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.rubocop_todo.yml
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# This configuration was generated by
# `rubocop --auto-gen-config --exclude-limit 10000`
# on 2022-04-28 09:45:06 UTC using RuboCop version 1.25.1.
# The point is for the user to remove these configuration records
# one by one as the offenses are removed from the code base.
# Note that changes in the inspected code, or installation of new
# versions of RuboCop, may require this file to be generated again.
# Offense count: 22
# Configuration parameters: IgnoredMethods.
Lint/AmbiguousBlockAssociation:
Exclude:
- 'app/models/qcable/statemachine.rb'
- '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
# Cop supports --auto-correct.
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
# Cop supports --auto-correct.
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: 1
Lint/FloatComparison:
Exclude:
- 'features/support/step_definitions/7119309_pulldown_cherrypick_pipeline_steps.rb'
# Offense count: 3
Lint/IneffectiveAccessModifier:
Exclude:
- 'app/helpers/plates_helper.rb'
- 'app/models/event_sender.rb'
- 'lib/authenticated_system.rb'
# Offense count: 29
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
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: 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: 5
# Cop supports --auto-correct.
# Configuration parameters: 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
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: 1
# Cop supports --auto-correct-all.
# Configuration parameters: AllowComments.
Lint/UselessMethodDefinition:
Exclude:
- 'app/uploaders/polymorphic_uploader.rb'
# Offense count: 15
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: (?-mix:(^|\s)(EO[A-Z]{1}|END)(\s|$))
Naming/HeredocDelimiterNaming:
Exclude:
- 'db/seeds/0001_snp_plate_purposes.rb'
# Offense count: 12
# 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'
- 'config/initializers/ruby_net_http_proxy_hack.rb'
# Offense count: 13
# Configuration parameters: MinNameLength, AllowNamesEndingInNumbers, AllowedNames, ForbiddenNames.
# AllowedNames: at, by, db, id, 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'
- 'app/models/metadata.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: 36
# 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: 218
# Configuration parameters: EnforcedStyle, CheckMethodNames, CheckSymbols, AllowedIdentifiers.
# SupportedStyles: snake_case, normalcase, non_integer
# AllowedIdentifiers: capture3, iso8601, rfc1123_date, rfc822, rfc2822, rfc3339
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: 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: 325
# Configuration parameters: Prefixes.
# 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/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
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: 198
# Configuration parameters: CountAsOne.
RSpec/ExampleLength:
Max: 28
# Offense count: 1
# Cop supports --auto-correct.
RSpec/ExpectActual:
Exclude:
- 'spec/models/qc_report_spec.rb'
# Offense count: 13
RSpec/ExpectInHook:
Exclude:
- 'spec/features/admin/changing_user_roles_spec.rb'
- 'spec/features/retrospective_failure_spec.rb'
- 'spec/features/submissions/bulk_submissions_spec.rb'
- 'spec/models/external_release_event_spec.rb'
- 'spec/models/specific_tube_creations_spec.rb'
- 'spec/models/transfer_request_collection_spec.rb'
- 'spec/uat_actions/test_submission_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: 240
# 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
# Cop supports --auto-correct.
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: 28
# Configuration parameters: .
# SupportedStyles: have_received, receive
RSpec/MessageSpies:
EnforcedStyle: receive
# 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: 676
RSpec/MultipleExpectations:
Max: 18
# Offense count: 865
# Configuration parameters: AllowSubject.
RSpec/MultipleMemoizedHelpers:
Max: 34
# Offense count: 377
# Configuration parameters: IgnoreSharedExamples.
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: 346
RSpec/NestedGroups:
Max: 6
# 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
# Cop supports --auto-correct.
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: 6
# Configuration parameters: IgnoreNameless, IgnoreSymbolicNames.
RSpec/VerifiedDoubles:
Exclude:
- 'spec/models/sample_manifest/generator_spec.rb'
- 'spec/sample_manifest_excel/download_spec.rb'
- 'spec/sample_manifest_excel/worksheet_spec.rb'
# Offense count: 3
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
# Cop supports --auto-correct.
Rails/ApplicationMailer:
Exclude:
- 'app/mailers/user_query_mailer.rb'
- 'lib/eventful_mailer.rb'
# Offense count: 15
# 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: 36
# 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/accession/accession.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
# Cop supports --auto-correct.
# 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: