Merge branch 'develop' into develop-Y24-190

.release-version

@@ -1 +1 @@
-14.42.2
+14.43.3

.rubocop_todo.yml

@@ -64,15 +64,14 @@ Lint/DuplicateBranch:
     - 'features/support/step_definitions/order_steps.rb'
     - 'test/shoulda_macros/sanger_macros.rb'
 
-# Offense count: 9
+# Offense count: 8
 Lint/DuplicateMethods:
   Exclude:
     - 'app/models/accessionable/submission.rb'
     - 'app/models/aliquot_indexer.rb'
     - 'app/models/lib_pool_norm_tube_generator.rb'
     - 'app/models/stock_stamper.rb'
     - 'lib/accession/accession/tag.rb'
-    - 'lib/label_printer/label_printer/label.rb'
 
 # Offense count: 66
 # Configuration parameters: AllowComments, AllowEmptyLambdas.
@@ -146,7 +145,7 @@ Lint/IneffectiveAccessModifier:
     - 'app/models/event_sender.rb'
     - 'lib/authenticated_system.rb'
 
-# Offense count: 29
+# Offense count: 15
 # Configuration parameters: AllowedParentClasses.
 Lint/MissingSuper:
   Exclude:
@@ -161,20 +160,6 @@ Lint/MissingSuper:
     - 'app/models/unsuitable_accession_service.rb'
     - 'app/uat_actions/uat_actions.rb'
     - 'lib/lab_where_client.rb'
-    - 'lib/label_printer/label_printer/label/asset_plate.rb'
-    - 'lib/label_printer/label_printer/label/asset_plate_double.rb'
-    - 'lib/label_printer/label_printer/label/asset_tube.rb'
-    - 'lib/label_printer/label_printer/label/batch_plate.rb'
-    - 'lib/label_printer/label_printer/label/batch_plate_double.rb'
-    - 'lib/label_printer/label_printer/label/batch_tube.rb'
-    - 'lib/label_printer/label_printer/label/multiplexed_tube.rb'
-    - 'lib/label_printer/label_printer/label/plate_creator.rb'
-    - 'lib/label_printer/label_printer/label/plate_to_tubes.rb'
-    - 'lib/label_printer/label_printer/label/robot_beds.rb'
-    - 'lib/label_printer/label_printer/label/sample_manifest_multiplex.rb'
-    - 'lib/label_printer/label_printer/label/sample_manifest_plate.rb'
-    - 'lib/label_printer/label_printer/label/sample_manifest_plate_double.rb'
-    - 'lib/label_printer/label_printer/label/sample_manifest_tube.rb'
     - 'test/unit/tasks/plate_transfer_task_test.rb'
 
 # Offense count: 1
@@ -190,13 +175,12 @@ Lint/NonLocalExitFromIterator:
     - 'app/api/core/io/json/grammar.rb'
     - 'app/models/create_asset_request.rb'
 
-# Offense count: 7
+# Offense count: 6
 # This cop supports safe autocorrection (--autocorrect).
 Lint/RedundantCopDisableDirective:
   Exclude:
     - 'app/controllers/npg_actions/assets_controller.rb'
     - 'app/helpers/submissions_helper.rb'
-    - 'app/heron/factories/event.rb'
     - 'app/models/barcode/format_handlers.rb'
     - 'app/models/illumina_htp/initial_stock_tube_purpose.rb'
     - 'app/models/metadata/form_builder.rb'
@@ -254,7 +238,7 @@ Lint/UselessAccessModifier:
     - 'app/models/event_sender.rb'
     - 'app/models/product_criteria/basic.rb'
 
-# Offense count: 67
+# Offense count: 66
 # This cop supports safe autocorrection (--autocorrect).
 # Configuration parameters: AutoCorrect.
 Lint/UselessAssignment:
@@ -300,7 +284,6 @@ Lint/UselessAssignment:
     - 'features/support/step_definitions/study_report_steps.rb'
     - 'features/support/step_definitions/study_steps.rb'
     - 'features/support/step_definitions/tube_steps.rb'
-    - 'lib/label_printer/label_printer/label/batch_tube.rb'
     - 'spec/features/sample_manifests/track_sample_manifest_updates_spec.rb'
     - 'spec/lib/accession/tag_list_spec.rb'
     - 'spec/models/study_spec.rb'
@@ -466,12 +449,12 @@ Naming/VariableNumber:
     - 'spec/features/retrospective_failure_spec.rb'
     - 'spec/features/sample_manifests/track_sample_manifest_updates_spec.rb'
     - 'spec/features/tag_layout_template_spec.rb'
-    - 'spec/heron/factories/tube_rack_spec.rb'
     - 'spec/lib/accession/tag_spec.rb'
     - 'spec/models/api/messages/flowcell_io_spec.rb'
     - 'spec/models/api/messages/pac_bio_run_io_spec.rb'
     - 'spec/models/api/messages/pac_bio_run_with_tag2_io_spec.rb'
     - 'spec/models/bulk_submission_spec.rb'
+    - 'spec/models/heron/factories/tube_rack_spec.rb'
     - 'spec/models/labware_spec.rb'
     - 'spec/models/labwhere_reception_spec.rb'
     - 'spec/models/linear_submission_spec.rb'
@@ -789,9 +772,9 @@ RSpec/ExampleWording:
     - 'spec/bulk_submission_excel/configuration_spec.rb'
     - 'spec/bulk_submission_excel/data_worksheet_spec.rb'
     - 'spec/features/gpl207_bug_incorrect_submission_id_on_transfer_spec.rb'
-    - 'spec/heron/factories/sample_spec.rb'
-    - 'spec/heron/factories/tube_rack_spec.rb'
     - 'spec/lib/accession/study_spec.rb'
+    - 'spec/models/heron/factories/sample_spec.rb'
+    - 'spec/models/heron/factories/tube_rack_spec.rb'
     - 'spec/models/plate/quad_creator_spec.rb'
     - 'spec/models/qc_result/qc_result_factory_spec.rb'
     - 'spec/models/qcable_creator_spec.rb'
@@ -956,10 +939,6 @@ RSpec/MultipleExpectations:
     - 'spec/controllers/submissions_controller_spec.rb'
     - 'spec/controllers/tag_sets_controller_spec.rb'
     - 'spec/helpers/compound_sample_helper_spec.rb'
-    - 'spec/heron/factories/concerns/contents_spec.rb'
-    - 'spec/heron/factories/plate_spec.rb'
-    - 'spec/heron/factories/sample_spec.rb'
-    - 'spec/heron/factories/tube_spec.rb'
     - 'spec/jobs/export_pool_xp_to_traction_job_spec.rb'
     - 'spec/lib/accession/accessionable_spec.rb'
     - 'spec/lib/accession/configuration_spec.rb'
@@ -1003,6 +982,10 @@ RSpec/MultipleExpectations:
     - 'spec/models/cherrypick_request_spec.rb'
     - 'spec/models/cherrypick_task/control_locator_spec.rb'
     - 'spec/models/comment_spec.rb'
+    - 'spec/models/heron/factories/concerns/contents_spec.rb'
+    - 'spec/models/heron/factories/plate_spec.rb'
+    - 'spec/models/heron/factories/sample_spec.rb'
+    - 'spec/models/heron/factories/tube_spec.rb'
     - 'spec/models/illumina_htp/requests/gbs_request_spec.rb'
     - 'spec/models/illumina_htp/requests/heron_request_spec.rb'
     - 'spec/models/illumina_htp/requests/heron_tailed_request_spec.rb'
@@ -1211,8 +1194,6 @@ RSpec/MultipleMemoizedHelpers:
     - 'spec/features/studies/view_study_request_links_spec.rb'
     - 'spec/features/submissions/bulk_submissions_spec.rb'
     - 'spec/helpers/batches_helper_spec.rb'
-    - 'spec/heron/factories/concerns/contents_spec.rb'
-    - 'spec/heron/factories/plate_spec.rb'
     - 'spec/insdc/import_countries_spec.rb'
     - 'spec/jobs/export_pool_xp_to_traction_job_spec.rb'
     - 'spec/lib/label_printer/batch_plate_spec.rb'
@@ -1236,6 +1217,8 @@ RSpec/MultipleMemoizedHelpers:
     - 'spec/models/bulk_submission_spec.rb'
     - 'spec/models/comment_spec.rb'
     - 'spec/models/external_release_event_spec.rb'
+    - 'spec/models/heron/factories/concerns/contents_spec.rb'
+    - 'spec/models/heron/factories/plate_spec.rb'
     - 'spec/models/illumina_htp/initial_stock_tube_purpose_spec.rb'
     - 'spec/models/labware_spec.rb'
     - 'spec/models/linear_submission_spec.rb'
@@ -1401,12 +1384,12 @@ RSpec/NestedGroups:
     - 'spec/features/sample_manifests/uploader_for_manifests_with_tag_sequences_spec.rb'
     - 'spec/features/submissions/bulk_submissions_spec.rb'
     - 'spec/helpers/assets_helper_spec.rb'
-    - 'spec/heron/factories/concerns/contents_spec.rb'
-    - 'spec/heron/factories/plate_spec.rb'
-    - 'spec/heron/factories/sample_spec.rb'
     - 'spec/models/api/messages/flowcell_io_spec.rb'
     - 'spec/models/broadcast_event/broadcast_event_spec.rb'
     - 'spec/models/broadcast_event/plate_cherrypicked_spec.rb'
+    - 'spec/models/heron/factories/concerns/contents_spec.rb'
+    - 'spec/models/heron/factories/plate_spec.rb'
+    - 'spec/models/heron/factories/sample_spec.rb'
     - 'spec/models/illumina_htp/initial_stock_tube_purpose_spec.rb'
     - 'spec/models/labware_spec.rb'
     - 'spec/models/linear_submission_spec.rb'
@@ -1587,7 +1570,7 @@ Rails/CompactBlank:
     - 'features/support/step_definitions/delayed_job_steps.rb'
     - 'lib/event_factory.rb'
 
