[release] Merge Develop into Master for 14.87.0

.gitignore

@@ -40,6 +40,10 @@ doc/*
 .yardoc/*
 app/sample_manifest_excel/doc/
 
+# Ignore generated diagrams from Mermaid
+docs/accessioning/**/*.png
+docs/accessioning/**/*.svg
+
 # Test files
 capybara*.html
 spec/examples.txt

.release-version

@@ -1 +1 @@
-14.86.0
+14.87.0

.rubocop_todo.yml

@@ -1,6 +1,6 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config --no-exclude-limit`
-# on 2026-02-06 11:06:52 UTC using RuboCop version 1.84.1.
+# on 2026-02-06 14:12:50 UTC using RuboCop version 1.84.1.
 # 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
@@ -126,7 +126,7 @@ Lint/DuplicateMethods:
     - 'app/models/stock_stamper.rb'
     - 'lib/accession/tag.rb'
 
-# Offense count: 63
+# Offense count: 62
 # Configuration parameters: AllowComments, AllowEmptyLambdas.
 Lint/EmptyBlock:
   Exclude:
@@ -164,7 +164,6 @@ Lint/EmptyBlock:
     - 'app/api/endpoints/users.rb'
     - 'app/api/endpoints/uuids.rb'
     - 'app/api/endpoints/wells.rb'
-    - 'app/models/accessionable/sample.rb'
     - 'app/models/plate.rb'
     - 'app/models/request/library_creation.rb'
     - 'app/sequencescape_excel/sequencescape_excel/list.rb'
@@ -194,12 +193,11 @@ Lint/IneffectiveAccessModifier:
     - 'app/helpers/plates_helper.rb'
     - 'lib/authenticated_system.rb'
 
-# Offense count: 14
+# Offense count: 13
 # Configuration parameters: AllowedParentClasses.
 Lint/MissingSuper:
   Exclude:
     - 'app/models/accession_service/no_service.rb'
-    - 'app/models/accession_service/unsuitable_service.rb'
     - 'app/models/delegate_validation.rb'
     - 'app/models/request/change_decision.rb'
     - 'app/models/sample_manifest/library_tube_behaviour.rb'
@@ -240,7 +238,7 @@ Lint/StructNewOverride:
   Exclude:
     - 'app/models/product_criteria/basic.rb'
 
-# Offense count: 61
+# Offense count: 57
 # This cop supports safe autocorrection (--autocorrect).
 Lint/UselessAssignment:
   Exclude:
@@ -580,18 +578,16 @@ Performance/MethodObjectAsBlock:
     - 'features/support/step_definitions/transfer_steps.rb'
     - 'lib/tasks/report.rake'
 
-# Offense count: 3
+# Offense count: 2
 RSpec/AnyInstance:
   Exclude:
-    - 'spec/controllers/samples_controller_spec.rb'
     - 'spec/controllers/studies_controller_spec.rb'
     - 'spec/models/lane_spec.rb'
 
-# Offense count: 24
+# Offense count: 22
 RSpec/BeforeAfterAll:
   Exclude:
     - 'spec/features/sample_manifests/uploader_for_manifests_with_tag_sequences_spec.rb'
-    - 'spec/lib/accession/contact_spec.rb'
     - 'spec/models/sample_manifest/generator_spec.rb'
     - 'spec/models/sample_manifest/uploader_spec.rb'
     - 'spec/sample_manifest_excel/download_spec.rb'
@@ -603,7 +599,7 @@ RSpec/BeforeAfterAll:
     - 'spec/sample_manifest_excel/worksheet_spec.rb'
     - 'spec/sequencescape_excel/worksheet_spec.rb'
 
-# Offense count: 341
+# Offense count: 342
 # Configuration parameters: Prefixes, AllowedPatterns.
 # Prefixes: when, with, without
 RSpec/ContextWording:
@@ -684,7 +680,7 @@ RSpec/EmptyExampleGroup:
     - 'spec/models/pulldown/requests_spec.rb'
     - 'spec/models/tag_substitutions_spec.rb'
 
-# Offense count: 376
+# Offense count: 377
 # Configuration parameters: Max, CountAsOne.
 RSpec/ExampleLength:
   Exclude:
@@ -828,14 +824,13 @@ RSpec/ExampleWording:
     - 'spec/sequencescape_excel/validation_spec.rb'
     - 'spec/sequencescape_excel/worksheet_spec.rb'
 
-# Offense count: 258
+# Offense count: 257
 # Configuration parameters: AssignmentOnly.
 RSpec/InstanceVariable:
   Exclude:
     - 'spec/api/extraction_attributes_spec.rb'
     - 'spec/controllers/studies_controller_spec.rb'
     - 'spec/controllers/submissions_controller_spec.rb'
-    - 'spec/lib/accession/contact_spec.rb'
     - 'spec/models/orders/order_spec.rb'
     - 'spec/models/pulldown/requests_spec.rb'
     - 'spec/models/qc_report_spec.rb'
@@ -877,7 +872,7 @@ RSpec/LeakyLocalVariable:
     - 'spec/models/well_spec.rb'
     - 'spec/shared_contexts/it_requires_login.rb'
 
