[release] Merge Develop into Master for 14.93.4

.rubocop.yml

@@ -284,6 +284,10 @@ Style/QuotedSymbols:
   Exclude:
   - bin/*
 
+# Keep consistency across attribute writers and readers
+Style/RedundantSelf:
+  Enabled: false
+
 # Files generated by Rails
 Style/StringLiterals:
   Exclude:

.rubocop_todo.yml

@@ -1,6 +1,6 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config --no-exclude-limit`
-# on 2026-04-22 15:46:09 UTC using RuboCop version 1.86.1.
+# on 2026-05-05 14:43:06 UTC using RuboCop version 1.86.1.
 # 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
@@ -301,12 +301,11 @@ Lint/UselessOr:
     - 'app/models/qcable/statemachine.rb'
     - 'app/models/ui_helper/summary.rb'
 
-# Offense count: 11
+# Offense count: 7
 # Configuration parameters: AllowedMethods, AllowedPatterns, CountRepeatedAttributes, Max.
 Metrics/AbcSize:
   Exclude:
     - 'app/controllers/api/v2/transfers_controller.rb'
-    - 'app/controllers/studies/information_controller.rb'
     - 'app/jobs/export_pool_xp_to_traction_job.rb'
     - 'app/models/accession_service/base_service.rb'
     - 'app/sample_manifest_excel/sample_manifest_excel/manifest_type_list.rb'
@@ -334,7 +333,7 @@ Metrics/CyclomaticComplexity:
     - 'app/models/accession_service/base_service.rb'
     - 'lib/limber/helper.rb'
 
-# Offense count: 19
+# Offense count: 18
 # Configuration parameters: CountComments, Max, CountAsOne, AllowedMethods, AllowedPatterns.
 Metrics/MethodLength:
   Exclude:
@@ -617,7 +616,7 @@ RSpec/BeforeAfterAll:
     - 'spec/sample_manifest_excel/worksheet_spec.rb'
     - 'spec/sequencescape_excel/worksheet_spec.rb'
 
-# Offense count: 342
+# Offense count: 330
 # Configuration parameters: Prefixes, AllowedPatterns.
 # Prefixes: when, with, without
 RSpec/ContextWording:
@@ -649,7 +648,6 @@ RSpec/ContextWording:
     - 'spec/models/barcode_spec.rb'
     - 'spec/models/broadcast_event/lab_event_spec.rb'
     - 'spec/models/broadcast_event/qc_assay_spec.rb'
-    - 'spec/models/bulk_submission_spec.rb'
     - 'spec/models/comment_spec.rb'
     - 'spec/models/illumina_htp/initial_stock_tube_purpose_spec.rb'
     - 'spec/models/location_report_form_spec.rb'
@@ -840,7 +838,7 @@ RSpec/ExampleWording:
     - 'spec/sequencescape_excel/validation_spec.rb'
     - 'spec/sequencescape_excel/worksheet_spec.rb'
 
-# Offense count: 27
+# Offense count: 26
 RSpec/ExpectInHook:
   Exclude:
     - 'spec/controllers/labwhere_receptions_controller_spec.rb'
@@ -1197,7 +1195,7 @@ RSpec/MultipleExpectations:
     - 'spec/views/labware/show_chromium_chip_spec.rb'
     - 'spec/views/samples/index_html_erb_spec.rb'
 
-# Offense count: 243
+# Offense count: 249
 # Configuration parameters: EnforcedStyle, IgnoreSharedExamples.
 # SupportedStyles: always, named_only
 RSpec/NamedSubject:

Gemfile

@@ -4,7 +4,7 @@ source 'https://rubygems.org'
 
 group :default do
   gem 'bootsnap'
-  gem 'concurrent-ruby', '1.3.5'
+  gem 'concurrent-ruby'
   gem 'configatron'
   gem 'formtastic'
   gem 'rails', '~> 8.0.0'
@@ -21,10 +21,6 @@ group :default do
   gem 'faraday-multipart'
   gem 'rest-client' # Deprecated, but still used in some places, replace with Faraday where possible
 
