.rubocop_todo.yml

# This configuration was generated by
# `rubocop --auto-gen-config --exclude-limit 1000`
# on 2022-04-26 14:16:25 UTC using RuboCop version 1.26.0.
# 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
# versions of RuboCop, may require this file to be generated again.

# Offense count: 16
# Configuration parameters: IgnoredMethods.
Lint/AmbiguousBlockAssociation:
  Exclude:
    - 'spec/controllers/steps_controller_spec.rb'
    - 'spec/models/step_spec.rb'
    - 'spec/models/steps/job_spec.rb'
    - 'spec/models/steps/task_spec.rb'

# Offense count: 3
# Configuration parameters: AllowedMethods.
# AllowedMethods: enums
Lint/ConstantDefinitionInBlock:
  Exclude:
    - 'spec/lib/parsers/csv_layout/barcode_creatable_parser_spec.rb'
    - 'spec/models/activities/background_tasks_spec.rb'

# Offense count: 3
Lint/DuplicateMethods:
  Exclude:
    - 'lib/parsers/csv_layout/barcode_parser.rb'
    - 'lib/support_n3.rb'

# Offense count: 1
# Configuration parameters: MaximumRangeSize.
Lint/MissingCopEnableDirective:
  Exclude:
    - 'lib/deployed_version.rb'

# Offense count: 4
# This cop supports unsafe auto-correction (--auto-correct-all).
Lint/NonDeterministicRequireOrder:
  Exclude:
    - 'lib/tasks/setup_templates.rake'
    - 'spec/rails_helper.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
Lint/RedundantCopDisableDirective:
  Exclude:
    - 'lib/deployed_version.rb'

# Offense count: 7
Lint/ShadowingOuterLocalVariable:
  Exclude:
    - 'app/models/printables/group.rb'
    - 'lib/actions/plate_transfer.rb'
    - 'lib/support_n3.rb'
    - 'spec/lib/support_n3_spec.rb'

# Offense count: 2
# Configuration parameters: AllowComments, AllowNil.
Lint/SuppressedException:
  Exclude:
    - 'spec/controllers/steps_controller_spec.rb'

# Offense count: 56
Lint/UselessAssignment:
  Exclude:
    - 'app/channels/activity_channel.rb'
    - 'app/controllers/activities_controller.rb'
    - 'app/helpers/application_helper.rb'
    - 'app/models/activities/json_attributes.rb'
    - 'app/models/assets/export.rb'
    - 'app/models/assets/facts_management.rb'
    - 'app/models/step_type.rb'
    - 'db/seeds.rb'
    - 'lib/actions/plate_transfer.rb'
    - 'lib/inference_engines/cwm/step_execution.rb'
    - 'lib/inference_engines/runner/step_execution.rb'
    - 'lib/parsers/csv_layout/location_parser.rb'
    - 'lib/sequencescape_client.rb'
    - 'lib/support_n3.rb'
    - 'script/fix_duplicated_tubes.rb'
    - 'script/recreate_steptypes.rb'
    - 'script/remove_duplicates.rb'
    - 'script/runners/put_tubes_into_rack_by_column_order.rb'
    - 'script/runners/transfer_plate_to_plate.rb'
    - 'script/runners/update_sequencescape.rb'
    - 'spec/controllers/assets_controller_spec.rb'
    - 'spec/controllers/steps_controller_spec.rb'
    - 'spec/lib/changes_support/disjoint_list_spec.rb'
    - 'spec/lib/support_n3_spec.rb'
    - 'spec/models/activity_spec.rb'
    - 'spec/models/asset_spec.rb'
    - 'spec/models/step_execution_spec.rb'
    - 'spec/models/step_spec.rb'
    - 'spec/models/steps/queueable_job_spec.rb'
    - 'spec/remote_assets_helper.rb'

# Offense count: 3
# Configuration parameters: CheckForMethodsWithNoSideEffects.
Lint/Void:
  Exclude:
    - 'app/models/printables/group.rb'
    - 'lib/inference_engines/default/step_execution.rb'
    - 'spec/models/assets/export_spec.rb'

# Offense count: 78
# Configuration parameters: IgnoredMethods, CountRepeatedAttributes.
Metrics/AbcSize:
  Max: 79

# Offense count: 13
# Configuration parameters: CountComments, CountAsOne, ExcludedMethods, IgnoredMethods.
# IgnoredMethods: refine
Metrics/BlockLength:
  Max: 68

# Offense count: 7
# Configuration parameters: CountBlocks.
Metrics/BlockNesting:
  Max: 5

# Offense count: 11
# Configuration parameters: CountComments, CountAsOne.
Metrics/ClassLength:
  Max: 489

# Offense count: 35
# Configuration parameters: IgnoredMethods.
Metrics/CyclomaticComplexity:
  Max: 26

# Offense count: 108
# Configuration parameters: CountComments, CountAsOne, ExcludedMethods, IgnoredMethods.
Metrics/MethodLength:
  Max: 363