-# Offense count: 15
+# Offense count: 13
 # This cop supports unsafe autocorrection (--autocorrect-all).
 # Configuration parameters: EnforcedStyle, AllowToTime.
 # SupportedStyles: strict, flexible
@@ -1598,8 +1581,6 @@ Rails/Date:
     - 'app/models/event/sample_manifest_event.rb'
     - 'app/models/event/scanned_into_lab_event.rb'
     - 'app/models/event_sender.rb'
-    - 'lib/label_printer/label_printer/label/base_plate.rb'
-    - 'lib/label_printer/label_printer/label/base_tube.rb'
     - 'test/lib/label_printer/plate_creator_test.rb'
     - 'test/lib/label_printer/plate_to_tube_test.rb'
     - 'test/lib/label_printer/print_job_test.rb'
@@ -1614,7 +1595,7 @@ Rails/DeprecatedActiveModelErrorsMethods:
   Exclude:
     - 'app/controllers/batches_controller.rb'
 
-# Offense count: 34
+# Offense count: 35
 # This cop supports safe autocorrection (--autocorrect).
 # Configuration parameters: EnforcedStyle.
 # SupportedStyles: slashes, arguments
@@ -1688,7 +1669,6 @@ Rails/HasManyOrHasOneDependent:
     - 'app/models/specific_tube_creation.rb'
     - 'app/models/stamp.rb'
     - 'app/models/study.rb'
-    - 'app/models/study/metadata.rb'
     - 'app/models/study_type.rb'
     - 'app/models/submission_pool.rb'
     - 'app/models/submission_template.rb'
@@ -1949,7 +1929,7 @@ Style/ExplicitBlockArgument:
     - 'app/models/submission/flexible_request_graph.rb'
     - 'features/support/step_definitions/web_steps.rb'
 
