Merge pull request #1454 from sanger/dpl951_ruby_3

DPL-951: Upgrade to Ruby 3

.ruby-version

@@ -1 +1 @@
-2.7.8
+3.0.6

Gemfile.lock

@@ -98,7 +98,6 @@ GEM
     ast (2.4.2)
     autoprefixer-rails (10.4.7.0)
       execjs (~> 2)
-    base64 (0.1.1)
     bindex (0.8.1)
     bootsnap (1.14.0)
       msgpack (~> 1.2)
@@ -248,8 +247,8 @@ GEM
     public_suffix (5.0.0)
     puma (6.3.1)
       nio4r (~> 2.0)
-    racc (1.7.1)
-    rack (2.2.8)
+    racc (1.7.3)
+    rack (2.2.4)
     rack-mini-profiler (3.0.0)
       rack (>= 1.2.0)
     rack-proxy (0.7.4)
@@ -317,8 +316,7 @@ GEM
       rspec-mocks (~> 3.12)
       rspec-support (~> 3.12)
     rspec-support (3.12.0)
-    rubocop (1.57.1)
-      base64 (~> 0.1.1)
+    rubocop (1.57.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -329,7 +327,7 @@ GEM
       rubocop-ast (>= 1.28.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.29.0)
+    rubocop-ast (1.30.0)
       parser (>= 3.2.1.0)
     rubocop-performance (1.15.1)
       rubocop (>= 1.7.0, < 2.0)
@@ -378,8 +376,8 @@ GEM
       actionpack (>= 5.2)
       activesupport (>= 5.2)
       sprockets (>= 3.0.0)
-    state_machines (0.5.0)
-    thor (1.3.0)
+    state_machines (0.6.0)
+    thor (1.2.1)
     tilt (2.0.11)
     timeout (0.4.0)
     tzinfo (2.0.6)
@@ -460,4 +458,4 @@ DEPENDENCIES
   yard
 
 BUNDLED WITH
-   2.1.4
+   2.2.33

app/controllers/labware_controller.rb

@@ -6,7 +6,7 @@
 # show => Looks up the presenter for the giver purpose and renders the appropriate show page
 # update => Used to update the state of a plate/tube
 class LabwareController < ApplicationController
-  UUID = /\A[\da-f]{8}(-[\da-f]{4}){3}-[\da-f]{12}\z/.freeze
+  UUID = /\A[\da-f]{8}(-[\da-f]{4}){3}-[\da-f]{12}\z/
 
   before_action :locate_labware, only: :show
   before_action :find_printers, only: [:show]

app/controllers/plates_controller.rb

@@ -36,7 +36,7 @@ def wells_to_fail
   private
 
   def locate_labware_identified_by_id
-    Sequencescape::Api::V2.plate_for_presenter(search_param) ||
+    Sequencescape::Api::V2.plate_for_presenter(**search_param) ||
       raise(ActionController::RoutingError, "Unknown resource #{search_param}")
   end
 end

app/helpers/application_helper.rb

@@ -7,7 +7,7 @@ module DeploymentInfo # rubocop:todo Style/Documentation
     rescue LoadError
       module Deployed
         VERSION_ID = 'LOCAL'
-        VERSION_STRING = "Limber LOCAL [#{ENV.fetch('RACK_ENV', nil)}]"
+        VERSION_STRING = "Limber LOCAL [#{ENV.fetch('RACK_ENV', nil)}]".freeze
       end
     end
 

app/helpers/page_helper.rb

@@ -6,7 +6,7 @@ def flash_messages
   end
 
   def grouping(_data_role, options = {}, &block)
-    tag.div(options, &block)
+    tag.div(**options, &block)
   end
   private :grouping
 
@@ -47,7 +47,7 @@ def jumbotron(jumbotron_id = nil, options = {}, &block)
     options[:class] ||= +''
     options[:class] << ' jumbotron'
     options[:id] = jumbotron_id
-    tag.div(options, &block)
+    tag.div(**options, &block)
   end
 
   # eg. state_badge('pending')

app/models/concerns/presenters/statemachine/allows_library_passing.rb

@@ -3,12 +3,15 @@
 # The state presents the library pass page for tagged assets
 module Presenters::Statemachine
   module AllowsLibraryPassing # rubocop:todo Style/Documentation
-    def control_library_passing
-      yield if libraries_passable? && !suggest_library_passing?
-    end
+    extend ActiveSupport::Concern
+    included do
+      def control_library_passing
+        yield if libraries_passable? && !suggest_library_passing?
+      end
 
