Merge pull request #4030 from sanger/depfu/update/group/rails-7.0.8.1

🚨 [security] [ruby] Update rails 6.1.7.10 → 7.0.8.1 (major)

Gemfile

@@ -4,7 +4,7 @@ source 'https://rubygems.org'
 
 group :default do
   gem 'bootsnap'
-  gem 'rails', '~> 6.1.7'
+  gem 'rails', '~> 7.0.8'
 
   # Fix incompatibility with between Ruby 3.1 and Psych 4 (used for yaml)
   # see https://stackoverflow.com/a/71192990

Gemfile.lock

@@ -34,70 +34,76 @@ GEM
   specs:
     aasm (5.5.0)
       concurrent-ruby (~> 1.0)
-    actioncable (6.1.7.10)
-      actionpack (= 6.1.7.10)
-      activesupport (= 6.1.7.10)
+    actioncable (7.0.8.1)
+      actionpack (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (6.1.7.10)
-      actionpack (= 6.1.7.10)
-      activejob (= 6.1.7.10)
-      activerecord (= 6.1.7.10)
-      activestorage (= 6.1.7.10)
-      activesupport (= 6.1.7.10)
+    actionmailbox (7.0.8.1)
+      actionpack (= 7.0.8.1)
+      activejob (= 7.0.8.1)
+      activerecord (= 7.0.8.1)
+      activestorage (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
       mail (>= 2.7.1)
-    actionmailer (6.1.7.10)
-      actionpack (= 6.1.7.10)
-      actionview (= 6.1.7.10)
-      activejob (= 6.1.7.10)
-      activesupport (= 6.1.7.10)
+      net-imap
+      net-pop
+      net-smtp
+    actionmailer (7.0.8.1)
+      actionpack (= 7.0.8.1)
+      actionview (= 7.0.8.1)
+      activejob (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
       mail (~> 2.5, >= 2.5.4)
+      net-imap
+      net-pop
+      net-smtp
       rails-dom-testing (~> 2.0)
-    actionpack (6.1.7.10)
-      actionview (= 6.1.7.10)
-      activesupport (= 6.1.7.10)
-      rack (~> 2.0, >= 2.0.9)
+    actionpack (7.0.8.1)
+      actionview (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
+      rack (~> 2.0, >= 2.2.4)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
     actionpack-xml_parser (2.0.1)
       actionpack (>= 5.0)
       railties (>= 5.0)
-    actiontext (6.1.7.10)
-      actionpack (= 6.1.7.10)
-      activerecord (= 6.1.7.10)
-      activestorage (= 6.1.7.10)
-      activesupport (= 6.1.7.10)
+    actiontext (7.0.8.1)
+      actionpack (= 7.0.8.1)
+      activerecord (= 7.0.8.1)
+      activestorage (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
+      globalid (>= 0.6.0)
       nokogiri (>= 1.8.5)
-    actionview (6.1.7.10)
-      activesupport (= 6.1.7.10)
+    actionview (7.0.8.1)
+      activesupport (= 7.0.8.1)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activejob (6.1.7.10)
-      activesupport (= 6.1.7.10)
+    activejob (7.0.8.1)
+      activesupport (= 7.0.8.1)
       globalid (>= 0.3.6)
-    activemodel (6.1.7.10)
-      activesupport (= 6.1.7.10)
-    activerecord (6.1.7.10)
-      activemodel (= 6.1.7.10)
-      activesupport (= 6.1.7.10)
+    activemodel (7.0.8.1)
+      activesupport (= 7.0.8.1)
+    activerecord (7.0.8.1)
+      activemodel (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
     activerecord-import (1.7.0)
       activerecord (>= 4.2)
-    activestorage (6.1.7.10)
-      actionpack (= 6.1.7.10)
-      activejob (= 6.1.7.10)
-      activerecord (= 6.1.7.10)
-      activesupport (= 6.1.7.10)
+    activestorage (7.0.8.1)
+      actionpack (= 7.0.8.1)
+      activejob (= 7.0.8.1)
+      activerecord (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (6.1.7.10)
+    activesupport (7.0.8.1)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
       tzinfo (~> 2.0)
-      zeitwerk (~> 2.3)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
     after_commit_everywhere (1.4.0)
@@ -279,7 +285,7 @@ GEM
     mustermann (3.0.0)
       ruby2_keywords (~> 0.0.1)
     mysql2 (0.5.6)
-    net-imap (0.5.0)
+    net-imap (0.5.1)
       date
       net-protocol
     net-ldap (0.19.0)
@@ -330,21 +336,20 @@ GEM
       rack
     rack-test (2.1.0)
       rack (>= 1.3)
-    rails (6.1.7.10)
-      actioncable (= 6.1.7.10)
-      actionmailbox (= 6.1.7.10)
-      actionmailer (= 6.1.7.10)
-      actionpack (= 6.1.7.10)
-      actiontext (= 6.1.7.10)
-      actionview (= 6.1.7.10)
-      activejob (= 6.1.7.10)
-      activemodel (= 6.1.7.10)
-      activerecord (= 6.1.7.10)
-      activestorage (= 6.1.7.10)
-      activesupport (= 6.1.7.10)
+    rails (7.0.8.1)
+      actioncable (= 7.0.8.1)
+      actionmailbox (= 7.0.8.1)
+      actionmailer (= 7.0.8.1)
+      actionpack (= 7.0.8.1)
+      actiontext (= 7.0.8.1)
+      actionview (= 7.0.8.1)
+      activejob (= 7.0.8.1)
+      activemodel (= 7.0.8.1)
+      activerecord (= 7.0.8.1)
+      activestorage (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
       bundler (>= 1.15.0)
-      railties (= 6.1.7.10)
-      sprockets-rails (>= 2.0.0)
+      railties (= 7.0.8.1)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
       actionview (>= 5.0.1.rc1)
@@ -362,12 +367,13 @@ GEM
       loofah (~> 2.21)
       nokogiri (~> 1.14)
     rails-perftest (0.0.7)
-    railties (6.1.7.10)
-      actionpack (= 6.1.7.10)
-      activesupport (= 6.1.7.10)
+    railties (7.0.8.1)
+      actionpack (= 7.0.8.1)
+      activesupport (= 7.0.8.1)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
+      zeitwerk (~> 2.5)
     rainbow (3.1.1)
     rake (13.2.1)
     rb-fsevent (0.11.2)
@@ -491,13 +497,6 @@ GEM
     sorted_set (1.0.3)
       rbtree
       set (~> 1.0)
-    sprockets (4.2.1)
-      concurrent-ruby (~> 1.0)
-      rack (>= 2.2.4, < 4)
-    sprockets-rails (3.5.2)
-      actionpack (>= 6.1)
-      activesupport (>= 6.1)
-      sprockets (>= 3.0.0)
     ssrf_filter (1.1.2)
     syntax_tree (6.2.0)
       prettier_print (>= 1.2.0)
@@ -516,7 +515,7 @@ GEM
     thor (1.3.2)
     tilt (2.4.0)
     timecop (0.9.10)
-    timeout (0.4.1)
+    timeout (0.4.2)
     traceroute (0.8.1)
       rails (>= 3.0.0)
     tzinfo (2.0.6)
@@ -610,7 +609,7 @@ DEPENDENCIES
   rack-acceptable
   rack-cors
   rack-mini-profiler
-  rails (~> 6.1.7)
+  rails (~> 7.0.8)
   rails-controller-testing
   rails-erd
   rails-perftest