-  # Fix incompatibility with between Ruby 3.1 and Psych 4 (used for yaml)
-  # see https://stackoverflow.com/a/71192990
-  gem 'psych', '< 4'
-
   # State machine
   gem 'aasm'
   gem 'after_commit_everywhere', '~> 1.0' # Required by AASM
@@ -34,7 +30,7 @@ group :default do
 
   # Provides bulk insert capabilities
   gem 'activerecord-import'
-  gem 'record_loader', git: 'https://github.com/sanger/record_loader', tag: 'v0.3.0'
+  gem 'record_loader', git: 'https://github.com/sanger/record_loader', tag: 'v1.1.0'
 
   gem 'mysql2', platforms: :mri
   gem 'will_paginate'

Gemfile.lock

@@ -16,10 +16,11 @@ GIT
 
 GIT
   remote: https://github.com/sanger/record_loader
-  revision: 238db7fa24fffee5ad413bd9cd4c6b857d1626c9
-  tag: v0.3.0
+  revision: 9e7f1b67c3eeee1895f1befc6a54682f11c02135
+  tag: v1.1.0
   specs:
-    record_loader (0.3.0)
+    record_loader (1.1.0)
+      psych (~> 5.0)
 
 GIT
   remote: https://github.com/sanger/sanger_barcode_format.git
@@ -170,7 +171,7 @@ GEM
     choice (0.2.0)
     chronic (0.10.2)
     coderay (1.1.3)
-    concurrent-ruby (1.3.5)
+    concurrent-ruby (1.3.6)
     configatron (4.5.1)
     connection_pool (2.5.5)
     crack (1.0.1)
@@ -233,7 +234,7 @@ GEM
     factory_bot_rails (6.5.1)
       factory_bot (~> 6.5)
       railties (>= 6.1.0)
-    faraday (2.14.1)
+    faraday (2.14.2)
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
@@ -244,14 +245,14 @@ GEM
     ffi (1.17.3-arm64-darwin)
     ffi (1.17.3-x86_64-darwin)
     ffi (1.17.3-x86_64-linux-gnu)
-    flipper (1.4.1)
+    flipper (1.4.2)
       concurrent-ruby (< 2)
-    flipper-active_record (1.4.1)
+    flipper-active_record (1.4.2)
       activerecord (>= 4.2, < 9)
-      flipper (~> 1.4.1)
-    flipper-ui (1.4.1)
+      flipper (~> 1.4.2)
+    flipper-ui (1.4.2)
       erubi (>= 1.0.0, < 2.0.0)
-      flipper (~> 1.4.1)
+      flipper (~> 1.4.2)
       rack (>= 1.4, < 4)
       rack-protection (>= 1.5.3, < 5.0.0)
       rack-session (>= 1.0.2, < 3.0.0)
@@ -280,16 +281,16 @@ GEM
       prism (>= 1.3.0)
       rdoc (>= 4.0.0)
       reline (>= 0.4.2)
-    json (2.19.4)
+    json (2.19.5)
     jsonapi-resources (0.9.0)
       activerecord (>= 4.1)
       concurrent-ruby
       railties (>= 4.1)
     jsonapi-resources-matchers (1.0.0)
       jsonapi-resources (>= 0.9.0)
-    knapsack_pro (9.2.3)
-      logger
+    knapsack_pro (10.0.0)
       rake
+      thor (~> 1.4)
     language_server-protocol (3.17.0.5)
     launchy (3.1.1)
       addressable (~> 2.8)
@@ -378,7 +379,9 @@ GEM
       pry (>= 0.13, < 0.17)
     pry-rails (0.3.11)
       pry (>= 0.13.0)
-    psych (3.3.4)
+    psych (5.3.1)
+      date
+      stringio
     public_suffix (7.0.5)
     puma (7.2.0)
       nio4r (~> 2.0)
@@ -499,8 +502,8 @@ GEM
       rspec-mocks (>= 3.13.0, < 5.0.0)
       rspec-support (>= 3.13.0, < 5.0.0)
     rspec-support (3.13.7)
-    ruboclean (0.7.1)
-    rubocop (1.86.1)
+    ruboclean (0.8.0)
+    rubocop (1.86.2)
       json (~> 2.3)
       language_server-protocol (~> 3.17.0.2)
       lint_roller (~> 1.1.0)
@@ -552,7 +555,7 @@ GEM
       ffi (~> 1.12)
       logger
     ruby2_keywords (0.0.5)
-    rubyzip (3.2.2)
+    rubyzip (3.3.0)
     sanger-jsonapi-resources (0.1.2)
       activerecord (>= 4.1)
       concurrent-ruby
@@ -562,7 +565,7 @@ GEM
       crass (~> 1.0.2)
       nokogiri (>= 1.16.8)
     securerandom (0.4.1)
-    selenium-webdriver (4.43.0)
+    selenium-webdriver (4.44.0)
       base64 (~> 0.2)
       logger (~> 1.4)
       rexml (~> 3.2, >= 3.2.5)
@@ -589,6 +592,7 @@ GEM
       rbtree
       set (~> 1.0)
     ssrf_filter (1.2.0)
+    stringio (3.2.0)
     syntax_tree (6.3.0)
       prettier_print (>= 1.2.0)
     syntax_tree-haml (4.0.3)
@@ -622,7 +626,7 @@ GEM
     uri (1.1.1)
     useragent (0.16.11)
     uuidtools (3.0.0)
-    vite_rails (3.10.0)
+    vite_rails (3.11.0)
       railties (>= 5.1, < 9)
       vite_ruby (~> 3.0, >= 3.2.2)
     vite_ruby (3.10.2)
@@ -680,7 +684,7 @@ DEPENDENCIES
   capybara
   carrierwave
   caxlsx
-  concurrent-ruby (= 1.3.5)
+  concurrent-ruby
   configatron
   csv (~> 3.3)
   cucumber-rails
@@ -716,7 +720,6 @@ DEPENDENCIES
   prettier_print
   pry-byebug
   pry-rails
-  psych (< 4)
   puma
   rack-acceptable
   rack-cors