-    def control_suggested_library_passing
-      yield if libraries_passable? && suggest_library_passing?
+      def control_suggested_library_passing
+        yield if libraries_passable? && suggest_library_passing?
+      end
     end
   end
 end

app/models/concerns/presenters/statemachine/does_not_allow_library_passing.rb

@@ -3,12 +3,15 @@
 # The state never presents the library pass button
 module Presenters::Statemachine
   module DoesNotAllowLibraryPassing # rubocop:todo Style/Documentation
-    def control_library_passing
-      false
-    end
+    extend ActiveSupport::Concern
+    included do
+      def control_library_passing
+        false
+      end
 
-    def control_suggested_library_passing
-      false
+      def control_suggested_library_passing
+        false
+      end
     end
   end
 end

app/models/concerns/presenters/statemachine/standard.rb

@@ -4,6 +4,7 @@
 module Presenters::Statemachine
   module Standard # rubocop:todo Style/Documentation
     extend ActiveSupport::Concern
+
     included do
       include Shared
 

app/models/concerns/presenters/statemachine/state_allows_child_creation.rb

@@ -3,8 +3,11 @@
 module Presenters::Statemachine
   # Supports creation of child assets in this state
   module StateAllowsChildCreation
-    def control_additional_creation
-      yield
+    extend ActiveSupport::Concern
+    included do
+      def control_additional_creation
+        yield
+      end
     end
   end
 end

app/models/concerns/presenters/statemachine/state_allows_single_child_creation.rb

@@ -3,8 +3,11 @@
 module Presenters::Statemachine
   # Supports creation of a single child asset in this state
   module StateAllowsSingleChildCreation
-    def control_additional_creation
-      yield if child_assets.blank?
+    extend ActiveSupport::Concern
+    included do
+      def control_additional_creation
+        yield if child_assets.blank?
+      end
     end
   end
 end

app/models/concerns/presenters/statemachine/state_does_not_allow_child_creation.rb

@@ -3,8 +3,11 @@
 module Presenters::Statemachine
   # Prevent creation of child assets while in this state
   module StateDoesNotAllowChildCreation
-    def control_additional_creation(&block)
-      # Does nothing because you can't!
+    extend ActiveSupport::Concern
+    included do
+      def control_additional_creation(&block)
+        # Does nothing because you can't!
+      end
     end
   end
 end

app/models/labware_creators/multi_stamp_tubes.rb

@@ -76,7 +76,7 @@ def parent_uuids
     end
 
     def parent_tubes
-      Sequencescape::Api::V2::Tube.find_all({ uuid: parent_uuids }, includes: 'receptacle,aliquots,aliquots.study')
+      Sequencescape::Api::V2::Tube.find_all(uuid: parent_uuids, includes: 'receptacle,aliquots,aliquots.study')
     end
 
     def transfer_material_from_parent!(child_plate)

app/models/labware_creators/pooled_tubes_by_submission_with_phi_x.rb

@@ -43,7 +43,8 @@ def tube_must_be_spiked_buffer
 
     # Only call this method if the spikedbuffer_tube_barcode is present
     def scanned_tube
-      @scanned_tube ||= Sequencescape::Api::V2::Tube.find_by(barcode: spikedbuffer_tube_barcode)
+      search_params = { barcode: spikedbuffer_tube_barcode }
+      @scanned_tube ||= Sequencescape::Api::V2::Tube.find_by(search_params)
     end
   end
 end

app/models/labware_creators/pooled_tubes_from_whole_tubes.rb

@@ -37,14 +37,12 @@ def available_tubes
       @search_options = OngoingTube.new(purpose_names: [parent.purpose.name], include_used: false)
       @search_results =
         Sequencescape::Api::V2::Tube.find_all(
-          @search_options.v2_search_parameters,
-          includes: 'purpose',
-          paginate: @search_options.v2_pagination
+          **@search_options.v2_search_parameters.merge({ includes: 'purpose', paginate: @search_options.v2_pagination })
         )
     end
 
