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.rubocop_todo.yml
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# This configuration was generated by
# `rubocop --auto-gen-config --exclude-limit 15000`
# on 2018-05-31 16:20:33 +0100 using RuboCop version 0.54.0.
# 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: 19
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# Offense count: 9
# Configuration parameters: AllowSafeAssignment.
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# Offense count: 11
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# Offense count: 4
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# Offense count: 10
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# Offense count: 7
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# Offense count: 1
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# Offense count: 1
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# Offense count: 4
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# Offense count: 10
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# Offense count: 453
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Metrics/CyclomaticComplexity:
Max: 87
# Offense count: 435
# Configuration parameters: CountComments.
Metrics/MethodLength:
Max: 76
# Offense count: 11
# Configuration parameters: CountComments.
Metrics/ModuleLength:
Max: 215
# Offense count: 13
# Configuration parameters: CountKeywordArgs.
Metrics/ParameterLists:
Max: 10
# Offense count: 57
Metrics/PerceivedComplexity:
Max: 35
# Offense count: 33
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.rb'
- 'app/models/asset/ownership.rb'
- 'app/models/broadcast_event.rb'
- 'app/models/field_info.rb'
- 'app/models/lib_pool_norm_tube_generator.rb'
- 'app/models/order.rb'
- 'app/models/plate.rb'
- 'app/models/presenters/batch_submenu_presenter.rb'
- 'app/models/robot_verification.rb'
- 'app/models/specific_tube_creation.rb'
- 'app/models/task.rb'
- 'app/models/tasks/plate_template_handler.rb'
- 'app/models/well.rb'
- 'db/seeds/0001_workflows.rb'
- 'lib/authenticated_system.rb'
- 'lib/external_resource.rb'
- 'lib/rails-authorization-plugin/lib/authorization.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/column.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/helpers/attributes.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/range.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/range_list.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/tags/aliquot_updater.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/upload/base.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/worksheet/data_worksheet.rb'
- 'lib/tasks/add_templates_and_printers_to_pmb.rake'
# Offense count: 1
Naming/BinaryOperatorParameterName:
Exclude:
- 'lib/libxml_helper.rb'
# Offense count: 12
Naming/ConstantName:
Exclude:
- 'app/models/accession_service.rb'
- 'app/models/field_info.rb'
- 'app/models/order.rb'
- 'app/models/sample.rb'
- 'app/models/study.rb'
- 'app/models/submission/state_machine.rb'
- 'app/models/uuid.rb'
- 'lib/acts_as_descriptable/rakeconfig.rb'
- 'lib/external_resource.rb'
# Offense count: 8
# Configuration parameters: ExpectMatchingDefinition, Regex, IgnoreExecutableScripts, AllowedAcronyms.
# 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:
- 'Gemfile'
- 'config/initializers/rails-authorization-plugin.rb'
- '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'
- 'lib/G1k_check.rb'
- 'lib/acts_as_descriptable/Rakefile'
- 'lib/informatics/Rakefile'
- 'lib/rails-authorization-plugin/Rakefile'
