.rubocop_todo.yml
# This configuration was generated by
# `rubocop --auto-gen-config --exclude-limit 10000`
# on 2024-03-15 15:37:36 UTC using RuboCop version 1.61.0.
# 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: 17
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: have_no, not_to
Capybara/NegationMatcher:
Exclude:
- 'features/support/step_definitions/web_steps.rb'
- 'spec/features/assets/asset_submission_spec.rb'
- 'spec/features/patient_consent_withdrawl_spec.rb'
- 'spec/features/pipelines/cherrypick/cherrypick_pipeline_spec.rb'
- 'spec/features/pipelines/sequencing/following_a_sequencing_pipeline_spec.rb'
- 'spec/features/sample_logistics/lab/stock_stamping_spec.rb'
- 'spec/features/sample_manifests/create_manifest_spec.rb'
- 'spec/features/shared_examples/sequencing.rb'
- 'spec/features/studies/change_study_roles_spec.rb'
- 'spec/features/studies/create_study_spec.rb'
- 'spec/features/studies/manage_study_spec.rb'
- 'spec/features/studies/view_study_request_links_spec.rb'
- 'spec/helpers/deprecation_helper_spec.rb'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: DefaultSelector.
Capybara/RSpec/HaveSelector:
Exclude:
- 'spec/features/plate_qc_display_spec.rb'
# Offense count: 21
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: AllowedMethods, AllowedPatterns.
Lint/AmbiguousBlockAssociation:
Exclude:
- 'features/support/step_definitions/bulk_submission_steps.rb'
- 'spec/features/sample_manifests/uploader_for_manifests_with_tag_sequences_spec.rb'
- 'spec/features/studies/accession_all_samples_spec.rb'
- 'spec/lib/accession/study_spec.rb'
- 'spec/lib/accession/submission_spec.rb'
- 'spec/sample_manifest_excel/worksheet_spec.rb'
- 'spec/sequencescape_excel/column_list_spec.rb'
- 'spec/sequencescape_excel/column_spec.rb'
- 'spec/sequencescape_excel/conditional_formatting_list_spec.rb'
- 'test/controllers/admin_users_controller_test.rb'
- 'test/unit/tasks/plate_transfer_task_test.rb'
# Offense count: 7
# This cop supports unsafe autocorrection (--autocorrect-all).
Lint/BooleanSymbol:
Exclude:
- 'app/models/qc_file.rb'
- 'lib/authenticated_system.rb'
- 'test/controllers/batches_controller_test.rb'
# Offense count: 15
# Configuration parameters: AllowedMethods.
# AllowedMethods: enums
Lint/ConstantDefinitionInBlock:
Exclude:
- 'app/jobs/asset_link/builder_job.rb'
- 'app/jobs/sample_accessioning_job.rb'
- 'app/models/sample.rb'
- 'app/models/study.rb'
- 'features/support/timecop.rb'
- 'lib/tasks/add_heron_product.rake'
- 'lib/tasks/add_templates_and_printers_to_pmb.rake'
- 'spec/lib/accession/accessionable_spec.rb'
- 'spec/sample_manifest_excel/tags_spec.rb'
- 'spec/sequencescape_excel/list_spec.rb'
- 'test/unit/qc_report_presenter_test.rb'
# Offense count: 17
# Configuration parameters: IgnoreLiteralBranches, IgnoreConstantBranches.
Lint/DuplicateBranch:
Exclude:
- 'app/api/core/io/base/json_formatting_behaviour/input.rb'
- 'app/api/core/io/json/stream.rb'
- 'app/helpers/submissions_helper.rb'
- 'app/models/aliquot.rb'
- 'app/models/receptacle.rb'
- 'app/models/sample.rb'
- 'app/models/submission/submission_creator.rb'
- 'app/models/submission_template.rb'
- 'app/models/well.rb'
- 'features/support/step_definitions/order_steps.rb'
- 'test/shoulda_macros/sanger_macros.rb'
# Offense count: 9
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: 1
# This cop supports safe autocorrection (--autocorrect).
Lint/DuplicateRegexpCharacterClassElement:
Exclude:
- 'app/models/barcode/format_handlers.rb'
# Offense count: 67
# Configuration parameters: AllowComments, AllowEmptyLambdas.
Lint/EmptyBlock:
Exclude:
- 'app/api/core/endpoint/basic_handler/actions/inner_action.rb'
- 'app/api/endpoints/asset_groups.rb'
- 'app/api/endpoints/assets.rb'
- 'app/api/endpoints/barcode_printers.rb'
- 'app/api/endpoints/batches.rb'
- 'app/api/endpoints/comments.rb'
- 'app/api/endpoints/lanes.rb'
- 'app/api/endpoints/lot_types.rb'
- 'app/api/endpoints/lots.rb'
- 'app/api/endpoints/order_templates.rb'
- 'app/api/endpoints/orders.rb'
- 'app/api/endpoints/pipelines.rb'
- 'app/api/endpoints/plate_templates.rb'
- 'app/api/endpoints/plates.rb'
- 'app/api/endpoints/projects.rb'
- 'app/api/endpoints/qcables.rb'
- 'app/api/endpoints/request_types.rb'
- 'app/api/endpoints/requests.rb'
- 'app/api/endpoints/robots.rb'
- 'app/api/endpoints/samples.rb'
- 'app/api/endpoints/searches.rb'
- 'app/api/endpoints/studies.rb'
- 'app/api/endpoints/submission_pools.rb'
- 'app/api/endpoints/suppliers.rb'
- 'app/api/endpoints/tag2_layout_templates.rb'
- 'app/api/endpoints/tag_groups.rb'
- 'app/api/endpoints/tag_layout_templates.rb'
- 'app/api/endpoints/transfer_requests.rb'
- 'app/api/endpoints/transfer_templates.rb'
- 'app/api/endpoints/transfers.rb'
- 'app/api/endpoints/tubes.rb'
- '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'
- 'db/seeds/0001_workflows.rb'
- 'lib/tasks/cucumber.rake'
- 'lib/validateable.rb'
- 'spec/factories/fragments.rb'
- 'spec/factories/qc_assays_factories.rb'
- 'spec/factories/racked_tube.rb'
- 'spec/factories/receptacles.rb'
- 'spec/factories/request_metadata.rb'
- 'spec/factories/submission_factories.rb'
- 'spec/factories/tasks.rb'
- 'spec/features/submissions/bulk_submissions_spec.rb'
- 'spec/requests/api/v2/plates_spec.rb'
- 'test/controllers/samples_controller_test.rb'
- 'test/factories/location_report_factories.rb'
- 'test/unit/data_release_test.rb'
- 'test/unit/fragment_test.rb'
- 'test/unit/tasks/plate_transfer_task_test.rb'
# Offense count: 1
# Configuration parameters: AllowComments.
Lint/EmptyFile:
Exclude:
- 'features/support/step_definitions/25387227_transfer_requests_request_type.rb'
# Offense count: 3
Lint/IneffectiveAccessModifier:
Exclude:
- 'app/helpers/plates_helper.rb'
- 'app/models/event_sender.rb'
- 'lib/authenticated_system.rb'
# Offense count: 29
# Configuration parameters: AllowedParentClasses.
Lint/MissingSuper:
Exclude:
- 'app/api/core/endpoint/basic_handler/actions/guards.rb'
- 'app/models/delegate_validation.rb'
- 'app/models/no_accession_service.rb'
- 'app/models/request/change_decision.rb'
- 'app/models/sample_manifest/library_tube_behaviour.rb'
- 'app/models/sample_manifest/multiplexed_library_behaviour.rb'
- 'app/models/sample_manifest/sample_tube_behaviour.rb'
- 'app/models/sample_manifest/tube_rack_behaviour.rb'
- '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: 3
# Configuration parameters: AllowedMethods, AllowedPatterns.
Lint/NestedMethodDefinition:
Exclude:
- 'app/api/endpoints/uuids.rb'
- 'app/middleware/api/root_service.rb'
- 'lib/eventful_record.rb'
# Offense count: 4
Lint/NonLocalExitFromIterator:
Exclude:
- 'app/api/core/io/base/json_formatting_behaviour/input.rb'
- 'app/api/core/io/json/grammar.rb'
- 'app/models/create_asset_request.rb'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
Lint/RedundantCopDisableDirective:
Enabled: false
# Offense count: 4
Lint/ReturnInVoidContext:
Exclude:
- 'app/models/qc_metric.rb'
- 'app/models/submission/request_options_behaviour.rb'
# Offense count: 24
Lint/ShadowingOuterLocalVariable:
Exclude:
- 'app/api/core/abilities.rb'
- 'app/api/core/io/base/json_formatting_behaviour/output.rb'
- 'app/api/core/io/json/grammar.rb'
- 'app/middleware/api/endpoint_handler.rb'
- 'app/models/bulk_submission.rb'
- 'app/models/external_release_event.rb'
- 'app/models/plate_volume.rb'
- 'app/models/submission/linear_request_graph.rb'
- 'features/support/step_definitions/4560014_refactoring_properties_descriptors_etc_to_table_columns_steps.rb'
- 'features/support/step_definitions/65192392_tag_qc_steps.rb'
- 'features/support/step_definitions/study_steps.rb'
- 'lib/api_tools.rb'
- 'spec/features/pipelines/cherrypick/cherrypick_for_fluidigm_pipeline_micro_litre_spec.rb'
- 'test/unit/accession_service_test.rb'
- 'test/unit/api/core/io/json/grammar_test.rb'
- 'test/unit/api/core/io/json/stream_test.rb'
# Offense count: 1
Lint/StructNewOverride:
Exclude:
- 'app/models/product_criteria/basic.rb'
# Offense count: 3
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: strict, consistent
Lint/SymbolConversion:
Exclude:
- 'lib/authenticated_test_helper.rb'
- 'lib/informatics/test/helpers/authentication_helper.rb'
- 'spec/factories/sample_manifest_excel/columns.rb'
# Offense count: 5
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: AutoCorrect, ContextCreatingMethods, MethodCreatingMethods.