# Offense count: 8
# Configuration parameters: CountComments, CountAsOne.
Metrics/ModuleLength:
  Max: 206

# Offense count: 31
# Configuration parameters: IgnoredMethods.
Metrics/PerceivedComplexity:
  Max: 26

# Offense count: 4
Naming/AccessorMethodName:
  Exclude:
    - 'app/models/fact.rb'
    - 'app/models/step.rb'
    - 'lib/fact_changes.rb'

# Offense count: 1
# Configuration parameters: ExpectMatchingDefinition, CheckDefinitionPathHierarchy, CheckDefinitionPathHierarchyRoots, Regex, IgnoreExecutableScripts, AllowedAcronyms.
# CheckDefinitionPathHierarchyRoots: lib, spec, test, src
# AllowedAcronyms: CLI, DSL, ACL, API, ASCII, CPU, CSS, DNS, EOF, GUID, HTML, HTTP, HTTPS, ID, IP, JSON, LHS, QPS, RAM, RHS, RPC, SLA, SMTP, SQL, SSH, TCP, TLS, TTL, UDP, UI, UID, UUID, URI, URL, UTF8, VM, XML, XMPP, XSRF, XSS
Naming/FileName:
  Exclude:
    - 'config/initializers/pmb_server-setup.rb'

# Offense count: 29
# Configuration parameters: MinNameLength, AllowNamesEndingInNumbers, AllowedNames, ForbiddenNames.
# AllowedNames: at, by, db, id, in, io, ip, of, on, os, pp, to
Naming/MethodParameterName:
  Exclude:
    - 'app/models/condition.rb'
    - 'app/models/fact.rb'
    - 'lib/actions/plate_transfer.rb'
    - 'lib/fact_changes.rb'
    - 'lib/inference_engines/cwm/step_execution.rb'
    - 'lib/support_n3.rb'
    - 'spec/lib/support_n3_spec.rb'
    - 'spec/models/step_spec.rb'
    - 'spec/models/step_type_spec.rb'
    - 'spec/models/steps/queueable_job_spec.rb'

# Offense count: 21
# Configuration parameters: NamePrefix, ForbiddenPrefixes, AllowedMethods, MethodDefinitionMacros.
# NamePrefix: is_, has_, have_
# ForbiddenPrefixes: is_, has_, have_
# AllowedMethods: is_a?
# MethodDefinitionMacros: define_method, define_singleton_method
Naming/PredicateName:
  Exclude:
    - 'app/models/activities/websocket_events.rb'
    - 'app/models/asset.rb'
    - 'app/models/asset_group.rb'
    - 'app/models/assets/export.rb'
    - 'app/models/assets/facts_management.rb'
    - 'app/models/assets/import.rb'
    - 'app/models/condition.rb'
    - 'app/models/condition_group.rb'
    - 'app/models/steps/queueable_job.rb'
    - 'app/models/steps/state.rb'
    - 'lib/fact_changes.rb'
    - 'lib/support_n3.rb'
    - 'lib/token_util.rb'

# Offense count: 36
# Configuration parameters: EnforcedStyle, AllowedIdentifiers.
# SupportedStyles: snake_case, camelCase
Naming/VariableName:
  Exclude:
    - 'app/helpers/application_helper.rb'
    - 'app/models/action.rb'
    - 'lib/actions/plate_transfer.rb'
    - 'lib/actions/racking.rb'
    - 'lib/actions/tube_transfer.rb'
    - 'spec/script/runners/transfer_samples_spec.rb'
    - 'spec/script/runners/transfer_tubes_to_tube_rack_by_position_spec.rb'

# Offense count: 84
# This cop supports safe auto-correction (--auto-correct).
Rails/ActiveRecordAliases:
  Exclude:
    - 'app/controllers/asset_groups_controller.rb'
    - 'app/controllers/changes_controller.rb'
    - 'app/models/activities/background_tasks.rb'
    - 'app/models/activities/state.rb'
    - 'app/models/activity_type.rb'
    - 'app/models/asset.rb'
    - 'app/models/assets/export.rb'
    - 'app/models/assets/import.rb'
    - 'app/models/concerns/deprecatable.rb'
    - 'app/models/fact.rb'
    - 'app/models/step_type.rb'
    - 'app/models/steps/retryable.rb'
    - 'app/models/uploaded_file.rb'
    - 'app/models/user.rb'
    - 'db/migrate/20170225191416_migrate_operations_to_object_asset.rb'
    - 'lib/fact_changes.rb'
    - 'lib/inference_engines/cwm/step_execution.rb'
    - 'lib/inference_engines/runner/step_execution.rb'
    - 'lib/support_n3.rb'
    - 'script/plate_to_code39.rb'
    - 'spec/helpers/application_helper_spec.rb'
    - 'spec/lib/fact_changes_spec.rb'
    - 'spec/models/activities/background_tasks_spec.rb'
    - 'spec/models/assets/import_spec.rb'
    - 'spec/models/step_spec.rb'
    - 'spec/models/steps/background_tasks/inference_spec.rb'
    - 'spec/models/steps/queueable_job_spec.rb'
    - 'spec/script/runners/transfer_tubes_to_tube_rack_by_position_spec.rb'
    - 'spec/shared_examples/background_step.rb'
    - 'test/factories/assets.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: Include.
# Include: app/models/**/*.rb
Rails/ActiveRecordCallbacksOrder:
  Exclude:
    - 'app/models/step_type.rb'