# Offense count: 9
# Configuration parameters: Blacklist.
# Blacklist: END, (?-mix:EO[A-Z]{1})
Naming/HeredocDelimiterNaming:
Exclude:
- 'app/api/core/logging.rb'
- 'app/models/metadata/form_builder.rb'
- 'app/models/well.rb'
- 'db/seeds.rb'
- 'db/seeds/0001_snp_plate_purposes.rb'
- 'lib/update_user_barcode.rb'
- 'test/controllers/projects_controller_test.rb'
# Offense count: 25
Naming/MemoizedInstanceVariableName:
Exclude:
- 'app/controllers/batches_controller.rb'
- 'app/controllers/npg_actions/assets_controller.rb'
- 'app/helpers/workflows_helper.rb'
- 'app/models/batch/pipeline_behaviour.rb'
- 'app/models/fluidigm_file.rb'
- 'app/models/metadata.rb'
- 'app/models/order.rb'
- 'app/models/plate.rb'
- 'app/models/plate/comments_proxy.rb'
- 'app/models/pre_capture_pool.rb'
- 'app/models/presenters/grouped_pipeline_inbox_presenter.rb'
- 'app/models/submission/flexible_request_graph.rb'
- 'app/models/submission/submission_creator.rb'
- 'app/models/tag_layout.rb'
- 'app/models/user_query.rb'
- 'bin/amqp_client'
- 'config/initializers/ruby_net_http_proxy_hack.rb'
- 'lib/limber/helper.rb'
- 'lib/postman.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/worksheet/base.rb'
- 'script/license_application.rb'
# Offense count: 67
# Configuration parameters: NamePrefix, NamePrefixBlacklist, NameWhitelist, MethodDefinitionMacros.
# NamePrefix: is_, has_, have_
# NamePrefixBlacklist: is_, has_, have_
# NameWhitelist: is_a?
# MethodDefinitionMacros: define_method, define_singleton_method
Naming/PredicateName:
Exclude:
- 'spec/**/*'
- '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/data_release_study_type.rb'
- 'app/models/db_file.rb'
- 'app/models/descriptor.rb'
- 'app/models/document.rb'
- 'app/models/extraction_attribute.rb'
- 'app/models/library_tube.rb'
- 'app/models/metadata.rb'
- 'app/models/multiplexed_library_tube.rb'
- 'app/models/order.rb'
- 'app/models/pipeline.rb'
- 'app/models/presenters/batch_submenu_presenter.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'
- 'app/models/user.rb'
- 'lib/eventful_record.rb'
- 'lib/has_behaviour.rb'
- 'lib/manifest_util.rb'
- 'lib/rails-authorization-plugin/lib/authorization.rb'
- 'lib/rails-authorization-plugin/lib/publishare/hardwired_roles.rb'
- 'lib/rails-authorization-plugin/lib/publishare/identity.rb'
- 'lib/rails-authorization-plugin/lib/publishare/object_roles_table.rb'
- 'lib/record_loader/plate_purpose_loader.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/subclass_checker.rb'
# Offense count: 102
# Configuration parameters: MinNameLength, AllowNamesEndingInNumbers, AllowedNames, ForbiddenNames.
# AllowedNames: io, id, to
Naming/UncommunicativeMethodParamName:
Exclude:
- 'app/api/core/endpoint/base.rb'
- 'app/api/core/endpoint/basic_handler/actions/factory.rb'
- 'app/api/core/endpoint/basic_handler/actions/inner_action.rb'
- 'app/api/core/endpoint/basic_handler/actions/standard.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/io/json/grammar.rb'
- 'app/api/model_extensions/stamp.rb'
- 'app/helpers/application_helper.rb'
- 'app/models/asset_shape.rb'
- 'app/models/attributable/association.rb'
- 'app/models/illumina_c/qc_pool_purpose.rb'
- 'app/models/illumina_htp/final_plate_purpose.rb'
- 'app/models/illumina_htp/initial_stock_tube_purpose.rb'
- 'app/models/illumina_htp/mx_tube_purpose.rb'
- 'app/models/illumina_htp/stock_tube_purpose.rb'
- 'app/models/map.rb'
