[release] Merge Develop into Master for 14.60.0

.github/workflows/ruby_test.yml

@@ -62,7 +62,7 @@ jobs:
           DBPORT: ${{ job.services.mysql.ports[3306] }}
         run: bundle exec rake test
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v5.4.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
@@ -141,7 +141,7 @@ jobs:
           path: tmp/capybara/
           retention-days: 5
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v5.4.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
@@ -228,7 +228,7 @@ jobs:
           path: tmp/capybara/
           retention-days: 5
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v5.4.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
@@ -301,7 +301,7 @@ jobs:
           path: tmp/capybara/
           retention-days: 5
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v5.4.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true

.prettierignore

@@ -26,6 +26,7 @@ capybara*.html
 config/cucumber.yml
 config/database.yml
 coverage
+data/avro_schema_cache/*
 database_suffix
 db/*.sql
 db/*test.sqlite3

.release-version

@@ -1 +1 @@
-14.59.0
+14.60.0

.rubocop.yml

@@ -3,12 +3,13 @@ inherit_from:
   - .rubocop_todo.yml
 require:
   - test_prof/rubocop
+plugins:
+  - rubocop-capybara
+  - rubocop-factory_bot
   - rubocop-performance
   - rubocop-rails
   - rubocop-rspec
   - rubocop-rspec_rails
-  - rubocop-capybara
-  - rubocop-factory_bot
 
 inherit_mode:
   merge:

Gemfile.lock

@@ -95,7 +95,7 @@ GEM
       activemodel (= 7.1.5.1)
       activesupport (= 7.1.5.1)
       timeout (>= 0.4.0)
-    activerecord-import (1.7.0)
+    activerecord-import (2.1.0)
       activerecord (>= 4.2)
     activestorage (7.1.5.1)
       actionpack (= 7.1.5.1)
@@ -121,8 +121,8 @@ GEM
     after_commit_everywhere (1.6.0)
       activerecord (>= 4.2)
       activesupport
-    amq-protocol (2.3.2)
-    ast (2.4.2)
+    amq-protocol (2.3.3)
+    ast (2.4.3)
     avro (1.11.3)
       multi_json (~> 1.0)
     backports (3.25.0)
@@ -132,13 +132,13 @@ GEM
     bootsnap (1.18.4)
       msgpack (~> 1.2)
     builder (3.3.0)
-    bullet (7.2.0)
+    bullet (8.0.1)
       activesupport (>= 3.0.0)
       uniform_notifier (~> 1.11)
-    bunny (2.22.0)
-      amq-protocol (~> 2.3, >= 2.3.1)
+    bunny (2.24.0)
+      amq-protocol (~> 2.3)
       sorted_set (~> 1, >= 1.0.2)
-    byebug (11.1.3)
+    byebug (12.0.0)
     cancancan (3.6.1)
     capybara (3.40.0)
       addressable
@@ -168,12 +168,12 @@ GEM
     coderay (1.1.3)
     concurrent-ruby (1.3.5)
     configatron (4.5.1)
-    connection_pool (2.4.1)
+    connection_pool (2.5.0)
     crack (1.0.0)
       bigdecimal
       rexml
     crass (1.0.6)
-    csv (3.3.2)
+    csv (3.3.3)
     cucumber (9.2.1)
       builder (~> 3.2)
       cucumber-ci-environment (> 9, < 11)
@@ -217,15 +217,15 @@ GEM
     delayed_job_active_record (4.1.11)
       activerecord (>= 3.0, < 9.0)
       delayed_job (>= 3.0, < 5)
-    diff-lcs (1.6.0)
+    diff-lcs (1.6.1)
     docile (1.4.0)
     domain_name (0.6.20240107)
     drb (2.2.1)
     dry-cli (1.2.0)
     erubi (1.13.1)
-    exception_notification (4.5.0)
-      actionmailer (>= 5.2, < 8)
-      activesupport (>= 5.2, < 8)
+    exception_notification (5.0.0)
+      actionmailer (>= 7.1, < 9)
+      activesupport (>= 7.1, < 9)
     factory_bot (6.5.0)
       activesupport (>= 5.0.0)
     factory_bot_rails (6.4.4)
@@ -267,20 +267,21 @@ GEM
       pp (>= 0.6.0)
       rdoc (>= 4.0.0)
       reline (>= 0.4.2)
-    json (2.7.2)
+    json (2.10.2)
     jsonapi-resources-matchers (1.0.0)
       jsonapi-resources (>= 0.9.0)
-    knapsack_pro (7.6.2)
+    knapsack_pro (8.1.0)
       rake
-    language_server-protocol (3.17.0.3)
+    language_server-protocol (3.17.0.4)
     launchy (3.1.1)
       addressable (~> 2.8)
       childprocess (~> 5.0)
       logger (~> 1.6)
+    lint_roller (1.1.0)
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    logger (1.6.6)
+    logger (1.7.0)
     loofah (2.24.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
@@ -320,31 +321,32 @@ GEM
       net-protocol
     net-protocol (0.2.2)
       timeout
-    net-smtp (0.5.0)
+    net-smtp (0.5.1)
       net-protocol
     netrc (0.11.0)
     nio4r (2.7.4)
-    nokogiri (1.18.5-arm64-darwin)
+    nokogiri (1.18.6-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.18.5-x86_64-darwin)
+    nokogiri (1.18.6-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.18.5-x86_64-linux-gnu)
+    nokogiri (1.18.6-x86_64-linux-gnu)
       racc (~> 1.4)
     ostruct (0.6.0)
     parallel (1.26.3)
-    parser (3.3.5.0)
+    parser (3.3.7.3)
       ast (~> 2.4.1)
       racc
     pp (0.6.2)
       prettyprint
     prettier_print (1.2.1)
     prettyprint (0.2.0)
-    pry (0.14.2)
+    prism (1.4.0)
+    pry (0.15.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    pry-byebug (3.10.1)
-      byebug (~> 11.0)
-      pry (>= 0.13, < 0.15)
+    pry-byebug (3.11.0)
+      byebug (~> 12.0)
+      pry (>= 0.13, < 0.16)
     pry-rails (0.3.11)
       pry (>= 0.13.0)
     psych (3.3.4)
@@ -437,60 +439,68 @@ GEM
       rspec-mocks (~> 3.13.0)
     rspec-collection_matchers (1.2.1)
       rspec-expectations (>= 2.99.0.beta1)
-    rspec-core (3.13.0)
+    rspec-core (3.13.3)
       rspec-support (~> 3.13.0)
-    rspec-expectations (3.13.2)
+    rspec-expectations (3.13.3)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-github (2.4.0)
+    rspec-github (3.0.0)
       rspec-core (~> 3.0)
     rspec-html-matchers (0.10.0)
       nokogiri (~> 1)
       rspec (>= 3.0.0.a)
     rspec-json_expectations (2.2.0)
     rspec-longrun (3.1.0)
       rspec-core (>= 3.5.0, < 4)
-    rspec-mocks (3.13.1)
+    rspec-mocks (3.13.2)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-rails (6.1.4)
-      actionpack (>= 6.1)
-      activesupport (>= 6.1)
-      railties (>= 6.1)
+    rspec-rails (7.1.1)
+      actionpack (>= 7.0)
+      activesupport (>= 7.0)
+      railties (>= 7.0)
       rspec-core (~> 3.13)
       rspec-expectations (~> 3.13)
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
-    rspec-support (3.13.1)
-    rubocop (1.66.1)
+    rspec-support (3.13.2)
+    rubocop (1.75.1)
       json (~> 2.3)
-      language_server-protocol (>= 3.17.0)
+      language_server-protocol (~> 3.17.0.2)
+      lint_roller (~> 1.1.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 2.4, < 3.0)
-      rubocop-ast (>= 1.32.2, < 2.0)
+      regexp_parser (>= 2.9.3, < 3.0)
+      rubocop-ast (>= 1.43.0, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.32.3)
-      parser (>= 3.3.1.0)
-    rubocop-capybara (2.21.0)
-      rubocop (~> 1.41)
-    rubocop-factory_bot (2.26.1)
-      rubocop (~> 1.61)
-    rubocop-performance (1.22.1)
-      rubocop (>= 1.48.1, < 2.0)
-      rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rails (2.26.2)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.43.0)
+      parser (>= 3.3.7.2)
+      prism (~> 1.4)
+    rubocop-capybara (2.22.1)
+      lint_roller (~> 1.1)
+      rubocop (~> 1.72, >= 1.72.1)
+    rubocop-factory_bot (2.27.1)
+      lint_roller (~> 1.1)
+      rubocop (~> 1.72, >= 1.72.1)
+    rubocop-performance (1.24.0)
+      lint_roller (~> 1.1)
+      rubocop (>= 1.72.1, < 2.0)
+      rubocop-ast (>= 1.38.0, < 2.0)
+    rubocop-rails (2.30.3)
       activesupport (>= 4.2.0)
+      lint_roller (~> 1.1)
       rack (>= 1.1)
-      rubocop (>= 1.52.0, < 2.0)
-      rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rspec (3.0.5)
-      rubocop (~> 1.61)
-    rubocop-rspec_rails (2.30.0)
-      rubocop (~> 1.61)
-      rubocop-rspec (~> 3, >= 3.0.1)
+      rubocop (>= 1.72.1, < 2.0)
+      rubocop-ast (>= 1.38.0, < 2.0)
+    rubocop-rspec (3.5.0)
+      lint_roller (~> 1.1)
+      rubocop (~> 1.72, >= 1.72.1)
+    rubocop-rspec_rails (2.31.0)
+      lint_roller (~> 1.1)
+      rubocop (~> 1.72, >= 1.72.1)
+      rubocop-rspec (~> 3.5)
     ruby-graphviz (1.2.5)
       rexml
     ruby-prof (1.7.1)
@@ -516,7 +526,7 @@ GEM
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
       websocket (~> 1.0)
-    set (1.1.0)
+    set (1.1.1)
     shoulda (4.0.0)
       shoulda-context (~> 2.0)
       shoulda-matchers (~> 4.0)
@@ -563,9 +573,11 @@ GEM
       rails (>= 3.0.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.6.0)
+    unicode-display_width (3.1.4)
+      unicode-emoji (~> 4.0, >= 4.0.4)
+    unicode-emoji (4.0.4)
     uniform_notifier (1.16.0)
-    uuidtools (2.2.0)
+    uuidtools (3.0.0)
     vite_rails (3.0.19)
       railties (>= 5.1, < 9)
       vite_ruby (~> 3.0, >= 3.2.2)