-# Offense count: 9
+# Offense count: 7
 # This cop supports safe autocorrection (--autocorrect).
 # Configuration parameters: EnforcedStyle.
 # SupportedStyles: format, sprintf, percent
@@ -1959,10 +1939,9 @@ Style/FormatString:
     - 'app/models/map.rb'
     - 'features/support/step_definitions/4560014_refactoring_properties_descriptors_etc_to_table_columns_steps.rb'
     - 'features/support/step_definitions/samples_steps.rb'
-    - 'lib/label_printer/label_printer/pmb_client.rb'
     - 'test/unit/fluidigm_plate_test.rb'
 
-# Offense count: 9
+# Offense count: 5
 # This cop supports safe autocorrection (--autocorrect).
 # Configuration parameters: EnforcedStyle, MaxUnannotatedPlaceholdersAllowed, AllowedMethods, AllowedPatterns.
 # SupportedStyles: annotated, template, unannotated
@@ -1972,7 +1951,6 @@ Style/FormatStringToken:
     - 'app/helpers/plates_helper.rb'
     - 'app/models/request_type/validation.rb'
     - 'app/uat_actions/uat_actions/generate_tag_group.rb'
-    - 'lib/label_printer/label_printer/pmb_client.rb'
     - 'lib/views_schema.rb'
 
 # Offense count: 1
@@ -1990,7 +1968,7 @@ Style/GlobalStdStream:
     - 'config/environments/production.rb'
     - 'lib/tasks/limber_dev.rake'
 
-# Offense count: 42
+# Offense count: 40
 # This cop supports safe autocorrection (--autocorrect).
 # Configuration parameters: MinBodyLength, AllowConsecutiveConditionals.
 Style/GuardClause:
@@ -2028,7 +2006,6 @@ Style/GuardClause:
     - 'lib/accession/accession/sample.rb'
     - 'lib/accession/accession/submission.rb'
     - 'lib/authenticated_system.rb'
-    - 'lib/label_printer/label_printer/pmb_client.rb'
     - 'lib/migration_extensions/db_table_archiver.rb'
     - 'lib/tasks/add_templates_and_printers_to_pmb.rake'
 
@@ -2138,15 +2115,14 @@ Style/NestedModifier:
     - 'app/uploaders/polymorphic_uploader.rb'
     - 'features/support/step_definitions/display_submitted_at_inbox_pipeline_steps.rb'
 
-# Offense count: 3
+# Offense count: 2
 # This cop supports safe autocorrection (--autocorrect).
 # Configuration parameters: AllowedMethods.
 # AllowedMethods: be, be_a, be_an, be_between, be_falsey, be_kind_of, be_instance_of, be_truthy, be_within, eq, eql, end_with, include, match, raise_error, respond_to, start_with
 Style/NestedParenthesizedCalls:
   Exclude:
     - 'app/controllers/uuids_controller.rb'
     - 'app/models/parsers/bioanalysis_csv_parser.rb'
-    - 'lib/label_printer/label_printer/pmb_client.rb'
 
 # Offense count: 2
 # This cop supports safe autocorrection (--autocorrect).
@@ -2156,13 +2132,12 @@ Style/NonNilCheck:
     - 'test/unit/product_criteria_test.rb'
     - 'test/unit/product_test.rb'
 