- 'app/models/metadata.rb'
- 'app/models/multiplexed_cherrypicking_task.rb'
- 'app/models/request.rb'
- 'app/models/request_type/pooling_method/submission.rb'
- 'app/models/sample_manifest/headers.rb'
- 'app/models/sequencing_request.rb'
- 'app/models/submission.rb'
- 'app/models/submission/linear_request_graph.rb'
- 'app/models/tag2_layout_template.rb'
- 'app/models/tag_layout_template.rb'
- 'app/models/transfer/between_plate_and_tubes.rb'
- 'app/models/tube/mixed_submission_mx.rb'
- 'app/models/tube/purpose.rb'
- 'app/models/tube/standard_mx.rb'
- 'app/models/tube/stock_mx.rb'
- 'app/models/well.rb'
- 'app/views/requests/expanded.xml.builder'
- 'app/views/requests/incomplete_requests_for_family.xml.builder'
- 'app/views/requests/pending.xml.builder'
- 'bin/amqp_client'
- 'db/migrate/20150825155128_set_base_request_purposes.rb'
- 'features/support/debug_formatter.rb'
- 'features/support/step_definitions/api_steps.rb'
- 'lib/hiseq_2500_helper.rb'
- 'lib/informatics/lib/informatics/application.rb'
- 'lib/informatics/lib/informatics/controller_helper.rb'
- 'lib/informatics/lib/informatics/deployment.rb'
- 'lib/informatics/lib/informatics/user/settings.rb'
- 'lib/oligo_enumerator.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/cell.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/upload/data.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/upload/row.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/upload/rows.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/worksheet/base.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/worksheet/test_worksheet.rb'
- 'lib/submission_serializer.rb'
- 'lib/tube_purpose_helper.rb'
- 'spec/models/submission_spec.rb'
# Offense count: 7
# Configuration parameters: EnforcedStyle.
# SupportedStyles: snake_case, camelCase
Naming/VariableName:
Exclude:
- 'app/models/pac_bio/sample_sheet.rb'
- 'app/models/presenters/batch_submenu_presenter.rb'
- 'app/views/batches/show.xml.builder'
- 'test/unit/import_fluidigm_data_test.rb'
# Offense count: 4
# Cop supports --auto-correct.
Performance/CompareWithBlock:
Exclude:
- 'lib/tasks/code_quality_tests.rake'
- 'lib/tecan_file_generation.rb'
# Offense count: 306
# Cop supports --auto-correct.
Rails/ActiveRecordAliases:
Exclude:
- 'app/api/core/service.rb'
- 'app/api/endpoints/sample_manifests.rb'
- 'app/controllers/admin/bait_libraries/bait_library_suppliers_controller.rb'
- 'app/controllers/admin/bait_libraries/bait_library_types_controller.rb'
- 'app/controllers/admin/bait_libraries_controller.rb'
- 'app/controllers/admin/custom_texts_controller.rb'
- 'app/controllers/admin/faculty_sponsors_controller.rb'
- 'app/controllers/admin/plate_purposes_controller.rb'
- 'app/controllers/admin/primer_panels_controller.rb'
- 'app/controllers/admin/programs_controller.rb'
- 'app/controllers/admin/projects_controller.rb'
- 'app/controllers/admin/robot_properties_controller.rb'
- 'app/controllers/admin/robots_controller.rb'
- 'app/controllers/admin/studies_controller.rb'
- 'app/controllers/admin/users_controller.rb'
- 'app/controllers/api/base_controller.rb'
- 'app/controllers/assets_controller.rb'
- 'app/controllers/barcode_printers_controller.rb'
- 'app/controllers/gels_controller.rb'
- 'app/controllers/projects_controller.rb'
- 'app/controllers/reference_genomes_controller.rb'
- 'app/controllers/requests_controller.rb'
- 'app/controllers/samples_controller.rb'