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

@@ -63,7 +63,7 @@ def encode(object, options = {}) # rubocop:todo Metrics/CyclomaticComplexity
       when ActiveSupport::TimeWithZone
         string_encode(object.to_s)
       when Time
-        string_encode(object.to_s(:compatible))
+        string_encode(object.to_fs(:compatible))
       when Hash
         hash_encode(object, options)
       when ZIPPABLE

app/models/accession_service.rb

@@ -122,9 +122,9 @@ def submit(user, *accessionables) # rubocop:todo Metrics/CyclomaticComplexity
       ensure
         files.each(&:close) # not really necessary but recommended
       end
-
-      return accessionables.map(&:accession_number) # rubocop:todo Rails/TransactionExitStatement
     end
+
+    accessionables.map(&:accession_number)
   end
 
   # rubocop:enable Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/BlockLength, Metrics/AbcSize

app/models/bait_library_type.rb

@@ -7,7 +7,7 @@ class BaitLibraryType < ApplicationRecord
 
   # category is used for billing, to differentiate between products with Custom and Standard bait libraries
   # Automated billing report stuff has been removed, but this is still useful downstream so we'll keep it
-  enum category: { standard: 0, custom: 1 }
+  enum :category, { standard: 0, custom: 1 }
 
   has_many :bait_libraries
 

app/models/barcode.rb

@@ -26,7 +26,8 @@ class Barcode < ApplicationRecord
   after_commit :broadcast_barcode
 
   # Caution! Do not adjust the index of existing formats.
-  enum format: {
+  enum :format,
+       {
          sanger_ean13: 0,
          infinium: 1,
          fluidigm: 2,

app/models/barcode_printer.rb

@@ -24,10 +24,10 @@ class BarcodePrinter < ApplicationRecord
   delegate :printer_type_id, to: :barcode_printer_type
 
   # this is for Limber. Moving it over to pmb v2 would allow this to be removed.
-  enum print_service: { 'PMB' => 0, 'SPrint' => 1 }
+  enum :print_service, { 'PMB' => 0, 'SPrint' => 1 }
 