-# Offense count: 20
+# Offense count: 18
 # This cop supports safe autocorrection (--autocorrect).
 Style/Not:
   Exclude:
     - 'app/api/core/endpoint/basic_handler.rb'
     - 'app/api/model_extensions/order.rb'
-    - 'app/controllers/assets/plate_layout.rb'
     - 'app/controllers/studies_controller.rb'
     - 'app/models/pipeline/batch_validation.rb'
     - 'app/models/request/change_decision.rb'
@@ -2192,7 +2167,7 @@ Style/NumericPredicate:
     - 'app/models/tag_layout/walk_wells_by_pools.rb'
     - 'app/models/well_attribute.rb'
     - 'features/support/step_definitions/samples_steps.rb'
-    - 'lib/deployed_version.rb'
+    - 'lib/deployed.rb'
     - 'lib/submission_serializer.rb'
     - 'test/shoulda_macros/sanger_macros/resource_test.rb'
 
@@ -2226,7 +2201,7 @@ Style/OrAssignment:
     - 'lib/informatics/lib/informatics/controller_helper.rb'
     - 'lib/informatics/lib/informatics/view/menu/list.rb'
 
-# Offense count: 72
+# Offense count: 71
 # This cop supports safe autocorrection (--autocorrect).
 Style/ParallelAssignment:
   Exclude:
@@ -2244,7 +2219,6 @@ Style/ParallelAssignment:
     - 'app/api/core/io/json/stream.rb'
     - 'app/api/core/io/list.rb'
     - 'app/api/core/service.rb'
-    - 'app/controllers/assets/plate_layout.rb'
     - 'app/controllers/requests_controller.rb'
     - 'app/controllers/studies_controller.rb'
     - 'app/helpers/application_helper.rb'
@@ -2352,14 +2326,11 @@ Style/SafeNavigation:
     - 'lib/event_factory.rb'
     - 'test/unit/qc_report_file_test.rb'
 
-# Offense count: 7
+# Offense count: 3
 # This cop supports unsafe autocorrection (--autocorrect-all).
 Style/SingleArgumentDig:
   Exclude:
     - 'app/controllers/plates_controller.rb'
-    - 'app/heron/factories/concerns/eventful.rb'
-    - 'app/heron/factories/event.rb'
-    - 'app/heron/factories/sample.rb'
     - 'spec/requests/api/v2/heron/plates_spec.rb'
 
 # Offense count: 8
@@ -2395,7 +2366,7 @@ Style/StderrPuts:
     - 'lib/volume_check.rb'
     - 'script/autospec'
 
-# Offense count: 75
+# Offense count: 74
 # This cop supports unsafe autocorrection (--autocorrect-all).
 # Configuration parameters: Mode.
 Style/StringConcatenation:
@@ -2414,7 +2385,6 @@ Style/StringConcatenation:
     - 'features/support/step_definitions/study_steps.rb'
     - 'lib/control_request_type_creation.rb'
     - 'lib/informatics/lib/informatics/application.rb'
-    - 'lib/label_printer/label_printer/pmb_client.rb'
     - 'lib/tasks/cucumber.rake'
     - 'script/dbconsole'
     - 'script/performance/benchmarker'

app/api/io/tube/purpose.rb

@@ -1,5 +1,4 @@
 # frozen_string_literal: true
-require_dependency 'tube/purpose'
 
 # Controls API V1 IO for Tube
 class Io::Tube::Purpose < Core::Io::Base

app/controllers/api/v2/concerns/disable_csrf_token_authentication.rb

@@ -10,7 +10,7 @@ module Concerns
       #
       # NB. APi key authentication is still in place, so the API is still secure.
       # Longer term solution is to rework the security of the v2 API.
-      module DisableCSRFTokenAuthentication
+      module DisableCsrfTokenAuthentication
         extend ActiveSupport::Concern
 
         included { skip_before_action :verify_authenticity_token }

app/controllers/application_controller.rb

@@ -1,5 +1,4 @@
 # frozen_string_literal: true
-require 'exceptions'
 require 'authenticated_system'
 
 # Filters added to this controller apply to all controllers in the application.