Lint/UselessAccessModifier:
Exclude:
- 'app/api/model_extensions/robot.rb'
- 'app/models/accessionable/sample.rb'
- 'app/models/accessionable/submission.rb'
- 'app/models/event_sender.rb'
- 'app/models/product_criteria/basic.rb'
# Offense count: 67
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: AutoCorrect.
Lint/UselessAssignment:
Exclude:
- 'app/api/core/endpoint/basic_handler/actions/bound.rb'
- 'app/api/core/endpoint/basic_handler/actions/bound/handler.rb'
- 'app/api/core/endpoint/basic_handler/endpoint_lookup.rb'
- 'app/api/core/io/json/grammar.rb'
- 'app/api/core/io/registry.rb'
- 'app/controllers/admin/studies_controller.rb'
- 'app/controllers/pipelines_controller.rb'
- 'app/controllers/projects_controller.rb'
- 'app/controllers/samples_controller.rb'
- 'app/controllers/studies_controller.rb'
- 'app/helpers/application_helper.rb'
- 'app/middleware/api/endpoint_handler.rb'
- 'app/models/accession_service.rb'
- 'app/models/accessionable/base.rb'
- 'app/models/accessionable/study.rb'
- 'app/models/asset_shape.rb'
- 'app/models/labwhere_reception.rb'
- 'app/models/pac_bio/worksheet.rb'
- 'app/models/parsers/bioanalysis_csv_parser.rb'
- 'app/models/plate_volume.rb'
- 'app/models/request/change_decision.rb'
- 'app/models/request_type/validation.rb'
- 'app/models/single_request_submission.rb'
- 'app/models/user/authentication.rb'
- 'app/models/uuid.rb'
- 'features/support/paths.rb'
- 'features/support/step_definitions/10071597_change_request_type_on_request_steps.rb'
- 'features/support/step_definitions/11438075_request_xml_exception_on_nil_study_steps.rb'
- 'features/support/step_definitions/20530077_weird_submission_link_behaviour.rb'
- 'features/support/step_definitions/3673146_tables_with_multiple_criteria_steps.rb'
- 'features/support/step_definitions/4759010_bug_on_reset_batches_steps.rb'
- 'features/support/step_definitions/5004860_change_decision_by_request_steps.rb'
- 'features/support/step_definitions/65192392_tag_qc_steps.rb'
- 'features/support/step_definitions/6679401_batch_request_recycling_broken_steps.rb'
- 'features/support/step_definitions/api_steps.rb'
- 'features/support/step_definitions/order_steps.rb'
- 'features/support/step_definitions/pipeline_steps.rb'
- 'features/support/step_definitions/samples_steps.rb'
- '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'
- 'test/lib/label_printer/plate_creator_test.rb'
- 'test/unit/tasks/plate_transfer_task_test.rb'
# Offense count: 4
# Configuration parameters: AllowedMethods, AllowedPatterns, CountRepeatedAttributes.
Metrics/AbcSize:
Max: 24
# Offense count: 1
# Configuration parameters: CountComments, CountAsOne.
Metrics/ClassLength:
Max: 205
# Offense count: 2
# Configuration parameters: AllowedMethods, AllowedPatterns.
Metrics/CyclomaticComplexity:
Max: 9
# Offense count: 2
# Configuration parameters: CountComments, CountAsOne, AllowedMethods, AllowedPatterns.
Metrics/MethodLength:
Max: 12
# Offense count: 1
# Configuration parameters: AllowedMethods, AllowedPatterns.
Metrics/PerceivedComplexity:
Max: 10
# Offense count: 14
Naming/AccessorMethodName:
Exclude:
- 'app/api/core/io/base/json_formatting_behaviour.rb'
- 'app/api/core/io/base/json_formatting_behaviour/input.rb'
- 'app/controllers/studies/documents_controller.rb'
- 'app/models/asset/ownership.rb'
- 'app/models/broadcast_event.rb'
- 'app/models/lib_pool_norm_tube_generator.rb'
- 'app/models/receptacle.rb'
- 'app/models/specific_tube_creation.rb'
- 'app/models/well.rb'
- 'lib/authenticated_system.rb'
- 'lib/tasks/add_templates_and_printers_to_pmb.rake'
# Offense count: 6
Naming/ConstantName:
Exclude:
- 'app/models/accession_service.rb'
- 'app/models/study.rb'
- 'app/models/submission/state_machine.rb'
- 'app/models/uuid.rb'
# Offense count: 2
# 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:
- 'features/support/step_definitions/11803383_bug_NPG_batch_state_released_steps.rb'
- 'features/support/step_definitions/641709_create_duplicate_SE_pipeline_with_no_controls_steps.rb'
# Offense count: 1
# Configuration parameters: ForbiddenDelimiters.
# ForbiddenDelimiters: (?i-mx:(^|\s)(EO[A-Z]{1}|END)(\s|$))
Naming/HeredocDelimiterNaming:
Exclude:
- 'db/seeds/0001_snp_plate_purposes.rb'
# Offense count: 11
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: EnforcedStyleForLeadingUnderscores.
# SupportedStylesForLeadingUnderscores: disallowed, required, optional
Naming/MemoizedInstanceVariableName:
Exclude:
- 'app/helpers/workflows_helper.rb'
- 'app/models/batch/pipeline_behaviour.rb'
- 'app/models/fluidigm_file.rb'
- 'app/models/metadata.rb'
- 'app/models/plate.rb'
- 'app/models/presenters/grouped_pipeline_inbox_presenter.rb'
- 'app/models/submission/flexible_request_graph.rb'
- 'app/models/tag_layout.rb'
- 'app/models/user_query.rb'
- 'app/uat_actions/uat_actions/generate_tag_group.rb'
# Offense count: 12
# Configuration parameters: MinNameLength, AllowNamesEndingInNumbers, AllowedNames, ForbiddenNames.
# AllowedNames: as, at, by, cc, db, id, if, in, io, ip, of, on, os, pp, to
Naming/MethodParameterName:
Exclude:
- 'app/api/model_extensions/stamp.rb'
- 'app/models/asset_shape.rb'
- 'app/models/map.rb'
- 'features/support/step_definitions/api_steps.rb'
- 'lib/informatics/lib/informatics/application.rb'
- 'lib/informatics/lib/informatics/controller_helper.rb'
- 'lib/oligo_enumerator.rb'
- 'lib/submission_serializer.rb'
# Offense count: 38
# 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/api/core/endpoint/basic_handler/associations/has_file.rb'
- 'app/api/core/endpoint/basic_handler/associations/has_many.rb'
- 'app/api/core/io/json/stream.rb'
- 'app/api/core/registry.rb'
- 'app/models/asset.rb'
- 'app/models/asset/stock.rb'
- 'app/models/asset_link.rb'
- 'app/models/batch.rb'
- 'app/models/batch/pipeline_behaviour.rb'
- 'app/models/broadcast_event/metadata_helpers.rb'
- 'app/models/broadcast_event/subject_helpers.rb'
- 'app/models/db_file.rb'
- 'app/models/descriptor.rb'
- 'app/models/document.rb'
- 'app/models/extraction_attribute.rb'
- 'app/models/metadata.rb'
- 'app/models/pipeline.rb'
- 'app/models/qc_file.rb'
- 'app/models/qc_report/file.rb'
- 'app/models/request.rb'
- 'app/models/sequencing_pipeline.rb'
- 'app/models/submission/asset_submission_finder.rb'
- 'lib/eventful_record.rb'
- 'lib/has_behaviour.rb'
- 'lib/manifest_util.rb'