     def parents
-      @parents ||= Sequencescape::Api::V2::Tube.find_all({ barcode: barcodes }, includes: [])
+      @parents ||= Sequencescape::Api::V2::Tube.find_all(barcode: barcodes, includes: [])
     end
 
     def parents_suitable

app/sequencescape/sequencescape/api/v2/plate.rb

@@ -29,11 +29,11 @@ class Sequencescape::Api::V2::Plate < Sequencescape::Api::V2::Base
   property :updated_at, type: :time
 
   def self.find_by(options)
-    Sequencescape::Api::V2.plate_for_presenter(options)
+    Sequencescape::Api::V2.plate_for_presenter(**options)
   end
 
   def self.find_all(options, includes: DEFAULT_INCLUDES)
-    Sequencescape::Api::V2::Plate.includes(*includes).where(options).all
+    Sequencescape::Api::V2::Plate.includes(*includes).where(**options).all
   end
 
   #

app/sequencescape/sequencescape/api/v2/sample.rb

@@ -10,7 +10,7 @@ class Sequencescape::Api::V2::Sample < Sequencescape::Api::V2::Base
   DEFAULT_INCLUDES = [].freeze
 
   def self.find_by(options, includes: DEFAULT_INCLUDES)
-    Sequencescape::Api::V2::Sample.includes(*includes).find(options).first
+    Sequencescape::Api::V2::Sample.includes(*includes).find(**options).first
   end
 
   def species

app/sequencescape/sequencescape/api/v2/sample_metadata.rb

@@ -7,6 +7,6 @@ class Sequencescape::Api::V2::SampleMetadata < Sequencescape::Api::V2::Base
   DEFAULT_INCLUDES = [].freeze
 
   def self.find_by(options, includes: DEFAULT_INCLUDES)
-    Sequencescape::Api::V2::SampleMetadata.includes(*includes).find(options).first
+    Sequencescape::Api::V2::SampleMetadata.includes(*includes).find(**options).first
   end
 end

app/sequencescape/sequencescape/api/v2/tube.rb

@@ -26,12 +26,17 @@ class Sequencescape::Api::V2::Tube < Sequencescape::Api::V2::Base
   property :created_at, type: :time
   property :updated_at, type: :time
 
-  def self.find_by(options, includes: DEFAULT_INCLUDES)
-    Sequencescape::Api::V2::Tube.includes(*includes).find(options).first
+  def self.find_by(params)
+    options = params.dup
+    includes = options.delete(:includes) || DEFAULT_INCLUDES
+    Sequencescape::Api::V2::Tube.includes(*includes).find(**options).first
   end
 
-  def self.find_all(options, includes: DEFAULT_INCLUDES, paginate: {})
-    Sequencescape::Api::V2::Tube.includes(*includes).where(options).paginate(paginate).all
+  def self.find_all(params)
+    options = params.dup
+    includes = options.delete(:includes) || DEFAULT_INCLUDES
+    paginate = options.delete(:paginate) || {}
+    Sequencescape::Api::V2::Tube.includes(*includes).where(**options).paginate(paginate).all
   end
 
   # Dummied out for the moment. But no real reason not to add it to the API.

config/initializers/cardinal_config.rb

@@ -4,7 +4,10 @@
 cardinal_pooling_csv =
   CSV.read(
     'config/cardinal_pooling.csv',
-    { encoding: 'UTF-8', headers: true, header_converters: :symbol, converters: :all }
+    encoding: 'UTF-8',
+    headers: true,
+    header_converters: :symbol,
+    converters: :all
   )
 
 Rails.application.config.cardinal_pooling_config = {}

config/initializers/settings.rb

@@ -18,7 +18,8 @@ def instance # rubocop:todo Metrics/AbcSize
       # but the creates an immutable setting object that messes with tests.
       # Immutability is good here though, so we should probably fix that.
       # Added flag onto safe_load to allow read of anchors (aliases) in yml files.
-      @instance = Hashie::Mash.new(YAML.safe_load(File.read(configuration_filename), [Symbol], [], true))
+      config_file_descriptor = File.open(configuration_filename, 'r:bom|utf-8')
+      @instance = Hashie::Mash.new(YAML.safe_load(config_file_descriptor, permitted_classes: [Symbol], aliases: true))
 