- 'app/controllers/sdb/sample_manifests_controller.rb'
- 'app/controllers/sdb/suppliers_controller.rb'
- 'app/controllers/studies/asset_groups_controller.rb'
- 'app/controllers/studies_controller.rb'
- 'app/controllers/submissions_controller.rb'
- 'app/controllers/tags_controller.rb'
- 'app/controllers/users_controller.rb'
- 'app/models/api/base.rb'
- 'app/models/asset.rb'
- 'app/models/asset/ownership.rb'
- 'app/models/batch.rb'
- 'app/models/batch_request.rb'
- 'app/models/billing/item.rb'
- 'app/models/create_asset_request.rb'
- 'app/models/customer_request.rb'
- 'app/models/extraction_attribute.rb'
- 'app/models/illumina_c/requests.rb'
- 'app/models/illumina_htp/pooled_plate_purpose.rb'
- 'app/models/library_creation_pipeline.rb'
- 'app/models/library_tube.rb'
- 'app/models/location_report.rb'
- 'app/models/pico_assay_plate.rb'
- 'app/models/plate.rb'
- 'app/models/plate/creator_parameters.rb'
- 'app/models/plate_purpose/request_attachment.rb'
- 'app/models/plate_volume.rb'
- 'app/models/request.rb'
- 'app/models/request_event.rb'
- 'app/models/sample.rb'
- 'app/models/sample_manifest/generator.rb'
- 'app/models/sample_manifest/input_behaviour.rb'
- 'app/models/sequencing_pipeline.rb'
- 'app/models/study_report.rb'
- 'app/models/submission.rb'
- 'app/models/submission/asset_group_behaviour.rb'
- 'app/models/submission/flexible_request_graph.rb'
- 'app/models/submission/linear_request_graph.rb'
- 'app/models/submission/submission_creator.rb'
- 'app/models/submission_template.rb'
- 'app/models/tasks/assign_tags_handler.rb'
- 'app/models/tasks/binding_kit_barcode_handler.rb'
- 'app/models/tasks/movie_length_handler.rb'
- 'app/models/tasks/prep_kit_barcode_handler.rb'
- 'app/models/tasks/sample_prep_qc_handler.rb'
- 'app/models/tasks/strip_tube_creation_handler.rb'
- 'app/models/transfer/between_plate_and_tubes.rb'
- 'app/models/transfer/between_specific_tubes.rb'
- 'app/models/transfer/between_tubes_by_submission.rb'
- 'app/models/transfer/from_plate_to_tube.rb'
- 'app/models/well.rb'
- 'app/models/work_completion/plate_completion.rb'
- 'app/models/work_completion/tube_completion.rb'
- 'db/migrate/20160413081206_unify_initial_downstream_classes.rb'
- 'db/migrate/20160413083640_eliminate_unnecessary_plate_purpose_classes.rb'
- 'db/migrate/20160914100113_make_user_requested_changes_to_hiseq_4000.rb'
- 'db/migrate/20161004142108_eliminate_redundant_plate_purpose_classes.rb'
- 'db/migrate/20170321132639_remove_plate_purpose_column_from_plate_creators.rb'
- 'db/migrate/20170925120658_migrate_request_state.rb'
- 'db/seeds/0019_plate_creators.rb'
- 'db/seeds/4000_mx_pacbio_workflows.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/269135815_add_bait_library_editor_to_admin_view.rb'
- 'features/support/step_definitions/27012705_prevent_inactive_projects_from_being_selected_at_submission.rb'
- 'features/support/step_definitions/3871492_links_from_study_workflow_view_steps.rb'
- 'features/support/step_definitions/4560014_refactoring_properties_descriptors_etc_to_table_columns_steps.rb'
- 'features/support/step_definitions/56037472_request_additional_sequencing_should_support_cross_project_submissions_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/7119309_pulldown_cherrypick_pipeline_steps.rb'
- 'features/support/step_definitions/9314145_pacbio_submission_steps.rb'
- 'features/support/step_definitions/api_steps.rb'
- 'features/support/step_definitions/asset_audit_steps.rb'
- 'features/support/step_definitions/asset_steps.rb'
- 'features/support/step_definitions/authentication_steps.rb'
- 'features/support/step_definitions/barcode_steps.rb'
- 'features/support/step_definitions/batch_steps.rb'
- 'features/support/step_definitions/pico_steps.rb'
- 'features/support/step_definitions/pipeline_steps.rb'
- 'features/support/step_definitions/plate_qc_display_steps.rb'
- 'features/support/step_definitions/plate_steps.rb'
- 'features/support/step_definitions/project_steps.rb'
- 'features/support/step_definitions/pulldown_steps.rb'
- 'features/support/step_definitions/request_steps.rb'
- 'features/support/step_definitions/robot_verification_steps.rb'
- 'features/support/step_definitions/sample_manifest_steps.rb'
- 'features/support/step_definitions/sample_metadata_steps.rb'
- 'features/support/step_definitions/samples_steps.rb'
- 'features/support/step_definitions/sequenom_qc_steps.rb'
- 'features/support/step_definitions/study_report_steps.rb'
- 'features/support/step_definitions/study_steps.rb'
- 'features/support/step_definitions/submission_steps.rb'
- 'features/support/step_definitions/tag_layout_steps.rb'
- 'features/support/step_definitions/transfer_steps.rb'
- 'features/support/step_definitions/user_steps.rb'
- 'features/support/step_definitions/uuid_steps.rb'
- 'lib/illumina_c/helper.rb'
- 'lib/limber/helper.rb'
- 'lib/request_class_deprecator.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/upload/processor/base.rb'
- 'lib/sequencing_qc_batch.rb'
- 'lib/submission_template_maker.rb'
- 'lib/tasks/advance_pulldows_submissions.rake'
- 'lib/tasks/billing_setup.rake'
- 'lib/tasks/uat_setup.rake'
- 'lib/tube_purpose_helper.rb'
- 'lib/working_setup/standard_seeder.rb'
- 'spec/api/extraction_attributes_spec.rb'
- 'spec/factories/request_factories.rb'
- 'spec/factories/study_factories.rb'
- 'spec/factories/submission_factories.rb'
- 'spec/factories/well_factories.rb'
- 'spec/features/pipelines/cherrypick/cherrypick_for_fluidigm_pipeline_micro_litre_spec.rb'
- 'spec/features/pipelines/cherrypick/cherrypick_pipeline_micro_litre_spec.rb'
- 'spec/features/pipelines/cherrypick/cherrypick_pipeline_nano_grams_per_micro_litre_spec.rb'
- 'spec/features/pipelines/cherrypick/cherrypick_pipeline_nano_grams_spec.rb'
- 'spec/features/sample_manifests/track_sample_manifest_updates_spec.rb'
- 'spec/models/aliquot_spec.rb'
- 'spec/models/billing/factories_spec.rb'
- 'spec/models/billing/product_catalogue_spec.rb'
- 'spec/models/orders/order_spec.rb'
- 'spec/models/pulldown/requests_spec.rb'
- 'spec/models/qc_report_spec.rb'
- 'spec/models/request_spec.rb'
- 'spec/models/sequencing_request_spec.rb'
- 'spec/models/study_spec.rb'
- 'spec/models/submission_spec.rb'
- 'spec/models/well_attribute_spec.rb'
- 'test/controllers/batches_controller_test.rb'
- 'test/functional/pre_cap_groups_test.rb'
- 'test/unit/asset_group_test.rb'
- 'test/unit/batch_test.rb'
- 'test/unit/cherrypick_task_test.rb'
- 'test/unit/custom_metadatum_collection_test.rb'
- 'test/unit/lab_interface/workflow_test.rb'
- 'test/unit/manifest_generator_test.rb'
- 'test/unit/product_criteria/advanced_test.rb'
- 'test/unit/qc_report_test.rb'
- 'test/unit/request_factory_test.rb'
- 'test/unit/tasks/assign_tubes_to_multiplexed_wells_task_test.rb'
- 'test/unit/tasks/multiplexed_cherrypicking_task_test.rb'