# Offense count: 242
# Configuration parameters: EnforcedStyle, CheckMethodNames, CheckSymbols, AllowedIdentifiers, AllowedPatterns.
# SupportedStyles: snake_case, normalcase, non_integer
# AllowedIdentifiers: capture3, iso8601, rfc1123_date, rfc822, rfc2822, rfc3339, x86_64
Naming/VariableNumber:
Exclude:
- 'app/controllers/quad_stamp_controller.rb'
- 'app/models/transfer_request.rb'
- 'config/application.rb'
- 'db/seeds/0015_transfer_templates.rb'
- 'spec/api/asset_audit_spec.rb'
- 'spec/controllers/api/v2/heron/tube_racks_controller_spec.rb'
- 'spec/controllers/labwhere_receptions_controller_spec.rb'
- 'spec/controllers/report_fails_controller_spec.rb'
- 'spec/factories/accession/tags.rb'
- 'spec/factories/purpose_factories.rb'
- 'spec/factories/sample_manifest_factories.rb'
- 'spec/features/creating_a_quad_stamp_spec.rb'
- 'spec/features/location_reports/location_reports_spec.rb'
- 'spec/features/pipelines/cherrypick/cherrypick_pipeline_spec.rb'
- '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/labware_spec.rb'
- 'spec/models/labwhere_reception_spec.rb'
- 'spec/models/linear_submission_spec.rb'
- 'spec/models/location_report_form_spec.rb'
- 'spec/models/location_report_spec.rb'
- 'spec/models/phi_x/stock_spec.rb'
- 'spec/models/qc_result/qc_result_factory_spec.rb'
- 'spec/models/report_fail_spec.rb'
- 'spec/models/robot/pick_data_spec.rb'
- 'spec/models/robot/verification/source_dest_beds_spec.rb'
- 'spec/models/robot/verification/source_dest_control_beds_spec.rb'
- 'spec/models/study_spec.rb'
- 'spec/models/submission_spec.rb'
- 'spec/models/tag_group_spec.rb'
- 'spec/models/transfer_request_spec.rb'
- 'spec/models/well_spec.rb'
- 'spec/requests/api/v2/pick_lists_spec.rb'
- 'spec/requests/api/v2/plates_spec.rb'
- 'spec/requests/api/v2/qc_assays_spec.rb'
- 'spec/requests/api/v2/qc_results_spec.rb'
- 'spec/sequencescape_excel/conditional_formatting_list_spec.rb'
- 'spec/uat_actions/generate_plates_spec.rb'
- 'spec/uat_actions/generate_tagged_plates_spec.rb'
- 'test/controllers/projects_controller_test.rb'
- 'test/performance/work_completion_tubes_test.rb'
- 'test/unit/batch_test.rb'
- 'test/unit/product_criteria_test.rb'
- 'test/unit/tag_qc/stamp_test.rb'
# Offense count: 6
# Configuration parameters: MinSize.
Performance/CollectionLiteralInLoop:
Exclude:
- 'db/seeds/3000_library_types_setup.rb'
- 'features/support/step_definitions/6040471_truncate_sample_name_barcode_steps.rb'
- 'features/support/step_definitions/pulldown_steps.rb'
- 'features/support/step_definitions/sample_manifest_steps.rb'
- 'script/spec'
- 'spec/models/transfer_request_spec.rb'
# Offense count: 25
Performance/MethodObjectAsBlock:
Exclude:
- 'app/api/core/endpoint/basic_handler/endpoint_lookup.rb'
- 'app/api/core/io/base/json_formatting_behaviour/input.rb'
- 'app/api/core/io/base/json_formatting_behaviour/output.rb'
- 'app/api/endpoints/uuids.rb'
- 'app/models/bulk_submission.rb'
- 'app/models/cherrypick/task/pick_by_nano_grams.rb'
- 'app/models/cherrypick/task/pick_by_nano_grams_per_micro_litre.rb'
- 'app/models/request/statistics.rb'
- 'features/support/step_definitions/6679401_batch_request_recycling_broken_steps.rb'
- 'features/support/step_definitions/aliquot_steps.rb'
- 'features/support/step_definitions/bait_library_steps.rb'
- 'features/support/step_definitions/pulldown_steps.rb'
- 'features/support/step_definitions/tag_layout_steps.rb'
- 'features/support/step_definitions/transfer_steps.rb'
- 'lib/tasks/report.rake'
# Offense count: 19
# This cop supports safe autocorrection (--autocorrect).
Performance/StringIdentifierArgument:
Exclude:
- 'app/models/role/user_role_helper.rb'
- 'app/models/search_behaviour.rb'
- 'app/models/submission/presenter_skeleton.rb'
- 'app/models/transfer/state.rb'
- 'app/sequencescape_excel/sequencescape_excel/column.rb'
- 'app/sequencescape_excel/sequencescape_excel/configuration.rb'
- 'app/sequencescape_excel/sequencescape_excel/helpers/attributes.rb'
- 'app/sequencescape_excel/sequencescape_excel/subclass_checker.rb'
- 'features/support/step_definitions/5393882_spiked_in_control_steps.rb'
- 'lib/accession/accession.rb'
- 'lib/accession/accession/configuration.rb'
- 'spec/models/user_spec.rb'
# Offense count: 3
RSpec/AnyInstance:
Exclude:
- 'spec/models/lane_spec.rb'
- 'spec/models/sample_spec.rb'
# Offense count: 24
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'
- 'spec/sample_manifest_excel/tags_spec.rb'
- 'spec/sample_manifest_excel/test_download_spec.rb'
- 'spec/sample_manifest_excel/upload/data_spec.rb'
- 'spec/sample_manifest_excel/upload/rows_spec.rb'
- 'spec/sample_manifest_excel/upload/upload_spec.rb'
- 'spec/sample_manifest_excel/worksheet_spec.rb'
- 'spec/sequencescape_excel/worksheet_spec.rb'
# Offense count: 335
# Configuration parameters: Prefixes, AllowedPatterns.
# Prefixes: when, with, without
RSpec/ContextWording:
Exclude:
- 'spec/api/extraction_attributes_spec.rb'
- 'spec/api/plate_purpose_spec.rb'
- 'spec/api/submission_pool_spec.rb'
- 'spec/bulk_submission_excel/data_worksheet_spec.rb'
- 'spec/bulk_submission_excel/download_spec.rb'
- 'spec/controllers/admin/primer_panels_controller_spec.rb'
- 'spec/controllers/lab_searches_controller_spec.rb'
- 'spec/controllers/labwhere_receptions_controller_spec.rb'
- 'spec/controllers/searches_controller_spec.rb'
- 'spec/controllers/submissions_controller_spec.rb'
- 'spec/features/gpl207_bug_incorrect_submission_id_on_transfer_spec.rb'
- 'spec/features/patient_consent_withdrawl_spec.rb'
- '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/lib/accession/study_spec.rb'
- 'spec/lib/label_printer/asset_labels_spec.rb'
- 'spec/lib/label_printer/asset_redirect_spec.rb'
- 'spec/lib/label_printer/batch_plate_spec.rb'
- 'spec/lib/label_printer/sample_manifest_plate_double_spec.rb'
- 'spec/lib/record_loader/plate_purpose_loader_spec.rb'
- 'spec/models/aliquot_spec.rb'
- 'spec/models/api/messages/qc_result_io_spec.rb'
- 'spec/models/api/request_io_spec.rb'
- 'spec/models/bait_library_type_spec.rb'
- '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'
- 'spec/models/location_report_spec.rb'
- 'spec/models/lot_type_spec.rb'
- 'spec/models/orders/order_spec.rb'
- 'spec/models/plate_spec.rb'
- 'spec/models/qc_report_spec.rb'
- 'spec/models/qc_result/qc_result_factory_spec.rb'
- 'spec/models/request/traction/grid_ion_spec.rb'
- 'spec/models/request_event_spec.rb'
- 'spec/models/request_spec.rb'
- 'spec/models/sample_manifest_spec.rb'
- 'spec/models/sample_spec.rb'
- 'spec/models/sequencing_request_spec.rb'
- 'spec/models/study_spec.rb'
- 'spec/models/submission/submission_creator_spec.rb'
- 'spec/models/tag_group_spec.rb'
- 'spec/models/tag_layout_spec.rb'
- 'spec/models/tag_layout_template_spec.rb'
- 'spec/models/transfer_request_collection_spec.rb'
- 'spec/models/transfer_request_spec.rb'
- 'spec/models/well_spec.rb'
- 'spec/models/work_order_spec.rb'
- 'spec/models/work_order_type_spec.rb'
- 'spec/resources/api/v2/plate_resource_spec.rb'
- 'spec/resources/api/v2/request_resource_spec.rb'
- 'spec/resources/api/v2/well_resource_spec.rb'
- 'spec/resources/api/v2/work_order_resource_spec.rb'
- 'spec/sample_manifest_excel/download_spec.rb'
- 'spec/sample_manifest_excel/tags_spec.rb'
- 'spec/sample_manifest_excel/upload/row_spec.rb'
- 'spec/sample_manifest_excel/upload/upload_spec.rb'
- 'spec/sample_manifest_excel/worksheet_spec.rb'
- 'spec/sequencescape_excel/column_spec.rb'
- 'spec/sequencescape_excel/conditional_formatting_default_spec.rb'
- 'spec/shared_contexts/limber_shared_context.rb'
- 'spec/uat_actions/integration_suite_tools_spec.rb'
- 'spec/uat_actions/test_submission_spec.rb'
# Offense count: 4
# This cop supports unsafe autocorrection (--autocorrect-all).
RSpec/EmptyExampleGroup:
Exclude:
- 'spec/models/illumina_htp/initial_stock_tube_purpose_spec.rb'
- 'spec/models/pulldown/requests_spec.rb'
- 'spec/models/tag_substitutions_spec.rb'
# Offense count: 345
# Configuration parameters: CountAsOne.
RSpec/ExampleLength:
Max: 21
# Offense count: 274
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: CustomTransform, IgnoredWords, DisallowedExamples.