-# Offense count: 38
+# Offense count: 39
 RSpec/LetSetup:
   Exclude:
     - 'spec/controllers/searches_controller_spec.rb'
@@ -938,7 +933,7 @@ RSpec/MultipleDescribes:
     - 'spec/lib/label_printer/asset_labels_spec.rb'
     - 'spec/models/qc_result/qc_result_spec.rb'
 
-# Offense count: 926
+# Offense count: 925
 # Configuration parameters: Max.
 RSpec/MultipleExpectations:
   Exclude:
@@ -980,7 +975,6 @@ RSpec/MultipleExpectations:
     - 'spec/jobs/export_pool_xp_to_traction_job_spec.rb'
     - 'spec/lib/accession/accessionable_spec.rb'
     - 'spec/lib/accession/configuration_spec.rb'
-    - 'spec/lib/accession/contact_spec.rb'
     - 'spec/lib/accession/sample_spec.rb'
     - 'spec/lib/accession/service_spec.rb'
     - 'spec/lib/accession/submission_spec.rb'
@@ -1168,7 +1162,7 @@ RSpec/MultipleExpectations:
     - 'spec/views/labware/show_chromium_chip_spec.rb'
     - 'spec/views/samples/index_html_erb_spec.rb'
 
-# Offense count: 248
+# Offense count: 246
 # Configuration parameters: EnforcedStyle, IgnoreSharedExamples.
 # SupportedStyles: always, named_only
 RSpec/NamedSubject:
@@ -1186,7 +1180,6 @@ RSpec/NamedSubject:
     - 'spec/api/work_completion_spec.rb'
     - 'spec/controllers/studies/information_controller_spec.rb'
     - 'spec/controllers/studies_controller_spec.rb'
-    - 'spec/lib/accession/contact_spec.rb'
     - 'spec/lib/label_printer/sample_manifest_plate_double_spec.rb'
     - 'spec/models/aliquot_spec.rb'
     - 'spec/models/api/library_tube_io_spec.rb'
@@ -1899,7 +1892,7 @@ Style/Not:
     - 'app/views/batches/show.xml.builder'
     - 'features/support/step_definitions/api_steps.rb'
 
-# Offense count: 32
+# Offense count: 30
 # This cop supports unsafe autocorrection (--autocorrect-all).
 # Configuration parameters: EnforcedStyle, AllowedMethods, AllowedPatterns.
 # SupportedStyles: predicate, comparison
@@ -1917,7 +1910,6 @@ Style/NumericPredicate:
     - 'app/models/study.rb'
     - 'app/models/tag_layout/walk_wells_by_pools.rb'
     - 'app/models/well_attribute.rb'
-    - 'features/support/step_definitions/samples_steps.rb'
     - 'lib/deployed.rb'
     - 'lib/submission_serializer.rb'
 
@@ -2035,14 +2027,13 @@ Style/Proc:
     - 'app/models/lib_pool_norm_tube_generator.rb'
     - 'app/models/qcable/statemachine.rb'
 
-# Offense count: 4
+# Offense count: 3
 # This cop supports unsafe autocorrection (--autocorrect-all).
 # Configuration parameters: Methods.
 Style/RedundantArgument:
   Exclude:
     - 'app/models/plate/fluidigm_behaviour.rb'
     - 'app/models/study_report/study_details.rb'
-    - 'features/support/step_definitions/samples_steps.rb'
     - 'spec/features/shared_examples/cherrypicking.rb'
 
 # Offense count: 7
@@ -2138,10 +2129,9 @@ Style/SymbolProc:
     - 'app/models/tasks/plate_transfer_handler.rb'
     - 'db/seeds/0001_workflows.rb'
 
-# Offense count: 8
+# Offense count: 6
 # This cop supports unsafe autocorrection (--autocorrect-all).
 Style/ZeroLengthPredicate:
   Exclude:
     - 'app/models/bulk_submission.rb'
     - 'app/models/sequencing_pipeline.rb'
-    - 'features/support/step_definitions/samples_steps.rb'

Gemfile.lock

@@ -134,7 +134,7 @@ GEM
     base64 (0.3.0)
     benchmark (0.5.0)
     bigdecimal (3.3.1)
-    bootsnap (1.21.1)
+    bootsnap (1.22.0)
       msgpack (~> 1.2)
     builder (3.3.0)
     bullet (8.1.0)
@@ -236,7 +236,7 @@ GEM
     factory_bot_rails (6.5.1)
       factory_bot (~> 6.5)
       railties (>= 6.1.0)
-    faraday (2.14.0)
+    faraday (2.14.1)
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
@@ -289,7 +289,7 @@ GEM
       railties (>= 4.1)
     jsonapi-resources-matchers (1.0.0)
       jsonapi-resources (>= 0.9.0)
-    knapsack_pro (9.2.1)
+    knapsack_pro (9.2.2)
       rake
     language_server-protocol (3.17.0.5)
     launchy (3.1.1)
@@ -338,8 +338,8 @@ GEM
     mutex_m (0.3.0)
     mysql2 (0.5.7)
       bigdecimal
-    net-http (0.7.0)
-      uri
+    net-http (0.9.1)
+      uri (>= 0.11.1)
     net-imap (0.5.9)
       date
       net-protocol

app/controllers/samples_controller.rb

@@ -149,7 +149,7 @@ def show_accession
     end
   end
 
-  def accession # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/MethodLength,Metrics/PerceivedComplexity
+  def accession # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
     # @sample needs to be set before initially for use in the ensure block
     @sample = Sample.find(params[:id])
 