app/api/core/endpoint/basic_handler/actions.rb

@@ -59,7 +59,7 @@ def check_request_io_class!(request)
     raise StandardError, 'Need an I/O class for this request' if request.io.nil?
   end
 
-  def does_not_require_an_io_class
+  def not_require_an_io_class?
     singleton_class.class_eval('def check_request_io_class!(_) ; end', __FILE__, __LINE__)
   end
 

app/api/core/endpoint/basic_handler/actions/bound.rb

@@ -17,5 +17,5 @@ def bound_#{name}(name, *args, &block)
   end
 
   delegate_to_bound_handler :action_guard
-  delegate_to_bound_handler :action_does_not_require_an_io_class, :does_not_require_an_io_class
+  delegate_to_bound_handler :action_not_require_an_io_class?, :not_require_an_io_class?
 end

app/api/core/endpoint/basic_handler/associations/belongs_to.rb

@@ -33,7 +33,7 @@ def initialize(endpoint_helper, children = nil)
       delegate :endpoint_details, to: :@endpoint
 
       def merge(node)
-        super(node) do |children|
+        super do |children|
           self.class.new(@endpoint_helper, children) # prettier-ignore
         end
       end

app/api/core/io/json/grammar.rb

@@ -130,7 +130,7 @@
     end
 
     def merge(node)
-      super(node) do |children|
+      super do |children|
         self.class.new(@name, children) # prettier-ignore
       end
     end

app/api/endpoints/uuids.rb

@@ -113,7 +113,7 @@ class << response
         'url' => request.service.api_path(uuid.external_id)
       }
     end
-    bound_action_does_not_require_an_io_class(:lookup)
+    bound_action_not_require_an_io_class?(:lookup)
 
     # Handles trying to find multiple resources
     bind_action(:create, to: 'bulk', as: :bulk) do |_, request, response|
@@ -135,6 +135,6 @@ class << response
         }
       end
     end
-    bound_action_does_not_require_an_io_class(:bulk)
+    bound_action_not_require_an_io_class?(:bulk)
   end
 end

app/controllers/admin/studies_controller.rb

@@ -36,7 +36,7 @@
   def filter # rubocop:todo Metrics/CyclomaticComplexity
     filter_conditions = { approved: false } if params[:filter][:by] == 'not approved' unless params[:filter].nil?
 
-    if params[:filter][:by] == 'not approved' || params[:filter][:by] == 'all'
+    if ['not approved', 'all'].include?(params[:filter][:by])
       @studies = Study.where(filter_conditions).alphabetical.select { |p| p.name.include? params[:q] }
     end
 

app/controllers/plates_controller.rb

@@ -65,7 +65,7 @@ def set_barcode_printers
   end
 
   def tube_rack_barcodes
-    return [] unless params.dig(:plates).dig(:source_plates)
+    return [] unless params.dig(:plates, :source_plates)
 
     params[:plates][:source_plates].split(/[\s,]+/)
   end