# DisallowedExamples: works
RSpec/ExampleWording:
Exclude:
- '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/parsers/cardinal_pbmc_count_parser_spec.rb'
- 'spec/models/plate/quad_creator_spec.rb'
- 'spec/models/qc_result/qc_result_factory_spec.rb'
- 'spec/models/qcable_creator_spec.rb'
- 'spec/models/sample_manifest/generator_spec.rb'
- 'spec/models/sample_manifest/uploader_spec.rb'
- 'spec/models/sample_spec.rb'
- 'spec/models/study_spec.rb'
- 'spec/models/transfer_request_spec.rb'
- 'spec/sample_manifest_excel/configuration_spec.rb'
- 'spec/sample_manifest_excel/upload/processor_spec.rb'
- 'spec/sample_manifest_excel/worksheet_spec.rb'
- 'spec/sequencescape_excel/column_spec.rb'
- 'spec/sequencescape_excel/conditional_formatting_spec.rb'
- 'spec/sequencescape_excel/configuration_spec.rb'
- 'spec/sequencescape_excel/range_list_spec.rb'
- 'spec/sequencescape_excel/specialised_field_spec.rb'
- 'spec/sequencescape_excel/validation_spec.rb'
- 'spec/sequencescape_excel/worksheet_spec.rb'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
RSpec/ExpectActual:
Exclude:
- 'spec/models/qc_report_spec.rb'
# Offense count: 12
# Configuration parameters: Include, CustomTransform, IgnoreMethods, SpecSuffixOnly.
# Include: **/*_spec*rb*, **/spec/**/*
RSpec/FilePath:
Exclude:
- 'spec/bulk_submission_excel/data_worksheet_spec.rb'
- 'spec/lib/accession/configuration_spec.rb'
- 'spec/lib/label_printer/sample_manifest_plate_double_spec.rb'
- 'spec/models/location_report_form_spec.rb'
- 'spec/models/std_library_request_spec.rb'
- 'spec/models/tag_group_form_object_spec.rb'
- 'spec/models/tube_purpose_spec.rb'
- 'spec/requests/api/v2/qc_assays_spec.rb'
- 'spec/requests/api/v2/qc_results_spec.rb'
- 'spec/resources/api/v2/project_resource_spec.rb'
- 'spec/sample_manifest_excel/upload/upload_spec.rb'
- 'spec/sequencescape_excel/configuration_spec.rb'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: implicit, each, example
RSpec/HookArgument:
Exclude:
- 'spec/spec_helper.rb'
# Offense count: 248
# 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'
- 'spec/models/request_event_spec.rb'
- 'spec/models/request_spec.rb'
- 'spec/models/request_type_spec.rb'
- 'spec/models/stock_stamper_spec.rb'
- 'spec/models/well_spec.rb'
- 'spec/sequencescape_excel/list_spec.rb'
- 'spec/shared_contexts/it_requires_login.rb'
# Offense count: 4
RSpec/IteratedExpectation:
Exclude:
- 'spec/features/pipelines/cherrypick/cherrypick_for_fluidigm_pipeline_micro_litre_spec.rb'
- 'spec/models/sample_spec.rb'
- 'spec/sample_manifest_excel/upload/upload_spec.rb'
# Offense count: 4
# This cop supports safe autocorrection (--autocorrect).
RSpec/LeadingSubject:
Exclude:
- 'spec/api/tag_layout_template_spec.rb'
- 'spec/api/transfer_request_collection_spec.rb'
- 'spec/api/work_completion_spec.rb'
- 'spec/models/plate_spec.rb'
# Offense count: 5
RSpec/LeakyConstantDeclaration:
Exclude:
- 'spec/lib/accession/accessionable_spec.rb'
- 'spec/sample_manifest_excel/tags_spec.rb'
- 'spec/sequencescape_excel/list_spec.rb'
# Offense count: 39
RSpec/LetSetup:
Exclude:
- 'spec/controllers/searches_controller_spec.rb'
- 'spec/features/assets/asset_submission_spec.rb'
- 'spec/features/location_reports/location_reports_spec.rb'
- 'spec/features/pipelines/cherrypick/cherrypick_for_fluidigm_pipeline_micro_litre_spec.rb'
- 'spec/features/sample_manifests/track_sample_manifest_updates_spec.rb'
- 'spec/lib/accession/study_spec.rb'
- 'spec/models/api/messages/flowcell_io_spec.rb'
- 'spec/models/broadcast_event/sequencing_complete_spec.rb'
- 'spec/models/bulk_submission_spec.rb'
- 'spec/models/external_release_event_spec.rb'
- 'spec/models/qc_result/qc_result_factory_spec.rb'
- 'spec/models/sample_spec.rb'
- 'spec/models/study_spec.rb'
- 'spec/models/tag2_layout_spec.rb'
- 'spec/models/tag_substitutions_spec.rb'
- 'spec/models/transfer_request_collection_spec.rb'
- 'spec/requests/api/v2/comments_spec.rb'
- 'spec/requests/api/v2/plates_spec.rb'
# Offense count: 40
# Configuration parameters: EnforcedStyle.
# SupportedStyles: have_received, receive
RSpec/MessageSpies:
Exclude:
- 'spec/api/dilution_plate_purpose_spec.rb'
- 'spec/api/plate_purpose_spec.rb'
- 'spec/controllers/labwhere_receptions_controller_spec.rb'
- 'spec/features/asset_information_spec.rb'
- 'spec/features/creating_a_quad_stamp_spec.rb'
- 'spec/features/sample_manifests/create_manifest_spec.rb'
- 'spec/features/sample_manifests/track_sample_manifest_updates_spec.rb'
- 'spec/insdc/import_countries_spec.rb'
- 'spec/lib/accession/study_spec.rb'
- 'spec/lib/method_benchmarking_spec.rb'
- 'spec/lib/migration_extensions/encoding_changes_spec.rb'
- 'spec/models/external_release_event_spec.rb'
- 'spec/models/plate/sample_tube_factory_spec.rb'
- 'spec/models/plate_barcode_spec.rb'
- 'spec/models/plate_purpose_spec.rb'
- 'spec/models/pooling_spec.rb'
- 'spec/models/qc_result/qc_result_spec.rb'
- 'spec/models/tasks/plate_template_task_spec.rb'
- 'spec/sample_manifest_excel/upload/upload_spec.rb'
- 'spec/sequencescape_excel/validation_spec.rb'
- 'spec/tasks/create_mbrave_tags_spec.rb'
- 'spec/uat_actions/test_submission_spec.rb'
# Offense count: 3
RSpec/MultipleDescribes:
Exclude:
- 'spec/api/plate_purpose_spec.rb'
- 'spec/lib/label_printer/asset_labels_spec.rb'
- 'spec/models/qc_result/qc_result_spec.rb'
# Offense count: 815
RSpec/MultipleExpectations:
Max: 18
# Offense count: 959
# Configuration parameters: AllowSubject.
RSpec/MultipleMemoizedHelpers:
Max: 46
# Offense count: 388
# Configuration parameters: EnforcedStyle, IgnoreSharedExamples.
# SupportedStyles: always, named_only
RSpec/NamedSubject:
Exclude:
- 'spec/api/api_root_spec.rb'
- 'spec/api/extraction_attributes_spec.rb'
- 'spec/api/multiplexed_library_tube_spec.rb'
- 'spec/api/plate_purpose_spec.rb'
- 'spec/api/plate_spec.rb'
- 'spec/api/qcable_creator_spec.rb'
- 'spec/api/tag_layout_template_spec.rb'
- 'spec/api/transfer_request_collection_spec.rb'
- 'spec/api/tube_purpose_spec.rb'
- 'spec/api/well_spec.rb'
- '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'
- 'spec/models/api/messages/flowcell_io_spec.rb'
- 'spec/models/api/messages/pac_bio_run_io_spec.rb'
- 'spec/models/api/messages/qc_result_io_spec.rb'
- 'spec/models/api/messages/well_stock_resource_io_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/illumina_htp/requests/gbs_request_spec.rb'
- 'spec/models/lab_event_spec.rb'
- 'spec/models/lot_type_spec.rb'
- 'spec/models/pick_list_spec.rb'
- 'spec/models/pulldown/requests/isc_library_request_spec.rb'
- 'spec/models/request/statistics/counter_spec.rb'
- 'spec/models/request/traction/grid_ion_spec.rb'
- 'spec/models/request_spec.rb'
- 'spec/models/sample_manifest_spec.rb'
- 'spec/models/std_library_request_spec.rb'
- 'spec/models/tag2_layout_spec.rb'
- 'spec/models/tag2_layout_template_spec.rb'
- 'spec/models/tag_layout_template_spec.rb'
- 'spec/models/tag_substitutions_spec.rb'
- 'spec/models/transfer_request_collection_spec.rb'
- 'spec/models/transfer_request_spec.rb'
- 'spec/models/well_spec.rb'
- 'spec/models/work_order_spec.rb'
- 'spec/resources/api/v2/aliquot_resource_spec.rb'
- 'spec/resources/api/v2/comment_resource_spec.rb'
- 'spec/resources/api/v2/custom_metadatum_collection_resource_spec.rb'
- 'spec/resources/api/v2/lane_resource_spec.rb'
- 'spec/resources/api/v2/lot_resource_spec.rb'
- 'spec/resources/api/v2/lot_type_resource_spec.rb'
- 'spec/resources/api/v2/order_resource_spec.rb'
- 'spec/resources/api/v2/pre_capture_pool_resource_spec.rb'
- 'spec/resources/api/v2/primer_panel_resource_spec.rb'
- 'spec/resources/api/v2/project_resource_spec.rb'
- 'spec/resources/api/v2/purpose_resource_spec.rb'
- 'spec/resources/api/v2/qcable_resource_spec.rb'
- 'spec/resources/api/v2/receptacle_resource_spec.rb'
- 'spec/resources/api/v2/request_resource_spec.rb'
- 'spec/resources/api/v2/request_type_resource_spec.rb'
- 'spec/resources/api/v2/sample_metadata_resource_spec.rb'
- 'spec/resources/api/v2/sample_resource_spec.rb'
- 'spec/resources/api/v2/study_resource_spec.rb'
- 'spec/resources/api/v2/submission_resource_spec.rb'
- 'spec/resources/api/v2/tag_group_resource_spec.rb'
- 'spec/resources/api/v2/tag_layout_template_resource_spec.rb'
- 'spec/resources/api/v2/tube_resource_spec.rb'
- 'spec/resources/api/v2/user_resource_spec.rb'