@@ -165,18 +165,11 @@ def accession # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Met
     #   return
     # end
 
+    # Must check if an accession number is assigned _before_ performing the accession
     accession_action = @sample.accession_number? ? :update : :create
 
-    if Flipper.enabled?(:y25_286_accession_individual_samples_with_sample_accessioning_job)
-      # Synchronously perform accessioning job
-      Accession.accession_sample(@sample, current_user, perform_now: true)
-    else
-      # TODO: when removing the y25_286_accession_individual_samples_with_sample_accessioning_job feature flag
-      #       and this accessioning path also remove the AccessionService and ActiveRecord errors below
-      @sample.validate_sample_for_accessioning!
-      accession_service = AccessionService.select_for_sample(@sample)
-      accession_service.submit_sample_for_user(@sample, current_user)
-    end
+    # Synchronously perform accessioning job
+    Accession.accession_sample(@sample, current_user, perform_now: true)
 
     if accession_action == :create
       flash[:notice] = "Accession number generated: #{@sample.sample_metadata.sample_ebi_accession_number}"
@@ -185,23 +178,18 @@ def accession # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Met
     end
 
     # Handle errors for both synchronous and asynchronous accessioning
-    # When the feature flag above (y25_286_accession_individual_samples_with_sample_accessioning_job) is removed,
-    # the AccessionService and ActiveRecord errors should also be removed. These errors are only raised in the old
-    # synchronous accessioning code path and are not required for the updated SampleAccessioningJob path.
-  rescue ActiveRecord::RecordInvalid, Accession::InternalValidationError
+  rescue Accession::InternalValidationError
     flash[:error] = "Please fill in the required fields: #{@sample.errors.full_messages.join(', ')}"
     redirect_to(edit_sample_path(@sample)) # send the user to edit the sample
-  rescue AccessionService::NumberNotRequired => e
-    flash[:warning] = e.message || 'An accession number is not required for this study'
-  rescue AccessionService::NumberNotGenerated, Accession::ExternalValidationError => e
+  rescue Accession::ExternalValidationError => e
     flash[:warning] = "No accession number was generated: #{e.message}"
-  rescue AccessionService::AccessionServiceError, Accession::Error => e
+  rescue Accession::Error => e
     flash[:error] = "Accessioning Service Failed: #{e.message}"
   rescue Faraday::Error => e
     flash[:error] = "Accessioning failed with a network error: #{e.message}"
   ensure
     # Redirect back to where we came from if not already redirected
-    redirect_back_with_anchor_or_to(sample_path(@sample), anchor: 'accession-statuses') unless performed?
+    redirect_back_with_anchor_or_to(sample_path(@sample)) unless performed?
   end
 
   private

app/controllers/studies_controller.rb

@@ -253,23 +253,49 @@ def accession
     end
   end
 
+  # Accession all samples in the study.
+  #
+  # If the study does not have an accession number, adds an error to the study and returns.
+  # Otherwise, iterates through each sample in the study and attempts to accession it,
+  # unless the sample already has an accession number.
+  # If an Accession::Error occurs for a sample, adds the error message to the study's errors.
+  #
+  # NOTE: this does not check if the current user has permission to accession samples in this study
+  #
+  # @return [void]
   def accession_all_samples # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
     @study = Study.find(params[:id])
     return accessioning_not_enabled_redirect unless accessioning_enabled?
 
     # TODO: Y26-026 - Enforce accessioning permissions
     # return accession_permission_denied_redirect unless permitted_to_accession?(@study)
 
-    @study.accession_all_samples(current_user)
+    unless @study.accession_number?
+      flash[:error] = 'Please accession the study before accessioning samples'
+      return redirect_to(study_path(@study))
+    end
+    unless @study.samples_accessionable?
+      flash[:error] = 'Study cannot accession samples, see Study Accessioning tab for details'
+      return redirect_to(study_path(@study))
+    end
+
+    @study.samples.find_each do |sample|
+      next if sample.accession_number?
+
+      begin
+        Accession.accession_sample(sample, current_user)
+      rescue Accession::Error => e
+        @study.errors.add(:base, e.message)
+      end
+    end
 
     if @study.errors.any?
-      error_messages = compile_accession_errors(@study.errors)
-      flash[:error] = error_messages
+      flash[:error] = compile_accession_errors(@study.errors)
     else
       flash[:notice] = 'All of the samples in this study have been sent for accessioning. ' \
                        'Please check back in 5 minutes to confirm that accessioning was successful.'
     end
-    redirect_to(study_path(@study, anchor: 'accession-statuses'))
+    redirect_to(study_path(@study))
   end
 
   def dac_accession