# Offense count: 2
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: NilOrEmpty, NotPresent, UnlessPresent.
Rails/Blank:
  Exclude:
    - 'app/models/action.rb'
    - 'app/models/steps/task.rb'

# Offense count: 4
# Configuration parameters: Database, Include.
# SupportedDatabases: mysql, postgresql
# Include: db/migrate/*.rb
Rails/BulkChangeTable:
  Exclude:
    - 'db/migrate/20160923094944_add_sessions_table.rb'
    - 'db/migrate/20170303142929_set_barcode_index_not_unique.rb'
    - 'db/migrate/20171009132757_add_next_step_to_steps.rb'
    - 'db/migrate/20180628135208_add_started_at_and_completed_at_to_step.rb'

# Offense count: 1
# Configuration parameters: Include.
# Include: db/migrate/*.rb
Rails/CreateTableWithTimestamps:
  Exclude:
    - 'db/migrate/20160626224627_create_condition_groups.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforceForPrefixed.
Rails/Delegate:
  Exclude:
    - 'lib/parsers/csv_metadata/csv_parser.rb'

# Offense count: 29
# This cop supports unsafe auto-correction (--auto-correct-all).
# Configuration parameters: Whitelist, AllowedMethods, AllowedReceivers.
# Whitelist: find_by_sql
# AllowedMethods: find_by_sql
# AllowedReceivers: Gem::Specification
Rails/DynamicFindBy:
  Exclude:
    - 'app/controllers/activities_controller.rb'
    - 'app/controllers/samples_status_controller.rb'
    - 'app/models/assets/import.rb'
    - 'spec/lib/support_n3_spec.rb'

# Offense count: 2
# Configuration parameters: EnforcedStyle.
# SupportedStyles: slashes, arguments
Rails/FilePath:
  Exclude:
    - 'script/runners/transfer_plate_to_plate_and_update_sequencescape.rb'

# Offense count: 2
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: Include, IgnoredMethods.
# Include: app/models/**/*.rb
# IgnoredMethods: order, limit, select, lock
Rails/FindEach:
  Exclude:
    - 'app/models/asset.rb'
    - 'app/models/steps/deprecatable.rb'

# Offense count: 2
# Configuration parameters: Include.
# Include: app/models/**/*.rb
Rails/HasAndBelongsToMany:
  Exclude:
    - 'app/models/activity_type.rb'
    - 'app/models/instrument.rb'

# Offense count: 22
# Configuration parameters: Include.
# Include: app/models/**/*.rb
Rails/HasManyOrHasOneDependent:
  Exclude:
    - 'app/models/activity.rb'
    - 'app/models/activity_type.rb'
    - 'app/models/asset.rb'
    - 'app/models/asset_group.rb'
    - 'app/models/concerns/deprecatable.rb'
    - 'app/models/condition_group.rb'
    - 'app/models/instrument.rb'
    - 'app/models/kit.rb'
    - 'app/models/kit_type.rb'
    - 'app/models/step.rb'
    - 'app/models/user.rb'

# Offense count: 8
# Configuration parameters: Include.
# Include: app/helpers/**/*.rb
Rails/HelperInstanceVariable:
  Exclude:
    - 'app/helpers/activities_helper.rb'
    - 'app/helpers/application_helper.rb'

# Offense count: 9
# Configuration parameters: IgnoreScopes, Include.
# Include: app/models/**/*.rb
Rails/InverseOf:
  Exclude:
    - 'app/models/activity.rb'
    - 'app/models/concerns/deprecatable.rb'
    - 'app/models/condition_group.rb'
    - 'app/models/step.rb'
    - 'app/models/user.rb'

# Offense count: 1
# Configuration parameters: Include.
# Include: app/controllers/**/*.rb
Rails/LexicallyScopedActionFilter:
  Exclude:
    - 'app/controllers/reracking_controller.rb'

# Offense count: 1
# This cop supports unsafe auto-correction (--auto-correct-all).
Rails/NegateInclude:
  Exclude:
    - 'lib/support_n3.rb'