# Offense count: 391
# Configuration parameters: AllowedGroups.
RSpec/NestedGroups:
Max: 6
# Offense count: 10
# This cop supports safe autocorrection (--autocorrect).
RSpec/Rails/MinitestAssertions:
Exclude:
- 'spec/models/robot/generator/beckman_spec.rb'
- 'spec/models/robot/generator/hamilton_spec.rb'
- 'spec/models/robot/generator/tecan_spec.rb'
- 'spec/models/tag_substitutions_spec.rb'
# Offense count: 6
RSpec/RepeatedDescription:
Exclude:
- 'spec/requests/api/v2/plates_spec.rb'
- 'spec/requests/api/v2/submissions_spec.rb'
- 'spec/sequencescape_excel/conditional_formatting_spec.rb'
# Offense count: 2
RSpec/RepeatedExample:
Exclude:
- 'spec/models/sample_manifest/uploader_spec.rb'
# Offense count: 2
RSpec/RepeatedExampleGroupBody:
Exclude:
- 'spec/models/well_spec.rb'
# Offense count: 9
RSpec/RepeatedExampleGroupDescription:
Exclude:
- 'spec/features/sample_manifests/uploader_for_manifests_with_tag_sequences_spec.rb'
- 'spec/features/submissions/bulk_submissions_spec.rb'
- 'spec/resources/api/v2/lot_type_resource_spec.rb'
# Offense count: 25
# This cop supports safe autocorrection (--autocorrect).
RSpec/ScatteredLet:
Exclude:
- 'spec/api/plate_spec.rb'
- 'spec/api/submission_pool_spec.rb'
- 'spec/features/submissions/bulk_submissions_spec.rb'
- 'spec/lib/record_loader/plate_purpose_loader_spec.rb'
- 'spec/models/api/messages/well_stock_resource_io_spec.rb'
- 'spec/models/bulk_submission_spec.rb'
- 'spec/models/qc_result/qc_result_spec.rb'
- 'spec/models/transfer_request_spec.rb'
- 'spec/models/work_completion_spec.rb'
- 'spec/requests/api/v2/work_orders_spec.rb'
# Offense count: 9
RSpec/StubbedMock:
Exclude:
- 'spec/api/dilution_plate_purpose_spec.rb'
- 'spec/api/plate_purpose_spec.rb'
- 'spec/controllers/labwhere_receptions_controller_spec.rb'
- 'spec/features/asset_information_spec.rb'
- 'spec/features/sample_manifests/create_manifest_spec.rb'
- 'spec/features/sample_manifests/track_sample_manifest_updates_spec.rb'
- 'spec/models/plate_purpose_spec.rb'
- 'spec/uat_actions/test_submission_spec.rb'
# Offense count: 4
RSpec/VoidExpect:
Exclude:
- 'spec/sample_manifest_excel/download_spec.rb'
- 'spec/sample_manifest_excel/test_download_spec.rb'
- 'spec/sequencescape_excel/column_spec.rb'
# Offense count: 2
# This cop supports unsafe autocorrection (--autocorrect-all).
Rails/ApplicationMailer:
Exclude:
- 'app/mailers/user_query_mailer.rb'
- 'lib/eventful_mailer.rb'
# Offense count: 5
# This cop supports unsafe autocorrection (--autocorrect-all).
Rails/CompactBlank:
Exclude:
- 'app/models/bulk_submission.rb'
- 'app/sample_manifest_excel/sample_manifest_excel/upload/base.rb'
- 'features/support/step_definitions/delayed_job_steps.rb'
- 'lib/event_factory.rb'
# Offense count: 15
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: EnforcedStyle, AllowToTime.
# SupportedStyles: strict, flexible
Rails/Date:
Exclude:
- 'app/models/event/plate_creation_event.rb'
- 'app/models/event/sample_logistics_qc_event.rb'
- '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'
- 'test/lib/label_printer/sample_manifest_multiplex_test.rb'
- 'test/lib/label_printer/sample_manifest_plate_test.rb'
- 'test/lib/label_printer/sample_manifest_tube_test.rb'
# Offense count: 2
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: Severity.
Rails/DeprecatedActiveModelErrorsMethods:
Exclude:
- 'app/controllers/batches_controller.rb'
# Offense count: 34
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: slashes, arguments
Rails/FilePath:
Exclude:
- 'app/middleware/api/root_service.rb'
- 'app/uploaders/polymorphic_uploader.rb'
- 'config/application.rb'
- 'config/config.rb'
- 'config/initializers/accession.rb'
- 'config/initializers/failure_reasons.rb'
- 'config/initializers/i18n.rb'
- 'config/initializers/load_config.rb'
- 'config/initializers/sample_manifest_excel.rb'
- 'features/support/step_definitions/49061511_qc_file_steps.rb'
- 'features/support/step_definitions/bulk_submission_steps.rb'
- 'lib/tasks/cucumber.rake'
- 'lib/tasks/sample_manifest_excel_tests.rake'
- 'test/test_helper.rb'
- 'test/unit/fluidigm_file_test.rb'
- 'test/unit/import_fluidigm_data_test.rb'
- 'test/unit/qc_report_file_test.rb'
# Offense count: 124
# Configuration parameters: Include.
# Include: app/models/**/*.rb
Rails/HasManyOrHasOneDependent:
Exclude:
- 'app/models/aliquot/aliquotable.rb'
- 'app/models/asset/ownership.rb'
- 'app/models/asset_group.rb'
- 'app/models/bait_library.rb'
- 'app/models/bait_library_type.rb'
- 'app/models/barcode_prefix.rb'
- 'app/models/barcode_printer_type.rb'
- 'app/models/batch.rb'
- 'app/models/budget_division.rb'
- 'app/models/bulk_transfer.rb'
- 'app/models/comment.rb'
- 'app/models/data_release_study_type.rb'
- 'app/models/faculty_sponsor.rb'
- 'app/models/item.rb'
- 'app/models/lane.rb'
- 'app/models/lot.rb'
- 'app/models/lot_type.rb'
- 'app/models/pipeline.rb'
- 'app/models/plate.rb'
- 'app/models/plate_creation.rb'
- 'app/models/plate_purpose.rb'
- 'app/models/pooled_plate_creation.rb'
- 'app/models/product.rb'
- 'app/models/product_catalogue.rb'
- 'app/models/product_line.rb'
- 'app/models/program.rb'
- 'app/models/project.rb'
- 'app/models/project_manager.rb'
- 'app/models/purpose.rb'
- 'app/models/qc_decision.rb'
- 'app/models/qc_report.rb'
- 'app/models/qcable.rb'
- 'app/models/qcable_creator.rb'
- 'app/models/receptacle.rb'
- 'app/models/reference_genome.rb'
- 'app/models/request.rb'
- 'app/models/request_information_type.rb'
- 'app/models/request_type.rb'
- 'app/models/request_type/pooling_method.rb'
- 'app/models/robot.rb'
- 'app/models/sample.rb'
- 'app/models/sample_manifest.rb'
- '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'
- 'app/models/tag.rb'
- 'app/models/transfer/between_plate_and_tubes.rb'
- 'app/models/tube/purpose.rb'
- 'app/models/tube_creation.rb'
- 'app/models/user.rb'
- 'app/models/well.rb'
- 'app/models/work_order.rb'
# Offense count: 4
# Configuration parameters: Include.
# Include: app/helpers/**/*.rb
Rails/HelperInstanceVariable:
Exclude:
- 'app/helpers/tag_substitution_helper.rb'
- 'app/helpers/workflows_helper.rb'
# Offense count: 19
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: numeric, symbolic
Rails/HttpStatus:
Exclude:
- 'app/controllers/admin/users_controller.rb'
- 'app/controllers/plate_picks_controller.rb'
- 'app/controllers/projects_controller.rb'
- 'app/controllers/studies/documents_controller.rb'
# Offense count: 42
# Configuration parameters: IgnoreScopes, Include.
# Include: app/models/**/*.rb
Rails/InverseOf:
Exclude:
- 'app/models/aliquot/aliquotable.rb'
- 'app/models/bait_library.rb'
- 'app/models/plate.rb'
- 'app/models/plate_creation.rb'
- 'app/models/pooled_plate_creation.rb'
- 'app/models/purpose/relationship.rb'
- 'app/models/qc_file.rb'
- 'app/models/receptacle.rb'
- 'app/models/request.rb'
- 'app/models/request_type.rb'
- 'app/models/robot.rb'
- 'app/models/spiked_buffer.rb'
- 'app/models/study.rb'
- 'app/models/submission_pool.rb'
- 'app/models/submission_template.rb'
- 'app/models/tag_group.rb'
- 'app/models/task.rb'
- 'app/models/transfer/between_plate_and_tubes.rb'
- 'app/models/tube.rb'
- 'app/models/tube/purpose.rb'
- 'app/models/well.rb'
- 'app/models/work_order.rb'
# Offense count: 4
# Configuration parameters: Include.
# Include: app/controllers/**/*.rb, app/mailers/**/*.rb
Rails/LexicallyScopedActionFilter:
Exclude:
- 'app/controllers/admin/programs_controller.rb'
- 'app/controllers/pipelines_controller.rb'
- 'app/controllers/projects_controller.rb'
- 'app/controllers/sdb/sample_manifests_controller.rb'
# Offense count: 1
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: Include.