# Offense count: 31
# Cop supports --auto-correct.
Rails/ApplicationRecord:
Exclude:
- 'app/models/billing/agresso_product.rb'
- 'app/models/billing/item.rb'
- 'app/models/billing/product.rb'
- 'app/models/billing/product_catalogue.rb'
- 'db/migrate/20150806102405_add_flexible_cherrypick_request.rb'
- 'db/migrate/20150825155128_set_base_request_purposes.rb'
- 'db/migrate/20151001150900_add_generic_product_catalogue.rb'
- 'db/migrate/20151002141446_add_product_catalogues_to_existing_templates.rb'
- 'db/migrate/20151002154511_add_product_to_existing_orders_by_role.rb'
- 'db/migrate/20160304095725_lib_pcr_plates_no_longer_need_special_behaviour.rb'
- 'db/migrate/20160412152411_pcr_plate_purpose_is_a_normal_plate_purpose.rb'
- 'db/migrate/20160413081206_unify_initial_downstream_classes.rb'
- 'db/migrate/20160413083640_eliminate_unnecessary_plate_purpose_classes.rb'
- 'db/migrate/20160921085248_remove_unused_tube_class.rb'
- 'db/migrate/20161004142108_eliminate_redundant_plate_purpose_classes.rb'
- 'db/migrate/20161214165052_unify_input_purposes.rb'
- 'db/migrate/20170118164446_remove_illumina_b_tubes_search.rb'
- 'db/migrate/20170321132639_remove_plate_purpose_column_from_plate_creators.rb'
- 'lib/acts_as_descriptable/test/test_helper.rb'
- 'lib/aliquot_tag_migration.rb'
- 'lib/metadata_migration.rb'
- 'lib/request_class_deprecator.rb'
- 'test/unit/eventful_entry_test.rb'
- 'test/unit/external_propertied_test.rb'
# Offense count: 34
# Cop supports --auto-correct.
# Configuration parameters: NilOrEmpty, NotPresent, UnlessPresent.
Rails/Blank:
Exclude:
- 'app/api/core/endpoint/basic_handler/associations/has_file.rb'
- 'app/controllers/assets_controller.rb'
- 'app/controllers/qc_reports_controller.rb'
- 'app/helpers/application_helper.rb'
- 'app/helpers/assets_helper.rb'
- 'app/models/accessionable/sample.rb'
- 'app/models/aliquot_indexer.rb'
- 'app/models/attributable/attribute.rb'
- 'app/models/billing/factory/base.rb'
- 'app/models/billing/factory/sequencing.rb'
- 'app/models/billing/item.rb'
- 'app/models/illumina_htp/initial_downstream_plate_purpose.rb'
- 'app/models/illumina_htp/initial_stock_tube_purpose.rb'
- 'app/models/lot.rb'
- 'app/models/pooling.rb'
- 'app/models/pulldown/initial_downstream_plate_purpose.rb'
- 'app/models/request/auto_multiplexing.rb'
- 'app/models/request_type/pooling_method/plate_row.rb'
- 'app/models/sample.rb'
- 'app/models/submission.rb'
- 'app/models/submission/submission_creator.rb'
- 'app/models/tasks/plate_transfer_handler.rb'
- 'app/views/batches/show.xml.builder'
- 'features/support/step_definitions/pulldown_steps.rb'
- 'features/support/step_definitions/request_steps.rb'
- 'lib/label_printer/label_printer/label/asset_redirect.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/manifest_type_list.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/specialised_field/library_type.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/upload/row.rb'
- 'lib/tasks/billing_setup.rake'
# Offense count: 2
# Configuration parameters: Include.
# Include: db/migrate/*.rb
Rails/CreateTableWithTimestamps:
Exclude:
- 'db/migrate/20160721144535_drop_sample_manifest_template.rb'
- 'db/migrate/20161219112914_add_work_completion_submission_table.rb'