# Offense count: 8
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: Include.
# Include: app/**/*.rb, config/**/*.rb, db/**/*.rb, lib/**/*.rb
Rails/Output:
  Exclude:
    - 'lib/inference_engines/cwm/step_execution.rb'
    - 'lib/inference_engines/runner/step_execution.rb'
    - 'lib/label_template_setup.rb'
    - 'lib/views_schema.rb'

# Offense count: 9
Rails/OutputSafety:
  Exclude:
    - 'app/helpers/activities_helper.rb'
    - 'app/helpers/application_helper.rb'
    - 'app/helpers/steps_helper.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
Rails/Presence:
  Exclude:
    - 'app/models/asset.rb'

# Offense count: 5
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: NotNilAndNotEmpty, NotBlank, UnlessBlank.
Rails/Present:
  Exclude:
    - 'app/helpers/activities_helper.rb'
    - 'lib/fact_changes.rb'
    - 'lib/support_n3.rb'

# Offense count: 5
# This cop supports safe auto-correction (--auto-correct).
Rails/RedundantForeignKey:
  Exclude:
    - 'app/models/concerns/deprecatable.rb'
    - 'app/models/step.rb'
    - 'app/models/user.rb'

# Offense count: 2
Rails/ReflectionClassName:
  Exclude:
    - 'app/models/concerns/deprecatable.rb'

# Offense count: 1
# Configuration parameters: Include.
# Include: db/**/*.rb
Rails/ReversibleMigration:
  Exclude:
    - 'db/migrate/20190516153622_remove_task_type.rb'

# Offense count: 23
# Configuration parameters: ForbiddenMethods, AllowedMethods.
# ForbiddenMethods: decrement!, decrement_counter, increment!, increment_counter, insert, insert!, insert_all, insert_all!, toggle!, touch, touch_all, update_all, update_attribute, update_column, update_columns, update_counters, upsert, upsert_all
Rails/SkipsModelValidations:
  Exclude:
    - 'app/channels/activity_channel.rb'
    - 'app/controllers/asset_groups_controller.rb'
    - 'app/controllers/assets_controller.rb'
    - 'app/models/asset_group.rb'
    - 'app/models/assets/import.rb'
    - 'app/models/step_type.rb'
    - 'app/models/steps/cancellable.rb'
    - 'app/models/steps/state.rb'
    - 'app/models/steps/websocket_events.rb'
    - 'app/models/uploaded_file.rb'
    - 'db/migrate/20190528125756_fix_incorrect_fact_literals.rb'
    - 'db/migrate/20190717130805_change_sti_type.rb'
    - 'lib/fact_changes.rb'
    - 'spec/models/steps/job_spec.rb'
    - 'spec/shared_examples/background_step.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
Rails/SquishedSQLHeredocs:
  Exclude:
    - 'db/migrate/20200709123033_create_heron_activities_view.rb'

# Offense count: 3
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: strict, flexible
Rails/TimeZone:
  Exclude:
    - 'app/controllers/assets_controller.rb'
    - 'spec/remote_assets_helper.rb'

# Offense count: 3
# This cop supports safe auto-correction (--auto-correct).
Rails/WhereNot:
  Exclude:
    - 'app/models/activities/state.rb'
    - 'app/models/step_type.rb'
    - 'db/migrate/20170225191416_migrate_operations_to_object_asset.rb'

# Offense count: 3
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: AllowOnConstant.
Style/CaseEquality:
  Exclude:
    - 'lib/sequencescape_client.rb'
    - 'lib/support_n3.rb'

# Offense count: 5
# This cop supports unsafe auto-correction (--auto-correct-all).
Style/CaseLikeIf:
  Exclude:
    - 'app/models/action.rb'
    - 'app/models/operation.rb'
    - 'app/models/step_type.rb'

# Offense count: 39
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: nested, compact
Style/ClassAndModuleChildren:
  Exclude:
    - 'app/models/activities/json_attributes.rb'
    - 'app/models/activities/state.rb'
    - 'app/models/activities/steps_management.rb'
    - 'app/models/activities/websocket_events.rb'
    - 'app/models/assets/export.rb'
    - 'app/models/assets/facts_management.rb'
    - 'app/models/assets/import.rb'
    - 'app/models/assets/traction_fields.rb'
    - 'app/models/printables/group.rb'
    - 'app/models/printables/instance.rb'
    - 'app/models/steps/background_tasks/inference.rb'
    - 'app/models/steps/background_tasks/runner.rb'
    - 'app/models/steps/cancellable.rb'
    - 'app/models/steps/compatible.rb'
    - 'app/models/steps/deprecatable.rb'
    - 'app/models/steps/job.rb'
    - 'app/models/steps/queueable_job.rb'
    - 'app/models/steps/retryable.rb'
    - 'app/models/steps/state.rb'
    - 'app/models/steps/stoppable.rb'
    - 'app/models/steps/task.rb'
    - 'app/models/steps/websocket_events.rb'
    - 'lib/changes_support/disjoint_list.rb'
    - 'lib/changes_support/transaction_scope.rb'
    - 'lib/sequencescape_client_v2.rb'
    - 'test/test_helper.rb'