# Include: app/**/*.rb, config/**/*.rb, db/**/*.rb, lib/**/*.rb
Rails/Output:
Exclude:
- 'lib/views_schema.rb'
# Offense count: 8
Rails/OutputSafety:
Exclude:
- 'app/helpers/application_helper.rb'
- 'app/helpers/bootstrap_helper.rb'
- 'app/helpers/submissions_helper.rb'
# Offense count: 2
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: Include.
# Include: **/Rakefile, **/*.rake
Rails/RakeEnvironment:
Exclude:
- 'lib/tasks/views_schema.rake'
# Offense count: 1
# Configuration parameters: TransactionMethods.
Rails/TransactionExitStatement:
Exclude:
- 'app/models/sample_manifest/uploader.rb'
# Offense count: 5
# This cop supports unsafe autocorrection (--autocorrect-all).
Rails/WhereEquals:
Exclude:
- 'app/models/request.rb'
- 'app/models/study.rb'
- 'app/models/transfer/associations.rb'
# Offense count: 4
# This cop supports safe autocorrection (--autocorrect).
Rails/WhereNot:
Exclude:
- 'app/models/qcable.rb'
- 'app/models/request.rb'
- 'app/models/well.rb'
# Offense count: 5
Security/Eval:
Exclude:
- 'app/models/uuid.rb'
- 'lib/tasks/add_templates_and_printers_to_pmb.rake'
- 'test/shoulda_macros/sanger_macros/resource_test.rb'
# Offense count: 1
Security/Open:
Exclude:
- 'app/api/core/io/json/stream.rb'
# Offense count: 4
# This cop supports unsafe autocorrection (--autocorrect-all).
Security/YAMLLoad:
Exclude:
- 'app/models/submission/request_options_behaviour.rb'
- 'config/initializers/failure_reasons.rb'
- 'config/initializers/process_locale_files_with_erb.rb'
- 'db/seeds/0001_snp_plate_purposes.rb'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: AllowOnConstant, AllowOnSelfClass.
Style/CaseEquality:
Exclude:
- 'app/models/parsers/bioanalysis_csv_parser.rb'
# Offense count: 14
Style/ClassVars:
Exclude:
- 'app/models/fluidigm_file.rb'
- 'app/models/implement.rb'
- 'app/models/item.rb'
- 'lib/authenticated_system.rb'
- 'lib/informatics.rb'
- 'lib/informatics/lib/informatics/application.rb'
- 'lib/informatics/lib/informatics/globals.rb'
# Offense count: 30
Style/DocumentDynamicEvalDefinition:
Exclude:
- 'app/api/core/abilities.rb'
- 'app/api/core/endpoint/basic_handler/actions.rb'
- 'app/api/core/endpoint/basic_handler/actions/bound.rb'
- 'app/api/core/endpoint/basic_handler/actions/guards.rb'
- 'app/api/core/endpoint/basic_handler/actions/inner_action.rb'
- 'app/api/core/endpoint/basic_handler/associations/has_many/handler.rb'
- 'app/api/core/initializable.rb'
- 'app/api/core/io/base/json_formatting_behaviour/input.rb'
- 'app/api/core/logging.rb'
- 'app/api/endpoints/studies.rb'
- 'app/api/endpoints/uuids.rb'
- 'app/models/asset_link.rb'
- 'app/models/attributable/association.rb'
- 'app/models/attributable/attribute.rb'
- 'app/models/delegate_validation.rb'
- 'app/models/document.rb'
- 'app/models/metadata.rb'
- 'app/models/metadata/form_builder.rb'
- 'app/models/request/statistics.rb'
- 'app/models/tube.rb'
- 'app/models/validation_state_guard.rb'
- 'app/models/well.rb'
- 'features/support/api.rb'
- 'lib/eventful_record.rb'
# Offense count: 5
# This cop supports safe autocorrection (--autocorrect).
Style/EmptyCaseCondition:
Exclude:
- 'app/api/core/endpoint/basic_handler/actions.rb'
- 'app/api/core/io/json/grammar.rb'
- 'app/models/aliquot.rb'
- 'app/models/request/change_decision.rb'
- 'app/models/request_type.rb'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: AutoCorrect, EnforcedStyle, AllowComments.
# SupportedStyles: empty, nil, both
Style/EmptyElse:
Exclude:
- 'app/controllers/requests/comments_controller.rb'
# Offense count: 8
# This cop supports safe autocorrection (--autocorrect).
Style/EmptyLiteral:
Exclude:
- 'app/api/model_extensions/order.rb'
- 'app/models/api/base.rb'
- 'app/models/bulk_submission.rb'
- 'app/models/metadata.rb'
- 'app/models/submission/presenter_skeleton.rb'
- 'app/models/transfer/from_plate_to_specific_tubes_by_pool.rb'
# Offense count: 4
# This cop supports safe autocorrection (--autocorrect).
Style/Encoding:
Exclude:
- 'app/controllers/bulk_submissions_controller.rb'
- 'app/models/bulk_submission.rb'
- 'app/models/sequencing_request.rb'
- 'config/initializers/formtastic.rb'
# Offense count: 30
# This cop supports safe autocorrection (--autocorrect).
Style/EvalWithLocation:
Exclude:
- 'app/api/core/abilities.rb'
- 'app/api/core/endpoint/basic_handler/actions.rb'
- 'app/api/core/endpoint/basic_handler/actions/bound.rb'
- 'app/api/core/endpoint/basic_handler/actions/guards.rb'
- 'app/api/core/endpoint/basic_handler/actions/inner_action.rb'
- 'app/api/core/endpoint/basic_handler/associations/has_many/handler.rb'
- 'app/api/core/initializable.rb'
- 'app/api/core/io/base/json_formatting_behaviour/input.rb'
- 'app/api/core/logging.rb'
- 'app/api/endpoints/studies.rb'
- 'app/api/endpoints/uuids.rb'
- 'app/models/asset_link.rb'
- 'app/models/attributable/association.rb'
- 'app/models/attributable/attribute.rb'
- 'app/models/delegate_validation.rb'
- 'app/models/document.rb'
- 'app/models/metadata.rb'
- 'app/models/metadata/form_builder.rb'
- 'app/models/request/statistics.rb'
- 'app/models/tube.rb'
- 'app/models/validation_state_guard.rb'
- 'app/models/well.rb'
- 'features/support/api.rb'
- 'lib/eventful_record.rb'
# Offense count: 4
# This cop supports safe autocorrection (--autocorrect).
Style/ExpandPathArguments:
Exclude:
- 'lib/generators/api_v2/api_v2_generator.rb'
- 'script/rails'
- 'spec/rails_helper.rb'
# Offense count: 5
# This cop supports safe autocorrection (--autocorrect).
Style/ExplicitBlockArgument:
Exclude:
- 'app/api/core/service/error_handling.rb'
- 'app/models/messenger_creator.rb'
- 'app/models/study.rb'
- 'app/models/submission/flexible_request_graph.rb'
- 'features/support/step_definitions/web_steps.rb'
# Offense count: 9
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: format, sprintf, percent
Style/FormatString:
Exclude:
- 'app/helpers/plates_helper.rb'
- '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
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: EnforcedStyle, MaxUnannotatedPlaceholdersAllowed, AllowedMethods, AllowedPatterns.
# SupportedStyles: annotated, template, unannotated
# AllowedMethods: redirect
Style/FormatStringToken:
Exclude:
- '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: 2
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: always, always_true, never
Style/FrozenStringLiteralComment:
Exclude:
- 'config/initializers/new_framework_defaults_6_1.rb'
- 'config/initializers/permissions_policy.rb'
# Offense count: 2
# This cop supports unsafe autocorrection (--autocorrect-all).
Style/GlobalStdStream:
Exclude:
- 'config/environments/production.rb'
- 'lib/tasks/limber_dev.rake'
# Offense count: 46
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: MinBodyLength, AllowConsecutiveConditionals.
Style/GuardClause:
Exclude:
- 'app/bulk_submission_excel/bulk_submission_excel/download.rb'
- 'app/controllers/assets_controller.rb'
- 'app/controllers/orders_controller.rb'
- 'app/controllers/plates_controller.rb'
- 'app/controllers/poolings_controller.rb'
- 'app/controllers/quad_stamp_controller.rb'
- 'app/models/batch.rb'
- 'app/models/broadcast_event/helpers/external_subjects.rb'
- 'app/models/bulk_submission.rb'
- 'app/models/cherrypick/volume_by_micro_litre.rb'
- 'app/models/cherrypick/volume_by_nano_grams.rb'
- 'app/models/cherrypick/volume_by_nano_grams_per_micro_litre.rb'
- 'app/models/document.rb'
- 'app/models/extraction_attribute.rb'
- 'app/models/failure.rb'
- 'app/models/lib_pool_norm_tube_generator.rb'
- 'app/models/location_report.rb'
- 'app/models/metadata/form_builder.rb'
- 'app/models/plate_template.rb'
- 'app/models/pooling.rb'
- 'app/models/presenters/grouped_pipeline_inbox_presenter.rb'
- 'app/models/pulldown/requests/bait_library_request.rb'
- 'app/models/qc_file.rb'
- 'app/models/request.rb'
- 'app/models/robot_property.rb'
- 'app/models/sample_manifest.rb'
- 'app/models/study.rb'
- 'app/models/transfer/between_plate_and_tubes.rb'
- 'features/support/step_definitions/tag_layout_steps.rb'
- 'lib/accession/accession/configuration.rb'
- 'lib/accession/accession/request.rb'
- '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'
# Offense count: 28
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: AllowedReceivers.