# Offense count: 32
# Configuration parameters: EnforcedStyle.
# 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_plate_double.rb'
- 'lib/label_printer/label_printer/label/base_tube.rb'
- 'spec/lib/label_printer/sample_manifest_plate_double_spec.rb'
- 'test/lib/label_printer/asset_plate_test.rb'
- 'test/lib/label_printer/asset_redirect_test.rb'
- 'test/lib/label_printer/asset_tube_test.rb'
- 'test/lib/label_printer/batch_multiplex_test.rb'
- 'test/lib/label_printer/batch_plate_test.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/sequenom_384plate_test.rb'
- 'test/lib/label_printer/sequenom_96plate_test.rb'
# Offense count: 57
Rails/FilePath:
Exclude:
- 'app/middleware/api/root_service.rb'
- 'app/models/search/find_illumina_b_plates.rb'
- 'app/models/search/find_illumina_b_plates_for_user.rb'
- 'app/models/search/find_illumina_b_stock_plates.rb'
- 'app/models/search/find_illumina_c_plates.rb'
- 'app/models/search/find_illumina_c_tubes.rb'
- 'app/uploaders/polymorphic_uploader.rb'
- 'config/application.rb'
- 'config/config.rb'
- 'config/initializers/accession.rb'
- 'config/initializers/acts_as_descriptable.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/poller.rb'
- 'lib/sample_manifest_excel/sample_manifest_excel/helpers.rb'
- 'lib/tasks/code_quality_tests.rake'
- 'lib/tasks/cucumber.rake'
- 'lib/tasks/cucumber_with_rcov.rake'
- 'lib/tasks/sample_manifest_excel_tests.rake'
- 'lib/tasks/test.rake'
- 'spec/rails_helper.rb'
- '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: 126
# Configuration parameters: Include.
# Include: app/models/**/*.rb
Rails/HasManyOrHasOneDependent:
Exclude:
- 'app/models/aliquot/aliquotable.rb'
- 'app/models/asset.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/billing/product.rb'
- 'app/models/billing/product_catalogue.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/family.rb'
- 'app/models/item.rb'
- 'app/models/lane.rb'
- 'app/models/lot.rb'
- 'app/models/lot_type.rb'
- 'app/models/order.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/role.rb'
- 'app/models/sample.rb'
- 'app/models/sample_manifest.rb'
- 'app/models/sample_manifest/input_behaviour.rb'
- 'app/models/specific_tube_creation.rb'
- 'app/models/stamp.rb'
- 'app/models/study.rb'
- 'app/models/study/metadata.rb'
- 'app/models/study_relation_type.rb'
- 'app/models/study_type.rb'
- 'app/models/submission.rb'
- 'app/models/submission_pool.rb'
- 'app/models/submission_template.rb'
- 'app/models/tag.rb'
- 'app/models/task.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: 2
# Cop supports --auto-correct.
# Configuration parameters: Include.
# Include: spec/**/*, test/**/*
Rails/HttpPositionalArguments:
Exclude:
- 'spec/shared_contexts/it_requires_login.rb'
- 'test/shoulda_macros/sanger_macros.rb'
# Offense count: 16
# Cop supports --auto-correct.
# Configuration parameters: EnforcedStyle.
# SupportedStyles: numeric, symbolic
Rails/HttpStatus:
Exclude:
- 'app/controllers/admin/users_controller.rb'
- 'app/controllers/projects_controller.rb'
- 'app/controllers/studies/documents_controller.rb'
# Offense count: 134
# Configuration parameters: Include.
# Include: app/models/**/*.rb
Rails/InverseOf:
Exclude:
- 'app/models/aliquot.rb'
- 'app/models/aliquot/aliquotable.rb'
- 'app/models/asset.rb'
- 'app/models/asset/ownership.rb'
- 'app/models/asset_creation.rb'
- 'app/models/bait_library.rb'
- 'app/models/batch.rb'
- 'app/models/billing/product.rb'
- 'app/models/billing/product_catalogue.rb'
- 'app/models/cherrypick_for_fluidigm_request.rb'
- 'app/models/comment.rb'
- 'app/models/db_file.rb'
- 'app/models/extended_validator.rb'
- 'app/models/extraction_attribute.rb'
- 'app/models/faculty_sponsor.rb'
- 'app/models/family.rb'