# Offense count: 38
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: is_a?, kind_of?
Style/ClassCheck:
  Exclude:
    - 'app/models/assets/facts_management.rb'
    - 'app/models/assets/traction_fields.rb'
    - 'app/models/condition.rb'
    - 'app/models/condition_group.rb'
    - 'app/models/steps/websocket_events.rb'
    - 'lib/actions/plate_transfer.rb'
    - 'lib/changes_support/disjoint_list.rb'
    - 'lib/changes_support/transaction_scope.rb'
    - 'lib/fact_changes.rb'
    - 'lib/parsers/csv_layout/line_reader.rb'
    - 'lib/token_util.rb'
    - 'spec/lib/changes_support/transaction_scope_spec.rb'
    - 'spec/lib/fact_changes_spec.rb'
    - 'spec/lib/parsers/csv_layout/barcode_creatable_parser_spec.rb'
    - 'spec/requests/api/v1/assets_spec.rb'

# Offense count: 3
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: IgnoredMethods.
# IgnoredMethods: ==, equal?, eql?
Style/ClassEqualityComparison:
  Exclude:
    - 'app/helpers/application_helper.rb'
    - 'lib/support_n3.rb'

# Offense count: 1
Style/ClassVars:
  Exclude:
    - 'app/models/action.rb'

# Offense count: 6
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforcedStyle, SingleLineConditionsOnly, IncludeTernaryExpressions.
# SupportedStyles: assign_to_condition, assign_inside_condition
Style/ConditionalAssignment:
  Exclude:
    - 'app/helpers/application_helper.rb'
    - 'app/models/asset_group.rb'
    - 'app/models/condition.rb'
    - 'lib/changes_support/transaction_scope.rb'
    - 'lib/inference_engines/runner/step_execution.rb'
    - 'script/runners/transfer_tubes_to_tube_rack_by_position.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: allowed_in_returns, forbidden
Style/DoubleNegation:
  Exclude:
    - 'app/channels/activity_channel.rb'

# Offense count: 25
# This cop supports safe auto-correction (--auto-correct).
Style/EachWithObject:
  Exclude:
    - 'app/channels/activity_channel.rb'
    - 'app/helpers/activities_helper.rb'
    - 'app/helpers/application_helper.rb'
    - 'app/helpers/step_types_helper.rb'
    - 'app/models/activities/background_tasks.rb'
    - 'app/models/activities/websocket_events.rb'
    - 'app/models/assets/traction_fields.rb'
    - 'app/models/printables/group.rb'
    - 'app/models/step_type.rb'
    - 'app/models/steps/cancellable.rb'
    - 'lib/actions/plate_transfer.rb'
    - 'lib/fact_changes.rb'
    - 'lib/parsers/csv_metadata/data_parser.rb'
    - 'lib/parsers/csv_metadata/line_parser.rb'
    - 'lib/support_n3.rb'
    - 'script/fix_duplicated_tubes.rb'
    - 'spec/lib/changes_support/disjoint_list_spec.rb'

# Offense count: 4
# This cop supports safe auto-correction (--auto-correct).
Style/EvenOdd:
  Exclude:
    - 'spec/models/condition_spec.rb'
    - 'spec/models/step_execution_spec.rb'

# Offense count: 4
# This cop supports safe auto-correction (--auto-correct).
Style/ExpandPathArguments:
  Exclude:
    - 'Rakefile'
    - 'config.ru'
    - 'spec/rails_helper.rb'
    - 'test/test_helper.rb'

# Offense count: 2
# Configuration parameters: EnforcedStyle, MaxUnannotatedPlaceholdersAllowed, IgnoredMethods.
# SupportedStyles: annotated, template, unannotated
Style/FormatStringToken:
  Exclude:
    - 'config/routes.rb'
    - 'lib/views_schema.rb'