# AllowedReceivers: Thread.current
Style/HashEachMethods:
Exclude:
- 'app/controllers/gels_controller.rb'
- 'app/models/api/base.rb'
- 'app/models/fluidigm_file.rb'
- 'app/models/pre_capture_pool.rb'
- 'app/models/request/sample_compound_aliquot_transfer.rb'
- 'app/models/request/statemachine.rb'
- 'app/models/tag.rb'
- 'app/models/tag_layout/walk_manual_wells_by_pools.rb'
- 'app/models/tasks/cherrypick_handler.rb'
- 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/tube_rack.rb'
- 'app/sequencescape_excel/sequencescape_excel/worksheet/ranges_worksheet.rb'
- 'app/views/studies/index_deprecated_xml.xml.builder'
- 'config/initializers/rails_rack_metal_fix.rb'
- 'lib/accession/accession/sample.rb'
- 'lib/accession/accession/tag_list.rb'
- 'spec/lib/accession/sample_spec.rb'
- 'spec/models/robot/verification/source_dest_beds_spec.rb'
- 'spec/sample_manifest_excel/configuration_spec.rb'
- 'spec/sequencescape_excel/column_spec.rb'
- 'spec/sequencescape_excel/conditional_formatting_default_list_spec.rb'
- 'spec/sequencescape_excel/configuration_spec.rb'
- 'spec/sequencescape_excel/range_list_spec.rb'
- 'test/unit/fluidigm_file_test.rb'
# Offense count: 5
# This cop supports unsafe autocorrection (--autocorrect-all).
Style/IdenticalConditionalBranches:
Exclude:
- 'app/controllers/studies/documents_controller.rb'
- 'features/support/step_definitions/api_steps.rb'
# Offense count: 3
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: AllowIfModifier.
Style/IfInsideElse:
Exclude:
- 'app/controllers/sessions_controller.rb'
- 'app/models/accession_service.rb'
- 'app/models/bulk_submission.rb'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
Style/IfUnlessModifier:
Exclude:
- 'app/models/delegate_validation.rb'
# Offense count: 5
# This cop supports safe autocorrection (--autocorrect).
Style/IfUnlessModifierOfIfUnless:
Exclude:
- 'app/controllers/admin/studies_controller.rb'
- 'app/models/parsers/plate_reader_parser.rb'
- 'app/models/robot/verification/base.rb'
- 'app/uploaders/polymorphic_uploader.rb'
- 'features/support/step_definitions/display_submitted_at_inbox_pipeline_steps.rb'
# Offense count: 2
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: InverseMethods, InverseBlocks.
Style/InverseMethods:
Exclude:
- 'app/models/batch.rb'
- 'app/models/extended_validator/species_validator.rb'
# Offense count: 1
# This cop supports unsafe autocorrection (--autocorrect-all).
Style/LineEndConcatenation:
Exclude:
- 'features/support/paths.rb'
# Offense count: 7
Style/MissingRespondToMissing:
Exclude:
- 'app/api/core/endpoint/basic_handler/actions/guards.rb'
- 'app/models/request_type/validator.rb'
- 'app/models/submission/order_presenter.rb'
- 'app/models/submission/presenter_skeleton.rb'
- 'lib/authenticated_test_helper.rb'
- 'lib/informatics/test/helpers/authentication_helper.rb'
- 'lib/validateable.rb'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: AllowMethodComparison, ComparisonsThreshold.
Style/MultipleComparison:
Exclude:
- 'app/helpers/application_helper.rb'
# Offense count: 4
# This cop supports safe autocorrection (--autocorrect).
Style/NegatedIfElseCondition:
Exclude:
- 'app/controllers/admin/studies_controller.rb'
- 'app/models/transfer/state.rb'
- 'config/initializers/api_routing.rb'
# Offense count: 5
# This cop supports safe autocorrection (--autocorrect).
Style/NestedModifier:
Exclude:
- 'app/controllers/admin/studies_controller.rb'
- 'app/models/parsers/plate_reader_parser.rb'
- 'app/models/robot/verification/base.rb'
- 'app/uploaders/polymorphic_uploader.rb'
- 'features/support/step_definitions/display_submitted_at_inbox_pipeline_steps.rb'
# Offense count: 3
# 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: 1
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: EnforcedStyle, MinBodyLength.
# SupportedStyles: skip_modifier_ifs, always
Style/Next:
Exclude:
- 'app/views/studies/show.xml.builder'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: predicate, comparison
Style/NilComparison:
Exclude:
- 'app/models/parsers/bioanalysis_csv_parser.rb'
# Offense count: 2
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: IncludeSemanticChanges.
Style/NonNilCheck:
Exclude:
- 'test/unit/product_criteria_test.rb'
- 'test/unit/product_test.rb'
# Offense count: 20
# 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'
- 'app/models/submission/accession_behaviour.rb'
- 'app/models/submission/asset_group_behaviour.rb'
- 'app/models/submission/project_validation.rb'
- 'app/models/user.rb'
- 'app/views/batches/show.xml.builder'
- 'features/support/step_definitions/api_steps.rb'
# Offense count: 32
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: EnforcedStyle, AllowedMethods, AllowedPatterns.
# SupportedStyles: predicate, comparison
Style/NumericPredicate:
Exclude:
- 'app/controllers/admin/bait_libraries/bait_library_suppliers_controller.rb'
- 'app/controllers/admin/bait_libraries/bait_library_types_controller.rb'
- 'app/controllers/plate_templates_controller.rb'
- 'app/models/bulk_submission.rb'
- 'app/models/bulk_transfer.rb'
- 'app/models/extraction_attribute.rb'
- 'app/models/implement.rb'
- 'app/models/map.rb'
- 'app/models/sequencing_pipeline.rb'
- '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_version.rb'
- 'lib/submission_serializer.rb'
- 'test/shoulda_macros/sanger_macros/resource_test.rb'
# Offense count: 18
# Configuration parameters: AllowedMethods.
# AllowedMethods: respond_to_missing?
Style/OptionalBooleanParameter:
Exclude:
- 'app/api/core/endpoint/basic_handler/actions/guards.rb'
- 'app/controllers/studies_controller.rb'
- 'app/models/accessionable/base.rb'
- 'app/models/attributable.rb'
- 'app/models/batch.rb'
- 'app/models/external_release_event.rb'
- 'app/models/metadata.rb'
- 'app/models/pipeline.rb'
- 'app/models/pipeline/group_by_parent.rb'
- 'app/models/pipeline/inbox_extensions.rb'
- 'app/models/presenters/grouped_pipeline_inbox_presenter.rb'
- 'app/sample_manifest_excel/sample_manifest_excel/tags/example_data.rb'
- 'db/seeds/0001_workflows.rb'
- 'features/support/step_definitions/web_form_steps.rb'
- 'lib/object_space_profile.rb'
- 'spec/sequencescape_excel/list_spec.rb'
# Offense count: 3
# This cop supports safe autocorrection (--autocorrect).
Style/OrAssignment:
Exclude:
- 'features/support/step_definitions/submission_steps.rb'
- 'lib/informatics/lib/informatics/controller_helper.rb'
- 'lib/informatics/lib/informatics/view/menu/list.rb'
# Offense count: 72
# This cop supports safe autocorrection (--autocorrect).
Style/ParallelAssignment:
Exclude:
- 'app/api/core/abilities.rb'
- 'app/api/core/endpoint/basic_handler.rb'
- 'app/api/core/endpoint/basic_handler/actions/guards.rb'
- 'app/api/core/endpoint/basic_handler/actions/inner_action.rb'
- 'app/api/core/endpoint/basic_handler/associations/belongs_to.rb'
- 'app/api/core/endpoint/basic_handler/associations/has_many/handler.rb'
- 'app/api/core/endpoint/basic_handler/paged.rb'
- 'app/api/core/io/base/json_formatting_behaviour.rb'
- 'app/api/core/io/base/json_formatting_behaviour/input.rb'
- 'app/api/core/io/buffer.rb'
- 'app/api/core/io/collection.rb'
- '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'
- 'app/helpers/assets_helper.rb'
- 'app/middleware/api/endpoint_handler.rb'
- 'app/models/api/base.rb'
- 'app/models/batch.rb'
- 'app/models/bulk_submission.rb'
- 'app/models/cherrypick/task/pick_by_nano_grams.rb'
- 'app/models/cherrypick/task/pick_by_nano_grams_per_micro_litre.rb'
- 'app/models/cherrypick/volume_by_nano_grams.rb'
- 'app/models/health.rb'
- 'app/models/metadata/builder_base.rb'
- 'app/models/metadata/form_builder.rb'
- 'app/models/presenters/grouped_pipeline_inbox_presenter.rb'
- 'app/models/submission/asset_submission_finder.rb'
- 'app/models/submission_template.rb'
- 'app/models/transfer/between_plate_and_tubes.rb'
- 'app/models/validation_state_guard.rb'
- 'app/views/studies/show.xml.builder'
- 'features/support/paths.rb'
- 'features/support/step_definitions/4560014_refactoring_properties_descriptors_etc_to_table_columns_steps.rb'
- 'features/support/step_definitions/tag_layout_steps.rb'
- 'features/support/step_definitions/transfer_steps.rb'
- 'test/unit/api/core/io/json/grammar_test.rb'
- 'test/unit/api/core/io/json/stream_test.rb'
- 'test/unit/api/core/io/json_output_test.rb'
- 'test/unit/batch_test.rb'
- 'test/unit/messaging/hash_generation_test.rb'
- 'test/unit/tag_qc/qcable_statemachine_checks.rb'
# Offense count: 4
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: AllowSafeAssignment, AllowInMultilineConditions.