app/controllers/qc_reports_controller.rb

@@ -45,12 +45,14 @@ def show # rubocop:todo Metrics/AbcSize
   def create # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
     study = Study.find_by(id: params[:qc_report][:study_id])
     exclude_existing = params[:qc_report][:exclude_existing] == '1'
+    plate_barcodes = format_plate_barcodes(params[:qc_report][:plate_barcodes_text])
     qc_report =
       QcReport.new(
         study: study,
         product_criteria: @product.stock_criteria,
         exclude_existing: exclude_existing,
-        plate_purposes: params[:qc_report][:plate_purposes].try(:reject, &:blank?)
+        plate_purposes: params[:qc_report][:plate_purposes].try(:reject, &:blank?),
+        plate_barcodes: plate_barcodes
       )
 
     if qc_report.save
@@ -64,6 +66,13 @@ def create # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
     end
   end
 
+  def format_plate_barcodes(plate_barcodes)
+    return nil if plate_barcodes.nil?
+
+    # Split the input string into an array of barcodes
+    plate_barcodes.split(/\s+/)
+  end
+
   # On form submit of a qc_file. Strictly speaking this should be an update action
   # on the qc_report itself. However we don't want to force the user to extract
   # the report identifier from the file.

app/models/broadcast_event.rb

@@ -19,7 +19,7 @@ class BroadcastEvent < ApplicationRecord
   # https://api.rubyonrails.org/classes/ActiveRecord/Inheritance/ClassMethods.html
   validates :sti_type, presence: true
 
-  serialize :properties, coder: YAML
+  serialize :properties, coder: YAML, yaml: { permitted_classes: [ActionController::Parameters] }
   self.inheritance_column = 'sti_type'
 
   broadcast_with_warren

app/models/presenters/qc_report_presenter.rb

@@ -31,7 +31,7 @@ def product_name
   end
 
   def study_name
-    qc_report.study.name
+    qc_report.study&.name || 'N/A'
   end
 