# Offense count: 351
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: always, always_true, never
Style/FrozenStringLiteralComment:
  Exclude:
    - 'Gemfile'
    - 'Rakefile'
    - 'app/channels/activity_channel.rb'
    - 'app/channels/application_cable/channel.rb'
    - 'app/channels/application_cable/connection.rb'
    - 'app/controllers/activities_controller.rb'
    - 'app/controllers/activity_types_controller.rb'
    - 'app/controllers/api/v1/assets_controller.rb'
    - 'app/controllers/application_controller.rb'
    - 'app/controllers/asset_groups_controller.rb'
    - 'app/controllers/assets_controller.rb'
    - 'app/controllers/changes_controller.rb'
    - 'app/controllers/history_controller.rb'
    - 'app/controllers/instruments_controller.rb'
    - 'app/controllers/kit_types_controller.rb'
    - 'app/controllers/kits_controller.rb'
    - 'app/controllers/printers_controller.rb'
    - 'app/controllers/reracking_controller.rb'
    - 'app/controllers/samples_not_started_controller.rb'
    - 'app/controllers/samples_started_controller.rb'
    - 'app/controllers/samples_status_controller.rb'
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# Offense count: 2
# This cop supports safe auto-correction (--auto-correct).
Style/GlobalStdStream:
  Exclude:
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# Offense count: 17
# Configuration parameters: MinBodyLength.
Style/GuardClause:
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# Offense count: 7
# This cop supports unsafe auto-correction (--auto-correct-all).
# Configuration parameters: AllowedReceivers.
Style/HashEachMethods:
  Exclude:
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    - 'spec/requests/api/v1/assets_spec.rb'

# Offense count: 5
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: AllowIfModifier.
Style/IfInsideElse:
  Exclude:
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    - 'lib/fact_changes.rb'
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    - 'lib/support_n3.rb'

# Offense count: 24
# This cop supports safe auto-correction (--auto-correct).
Style/IfUnlessModifier:
  Exclude:
    - 'app/models/action.rb'
    - 'app/models/asset.rb'
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# Offense count: 1
# This cop supports unsafe auto-correction (--auto-correct-all).
# Configuration parameters: InverseMethods, InverseBlocks.
Style/InverseMethods:
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# Offense count: 2
Style/MixinUsage:
  Exclude:
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# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: AllowMethodComparison.
Style/MultipleComparison:
  Exclude:
    - 'script/runners/load_metadata.rb'

# Offense count: 18
# This cop supports safe auto-correction (--auto-correct).
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# SupportedStyles: literals, strict
Style/MutableConstant:
  Exclude:
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    - 'lib/actions/racking.rb'
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# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: both, prefix, postfix
Style/NegatedIf:
  Exclude:
    - 'app/models/printables/instance.rb'

# Offense count: 11
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforcedStyle, MinBodyLength.
# SupportedStyles: skip_modifier_ifs, always
Style/Next:
  Exclude:
    - 'app/models/asset_group.rb'
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# Offense count: 57
# This cop supports unsafe auto-correction (--auto-correct-all).
# Configuration parameters: EnforcedStyle, IgnoredMethods.
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Style/NumericPredicate:
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    - 'app/helpers/application_helper.rb'
    - 'app/models/action.rb'
    - 'app/models/activities/state.rb'
    - 'app/models/activities/websocket_events.rb'
    - 'app/models/asset.rb'
    - 'app/models/asset_group.rb'
    - 'app/models/assets/import.rb'
    - 'app/models/assets/traction_fields.rb'
    - 'app/models/condition.rb'
    - 'app/models/condition_group.rb'
    - 'app/models/step_type.rb'
    - 'app/models/steps/task.rb'
    - 'lib/actions/racking.rb'
    - 'lib/actions/tube_transfer.rb'
    - 'lib/changes_support/transaction_scope.rb'
    - 'lib/deployed_version.rb'
    - 'lib/fact_changes.rb'
    - 'lib/inference_engines/cwm/step_execution.rb'
    - 'lib/inference_engines/runner/step_execution.rb'
    - 'lib/parsers/csv_layout/line_parser.rb'
    - 'lib/parsers/csv_metadata/line_parser.rb'
    - 'lib/support_n3.rb'
    - 'script/aliquot_type_inference.rb'
    - 'script/container_inferences.rb'
    - 'script/purpose_name_inference.rb'
    - 'script/runners/load_metadata.rb'
    - 'script/runners/print_barcodes.rb'
    - 'script/runners/rack_layout.rb'
    - 'script/runners/rack_layout_any_barcode.rb'
    - 'script/runners/transfer_plate_to_plate.rb'
    - 'script/runners/transfer_samples.rb'
    - 'script/runners/transfer_tubes_to_tube_rack_by_position.rb'
    - 'script/runners/update_sequencescape.rb'
    - 'script/study_name_inference.rb'
    - 'script/tasks/runners/aliquot_type_inference.rb'

# Offense count: 1
Style/OpenStructUse:
  Exclude:
    - 'lib/deployed_version.rb'

# Offense count: 15
# Configuration parameters: AllowedMethods.
# AllowedMethods: respond_to_missing?
Style/OptionalBooleanParameter:
  Exclude:
    - 'app/helpers/application_helper.rb'
    - 'app/models/steps/cancellable.rb'
    - 'lib/fact_changes.rb'
    - 'lib/support_n3.rb'