   # it would possibly make more sense to have squix as 0 but this fits with PMB but creates no dependency
-  enum printer_type: { squix: 1, toshiba: 0 }
+  enum :printer_type, { squix: 1, toshiba: 0 }
 
   def plate384_printer?
     barcode_printer_type.name == '384 Well Plate'

app/models/failure.rb

@@ -1,11 +1,4 @@
 # frozen_string_literal: true
 class Failure < ApplicationRecord
   belongs_to :failable, polymorphic: true
-  after_create :notify_remote
-
-  def notify_remote
-    if notify_remote?
-      # Send event to Studies here
-    end
-  end
 end

app/models/insdc/country.rb

@@ -30,7 +30,7 @@ class Country < ApplicationRecord
     #   Indicates if a region is valid for selection or not
     #   @note This has been implemented as an enum for flexible extension at a later date.
     #   @return [Symbol] :valid or :invalid
-    enum validation_state: { valid: 0, invalid: 1 }, _suffix: :state
+    enum :validation_state, { valid: 0, invalid: 1 }, suffix: :state
 
     validates :name, presence: true, uniqueness: { case_sensitive: false }
     validates :sort_priority, presence: true

app/models/labware.rb

@@ -11,7 +11,7 @@ class Labware < Asset
 
   attr_reader :storage_location_service
 
-  enum retention_instruction: { destroy_after_2_years: 0, return_to_customer_after_2_years: 1, long_term_storage: 2 }
+  enum :retention_instruction, { destroy_after_2_years: 0, return_to_customer_after_2_years: 1, long_term_storage: 2 }
 
   delegate :metadata, to: :custom_metadatum_collection, allow_nil: true
 

app/models/location_report.rb

@@ -10,7 +10,7 @@ class LocationReport < ApplicationRecord
   serialize :plate_purpose_ids, Array
   serialize :barcodes, Array
   self.per_page = 20
-  enum report_type: { type_selection: 0, type_labwhere: 1 }
+  enum :report_type, { type_selection: 0, type_labwhere: 1 }
 
   # relations
   belongs_to :study, optional: true

app/models/location_report/location_report_form.rb

@@ -24,7 +24,7 @@ class LocationReport::LocationReportForm
 
   def name=(input_name)
     @name = input_name.gsub(/[^A-Za-z0-9_\-.\s]/, '').squish.gsub(/\s/, '_') if input_name.present?
-    @name = Time.current.to_formatted_s(:number) if input_name.blank?
+    @name = Time.current.to_fs(:number) if input_name.blank?
   end
 
   def location_barcode=(location_barcode)

app/models/pick_list.rb

@@ -15,7 +15,7 @@ class PickList < ApplicationRecord
   belongs_to :submission, optional: false, autosave: true
   has_many :batches, -> { distinct }, through: :submission
 
-  enum state: { pending: 0, built: 1 }
+  enum :state, { pending: 0, built: 1 }
 
   delegate :orders, to: :submission
 

app/models/plate/fluidigm_behaviour.rb

@@ -36,7 +36,6 @@ def retrieve_fluidigm_data
       # rubocop:enable Rails/TransactionExitStatement
 
       apply_fluidigm_data(FluidigmFile.new(fluidigm_data.content))
-      return true # rubocop:todo Rails/TransactionExitStatement
     end
   end
 

app/models/plate/sample_tube_factory.rb

@@ -26,10 +26,7 @@ def self.create_sample_tubes_asset_group_and_print_barcodes(plates, barcode_prin
 
     plate_barcodes = plates.map(&:barcode_number)
     asset_group =
-      AssetGroup.find_or_create_asset_group(
-        "#{plate_barcodes.join('-')} #{Time.current.to_formatted_s(:sortable)} ",
-        study
-      )
+      AssetGroup.find_or_create_asset_group("#{plate_barcodes.join('-')} #{Time.current.to_fs(:sortable)} ", study)
     plates.each do |plate|
       factory = Plate::SampleTubeFactory.new(plate)
       next if factory.wells.empty?

app/models/presenters/qc_report_presenter.rb

@@ -47,7 +47,7 @@ def new_or_all
   end
 
   def created_date
-    qc_report.created_at.to_formatted_s(:rfc822)
+    qc_report.created_at.to_fs(:rfc822)
   end
 
   def state_description

app/models/product.rb

@@ -23,6 +23,6 @@ def stock_criteria
   end
 
   def display_name
-    deprecated? ? "#{name} (Deprecated #{deprecated_at.to_formatted_s(:iso8601)})" : name
+    deprecated? ? "#{name} (Deprecated #{deprecated_at.to_fs(:iso8601)})" : name
   end
 end

app/models/qc_report.rb

@@ -168,7 +168,7 @@ def identifier_required?
   def generate_report_identifier
     return true if study.nil? || product_criteria.nil?
 
-    rid = [study.abbreviation, product_criteria.product.name, DateTime.now.to_formatted_s(:number)].compact
+    rid = [study.abbreviation, product_criteria.product.name, DateTime.now.to_fs(:number)].compact
       .join('_')
       .downcase
       .gsub(/[^\w]/, '_')

app/models/request.rb

@@ -108,7 +108,7 @@ def date_for_state(state)
   # cf. RequestType which defines how it will be fulfilled.
   # Both RequestType and Request have a purpose, with the former acting as the default for
   # the latter.
-  enum request_purpose: { standard: 1, internal: 2, qc: 3, control: 4 }
+  enum :request_purpose, { standard: 1, internal: 2, qc: 3, control: 4 }
 
   # Validations
   # On create we perform a full and complete validation.