   def study_abbreviation

app/models/qc_report.rb

@@ -82,10 +82,12 @@ module ReportBehaviour
     # You can trigger a synchronous report manually by calling #generate!
     # rubocop:todo Metrics/MethodLength
     def generate_report # rubocop:todo Metrics/AbcSize
-      study.each_well_for_qc_report_in_batches(
+      Well.qc_report_in_batches(
+        study,
         exclude_existing,
         product_criteria,
-        (plate_purposes.empty? ? nil : plate_purposes)
+        (plate_purposes.empty? ? nil : plate_purposes),
+        (plate_barcodes.empty? ? nil : plate_barcodes)
       ) do |assets|
         # If there are some wells of interest, we get them in a list
         connected_wells = Well.hash_stock_with_targets(assets, product_criteria.target_plate_purposes)
@@ -128,17 +130,30 @@ def generate_report # rubocop:todo Metrics/AbcSize
   has_many :qc_metrics
 
   serialize :plate_purposes, type: Array, coder: YAML
+  serialize :plate_barcodes, type: Array, coder: YAML
 
   before_validation :generate_report_identifier, if: :identifier_required?
 
   after_create :schedule_report
 
   scope :for_report_page, ->(conditions) { order(id: :desc).where(conditions).joins(:product_criteria) }
 
-  validates :product_criteria, :study, :state, presence: true
+  validates :product_criteria, :state, presence: true
 
   validates :exclude_existing, inclusion: { in: [true, false], message: 'should be true or false.' }
 
+  validate :check_valid_plate_barcodes, if: -> { plate_barcodes.present? }
+
+  # We allow null values for study_id to allow qc_reports to be created without a study (just plate_barcodes)
+  validates :study, presence: true, unless: -> { plate_barcodes.present? }
+
+  def check_valid_plate_barcodes
+    invalid_barcodes = plate_barcodes.reject { |barcode| Plate.find_by_barcode(barcode) }
+    return unless invalid_barcodes.any?
+
+    errors.add(:plate_barcodes, "contain invalid barcodes: #{invalid_barcodes.join(', ')}")
+  end
+
   # Reports are handled asynchronously
   def schedule_report
     Delayed::Job.enqueue QcReportJob.new(id)
@@ -166,9 +181,9 @@ def identifier_required?
   # same product / study abbreviation combo within one second
   # of each other.
   def generate_report_identifier
-    return true if study.nil? || product_criteria.nil?
+    return true if product_criteria.nil?
 
-    rid = [study.abbreviation, product_criteria.product.name, DateTime.now.to_fs(:number)].compact
+    rid = [study&.abbreviation, product_criteria.product.name, DateTime.now.to_fs(:number)].compact
       .join('_')
       .downcase
       .gsub(/[^\w]/, '_')

app/models/request_type/validator.rb

@@ -104,7 +104,14 @@ def valid_options
 
   belongs_to :request_type, optional: false
   validates :request_option, :valid_options, presence: true
-  serialize :valid_options, coder: YAML
+  serialize :valid_options, coder: YAML, yaml: {
+    permitted_classes: [
+      Range,
+      RequestType::Validator::ArrayWithDefault,
+      RequestType::Validator::FlowcellTypeValidator,
+      RequestType::Validator::LibraryTypeValidator
+    ]
+  }
 
   delegate :include?, to: :valid_options
 

app/models/study.rb

@@ -446,20 +446,6 @@ def validate_ethically_approved
     false
   end
 
-  def each_well_for_qc_report_in_batches(exclude_existing, product_criteria, plate_purposes = nil)
-    # @note We include aliquots here, despite the fact they are only needed if we have to set a poor-quality flag
-    #       as in some cases failures are not as rare as you may imagine, and it can cause major performance issues.
-    base_scope =
-      Well
-        .on_plate_purpose_included(PlatePurpose.where(name: plate_purposes || STOCK_PLATE_PURPOSES))
-        .for_study_through_aliquot(self)
-        .without_blank_samples
-        .includes(:well_attribute, :aliquots, :map, samples: :sample_metadata)
-        .readonly(true)
-    scope = exclude_existing ? base_scope.without_report(product_criteria) : base_scope
-    scope.find_in_batches { |wells| yield wells }
-  end
-
   def warnings
     # These studies are now invalid, but the warning should remain until existing studies are fixed.
     if study_metadata.managed? && study_metadata.data_access_group.blank?