# Offense count: 4
# This cop supports safe auto-correction (--auto-correct).
Style/OrAssignment:
  Exclude:
    - 'app/controllers/asset_groups_controller.rb'
    - 'app/helpers/application_helper.rb'
    - 'lib/inference_engines/cwm/step_execution.rb'
    - 'lib/inference_engines/runner/step_execution.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
Style/ParallelAssignment:
  Exclude:
    - 'spec/models/step_spec.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: PreferredDelimiters.
Style/PercentLiteralDelimiters:
  Exclude:
    - 'spec/lib/support_n3_spec.rb'

# Offense count: 8
# This cop supports unsafe auto-correction (--auto-correct-all).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: short, verbose
Style/PreferredHashMethods:
  Exclude:
    - 'lib/changes_support/disjoint_list.rb'
    - 'lib/changes_support/transaction_scope.rb'
    - 'spec/models/asset_spec.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
Style/RedundantCondition:
  Exclude:
    - 'spec/integration/inference_spec.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
Style/RedundantFreeze:
  Exclude:
    - 'lib/psd_formatter.rb'

# Offense count: 4
# This cop supports safe auto-correction (--auto-correct).
Style/RedundantInterpolation:
  Exclude:
    - 'app/helpers/application_helper.rb'

# Offense count: 22
# This cop supports safe auto-correction (--auto-correct).
Style/RedundantParentheses:
  Exclude:
    - 'app/models/action.rb'
    - 'app/models/asset.rb'
    - 'app/models/assets/import.rb'
    - 'app/models/condition_group.rb'
    - 'lib/actions/plate_transfer.rb'
    - 'lib/actions/racking.rb'
    - 'lib/actions/tube_transfer.rb'
    - 'lib/changes_support/disjoint_list.rb'
    - 'lib/changes_support/transaction_scope.rb'
    - 'lib/fact_changes.rb'
    - 'lib/support_n3.rb'
    - 'script/runners/create_stamped_plate.rb'

# Offense count: 36
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: AllowMultipleReturnValues.
Style/RedundantReturn:
  Exclude:
    - 'app/helpers/steps_helper.rb'
    - 'app/models/action.rb'
    - 'app/models/activities/background_tasks.rb'
    - 'app/models/asset.rb'
    - 'app/models/asset_group.rb'
    - 'app/models/assets/import.rb'
    - 'app/models/condition.rb'
    - 'app/models/step_type.rb'
    - 'app/models/steps/compatible.rb'
    - 'app/models/uploaded_file.rb'
    - 'lib/actions/racking.rb'
    - 'lib/inference_engines/cwm/step_execution.rb'
    - 'lib/label_template_setup.rb'
    - 'lib/sequencescape_client.rb'
    - 'lib/step_execution_process.rb'
    - 'lib/token_util.rb'
    - 'script/aliquot_type_inference.rb'
    - 'script/container_inferences.rb'
    - 'script/purpose_name_inference.rb'
    - 'script/runners/load_metadata.rb'
    - 'script/runners/transfer_tubes_to_tube_rack_by_position.rb'
    - 'script/runners/update_sequencescape.rb'
    - 'script/study_name_inference.rb'
    - 'spec/requests/api/v1/assets_spec.rb'

# Offense count: 22
# This cop supports safe auto-correction (--auto-correct).
Style/RedundantSelf:
  Exclude:
    - 'app/channels/activity_channel.rb'
    - 'app/channels/application_cable/connection.rb'
    - 'app/models/activities/json_attributes.rb'
    - 'app/models/asset.rb'
    - 'app/models/asset_group.rb'
    - 'app/models/concerns/deprecatable.rb'
    - 'app/models/operation.rb'
    - 'app/models/step.rb'
    - 'app/models/steps/stoppable.rb'
    - 'app/models/steps/websocket_events.rb'
    - 'lib/sequencescape_client.rb'

# Offense count: 15
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: ConvertCodeThatCanStartToReturnNil, AllowedMethods.
# AllowedMethods: present?, blank?, presence, try, try!
Style/SafeNavigation:
  Exclude:
    - 'app/controllers/steps_controller.rb'
    - 'app/controllers/user_sessions_controller.rb'
    - 'app/helpers/activities_helper.rb'
    - 'app/models/activities/json_attributes.rb'
    - 'app/models/asset_group.rb'
    - 'app/models/condition.rb'
    - 'app/models/steps/queueable_job.rb'
    - 'app/models/user.rb'
    - 'lib/changes_support/disjoint_list.rb'
    - 'lib/fact_changes.rb'
    - 'lib/support_n3.rb'
    - 'spec/models/steps/background_tasks/inference_spec.rb'

# Offense count: 5
# This cop supports safe auto-correction (--auto-correct).
Style/SelfAssignment:
  Exclude:
    - 'lib/parsers/csv_metadata/line_parser.rb'
    - 'script/runners/create_file.rb'
    - 'script/runners/create_layout.rb'
    - 'spec/models/action_spec.rb'