Style/ParenthesesAroundCondition:
Exclude:
- 'app/api/core/io/base/json_formatting_behaviour.rb'
- 'app/models/parsers/bioanalysis_csv_parser.rb'
# Offense count: 34
# This cop supports safe autocorrection (--autocorrect).
Style/PerlBackrefs:
Exclude:
- 'app/models/validation_state_guard.rb'
- 'features/support/paths.rb'
- 'features/support/step_definitions/submission_steps.rb'
- 'features/support/step_definitions/tag_layout_steps.rb'
- 'lib/validateable.rb'
# Offense count: 4
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: short, verbose
Style/PreferredHashMethods:
Exclude:
- 'lib/authenticated_system.rb'
- 'lib/submission_serializer.rb'
- 'script/poller'
# Offense count: 2
# This cop supports safe autocorrection (--autocorrect).
Style/Proc:
Exclude:
- 'app/models/lib_pool_norm_tube_generator.rb'
- 'app/models/qcable/statemachine.rb'
# Offense count: 4
# 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: 5
# This cop supports safe autocorrection (--autocorrect).
Style/RedundantBegin:
Exclude:
- 'app/controllers/bulk_submissions_controller.rb'
- 'app/controllers/studies_controller.rb'
- 'app/models/qc_report.rb'
- 'app/models/request/change_decision.rb'
- 'app/models/submission/project_validation.rb'
# Offense count: 2
# This cop supports safe autocorrection (--autocorrect).
Style/RedundantException:
Exclude:
- 'app/models/request.rb'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
Style/RedundantFreeze:
Exclude:
- 'lib/psd_formatter.rb'
# Offense count: 61
# This cop supports safe autocorrection (--autocorrect).
Style/RedundantParentheses:
Exclude:
- 'app/controllers/admin/studies_controller.rb'
- 'app/models/asset_barcode.rb'
- 'app/models/map.rb'
- 'app/models/parsers/bioanalysis_csv_parser.rb'
- 'app/models/plate/creator_parameters.rb'
- 'app/models/qc_result_factory.rb'
- 'app/models/sequencing_pipeline.rb'
- 'app/models/study.rb'
- 'app/models/user.rb'
- 'app/resources/api/v2/shared_behaviour/labware.rb'
- 'app/sample_manifest_excel/sample_manifest_excel/worksheet/test_worksheet.rb'
- 'app/views/samples/show.xml.builder'
- 'app/views/studies/show.xml.builder'
- 'features/support/step_definitions/debug_steps.rb'
- 'lib/accession/accession/sample.rb'
- 'lib/eventful_mailer.rb'
- 'lib/label_printer/label_printer/label/robot_beds.rb'
- 'lib/manifest_util.rb'
- 'lib/submission_serializer.rb'
- 'lib/tasks/limber.rake'
- 'spec/features/pooling_spec.rb'
- 'spec/features/sample_logistics/lab/stock_stamping_spec.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'
- 'test/lib/label_printer/sample_manifest_multiplex_test.rb'
- 'test/lib/label_printer/sample_manifest_plate_test.rb'
- 'test/lib/label_printer/sample_manifest_tube_test.rb'
- 'test/lib/label_printer/shared_tests.rb'
- 'test/unit/custom_metadatum_collection_test.rb'
# Offense count: 10
# This cop supports safe autocorrection (--autocorrect).
Style/RedundantRegexpEscape:
Exclude:
- 'features/support/step_definitions/api_steps.rb'
- 'features/support/step_definitions/web_form_steps.rb'
- 'features/support/step_definitions/web_steps.rb'
- 'features/support/step_definitions/xml_steps.rb'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: AllowMultipleReturnValues.
Style/RedundantReturn:
Exclude:
- 'lib/lab_where_client.rb'
# Offense count: 7
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: EnforcedStyle.
# SupportedStyles: implicit, explicit
Style/RescueStandardError:
Exclude:
- 'app/api/core/endpoint/basic_handler/actions/bound/handler.rb'
- 'app/controllers/requests_controller.rb'
- 'app/models/bulk_submission.rb'
- 'app/models/lib_pool_norm_tube_generator.rb'
- 'app/models/plate_volume.rb'
- 'app/models/qc_report.rb'
- 'app/models/submission/delayed_job_behaviour.rb'
# Offense count: 17
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: ConvertCodeThatCanStartToReturnNil, AllowedMethods, MaxChainLength.
# AllowedMethods: present?, blank?, presence, try, try!
Style/SafeNavigation:
Exclude:
- 'app/controllers/events_controller.rb'
- 'app/controllers/qc_reports_controller.rb'
- 'app/models/batch.rb'
- 'app/models/product_criteria/basic.rb'
- 'app/models/request/statemachine.rb'
- 'app/models/user/authentication.rb'
- 'app/models/uuid.rb'
- 'lib/authenticated_system.rb'
- 'lib/event_factory.rb'
- 'test/unit/qc_report_file_test.rb'
# Offense count: 2
# This cop supports safe autocorrection (--autocorrect).
Style/SelfAssignment:
Exclude:
- 'app/helpers/application_helper.rb'
- 'app/views/batches/released.xml.builder'
# Offense count: 7
# 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
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: AllowModifier.
Style/SoleNestedConditional:
Exclude:
- 'app/controllers/admin/studies_controller.rb'
- 'app/controllers/requests_controller.rb'
- 'app/models/order.rb'
- 'app/models/parsers/plate_reader_parser.rb'
- 'app/models/robot/verification/base.rb'
- 'app/uploaders/polymorphic_uploader.rb'
- 'features/support/step_definitions/display_submitted_at_inbox_pipeline_steps.rb'
# Offense count: 5
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: RequireEnglish, EnforcedStyle.
# SupportedStyles: use_perl_names, use_english_names, use_builtin_english_names
Style/SpecialGlobalVars:
Exclude:
- 'app/models/accession_service.rb'
- 'lib/informatics/lib/platform.rb'
# Offense count: 9
# This cop supports safe autocorrection (--autocorrect).
Style/StderrPuts:
Exclude:
- 'app/api/core/service.rb'
- 'features/support/step_definitions/api_steps.rb'
- 'features/support/step_definitions/tag_layout_steps.rb'
- 'lib/cron_scripts/import_fluidigm_data.rb'
- 'lib/volume_check.rb'
- 'script/autospec'
# Offense count: 75
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: Mode.
Style/StringConcatenation:
Exclude:
- 'app/helpers/application_helper.rb'
- 'app/helpers/submissions_helper.rb'
- 'app/models/accessionable/submission.rb'
- 'app/models/concerns/squishify.rb'
- 'app/models/location_report.rb'
- 'app/models/robot_property.rb'
- 'app/sample_manifest_excel/sample_manifest_excel/worksheet/test_worksheet.rb'
- 'app/views/requests/list_inboxes.xml.builder'
- 'config/application.rb'
- 'config/initializers/informatics.rb'
- 'features/support/paths.rb'
- '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'
- 'script/performance/profiler'
- 'script/performance/request'
- 'script/plugin'
- 'script/process/inspector'
- 'script/process/reaper'
- 'script/process/spawner'
- 'script/spec'
- 'spec/api/dilution_plate_purpose_spec.rb'
- 'spec/api/labware_spec.rb'
- 'spec/api/multiplexed_library_tube_spec.rb'
- 'spec/api/plate_purpose_spec.rb'
- 'spec/api/plate_spec.rb'
- 'spec/api/receptacle_spec.rb'
- 'spec/api/request_types_spec.rb'
- 'spec/api/submission_pool_spec.rb'
- 'spec/api/well_spec.rb'
- 'spec/factories/barcode_factories.rb'
- 'spec/models/location_report_spec.rb'
- 'spec/models/stock_stamper_spec.rb'
- 'spec/requests/api/v2/purposes_spec.rb'
- 'spec/requests/api/v2/studies_spec.rb'
- 'test/controllers/plates_controller_test.rb'
- 'test/lib/linefeed_fix_test.rb'
- 'test/test_helper.rb'
- 'test/unit/accession_service_test.rb'
- 'test/unit/parsers/bioanalysis_csv_parser_test.rb'
- 'test/unit/parsers/plate_reader_parser_test.rb'
- 'test/unit/parsers/quant_parser_test.rb'
- 'test/unit/product_criteria/basic_test.rb'
- 'test/unit/qc_file_test.rb'
# Offense count: 4
# This cop supports unsafe autocorrection (--autocorrect-all).
# Configuration parameters: AllowMethodsWithArguments, AllowedMethods, AllowedPatterns, AllowComments.
# AllowedMethods: define_method, mail, respond_to
Style/SymbolProc:
Exclude:
- 'app/models/sample.rb'
- 'app/models/study.rb'
- 'app/models/tasks/plate_transfer_handler.rb'
- 'db/seeds/0001_workflows.rb'
# Offense count: 1
# This cop supports safe autocorrection (--autocorrect).
# Configuration parameters: EnforcedStyle, AllowSafeAssignment.
# SupportedStyles: require_parentheses, require_no_parentheses, require_parentheses_when_complex
Style/TernaryParentheses:
Exclude:
- 'app/models/parsers/bioanalysis_csv_parser.rb'
# Offense count: 9
# 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'
- 'test/shoulda_macros/sanger_macros/resource_test.rb'