       # To view a list of pipeline groups and respective pipelines:
       # e.g. Settings.pipelines.group_by(&:pipeline_group).transform_values { |pipelines| pipelines.map(&:name) }

config/initializers/version_strings.rb

@@ -10,7 +10,7 @@ module Deployed
     ENVIRONMENT = 'Dev'
 
     VERSION_ID = 'LOCAL'
-    VERSION_STRING = "Limber LOCAL [#{Deployed::ENVIRONMENT}]"
+    VERSION_STRING = "Limber LOCAL [#{Deployed::ENVIRONMENT}]".freeze
 
     APP_NAME = 'Limber'
     RELEASE_NAME = 'DEV'

lib/colour_helper.rb

@@ -7,7 +7,7 @@
 # or black text has better contrast for a given colour.
 # https://www.w3.org/TR/WCAG20-TECHS/G17.html#G17-tests
 class ColourConverter
-  HEX = /#([0-f]{2})([0-f]{2})([0-f]{2})/.freeze
+  HEX = /#([0-f]{2})([0-f]{2})([0-f]{2})/
 
   RED_MULTIPLIER = 0.2126
   GREEN_MULTIPLIER = 0.7152

lib/deployed_version.rb

@@ -107,8 +107,8 @@ def read_file(filename)
   COMMIT = REPO_DATA.revision.presence || 'unknown_revision'
   ABBREV_COMMIT = REPO_DATA.revision_short.presence || 'unknown_revision'
 
-  VERSION_STRING = "#{APP_NAME} #{VERSION_ID} [#{ENVIRONMENT}]"
-  VERSION_COMMIT = "#{BRANCH}@#{ABBREV_COMMIT}"
+  VERSION_STRING = "#{APP_NAME} #{VERSION_ID} [#{ENVIRONMENT}]".freeze
+  VERSION_COMMIT = "#{BRANCH}@#{ABBREV_COMMIT}".freeze
   REPO_URL = REPO_DATA.release_url.presence || '#'
   HOSTNAME = Socket.gethostname
 

script/limber

@@ -3,7 +3,7 @@
 
 require 'uri'
 
-CONFIG_FILE = "#{Dir.home}/.limber.environments.yml"
+CONFIG_FILE = "#{Dir.home}/.limber.environments.yml".freeze
 
 if ARGV[0].nil?
   $stdout.puts <<-HELP

spec/features/pooling_multiple_tubes_into_one_tube_spec.rb

@@ -144,6 +144,25 @@
     stub_api_post('sub-uuid', 'submit')
   end
 
+  before do
+    allow(Sequencescape::Api::V2::Tube).to receive(:find_all)
+      .with(
+        include_used: false,
+        purpose_name: ['example-purpose'],
+        includes: 'purpose',
+        paginate: {
+          size: 30,
+          number: 1
+        }
+      )
+      .and_return([example_v2_tube, example_v2_tube2])
+
+    # Parent lookup
+    allow(Sequencescape::Api::V2::Tube).to receive(:find_all)
+      .with(barcode: [tube_barcode_1, tube_barcode_2], includes: [])
+      .and_return([example_v2_tube, example_v2_tube2])
+  end
+
   background do
     create :tube_config, name: parent_purpose_name, uuid: 'example-purpose-uuid'
     create :pooled_tube_from_tubes_purpose_config,
@@ -165,7 +184,8 @@
     # Available tubes search
     allow(Sequencescape::Api::V2::Tube).to receive(:find_all)
       .with(
-        { include_used: false, purpose_name: ['example-purpose'] },
+        include_used: false,
+        purpose_name: ['example-purpose'],
         includes: 'purpose',
         paginate: {
           size: 30,
@@ -176,7 +196,7 @@
 
     # Parent lookup
     allow(Sequencescape::Api::V2::Tube).to receive(:find_all)
-      .with({ barcode: [tube_barcode_1, tube_barcode_2] }, includes: [])
+      .with(barcode: [tube_barcode_1, tube_barcode_2], includes: [])
       .and_return([example_v2_tube, example_v2_tube2])
 
     # Old API still used when loading parent

spec/models/labware_creators/pooled_tubes_from_whole_tubes_spec.rb

@@ -100,7 +100,7 @@
 
     before do
       allow(Sequencescape::Api::V2::Tube).to receive(:find_all)
-        .with({ barcode: barcodes }, includes: [])
+        .with(barcode: barcodes, includes: [])
         .and_return([parent, parent2])
 
       tube_creation_request