# Offense count: 3
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: only_raise, only_fail, semantic
Style/SignalException:
  Exclude:
    - 'spec/inferences_helper.rb'

# Offense count: 1
# This cop supports unsafe auto-correction (--auto-correct-all).
Style/SlicingWithRange:
  Exclude:
    - 'script/runners/transfer_tubes_to_tube_rack_by_position.rb'

# Offense count: 12
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: AllowModifier.
Style/SoleNestedConditional:
  Exclude:
    - 'app/models/action.rb'
    - 'app/models/asset.rb'
    - 'app/models/condition_group.rb'
    - 'lib/actions/plate_transfer.rb'
    - 'lib/actions/racking.rb'
    - 'lib/changes_support/transaction_scope.rb'
    - 'lib/parsers/csv_layout/csv_parser.rb'
    - 'lib/support_n3.rb'
    - 'script/runners/transfer_tubes_to_tube_rack_by_position.rb'
    - 'spec/integration/inference_spec.rb'

# Offense count: 18
# This cop supports unsafe auto-correction (--auto-correct-all).
# Configuration parameters: Mode.
Style/StringConcatenation:
  Exclude:
    - 'app/controllers/assets_controller.rb'
    - 'app/helpers/activities_helper.rb'
    - 'lib/inference_engines/cwm/step_execution.rb'
    - 'lib/inference_engines/runner/step_execution.rb'
    - 'script/runners/load_metadata.rb'
    - 'script/runners/rack_layout.rb'
    - 'script/runners/rack_layout_any_barcode.rb'
    - 'spec/inferences_helper.rb'
    - 'spec/lib/parsers/csv_layout/csv_parser_spec.rb'
    - 'spec/lib/parsers/csv_metadata/csv_parser_spec.rb'
    - 'spec/script/runners/load_metadata_spec.rb'
    - 'spec/script/runners/transfer_plate_to_plate_spec.rb'
    - 'spec/script/runners/transfer_samples_spec.rb'
    - 'spec/script/runners/transfer_tubes_to_tube_rack_by_position_spec.rb'

# Offense count: 2
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforcedStyle, ConsistentQuotesInMultiline.
# SupportedStyles: single_quotes, double_quotes
Style/StringLiterals:
  Exclude:
    - 'spec/lib/token_util_spec.rb'

# Offense count: 15
# This cop supports unsafe auto-correction (--auto-correct-all).
# Configuration parameters: AllowMethodsWithArguments, IgnoredMethods.
# IgnoredMethods: respond_to, define_method
Style/SymbolProc:
  Exclude:
    - 'app/models/assets/import.rb'
    - 'lib/label_template_setup.rb'
    - 'lib/parsers/csv_metadata/headers_parser.rb'
    - 'lib/support_n3.rb'
    - 'spec/controllers/steps_controller_spec.rb'
    - 'spec/models/steps/cancellable_spec.rb'

# Offense count: 9
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: EnforcedStyle, AllowSafeAssignment.
# SupportedStyles: require_parentheses, require_no_parentheses, require_parentheses_when_complex
Style/TernaryParentheses:
  Exclude:
    - 'app/helpers/activities_helper.rb'
    - 'app/helpers/application_helper.rb'
    - 'lib/changes_support/disjoint_list.rb'
    - 'lib/fact_changes.rb'
    - 'spec/models/condition_spec.rb'
    - 'spec/models/step_execution_spec.rb'
    - 'spec/models/step_spec.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
# Configuration parameters: ExactNameMatch, AllowPredicates, AllowDSLWriters, IgnoreClassMethods, AllowedMethods.
# AllowedMethods: to_ary, to_a, to_c, to_enum, to_h, to_hash, to_i, to_int, to_io, to_open, to_path, to_proc, to_r, to_regexp, to_str, to_s, to_sym
Style/TrivialAccessors:
  Exclude:
    - 'lib/support_n3.rb'

# Offense count: 1
# This cop supports safe auto-correction (--auto-correct).
Style/UnlessElse:
  Exclude:
    - 'spec/inferences_helper.rb'

# Offense count: 19
# This cop supports unsafe auto-correction (--auto-correct-all).
Style/ZeroLengthPredicate:
  Exclude:
    - 'app/models/action.rb'
    - 'app/models/asset.rb'
    - 'app/models/asset_group.rb'
    - 'app/models/assets/traction_fields.rb'
    - 'app/models/steps/task.rb'
    - 'lib/changes_support/transaction_scope.rb'
    - 'lib/fact_changes.rb'
    - 'lib/parsers/csv_layout/line_parser.rb'
    - 'lib/parsers/csv_metadata/line_parser.rb'
    - 'script/runners/transfer_tubes_to_tube_rack_by_position.rb'