+    oj (3.16.16)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     ostruct (0.6.3)
     parallel (1.27.0)
-    parser (3.3.10.1)
+    parser (3.3.11.1)
       ast (~> 2.4.1)
       racc
     prism (1.9.0)
@@ -228,7 +228,7 @@ GEM
       method_source (~> 1.0)
     pry-rails (0.3.11)
       pry (>= 0.13.0)
-    public_suffix (6.0.1)
+    public_suffix (7.0.5)
     puma (7.2.0)
       nio4r (~> 2.0)
     racc (1.8.1)
@@ -277,7 +277,7 @@ GEM
     roo (2.8.3)
       nokogiri (~> 1)
       rubyzip (>= 1.3.0, < 3.0.0)
-    rubocop (1.84.1)
+    rubocop (1.86.0)
       json (~> 2.3)
       language_server-protocol (~> 3.17.0.2)
       lint_roller (~> 1.1.0)
@@ -288,7 +288,7 @@ GEM
       rubocop-ast (>= 1.49.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 4.0)
-    rubocop-ast (1.49.0)
+    rubocop-ast (1.49.1)
       parser (>= 3.3.7.2)
       prism (~> 1.7)
     rubocop-rails (2.34.3)

README.md

@@ -1,7 +1,7 @@
 [![Ruby Tests](https://github.com/sanger/gatekeeper/actions/workflows/ruby_test.yml/badge.svg)](https://github.com/sanger/gatekeeper/actions/workflows/ruby_test.yml)
 [![codecov](https://codecov.io/gh/sanger/gatekeeper/graph/badge.svg?token=VbxDtCNFAh)](https://codecov.io/gh/sanger/gatekeeper)
 
-# Gatekeeper
+# <img src="public/images/gate-kk.svg" alt="Reflected K Logo" height="20pt" /> Gatekeeper
 
 Gatekeeper is used to track the production and validation of batches of tag plates for sequencing.
 It is designed to interface with the [Sequencescape](https://github.com/sanger/sequencescape) LIMS.

app/assets/config/manifest.js

@@ -1,2 +1,3 @@
 //= link application.css
 //= link application.js
+//= link gate-kk.svg

app/assets/stylesheets/gatekeeper.scss

@@ -24,6 +24,12 @@ h1 {
   padding: 0.5em;
 }
 
+.logo {
+  margin-bottom: -11px;
+  margin-right: -11px;
+  vertical-align: baseline;
+}
+
 .gk-section {
   text-align: justify;
 }

app/views/pages/index.erb

@@ -1,5 +1,8 @@
 <div id='gk-index-page' class='gk-page'>
-  <h1 id='gk-index-title' class='gk-page-title'><%= Gatekeeper::Application.config.name %></h1>
+  <h1 id='gk-index-title' class='gk-page-title'>
+    <%= image_tag 'gate-kk.svg', alt: 'Reflected K Logo', class: 'logo'%>
+    <%= Gatekeeper::Application.config.name %>
+  </h1>
   <div class="col-sm-6">
     <div id='gk-index-menu' class='panel panel-primary'>
       <div class="panel-heading">Register Lots</div>

config/application.rb

@@ -34,7 +34,7 @@ class Application < Rails::Application
     config.i18n.fallbacks = [I18n.default_locale]
 
     # Ensures precompiling is faster by not loading the application
-    config.assets.initialize_on_precompile = false
+    config.assets.initialize_on_precompile = true
     config.disable_animations = false
 
     config.destroyable_states = %w[pending available]

config/initializers/request_logger.rb

@@ -0,0 +1,11 @@
+# frozen_string_literal: true
+
+require_relative '../../lib/middleware/request_logger'
+
+Rails.application.configure do
+  # Insert RequestLogger near the top, before Rails::Rack::Logger
+  config.middleware.insert_before(Rails::Rack::Logger, Middleware::RequestLogger)
+end
+
+# Add backtrace silencers for middleware so that we don't see it in backtraces.
+Rails.backtrace_cleaner.add_silencer { |line| line.include?('request_logger') }