├── .browserslistrc ├── .git-blame-ignore-revs ├── .github └── workflows │ ├── add_prs_to_tech_debt_project.yml │ ├── assign_issue_number.yml │ ├── automated_docker_release.yml │ ├── automated_release.yml │ ├── build_and_release.yml │ ├── check_release_version.yml │ ├── create_release_pr.yml │ ├── cucumber_tests.yml │ ├── generate_pages.yml │ ├── lint.yml │ ├── rake_tests.yml │ ├── rspec_feature_tests.yml │ ├── rspec_unit_tests.yml │ └── update_rubocop.yml ├── .gitignore ├── .master_fork ├── .nvmrc ├── .prettierignore ├── .prettierrc.json ├── .pryrc ├── .reek.yml ├── .release-version ├── .rspec ├── .rubocop ├── .rubocop.yml ├── .rubocop_todo.yml ├── .ruby-version ├── .rvmrc ├── .simplecov ├── .yardopts ├── Dockerfile ├── Gemfile ├── Gemfile.lock ├── LICENSE ├── Procfile ├── Procfile.dev ├── README.md ├── Rakefile ├── app ├── api │ ├── core │ │ ├── abilities.rb │ │ ├── benchmarking.rb │ │ ├── endpoint │ │ │ ├── base.rb │ │ │ ├── basic_handler.rb │ │ │ └── basic_handler │ │ │ │ ├── actions.rb │ │ │ │ ├── actions │ │ │ │ ├── bound.rb │ │ │ │ ├── bound │ │ │ │ │ └── handler.rb │ │ │ │ ├── factory.rb │ │ │ │ ├── guards.rb │ │ │ │ ├── inner_action.rb │ │ │ │ └── standard.rb │ │ │ │ ├── associations │ │ │ │ ├── belongs_to.rb │ │ │ │ ├── has_file.rb │ │ │ │ ├── has_many.rb │ │ │ │ └── has_many │ │ │ │ │ └── handler.rb │ │ │ │ ├── endpoint_lookup.rb │ │ │ │ ├── handlers.rb │ │ │ │ └── paged.rb │ │ ├── initializable.rb │ │ ├── io │ │ │ ├── base.rb │ │ │ ├── base │ │ │ │ ├── eager_loading_behaviour.rb │ │ │ │ ├── json_formatting_behaviour.rb │ │ │ │ └── json_formatting_behaviour │ │ │ │ │ ├── input.rb │ │ │ │ │ └── output.rb │ │ │ ├── buffer.rb │ │ │ ├── collection.rb │ │ │ ├── json │ │ │ │ ├── grammar.rb │ │ │ │ └── stream.rb │ │ │ ├── list.rb │ │ │ └── registry.rb │ │ ├── logging.rb │ │ ├── references.rb │ │ ├── registry.rb │ │ ├── service.rb │ │ └── service │ │ │ ├── authentication.rb │ │ │ ├── content_filtering.rb │ │ │ ├── endpoint_handling.rb │ │ │ └── error_handling.rb │ ├── docs.md │ ├── endpoints │ │ ├── asset_audits.rb │ │ ├── asset_groups.rb │ │ ├── assets.rb │ │ ├── bait_library_layouts.rb │ │ ├── barcode_printers.rb │ │ ├── batches.rb │ │ ├── bulk_transfers.rb │ │ ├── comments.rb │ │ ├── custom_metadatum_collections.rb │ │ ├── dilution_plate_purposes.rb │ │ ├── extraction_attributes.rb │ │ ├── lanes.rb │ │ ├── library_creation_requests.rb │ │ ├── library_events.rb │ │ ├── library_tubes.rb │ │ ├── lot_types.rb │ │ ├── lots.rb │ │ ├── multiplexed_library_creation_requests.rb │ │ ├── multiplexed_library_tubes.rb │ │ ├── order_templates.rb │ │ ├── orders.rb │ │ ├── pipelines.rb │ │ ├── plate_conversions.rb │ │ ├── plate_creations.rb │ │ ├── plate_purposes.rb │ │ ├── plate_templates.rb │ │ ├── plates.rb │ │ ├── pooled_plate_creations.rb │ │ ├── projects.rb │ │ ├── qc_decisions.rb │ │ ├── qc_files.rb │ │ ├── qcable_creators.rb │ │ ├── qcables.rb │ │ ├── reference_genomes.rb │ │ ├── request_types.rb │ │ ├── requests.rb │ │ ├── robots.rb │ │ ├── sample_manifests.rb │ │ ├── sample_tubes.rb │ │ ├── samples.rb │ │ ├── searches.rb │ │ ├── sequencing_requests.rb │ │ ├── specific_tube_creations.rb │ │ ├── stamps.rb │ │ ├── state_changes.rb │ │ ├── studies.rb │ │ ├── submission_pools.rb │ │ ├── submissions.rb │ │ ├── suppliers.rb │ │ ├── tag2_layout_templates.rb │ │ ├── tag2_layouts.rb │ │ ├── tag_groups.rb │ │ ├── tag_layout_templates.rb │ │ ├── tag_layouts.rb │ │ ├── transfer_request_collections.rb │ │ ├── transfer_requests.rb │ │ ├── transfer_templates.rb │ │ ├── transfers.rb │ │ ├── tube │ │ │ └── purposes.rb │ │ ├── tube_creations.rb │ │ ├── tube_from_tube_creations.rb │ │ ├── tubes.rb │ │ ├── users.rb │ │ ├── uuids.rb │ │ ├── volume_updates.rb │ │ ├── wells.rb │ │ └── work_completions.rb │ ├── io │ │ ├── active_record │ │ │ └── relation.rb │ │ ├── aliquot.rb │ │ ├── array.rb │ │ ├── asset.rb │ │ ├── asset_audit.rb │ │ ├── asset_group.rb │ │ ├── bait_library.rb │ │ ├── bait_library_layout.rb │ │ ├── barcode_printer.rb │ │ ├── batch.rb │ │ ├── bulk_transfer.rb │ │ ├── comment.rb │ │ ├── custom_metadatum_collection.rb │ │ ├── dilution_plate_purpose.rb │ │ ├── endpoints │ │ │ └── uuids │ │ │ │ └── search.rb │ │ ├── extraction_attribute.rb │ │ ├── labware.rb │ │ ├── lane.rb │ │ ├── library_creation_request.rb │ │ ├── library_event.rb │ │ ├── library_tube.rb │ │ ├── lot.rb │ │ ├── lot_type.rb │ │ ├── multiplexed_library_creation_request.rb │ │ ├── multiplexed_library_tube.rb │ │ ├── order.rb │ │ ├── pac_bio_library_tube.rb │ │ ├── pipeline.rb │ │ ├── plate.rb │ │ ├── plate_conversion.rb │ │ ├── plate_creation.rb │ │ ├── plate_purpose.rb │ │ ├── plate_template.rb │ │ ├── pooled_plate_creation.rb │ │ ├── project.rb │ │ ├── purpose.rb │ │ ├── qc_decision.rb │ │ ├── qc_file.rb │ │ ├── qcable.rb │ │ ├── qcable_creator.rb │ │ ├── receptacle.rb │ │ ├── reference_genome.rb │ │ ├── request.rb │ │ ├── request_type.rb │ │ ├── robot.rb │ │ ├── sample.rb │ │ ├── sample_manifest.rb │ │ ├── sample_tube.rb │ │ ├── search.rb │ │ ├── sequencing_request.rb │ │ ├── specific_tube_creation.rb │ │ ├── stamp.rb │ │ ├── state_change.rb │ │ ├── stock_multiplexed_library_tube.rb │ │ ├── study.rb │ │ ├── submission.rb │ │ ├── submission_pool.rb │ │ ├── submission_template.rb │ │ ├── supplier.rb │ │ ├── tag2_layout.rb │ │ ├── tag2_layout_template.rb │ │ ├── tag_group.rb │ │ ├── tag_layout.rb │ │ ├── tag_layout_template.rb │ │ ├── transfer.rb │ │ ├── transfer │ │ │ ├── between_plates.rb │ │ │ ├── between_plates_by_submission.rb │ │ │ ├── between_specific_tubes.rb │ │ │ ├── between_tubes_by_submission.rb │ │ │ ├── from_plate_to_specific_tubes.rb │ │ │ ├── from_plate_to_specific_tubes_by_pool.rb │ │ │ ├── from_plate_to_tube.rb │ │ │ ├── from_plate_to_tube_by_multiplex.rb │ │ │ └── from_plate_to_tube_by_submission.rb │ │ ├── transfer_request.rb │ │ ├── transfer_request_collection.rb │ │ ├── transfer_template.rb │ │ ├── tube.rb │ │ ├── tube │ │ │ └── purpose.rb │ │ ├── tube_creation.rb │ │ ├── tube_from_tube_creation.rb │ │ ├── user.rb │ │ ├── volume_update.rb │ │ ├── well.rb │ │ └── work_completion.rb │ └── model_extensions │ │ ├── asset_group.rb │ │ ├── bait_library_layout.rb │ │ ├── barcode_printer.rb │ │ ├── library_tube.rb │ │ ├── multiplexed_library_tube.rb │ │ ├── order.rb │ │ ├── plate.rb │ │ ├── project.rb │ │ ├── request.rb │ │ ├── robot.rb │ │ ├── sample.rb │ │ ├── sample_manifest.rb │ │ ├── sample_tube.rb │ │ ├── stamp.rb │ │ ├── study.rb │ │ ├── submission.rb │ │ ├── tag_layout.rb │ │ ├── tube.rb │ │ └── well.rb ├── bulk_submission_excel │ ├── bulk_submission_excel.rb │ └── bulk_submission_excel │ │ ├── configuration.rb │ │ ├── download.rb │ │ └── worksheet │ │ └── data_worksheet.rb ├── controllers │ ├── admin │ │ ├── abilities_controller.rb │ │ ├── bait_libraries │ │ │ ├── bait_library_suppliers_controller.rb │ │ │ └── bait_library_types_controller.rb │ │ ├── bait_libraries_controller.rb │ │ ├── custom_texts_controller.rb │ │ ├── delayed_jobs_controller.rb │ │ ├── faculty_sponsors_controller.rb │ │ ├── plate_purposes_controller.rb │ │ ├── primer_panels_controller.rb │ │ ├── programs_controller.rb │ │ ├── projects_controller.rb │ │ ├── robot_properties_controller.rb │ │ ├── robots_controller.rb │ │ ├── roles │ │ │ └── users_controller.rb │ │ ├── roles_controller.rb │ │ ├── studies_controller.rb │ │ └── users_controller.rb │ ├── admin_controller.rb │ ├── advanced_search_controller.rb │ ├── api │ │ └── v2 │ │ │ ├── aliquots_controller.rb │ │ │ ├── asset_audits_controller.rb │ │ │ ├── assets_controller.rb │ │ │ ├── bait_library_layouts_controller.rb │ │ │ ├── barcode_printers_controller.rb │ │ │ ├── bioscan │ │ │ └── export_pool_xp_to_traction_controller.rb │ │ │ ├── bulk_transfers_controller.rb │ │ │ ├── comments_controller.rb │ │ │ ├── concerns │ │ │ ├── api_key_authenticatable.rb │ │ │ ├── disable_csrf_token_authentication.rb │ │ │ └── disable_destroy_action.rb │ │ │ ├── custom_metadatum_collections_controller.rb │ │ │ ├── heron │ │ │ ├── plates_controller.rb │ │ │ ├── tube_rack_statuses_controller.rb │ │ │ └── tube_racks_controller.rb │ │ │ ├── labware_controller.rb │ │ │ ├── lanes_controller.rb │ │ │ ├── lot_types_controller.rb │ │ │ ├── lots_controller.rb │ │ │ ├── orders_controller.rb │ │ │ ├── pick_lists_controller.rb │ │ │ ├── plate_conversions_controller.rb │ │ │ ├── plate_creations_controller.rb │ │ │ ├── plate_purposes_controller.rb │ │ │ ├── plate_templates_controller.rb │ │ │ ├── plates_controller.rb │ │ │ ├── poly_metadata_controller.rb │ │ │ ├── pooled_plate_creations_controller.rb │ │ │ ├── pre_capture_pools_controller.rb │ │ │ ├── primer_panels_controller.rb │ │ │ ├── projects_controller.rb │ │ │ ├── purposes_controller.rb │ │ │ ├── qc_assays_controller.rb │ │ │ ├── qc_files_controller.rb │ │ │ ├── qc_results_controller.rb │ │ │ ├── qcable_creators_controller.rb │ │ │ ├── qcables_controller.rb │ │ │ ├── racked_tubes_controller.rb │ │ │ ├── receptacles_controller.rb │ │ │ ├── request_metadata_controller.rb │ │ │ ├── request_types_controller.rb │ │ │ ├── requests_controller.rb │ │ │ ├── sample_manifests_controller.rb │ │ │ ├── sample_metadata_controller.rb │ │ │ ├── samples_controller.rb │ │ │ ├── specific_tube_creations_controller.rb │ │ │ ├── specific_tube_rack_creations_controller.rb │ │ │ ├── state_changes_controller.rb │ │ │ ├── studies_controller.rb │ │ │ ├── submission_pools_controller.rb │ │ │ ├── submission_templates_controller.rb │ │ │ ├── submissions_controller.rb │ │ │ ├── tag_group_adapter_types_controller.rb │ │ │ ├── tag_groups_controller.rb │ │ │ ├── tag_layout_templates_controller.rb │ │ │ ├── tag_layouts_controller.rb │ │ │ ├── tag_sets_controller.rb │ │ │ ├── tags_controller.rb │ │ │ ├── templates_controller.rb │ │ │ ├── transfer_request_collections_controller.rb │ │ │ ├── transfer_requests_controller.rb │ │ │ ├── transfer_templates_controller.rb │ │ │ ├── transfers_controller.rb │ │ │ ├── tube_from_plate_creations_controller.rb │ │ │ ├── tube_from_tube_creations_controller.rb │ │ │ ├── tube_purposes_controller.rb │ │ │ ├── tube_rack_purposes_controller.rb │ │ │ ├── tube_rack_statuses_controller.rb │ │ │ ├── tube_racks_controller.rb │ │ │ ├── tubes_controller.rb │ │ │ ├── users_controller.rb │ │ │ ├── volume_updates_controller.rb │ │ │ ├── wells_controller.rb │ │ │ ├── work_completions_controller.rb │ │ │ └── work_orders_controller.rb │ ├── application_controller.rb │ ├── asset_audits_controller.rb │ ├── assets_controller.rb │ ├── aviti_sample_sheet │ │ └── sample_sheet_generator.rb │ ├── barcode_printers_controller.rb │ ├── batches │ │ ├── comments_controller.rb │ │ └── requests_controller.rb │ ├── batches_controller.rb │ ├── bioscan_control_locations_controller.rb │ ├── bulk_submission_excel │ │ └── downloads_controller.rb │ ├── bulk_submissions_controller.rb │ ├── concerns │ │ ├── flash_truncation.rb │ │ └── plate_picks │ │ │ └── batches_json.rb │ ├── documents_controller.rb │ ├── driver_files_controller.rb │ ├── errors_controller.rb │ ├── events_controller.rb │ ├── gels_controller.rb │ ├── get_your_qc_completed_tubes_here_controller.rb │ ├── health_controller.rb │ ├── homes_controller.rb │ ├── lab_searches_controller.rb │ ├── labware │ │ └── comments_controller.rb │ ├── labware_controller.rb │ ├── labwhere_receptions_controller.rb │ ├── location_reports_controller.rb │ ├── messengers_controller.rb │ ├── npg_actions │ │ └── assets_controller.rb │ ├── orders_controller.rb │ ├── parents_controller.rb │ ├── phi_x │ │ ├── spiked_buffers_controller.rb │ │ └── stocks_controller.rb │ ├── phi_xes_controller.rb │ ├── pick_lists_controller.rb │ ├── pipelines_controller.rb │ ├── plate_picks_controller.rb │ ├── plate_summaries_controller.rb │ ├── plate_templates_controller.rb │ ├── plates_controller.rb │ ├── plates_from_tubes_controller.rb │ ├── poolings_controller.rb │ ├── projects_controller.rb │ ├── qc_files_controller.rb │ ├── qc_reports_controller.rb │ ├── quad_stamp_controller.rb │ ├── receptacles │ │ └── comments_controller.rb │ ├── receptacles_controller.rb │ ├── reference_genomes_controller.rb │ ├── report_fails_controller.rb │ ├── requests │ │ └── comments_controller.rb │ ├── requests_controller.rb │ ├── robot_verifications_controller.rb │ ├── sample_logistics_controller.rb │ ├── sample_manifest_upload_with_tag_sequences_controller.rb │ ├── samples │ │ ├── comments_controller.rb │ │ └── studies_controller.rb │ ├── samples_controller.rb │ ├── sdb │ │ ├── base_controller.rb │ │ ├── home_controller.rb │ │ ├── sample_manifests_controller.rb │ │ └── suppliers_controller.rb │ ├── searches_controller.rb │ ├── sequenom_qc_plates_controller.rb │ ├── sessions_controller.rb │ ├── stock_stampers_controller.rb │ ├── studies │ │ ├── asset_groups_controller.rb │ │ ├── comments_controller.rb │ │ ├── documents_controller.rb │ │ ├── events_controller.rb │ │ ├── information_controller.rb │ │ └── samples_controller.rb │ ├── studies_controller.rb │ ├── study_reports_controller.rb │ ├── submissions_controller.rb │ ├── tag_groups_controller.rb │ ├── tag_layout_templates_controller.rb │ ├── tag_sets_controller.rb │ ├── tag_substitutions_controller.rb │ ├── taxa_controller.rb │ ├── tube_rack_statuses_controller.rb │ ├── tube_rack_summaries_controller.rb │ ├── uat_actions_controller.rb │ ├── ultima_sample_sheet │ │ └── sample_sheet_generator.rb │ ├── users_controller.rb │ ├── uuids_controller.rb │ └── workflows_controller.rb ├── frontend │ ├── barcodeRendering │ │ └── index.js │ ├── datatables │ │ ├── config.js │ │ ├── index.js │ │ ├── tableBatchEdit.js │ │ ├── tablePipelineInboxColumnSearch.js │ │ └── tableSortable.js │ ├── entrypoints │ │ ├── application.js │ │ ├── application.scss │ │ ├── bulk_submissions.js │ │ ├── cherrypick.js │ │ ├── cherrypick_strategies.js │ │ ├── disable_animations.css │ │ ├── fail_batch.js │ │ ├── labwhere_reception.js │ │ ├── lane_edit.js │ │ ├── organism_validation.js │ │ ├── pipeline.js │ │ ├── plates_from_tubes.js │ │ ├── plates_new.js │ │ ├── pooling.js │ │ ├── print.css │ │ ├── report_fails.js │ │ ├── robot_behaviours.js │ │ ├── submissions.js │ │ ├── tab_anchor.js │ │ └── worksheet.js │ ├── images │ │ ├── icon_0_flag.png │ │ ├── icon_1_flag.png │ │ ├── icon_2_flag.png │ │ ├── icon_3_flag.png │ │ ├── icon_f_flag.png │ │ ├── logo-gradient-development.svg │ │ ├── logo-gradient-staging.svg │ │ ├── logo-gradient-training.svg │ │ ├── logo-gradient.svg │ │ └── sanger-pattern-corner.svg │ ├── legacy │ │ ├── ajax_handling.js │ │ ├── comment_dropdown_handler.js │ │ ├── index.js │ │ ├── select_2_handling.js │ │ └── sequencescape.js │ ├── libs │ │ └── speechSynth.js │ ├── shared │ │ └── scanned_barcode.js │ └── stylesheets │ │ ├── all │ │ ├── asset_audits.scss │ │ ├── bootstrap_variables.scss │ │ ├── colours.scss │ │ ├── comments_box.scss │ │ ├── components.scss │ │ ├── datatables-bootstrap.scss │ │ ├── floating-labels.css │ │ ├── footer.scss │ │ ├── header.scss │ │ ├── misc_buttons.scss │ │ ├── page_specific_hacks.css │ │ ├── pipelines_pages.scss │ │ ├── robot_behaviours.scss │ │ ├── search.scss │ │ ├── sequencescape.scss │ │ ├── sessions.scss │ │ ├── sidebar.scss │ │ ├── tag-substitutions.scss │ │ └── uat_actions.scss │ │ └── application.scss ├── helpers │ ├── application_helper.rb │ ├── assets_helper.rb │ ├── barcode_printers_helper.rb │ ├── batches_helper.rb │ ├── bootstrap_helper.rb │ ├── cherrypick_form_helper.rb │ ├── compound_sample_helper.rb │ ├── delayed_jobs_helper.rb │ ├── descriptor_javascript_helper.rb │ ├── field_infos_helper.rb │ ├── fontawesome_helper.rb │ ├── pipelines_helper.rb │ ├── plates_helper.rb │ ├── prototype_replacement_helper.rb │ ├── report_fails_helper.rb │ ├── request_types_helper.rb │ ├── requests_helper.rb │ ├── retention_instruction_helper.rb │ ├── sdb │ │ └── sample_manifests_helper.rb │ ├── studies_helper.rb │ ├── submissions_helper.rb │ ├── tag_substitution_helper.rb │ ├── users_helper.rb │ └── workflows_helper.rb ├── jobs │ ├── asset_link │ │ ├── builder_job.rb │ │ └── job.rb │ ├── export_pool_xp_to_traction_job.rb │ ├── generate_create_asset_requests_job.rb │ ├── location_report_job.rb │ ├── pick_list_job.rb │ ├── qc_report_job.rb │ ├── sample_accessioning_job.rb │ ├── sample_manifest │ │ └── generate_wells_job.rb │ ├── study_report_job.rb │ └── submission_builder_job.rb ├── middleware │ └── api │ │ ├── endpoint_handler.rb │ │ └── root_service.rb ├── models │ ├── ability.rb │ ├── ability │ │ ├── administrator.rb │ │ ├── base_user.rb │ │ ├── data_access_coordinator.rb │ │ ├── lab_manager.rb │ │ ├── manager.rb │ │ ├── qa_manager.rb │ │ ├── sample_management_gel.rb │ │ ├── sample_management_manager.rb │ │ └── shared │ │ │ ├── lab_user.rb │ │ │ ├── power_user.rb │ │ │ ├── sample_management_user.rb │ │ │ ├── super_user.rb │ │ │ └── tag_creation_user.rb │ ├── accession.rb │ ├── accession │ │ ├── README.md │ │ └── sample_status.rb │ ├── accession_service.rb │ ├── accession_service │ │ ├── base_service.rb │ │ ├── ega_service.rb │ │ ├── ena_service.rb │ │ ├── no_service.rb │ │ └── unsuitable_service.rb │ ├── accessionable │ │ ├── base.rb │ │ ├── dac.rb │ │ ├── policy.rb │ │ ├── sample.rb │ │ ├── study.rb │ │ └── submission.rb │ ├── add_spiked_in_control_task.rb │ ├── aliquot.rb │ ├── aliquot │ │ ├── aliquotable.rb │ │ ├── data_for_substitution.rb │ │ ├── deprecated_behaviours.rb │ │ └── remover.rb │ ├── aliquot_index.rb │ ├── aliquot_indexer.rb │ ├── api │ │ ├── aliquot_io.rb │ │ ├── asset_link_io.rb │ │ ├── base.rb │ │ ├── batch_io.rb │ │ ├── batch_request_io.rb │ │ ├── lane_io.rb │ │ ├── library_tube_io.rb │ │ ├── messages │ │ │ ├── barcode_io.rb │ │ │ ├── flowcell_io.rb │ │ │ ├── fluidigm_plate_io.rb │ │ │ ├── pac_bio_run_io.rb │ │ │ ├── pac_bio_run_with_tag2_io.rb │ │ │ ├── qc_result_io.rb │ │ │ ├── tube_stock_resource_io.rb │ │ │ ├── useq_wafer_io.rb │ │ │ └── well_stock_resource_io.rb │ │ ├── multiplexed_library_tube_io.rb │ │ ├── order_io.rb │ │ ├── pac_bio_library_tube_io.rb │ │ ├── plate_io.rb │ │ ├── plate_purpose_io.rb │ │ ├── project_io.rb │ │ ├── pulldown_multiplexed_library_tube_io.rb │ │ ├── reference_genome_io.rb │ │ ├── request_io.rb │ │ ├── sample_io.rb │ │ ├── sample_tube_io.rb │ │ ├── study_io.rb │ │ ├── study_sample_io.rb │ │ ├── submission_io.rb │ │ ├── tag_io.rb │ │ └── well_io.rb │ ├── api_application.rb │ ├── application_record.rb │ ├── asset.rb │ ├── asset │ │ ├── apply_id_to_name_on_create.rb │ │ ├── finder.rb │ │ ├── ownership.rb │ │ ├── shared_library_tube_behaviour.rb │ │ └── stock.rb │ ├── asset_audit.rb │ ├── asset_barcode.rb │ ├── asset_creation.rb │ ├── asset_group.rb │ ├── asset_group_asset.rb │ ├── asset_link.rb │ ├── asset_shape.rb │ ├── assign_tags_task.rb │ ├── assign_tags_to_tubes_task.rb │ ├── assign_tubes_to_multiplexed_wells_task.rb │ ├── attributable.rb │ ├── attributable │ │ ├── association.rb │ │ ├── attribute.rb │ │ └── custom_validator.rb │ ├── automated_order.rb │ ├── bait_library.rb │ ├── bait_library_layout.rb │ ├── bait_library_type.rb │ ├── barcode.rb │ ├── barcode │ │ ├── barcodeable.rb │ │ └── format_handlers.rb │ ├── barcode_prefix.rb │ ├── barcode_printer.rb │ ├── barcode_printer_type.rb │ ├── barcode_printer_type1_d_tube.rb │ ├── barcode_printer_type384_double_plate.rb │ ├── barcode_printer_type384_plate.rb │ ├── barcode_printer_type96_plate.rb │ ├── batch.rb │ ├── batch │ │ ├── pipeline_behaviour.rb │ │ ├── request_behaviour.rb │ │ ├── request_fail_and_remover.rb │ │ └── state_machine_behaviour.rb │ ├── batch_request.rb │ ├── binding_kit_barcode_task.rb │ ├── broadcast_event.rb │ ├── broadcast_event │ │ ├── asset_audit.rb │ │ ├── helpers │ │ │ └── external_subjects.rb │ │ ├── lab_event.rb │ │ ├── labware_failed.rb │ │ ├── labware_received.rb │ │ ├── library_complete.rb │ │ ├── library_start.rb │ │ ├── metadata_helpers.rb │ │ ├── order_made.rb │ │ ├── plate_cherrypicked.rb │ │ ├── plate_library_complete.rb │ │ ├── pool_released.rb │ │ ├── qc_assay.rb │ │ ├── render_helpers.rb │ │ ├── sample_manifest_created.rb │ │ ├── sample_manifest_updated.rb │ │ ├── sequencing_complete.rb │ │ ├── sequencing_start.rb │ │ └── subject_helpers.rb │ ├── budget_division.rb │ ├── bulk_submission.rb │ ├── bulk_transfer.rb │ ├── cherrypick.rb │ ├── cherrypick │ │ ├── task │ │ │ ├── pick_by_micro_litre.rb │ │ │ ├── pick_by_nano_grams.rb │ │ │ ├── pick_by_nano_grams_per_micro_litre.rb │ │ │ └── pick_helpers.rb │ │ ├── volume_by_micro_litre.rb │ │ ├── volume_by_nano_grams.rb │ │ └── volume_by_nano_grams_per_micro_litre.rb │ ├── cherrypick_for_fluidigm_request.rb │ ├── cherrypick_for_pulldown_pipeline.rb │ ├── cherrypick_for_pulldown_request.rb │ ├── cherrypick_pipeline.rb │ ├── cherrypick_request.rb │ ├── cherrypick_task.rb │ ├── cherrypick_task │ │ ├── control_locator.rb │ │ └── pick_target.rb │ ├── cherrypicking_pipeline.rb │ ├── comment.rb │ ├── comments_proxy │ │ ├── base.rb │ │ ├── plate.rb │ │ ├── tube.rb │ │ └── tube_rack.rb │ ├── compound_aliquot.rb │ ├── concerns │ │ ├── aasm │ │ │ └── extensions.rb │ │ ├── commentable.rb │ │ ├── programs_validator.rb │ │ ├── request │ │ │ └── has_primer_panel.rb │ │ ├── single_receptacle_labware.rb │ │ └── squishify.rb │ ├── control.rb │ ├── control_plate.rb │ ├── control_request.rb │ ├── create_asset_request.rb │ ├── custom_metadatum.rb │ ├── custom_metadatum_collection.rb │ ├── custom_text.rb │ ├── customer_request.rb │ ├── data_release.rb │ ├── data_release_study_type.rb │ ├── db_file.rb │ ├── delegate_validation.rb │ ├── descriptor.rb │ ├── dilution_plate.rb │ ├── dilution_plate_purpose.rb │ ├── document.rb │ ├── element_aviti_sequencing_pipeline.rb │ ├── element_aviti_sequencing_request.rb │ ├── equipment.rb │ ├── event.rb │ ├── event │ │ ├── asset_set_qc_state_event.rb │ │ ├── labware_failed_event.rb │ │ ├── plate_creation_event.rb │ │ ├── plate_events.rb │ │ ├── request_descriptor_update_event.rb │ │ ├── sample_logistics_qc_event.rb │ │ ├── sample_manifest_event.rb │ │ ├── scanned_into_lab_event.rb │ │ └── sequenom_loading.rb │ ├── event_sender.rb │ ├── extended_validator.rb │ ├── extended_validator │ │ └── species_validator.rb │ ├── external_library_creation_request.rb │ ├── external_property.rb │ ├── external_release_event.rb │ ├── extraction_attribute.rb │ ├── faculty_sponsor.rb │ ├── failure.rb │ ├── field_info.rb │ ├── flexible_cherrypick_pipeline.rb │ ├── flexible_submission.rb │ ├── flowcell_type.rb │ ├── flowcell_types_request_type.rb │ ├── fluidigm_file.rb │ ├── fluidigm_template_task.rb │ ├── fragment.rb │ ├── gel_dilution_plate.rb │ ├── genotyping_pipeline.rb │ ├── genotyping_request.rb │ ├── health.rb │ ├── heron │ │ └── factories │ │ │ ├── README.md │ │ │ ├── concerns │ │ │ ├── contents.rb │ │ │ ├── coordinates_support.rb │ │ │ ├── eventful.rb │ │ │ ├── foreign_barcodes.rb │ │ │ ├── recipients.rb │ │ │ └── recipients_coordinates.rb │ │ │ ├── event.rb │ │ │ ├── plate.rb │ │ │ ├── plate_from_rack.rb │ │ │ ├── sample.rb │ │ │ ├── tube.rb │ │ │ ├── tube_rack.rb │ │ │ └── tube_rack_status.rb │ ├── hi_seq_sequencing_request.rb │ ├── identifier.rb │ ├── illumina_b │ │ └── requests.rb │ ├── illumina_c │ │ └── requests.rb │ ├── illumina_htp │ │ ├── initial_stock_tube_purpose.rb │ │ ├── mx_tube_purpose.rb │ │ ├── requests.rb │ │ ├── requests │ │ │ ├── gbs_request.rb │ │ │ ├── heron_request.rb │ │ │ ├── heron_tailed_request.rb │ │ │ ├── library_completion.rb │ │ │ ├── shared_library_prep.rb │ │ │ └── std_library_request.rb │ │ └── stock_tube_purpose.rb │ ├── implement.rb │ ├── index.html │ ├── insdc.rb │ ├── insdc │ │ └── country.rb │ ├── item.rb │ ├── lab_event.rb │ ├── labware.rb │ ├── labwhere_reception.rb │ ├── lane.rb │ ├── lane │ │ └── labware.rb │ ├── legacy_pipeline.rb │ ├── lib_pool_norm_tube_generator.rb │ ├── library_creation_request.rb │ ├── library_event.rb │ ├── library_tube.rb │ ├── library_type.rb │ ├── library_types_request_type.rb │ ├── linear_submission.rb │ ├── location_report.rb │ ├── location_report │ │ └── location_report_form.rb │ ├── lot.rb │ ├── lot_type.rb │ ├── map.rb │ ├── messenger.rb │ ├── messenger_creator.rb │ ├── metadata.rb │ ├── metadata │ │ ├── builder_base.rb │ │ ├── form_builder.rb │ │ └── view_builder.rb │ ├── mi_seq_sequencing_request.rb │ ├── movie_length_task.rb │ ├── multiplexed_cherrypicking_task.rb │ ├── multiplexed_library_creation_request.rb │ ├── multiplexed_library_tube.rb │ ├── null_custom_metadatum_collection.rb │ ├── order.rb │ ├── order_role.rb │ ├── order_template.rb │ ├── pac_bio │ │ └── worksheet.rb │ ├── pac_bio_library_tube.rb │ ├── pac_bio_sample_prep_pipeline.rb │ ├── pac_bio_sample_prep_request.rb │ ├── pac_bio_sequencing_pipeline.rb │ ├── pac_bio_sequencing_request.rb │ ├── parsers.rb │ ├── parsers │ │ ├── bioanalysis_csv_parser.rb │ │ ├── dilution_parser.rb │ │ ├── pbmc_count_parser.rb │ │ ├── plate_reader_parser.rb │ │ └── quant_parser.rb │ ├── pbmc_pooling_customer_request.rb │ ├── permission.rb │ ├── phi_x.rb │ ├── phi_x │ │ ├── spiked_buffer.rb │ │ └── stock.rb │ ├── pick_list.rb │ ├── pick_list │ │ ├── pick.rb │ │ └── record_cache.rb │ ├── pico_assay_plate.rb │ ├── pico_dilution_plate.rb │ ├── pipeline.rb │ ├── pipeline │ │ ├── batch_validation.rb │ │ ├── group_by_parent.rb │ │ ├── grouper_by_parent.rb │ │ ├── grouper_by_parent_and_submission.rb │ │ ├── grouper_by_submission.rb │ │ ├── grouper_for_pipeline.rb │ │ ├── inbox_extensions.rb │ │ ├── inbox_grouped_by_submission.rb │ │ └── requests_in_storage.rb │ ├── pipeline_request_information_type.rb │ ├── pipelines_request_type.rb │ ├── plate.rb │ ├── plate │ │ ├── creator.rb │ │ ├── creator_parameters.rb │ │ ├── fluidigm_behaviour.rb │ │ ├── pooling_metadata.rb │ │ ├── quad_creator.rb │ │ └── sample_tube_factory.rb │ ├── plate_barcode.rb │ ├── plate_conversion.rb │ ├── plate_creation.rb │ ├── plate_owner.rb │ ├── plate_purpose.rb │ ├── plate_purpose │ │ ├── initial_purpose.rb │ │ └── input.rb │ ├── plate_template.rb │ ├── plate_template_task.rb │ ├── plate_transfer_task.rb │ ├── plate_type.rb │ ├── plate_volume.rb │ ├── poly_metadatum.rb │ ├── pooled_cherrypick_request.rb │ ├── pooled_plate_creation.rb │ ├── pooling.rb │ ├── pooling │ │ └── tag_clash_report.rb │ ├── pre_capture_pool.rb │ ├── prep_kit_barcode_task.rb │ ├── presenters │ │ ├── batch_submenu_presenter.rb │ │ ├── grouped_pipeline_inbox_presenter.rb │ │ └── qc_report_presenter.rb │ ├── primer_panel.rb │ ├── product.rb │ ├── product_catalogue.rb │ ├── product_catalogue │ │ ├── library_driven.rb │ │ ├── manual.rb │ │ └── single_product.rb │ ├── product_criteria.rb │ ├── product_criteria │ │ ├── advanced.rb │ │ └── basic.rb │ ├── product_line.rb │ ├── product_product_catalogue.rb │ ├── program.rb │ ├── project.rb │ ├── project_manager.rb │ ├── pulldown │ │ ├── plate_purposes.rb │ │ ├── requests.rb │ │ └── requests │ │ │ ├── bait_library_request.rb │ │ │ ├── isc_library_request.rb │ │ │ ├── isc_library_request_part.rb │ │ │ ├── library_creation.rb │ │ │ ├── re_isc_library_request.rb │ │ │ ├── sc_library_request.rb │ │ │ └── wgs_library_request.rb │ ├── pulldown_multiplexed_library_creation_request.rb │ ├── pulldown_multiplexed_library_tube.rb │ ├── purpose.rb │ ├── purpose │ │ └── relationship.rb │ ├── qc_assay.rb │ ├── qc_decision.rb │ ├── qc_file.rb │ ├── qc_metric.rb │ ├── qc_metric │ │ └── qc_state.rb │ ├── qc_metric_request.rb │ ├── qc_report.rb │ ├── qc_report │ │ └── file.rb │ ├── qc_request.rb │ ├── qc_result.rb │ ├── qc_result_factory.rb │ ├── qc_tube.rb │ ├── qcable.rb │ ├── qcable │ │ └── statemachine.rb │ ├── qcable_creator.rb │ ├── qcable_library_plate_purpose.rb │ ├── qcable_plate_purpose.rb │ ├── qcable_tube_purpose.rb │ ├── racked_tube.rb │ ├── re_request_submission.rb │ ├── receptacle.rb │ ├── receptacle │ │ ├── downstream_aliquots_removal.rb │ │ └── qc.rb │ ├── reference_genome.rb │ ├── report_fail.rb │ ├── request.rb │ ├── request │ │ ├── accessioning_required.rb │ │ ├── auto_multiplexing.rb │ │ ├── change_decision.rb │ │ ├── customer_responsibility.rb │ │ ├── grouping_helpers.rb │ │ ├── has_no_target_asset.rb │ │ ├── library_creation.rb │ │ ├── library_manufacture.rb │ │ ├── multiplexing.rb │ │ ├── none.rb │ │ ├── sample_compound_aliquot_transfer.rb │ │ ├── statemachine.rb │ │ ├── statistics.rb │ │ ├── traction.rb │ │ └── traction │ │ │ └── grid_ion.rb │ ├── request_event.rb │ ├── request_factory.rb │ ├── request_information.rb │ ├── request_information_type.rb │ ├── request_type.rb │ ├── request_type │ │ ├── pooling_method.rb │ │ ├── pooling_method │ │ │ ├── plate_row.rb │ │ │ └── submission.rb │ │ ├── validation.rb │ │ └── validator.rb │ ├── robot.rb │ ├── robot │ │ ├── generator.rb │ │ ├── generator │ │ │ ├── base.rb │ │ │ ├── beckman.rb │ │ │ ├── behaviours │ │ │ │ ├── hamilton_default.rb │ │ │ │ └── tecan_default.rb │ │ │ ├── hamilton.rb │ │ │ ├── tecan.rb │ │ │ ├── tecan_v2.rb │ │ │ └── tecan_v3.rb │ │ ├── pick_data.rb │ │ ├── verification.rb │ │ └── verification │ │ │ ├── base.rb │ │ │ ├── source_dest_beds.rb │ │ │ └── source_dest_control_beds.rb │ ├── robot_property.rb │ ├── role.rb │ ├── role │ │ ├── authorized.rb │ │ ├── user_role.rb │ │ └── user_role_helper.rb │ ├── sample.rb │ ├── sample_compound_component.rb │ ├── sample_manifest.rb │ ├── sample_manifest │ │ ├── barcode_printer_behaviour.rb │ │ ├── core_behaviour.rb │ │ ├── generator.rb │ │ ├── library_plate_behaviour.rb │ │ ├── library_tube_behaviour.rb │ │ ├── multiplexed_library_behaviour.rb │ │ ├── plate_behaviour.rb │ │ ├── sample_tube_behaviour.rb │ │ ├── shared_tube_behaviour.rb │ │ ├── state_machine.rb │ │ ├── tube_rack_behaviour.rb │ │ ├── unspecified_behaviour.rb │ │ └── uploader.rb │ ├── sample_manifest_asset.rb │ ├── sample_prep_qc_task.rb │ ├── sample_tube.rb │ ├── sanger_sample_id.rb │ ├── search.rb │ ├── search │ │ ├── deprecated_search.rb │ │ ├── find_asset_by_barcode.rb │ │ ├── find_illumina_a_plates.rb │ │ ├── find_illumina_a_stock_plates.rb │ │ ├── find_illumina_b_plates.rb │ │ ├── find_illumina_b_plates_for_user.rb │ │ ├── find_illumina_b_stock_plates.rb │ │ ├── find_illumina_c_plates.rb │ │ ├── find_illumina_c_tubes.rb │ │ ├── find_lot_by_batch_id.rb │ │ ├── find_lot_by_lot_number.rb │ │ ├── find_model_by_name.rb │ │ ├── find_outstanding_illumina_b_pre_pcr_plates.rb │ │ ├── find_plates.rb │ │ ├── find_plates_for_user.rb │ │ ├── find_pulldown_plates.rb │ │ ├── find_pulldown_plates_for_user.rb │ │ ├── find_pulldown_stock_plates.rb │ │ ├── find_qcable_by_barcode.rb │ │ ├── find_robot_by_barcode.rb │ │ ├── find_source_assets_by_destination_asset_barcode.rb │ │ ├── find_tubes.rb │ │ ├── find_user_by_login.rb │ │ └── find_user_by_swipecard_code.rb │ ├── search_behaviour.rb │ ├── sequencing_pipeline.rb │ ├── sequencing_request.rb │ ├── sequenom_qc_plate.rb │ ├── set_descriptors_task.rb │ ├── shared_behaviour │ │ ├── deprecatable.rb │ │ ├── immutable.rb │ │ ├── indestructable.rb │ │ ├── named.rb │ │ └── qcable_asset.rb │ ├── single_request_submission.rb │ ├── specific_tube_creation.rb │ ├── specific_tube_rack_creation.rb │ ├── spiked_buffer.rb │ ├── stamp.rb │ ├── standard_named_scopes.rb │ ├── state_change.rb │ ├── state_changer │ │ ├── base.rb │ │ ├── initial_stock_tube.rb │ │ ├── input_plate.rb │ │ ├── mx_tube.rb │ │ ├── qcable_labware.rb │ │ ├── qcable_library_plate.rb │ │ ├── standard_plate.rb │ │ ├── stock_tube.rb │ │ ├── tube_base.rb │ │ └── tube_rack.rb │ ├── stock_library_tube.rb │ ├── stock_multiplexed_library_tube.rb │ ├── stock_stamper.rb │ ├── strip_creation_request.rb │ ├── strip_tube.rb │ ├── study.rb │ ├── study_report.rb │ ├── study_report │ │ ├── asset_details.rb │ │ ├── study_details.rb │ │ └── well_details.rb │ ├── study_sample.rb │ ├── study_type.rb │ ├── submission.rb │ ├── submission │ │ ├── accession_behaviour.rb │ │ ├── asset_group_behaviour.rb │ │ ├── asset_submission_finder.rb │ │ ├── crossable.rb │ │ ├── delayed_job_behaviour.rb │ │ ├── flexible_request_graph.rb │ │ ├── linear_request_graph.rb │ │ ├── order_presenter.rb │ │ ├── presenter_skeleton.rb │ │ ├── priorities.rb │ │ ├── project_validation.rb │ │ ├── request_options_behaviour.rb │ │ ├── scrna_core_cdna_prep_feasibility_calculator.rb │ │ ├── scrna_core_cdna_prep_feasibility_validator.rb │ │ ├── state_machine.rb │ │ ├── submission_creator.rb │ │ ├── submission_presenter.rb │ │ └── validations_by_template_name.rb │ ├── submission_pool.rb │ ├── submission_template.rb │ ├── submission_template_request_type.rb │ ├── submitted_asset.rb │ ├── supplier.rb │ ├── swipecardable.rb │ ├── system_request.rb │ ├── tag.rb │ ├── tag2_layout.rb │ ├── tag2_layout_template.rb │ ├── tag_group.rb │ ├── tag_group │ │ ├── adapter_type.rb │ │ └── form_object.rb │ ├── tag_groups_task.rb │ ├── tag_layout.rb │ ├── tag_layout │ │ ├── as_fixed_group_by_plate.rb │ │ ├── as_group_by_plate.rb │ │ ├── comb_by_rows.rb │ │ ├── combinatorial_sequential.rb │ │ ├── dual_index_walker.rb │ │ ├── in_columns.rb │ │ ├── in_columns_then_columns.rb │ │ ├── in_columns_then_rows.rb │ │ ├── in_inverse_columns.rb │ │ ├── in_inverse_rows.rb │ │ ├── in_rows.rb │ │ ├── quadrants.rb │ │ ├── template_submission.rb │ │ ├── walk_manual_wells_by_pools.rb │ │ ├── walk_manual_wells_of_plate.rb │ │ ├── walk_wells_by_pools.rb │ │ ├── walk_wells_of_plate.rb │ │ └── walker.rb │ ├── tag_layout_template.rb │ ├── tag_set.rb │ ├── tag_substitution.rb │ ├── tag_substitution │ │ └── substitution.rb │ ├── task.rb │ ├── tasks │ │ ├── add_spiked_in_control_handler.rb │ │ ├── base_handler.rb │ │ ├── cherrypick_handler.rb │ │ ├── plate_template_handler.rb │ │ ├── plate_transfer_handler.rb │ │ └── set_descriptors_handler.rb │ ├── transfer.rb │ ├── transfer │ │ ├── associations.rb │ │ ├── between_plate_and_tubes.rb │ │ ├── between_plates.rb │ │ ├── between_plates_by_submission.rb │ │ ├── between_specific_tubes.rb │ │ ├── between_tubes_by_submission.rb │ │ ├── controlled_destinations.rb │ │ ├── from_plate_to_specific_tubes.rb │ │ ├── from_plate_to_specific_tubes_by_pool.rb │ │ ├── from_plate_to_tube.rb │ │ ├── from_plate_to_tube_by_multiplex.rb │ │ ├── from_plate_to_tube_by_submission.rb │ │ ├── state.rb │ │ ├── transfers_by_schema.rb │ │ └── transfers_to_known_destination.rb │ ├── transfer_request.rb │ ├── transfer_request_collection.rb │ ├── transfer_request_collection_transfer_request.rb │ ├── transfer_template.rb │ ├── tube.rb │ ├── tube │ │ ├── attribute_updater.rb │ │ ├── purpose.rb │ │ ├── standard_mx.rb │ │ └── stock_mx.rb │ ├── tube_creation.rb │ ├── tube_from_plate_creation.rb │ ├── tube_from_tube_creation.rb │ ├── tube_rack.rb │ ├── tube_rack │ │ └── purpose.rb │ ├── tube_rack_status.rb │ ├── ui_helper.rb │ ├── ui_helper │ │ ├── summary.rb │ │ └── summary_item.rb │ ├── ultima_global.rb │ ├── ultima_sequencing_pipeline.rb │ ├── ultima_sequencing_request.rb │ ├── user.rb │ ├── user │ │ └── authentication.rb │ ├── uuid.rb │ ├── validate_sample_sheet_task.rb │ ├── validation_state_guard.rb │ ├── volume_update.rb │ ├── warren │ │ └── subscriber │ │ │ └── queue_broadcast_consumer.rb │ ├── well.rb │ ├── well │ │ └── attribute_updater.rb │ ├── well_attribute.rb │ ├── work_completion.rb │ ├── work_completion │ │ ├── labware_completion.rb │ │ ├── plate_completion.rb │ │ ├── tube_completion.rb │ │ └── tube_rack_completion.rb │ ├── work_completions_submission.rb │ ├── work_order.rb │ ├── work_order │ │ └── factory.rb │ ├── work_order_type.rb │ ├── workflow.rb │ └── working_dilution_plate.rb ├── resources │ └── api │ │ └── v2 │ │ ├── aliquot_resource.rb │ │ ├── asset_audit_resource.rb │ │ ├── asset_resource.rb │ │ ├── bait_library_layout_resource.rb │ │ ├── barcode_printer_resource.rb │ │ ├── base_resource.rb │ │ ├── bulk_transfer_resource.rb │ │ ├── comment_resource.rb │ │ ├── custom_metadatum_collection_resource.rb │ │ ├── faculty_sponsor_resource.rb │ │ ├── fragment_resource.rb │ │ ├── labware_resource.rb │ │ ├── lane_resource.rb │ │ ├── lot_resource.rb │ │ ├── lot_type_resource.rb │ │ ├── order_resource.rb │ │ ├── pick_list_resource.rb │ │ ├── plate_conversion_resource.rb │ │ ├── plate_creation_resource.rb │ │ ├── plate_purpose_resource.rb │ │ ├── plate_resource.rb │ │ ├── plate_template_resource.rb │ │ ├── poly_metadatum_resource.rb │ │ ├── pooled_plate_creation_resource.rb │ │ ├── pre_capture_pool_resource.rb │ │ ├── primer_panel_resource.rb │ │ ├── project_resource.rb │ │ ├── purpose_resource.rb │ │ ├── qc_assay_resource.rb │ │ ├── qc_file_resource.rb │ │ ├── qc_result_resource.rb │ │ ├── qcable_creator_resource.rb │ │ ├── qcable_resource.rb │ │ ├── racked_tube_resource.rb │ │ ├── receptacle_resource.rb │ │ ├── request_metadata_resource.rb │ │ ├── request_resource.rb │ │ ├── request_type_resource.rb │ │ ├── sample_manifest_resource.rb │ │ ├── sample_metadata_resource.rb │ │ ├── sample_resource.rb │ │ ├── shared_behaviour │ │ ├── labware.rb │ │ └── receptacle.rb │ │ ├── specific_tube_creation_resource.rb │ │ ├── specific_tube_rack_creation_resource.rb │ │ ├── state_change_resource.rb │ │ ├── study_metadata_resource.rb │ │ ├── study_resource.rb │ │ ├── submission_pool_resource.rb │ │ ├── submission_resource.rb │ │ ├── submission_template_resource.rb │ │ ├── tag_group_adapter_type_resource.rb │ │ ├── tag_group_resource.rb │ │ ├── tag_layout_resource.rb │ │ ├── tag_layout_template_resource.rb │ │ ├── tag_resource.rb │ │ ├── tag_set_resource.rb │ │ ├── template_resource.rb │ │ ├── transfer_request_collection_resource.rb │ │ ├── transfer_request_resource.rb │ │ ├── transfer_resource.rb │ │ ├── transfer_template_resource.rb │ │ ├── tube_from_plate_creation_resource.rb │ │ ├── tube_from_tube_creation_resource.rb │ │ ├── tube_purpose_resource.rb │ │ ├── tube_rack_purpose_resource.rb │ │ ├── tube_rack_resource.rb │ │ ├── tube_rack_status_resource.rb │ │ ├── tube_resource.rb │ │ ├── user_resource.rb │ │ ├── volume_update_resource.rb │ │ ├── well_resource.rb │ │ ├── work_completion_resource.rb │ │ └── work_order_resource.rb ├── sample_manifest_excel │ ├── sample_manifest_excel.rb │ └── sample_manifest_excel │ │ ├── configuration.rb │ │ ├── download.rb │ │ ├── manifest_type_list.rb │ │ ├── tags.rb │ │ ├── tags │ │ ├── aliquot_updater.rb │ │ ├── clashes_finder.rb │ │ ├── example_data.rb │ │ └── validator │ │ │ ├── formatting.rb │ │ │ └── uniqueness.rb │ │ ├── test_download.rb │ │ ├── upload │ │ ├── base.rb │ │ ├── cache.rb │ │ ├── converters.rb │ │ ├── data.rb │ │ ├── processor.rb │ │ ├── processor │ │ │ ├── base.rb │ │ │ ├── library_tube.rb │ │ │ ├── multiplexed_library_tube.rb │ │ │ ├── one_d_tube.rb │ │ │ ├── plate.rb │ │ │ └── tube_rack.rb │ │ ├── row.rb │ │ └── rows.rb │ │ └── worksheet │ │ ├── data_worksheet.rb │ │ └── test_worksheet.rb ├── sequencescape_excel │ ├── sequencescape_excel.rb │ └── sequencescape_excel │ │ ├── cell.rb │ │ ├── column.rb │ │ ├── column_list.rb │ │ ├── conditional_formatting.rb │ │ ├── conditional_formatting_default.rb │ │ ├── conditional_formatting_default_list.rb │ │ ├── conditional_formatting_list.rb │ │ ├── configuration.rb │ │ ├── core_extensions.rb │ │ ├── formula.rb │ │ ├── helpers.rb │ │ ├── helpers │ │ ├── attributes.rb │ │ ├── download.rb │ │ └── worksheet.rb │ │ ├── list.rb │ │ ├── null_objects.rb │ │ ├── null_objects │ │ ├── null_column.rb │ │ ├── null_column_list.rb │ │ ├── null_configuration.rb │ │ └── null_processor.rb │ │ ├── null_range.rb │ │ ├── null_validation.rb │ │ ├── range.rb │ │ ├── range_list.rb │ │ ├── specialised_field.rb │ │ ├── specialised_field │ │ ├── base.rb │ │ ├── bioscan_control_type.rb │ │ ├── bioscan_supplier_name.rb │ │ ├── chromium_tag_group.rb │ │ ├── chromium_tag_well.rb │ │ ├── control_type.rb │ │ ├── dual_index_tag_set.rb │ │ ├── dual_index_tag_well.rb │ │ ├── i5.rb │ │ ├── i7.rb │ │ ├── insert_size_from.rb │ │ ├── insert_size_to.rb │ │ ├── library_type.rb │ │ ├── primer_panel.rb │ │ ├── priority.rb │ │ ├── reference_genome.rb │ │ ├── retention_instruction.rb │ │ ├── sample_ebi_accession_number.rb │ │ ├── sanger_plate_id.rb │ │ ├── sanger_sample_id.rb │ │ ├── sanger_sample_id_value.rb │ │ ├── sanger_tube_id.rb │ │ ├── tag2_group.rb │ │ ├── tag2_index.rb │ │ ├── tag_group.rb │ │ ├── tag_index.rb │ │ ├── value_required.rb │ │ ├── value_to_integer.rb │ │ ├── value_to_upcase.rb │ │ ├── volume.rb │ │ └── well.rb │ │ ├── subclass_checker.rb │ │ ├── upload.rb │ │ ├── validation.rb │ │ ├── worksheet.rb │ │ └── worksheet │ │ ├── base.rb │ │ └── ranges_worksheet.rb ├── uat_actions │ ├── uat_actions.rb │ └── uat_actions │ │ ├── form_field.rb │ │ ├── generate_fluidx_barcodes.rb │ │ ├── generate_plate_concentrations.rb │ │ ├── generate_plate_volumes.rb │ │ ├── generate_plates.rb │ │ ├── generate_primer_panel.rb │ │ ├── generate_project.rb │ │ ├── generate_qc_results.rb │ │ ├── generate_sample_manifest.rb │ │ ├── generate_spiked_buffer_tube.rb │ │ ├── generate_study.rb │ │ ├── generate_supplier.rb │ │ ├── generate_tag_group.rb │ │ ├── generate_tag_layout_template.rb │ │ ├── generate_tag_plates.rb │ │ ├── generate_tag_set.rb │ │ ├── generate_tagged_plates.rb │ │ ├── generate_tube_racks.rb │ │ ├── generate_tubes.rb │ │ ├── integration_suite_tools.rb │ │ ├── plate_information.rb │ │ ├── shared │ │ ├── study_helper.rb │ │ └── supplier_helper.rb │ │ ├── static_records.rb │ │ ├── test_submission.rb │ │ ├── tube_submission.rb │ │ └── update_state_of_requests_in_labware.rb ├── uploaders │ └── polymorphic_uploader.rb ├── validators │ ├── batch_creation_validator.rb │ ├── element_aviti_validator.rb │ ├── latin1_validator.rb │ ├── novaseqx_pe_validator.rb │ ├── order_compatibility_validator.rb │ ├── ultima_validator.rb │ └── utf8mb3_validator.rb └── views │ ├── admin │ ├── abilities │ │ └── index.html.erb │ ├── bait_libraries │ │ ├── _edit_form.html.erb │ │ ├── _supplier_index.html.erb │ │ ├── _type_index.html.erb │ │ ├── bait_library_suppliers │ │ │ ├── _edit_form.html.erb │ │ │ ├── edit.html.erb │ │ │ └── new.html.erb │ │ ├── bait_library_types │ │ │ ├── _edit_form.html.erb │ │ │ ├── edit.html.erb │ │ │ └── new.html.erb │ │ ├── edit.html.erb │ │ ├── index.html.erb │ │ └── new.html.erb │ ├── custom_texts │ │ ├── _edit_custom_text.html.erb │ │ ├── edit.html.erb │ │ ├── index.html.erb │ │ ├── new.html.erb │ │ └── show.html.erb │ ├── delayed_jobs │ │ └── index.html.erb │ ├── faculty_sponsors │ │ ├── edit.html.erb │ │ ├── index.html.erb │ │ ├── new.html.erb │ │ └── show.html.erb │ ├── index.html.erb │ ├── plate_purposes │ │ ├── edit.html.erb │ │ ├── index.html.erb │ │ ├── new.html.erb │ │ └── show.html.erb │ ├── primer_panels │ │ ├── _edit_form.html.erb │ │ ├── edit.html.erb │ │ ├── index.html.erb │ │ └── new.html.erb │ ├── programs │ │ ├── edit.html.erb │ │ ├── index.html.erb │ │ ├── new.html.erb │ │ └── show.html.erb │ ├── projects │ │ ├── _edit.html.erb │ │ ├── _filtered_projects.html.erb │ │ ├── _manage_single_project.html.erb │ │ ├── index.html.erb │ │ └── show.html.erb │ ├── robot_properties │ │ ├── edit.html.erb │ │ ├── index.html.erb │ │ ├── new.html.erb │ │ └── show.html.erb │ ├── robots │ │ ├── edit.html.erb │ │ ├── index.html.erb │ │ ├── new.html.erb │ │ └── show.html.erb │ ├── roles │ │ ├── index.html.erb │ │ ├── new.html.erb │ │ ├── show.html.erb │ │ └── users │ │ │ └── index.html.erb │ ├── studies │ │ ├── _edit.html.erb │ │ ├── _filtered_studies.html.erb │ │ ├── _manage_single_study.html.erb │ │ ├── index.html.erb │ │ └── show.html.erb │ └── users │ │ ├── _add_role.html.erb │ │ ├── _add_role.js.rjs │ │ ├── _roles.html.erb │ │ ├── _user.html.erb │ │ ├── _users.html.erb │ │ ├── edit.html.erb │ │ ├── filter.html.erb │ │ ├── index.html.erb │ │ └── show.html.erb │ ├── advanced_search │ └── index.html.erb │ ├── approval_mailer │ ├── approved.html.erb │ ├── on_hold.html.erb │ └── rejected.html.erb │ ├── asset_audits │ └── index.html.erb │ ├── assets │ ├── _print_form.html.erb │ ├── _scan_message.html.erb │ ├── _table_of_assets.html.erb │ ├── create_plate_layout.html.erb │ ├── lookup.html.erb │ ├── reset_values_for_move.html.erb │ ├── samples_partials │ │ ├── _asset_samples.erb │ │ ├── _blank.erb │ │ ├── _lane_samples.erb │ │ ├── _plate_samples.erb │ │ └── _tube_rack_samples.erb │ ├── show.html.erb │ ├── show.xml.builder │ └── show_plate.html.erb │ ├── barcode_printers │ ├── __edit_barcode_printer.html.erb │ ├── edit.html.erb │ ├── index.html.erb │ ├── new.html.erb │ └── show.html.erb │ ├── batches │ ├── _assets.html.erb │ ├── _batch_fail.html.erb │ ├── _cherrypick_single_worksheet.html.erb │ ├── _cherrypick_worksheet_plate_list.html.erb │ ├── _events.html.erb │ ├── _printable.html.erb │ ├── _submenu.erb │ ├── _user_not_found.html.erb │ ├── _workflow.html.erb │ ├── auto_qc.html.erb │ ├── auto_qc.xml.erb │ ├── batch_error.xml.builder │ ├── by_study.html.erb │ ├── cherrypick_worksheet.html.erb │ ├── comments │ │ ├── _list.html.erb │ │ └── index.html.erb │ ├── completed.html.erb │ ├── edit.html.erb │ ├── fail.html.erb │ ├── failed.html.erb │ ├── filtered.html.erb │ ├── index.html.erb │ ├── legacy_worksheet.html.erb │ ├── pending.html.erb │ ├── pipeline.html.erb │ ├── print_amp_plate_labels.html.erb │ ├── print_labels.html.erb │ ├── print_plate_labels.html.erb │ ├── released.html.erb │ ├── released.xml.builder │ ├── show.html.erb │ ├── show.xml.builder │ ├── simplified_worksheet.html.erb │ ├── started.html.erb │ └── verify.html.erb │ ├── bulk_submission_excel │ └── downloads │ │ └── new.html.erb │ ├── bulk_submissions │ ├── _bulk_submission_template.html.erb │ ├── _guidance.html.erb │ ├── _submission_templates.html.erb │ ├── _upload.html.erb │ ├── _warnings.erb │ ├── create.html.erb │ └── new.html.erb │ ├── errors │ ├── internal_server_error.html.erb │ ├── not_found.html.erb │ └── service_unavailable.html.erb │ ├── eventful_mailer │ ├── confirm_event.html.erb │ ├── confirm_event.text.erb │ ├── confirm_external_release_event.html.erb │ ├── confirm_sample_event.html.erb │ ├── confirm_sample_event.text.erb │ ├── fail_attempt.html.erb │ ├── fail_attempt.text.erb │ ├── notify_request_fail.html.erb │ ├── notify_request_fail.text.erb │ ├── update_event.html.erb │ └── update_event.text.erb │ ├── events │ └── new.html.erb │ ├── gels │ ├── _gel_plate.html.erb │ ├── find.html.erb │ ├── index.html.erb │ └── show.html.erb │ ├── get_your_qc_completed_tubes_here │ └── new.html.erb │ ├── homes │ ├── _batches.html.erb │ ├── _studies.html.erb │ ├── _submissions.html.erb │ └── show.html.erb │ ├── lab_searches │ ├── _search.html.erb │ ├── new.html.erb │ └── show │ │ ├── _asset.html.erb │ │ └── _batch.html.erb │ ├── labware │ ├── _asset_summary.html.erb │ ├── _find_form.html.erb │ ├── _metadata.html.erb │ ├── _print_form.html.erb │ ├── _qc_files.html.erb │ ├── _relations.html.erb │ ├── _requests.html.erb │ ├── _scan_message.html.erb │ ├── _table_of_assets.html.erb │ ├── comments │ │ ├── _list.html.erb │ │ ├── _simple_list.erb │ │ └── index.html.erb │ ├── create_plate_layout.html.erb │ ├── edit.html.erb │ ├── find_by_barcode.html.erb │ ├── history.html.erb │ ├── index.html.erb │ ├── lab_view.html.erb │ ├── lookup.html.erb │ ├── print.html.erb │ ├── reset_values_for_move.html.erb │ ├── retention_instruction.html.erb │ ├── samples_partials │ │ ├── _asset_samples.erb │ │ ├── _blank.erb │ │ ├── _lane_samples.erb │ │ └── _plate_samples.erb │ ├── show.html.erb │ ├── show.xml.builder │ ├── show_plate.html.erb │ └── summary.html.erb │ ├── labwhere_receptions │ ├── _form.html.erb │ ├── create.html.erb │ └── index.html.erb │ ├── layouts │ ├── _readable_error.html.erb │ ├── application.html.erb │ ├── home.xml.erb │ └── sessions.html.erb │ ├── location_reports │ ├── _location_labware_selection_form.html.erb │ ├── _location_labwhere_form.html.erb │ ├── _location_report.html.erb │ ├── _location_reports.html.erb │ └── index.html.erb │ ├── parents │ ├── _parent.html.erb │ └── show.html.erb │ ├── phi_x │ ├── spiked_buffers │ │ ├── new.html.erb │ │ └── show.html.erb │ └── stocks │ │ ├── new.html.erb │ │ └── show.html.erb │ ├── phi_xes │ ├── _spiked_buffer.html.erb │ ├── _stock.html.erb │ └── show.html.erb │ ├── pick_lists │ ├── index.html.erb │ └── show.html.erb │ ├── pipelines │ ├── _assets.html.erb │ ├── _batch_statuses.html.erb │ ├── _default_inbox.html.erb │ ├── _deprecated_inbox.html.erb │ ├── _event.html.erb │ ├── _event_request.html.erb │ ├── _event_requests.html.erb │ ├── _group_by_parent.html.erb │ ├── _inbox_submission_button.html.erb │ ├── _pipeline_limit.html.erb │ ├── _pipelines.html.erb │ ├── _previous_failed_requests.erb │ ├── _request.html.erb │ ├── _request_comments.html.erb │ ├── _requests.html.erb │ ├── _requests_footer.html.erb │ ├── _requests_header.html.erb │ ├── _show_held_requests.html.erb │ ├── batches.html.erb │ ├── finish.html.erb │ ├── index.html.erb │ ├── show.html.erb │ ├── summary.html.erb │ ├── update_priority.html.erb │ └── update_priority_mx.html.erb │ ├── plate_picks │ └── show.html.erb │ ├── plate_summaries │ ├── _custom_metadatum_collection.html.erb │ ├── _descendant.html.erb │ ├── index.html.erb │ ├── search.html.erb │ └── show.html.erb │ ├── plate_templates │ ├── _layout_plate.html.erb │ ├── edit.html.erb │ ├── index.html.erb │ └── new.html.erb │ ├── plates │ ├── _concentration.html.erb │ ├── _loci_passed.html.erb │ ├── _plate_schematic.html.erb │ ├── _quantity_in_nano_grams.html.erb │ ├── _rin.html.erb │ ├── _volume.html.erb │ ├── creator │ │ └── _printed_barcodes.html.erb │ ├── fluidigm_file.csv.erb │ ├── new.html.erb │ ├── show.html.erb │ └── to_sample_tubes.html.erb │ ├── plates_from_tubes │ ├── _created_plates.html.erb │ └── new.html.erb │ ├── poolings │ ├── _tag_clash_report.html.erb │ └── new.html.erb │ ├── projects │ ├── _managed_project.html.erb │ ├── _project_form.html.erb │ ├── _role.html.erb │ ├── _roles.html.erb │ ├── collaborators.html.erb │ ├── edit.html.erb │ ├── index.html.erb │ ├── new.html.erb │ ├── related_studies.html.erb │ ├── related_studies.xml.builder │ ├── show.html.erb │ └── show.xml.builder │ ├── qc_reports │ ├── _filter_criteria.html.erb │ ├── _qc_report.html.erb │ ├── _qc_report_form.html.erb │ ├── _qc_report_upload.html.erb │ ├── _qc_reports.html.erb │ ├── index.html.erb │ └── show.html.erb │ ├── quad_stamp │ └── new.html.erb │ ├── receptacles │ ├── _asset_summary.html.erb │ ├── _find_form.html.erb │ ├── _print_form.html.erb │ ├── _qc_files.html.erb │ ├── _requests.html.erb │ ├── _samples.erb │ ├── _scan_message.html.erb │ ├── _table_of_assets.html.erb │ ├── comments │ │ ├── _list.html.erb │ │ ├── _simple_list.erb │ │ └── index.html.erb │ ├── create_plate_layout.html.erb │ ├── edit.html.erb │ ├── find_by_barcode.html.erb │ ├── history.html.erb │ ├── index.html.erb │ ├── lookup.html.erb │ ├── new_request.html.erb │ ├── print.html.erb │ ├── reset_values_for_move.html.erb │ ├── show.html.erb │ ├── show.xml.builder │ ├── show_plate.html.erb │ └── summary.html.erb │ ├── reference_genomes │ ├── edit.html.erb │ ├── index.html.erb │ ├── new.html.erb │ └── show.html.erb │ ├── report_fails │ ├── _form.html.erb │ ├── create.html.erb │ └── index.html.erb │ ├── requests │ ├── _event.html.erb │ ├── _form.html.erb │ ├── _qc_information.html.erb │ ├── _submitted.html.erb │ ├── comments │ │ ├── _list.html.erb │ │ ├── _simple_list.erb │ │ └── index.html.erb │ ├── edit.html.erb │ ├── filter_change_decision.html.erb │ ├── history.html.erb │ ├── index.html.erb │ ├── index.xml.builder │ ├── list_inboxes.xml.builder │ ├── show.html.erb │ └── show.xml.builder │ ├── robot_verifications │ ├── download.html.erb │ ├── index.html.erb │ └── submission.html.erb │ ├── sample_logistics │ ├── index.html.erb │ └── lab.html.erb │ ├── sample_manifest_upload_with_tag_sequences │ ├── _side_links.html.erb │ ├── _upload.html.erb │ └── new.html.erb │ ├── samples │ ├── _accession_statuses.html.erb │ ├── _asset_groups.html.erb │ ├── _assets.html.erb │ ├── _component_samples.html.erb │ ├── _consent_withdrawn.html.erb │ ├── _receptacles.html.erb │ ├── _sample.html.erb │ ├── _studies.html.erb │ ├── _submissions.html.erb │ ├── _summary.html.erb │ ├── comments │ │ ├── _list.html.erb │ │ └── index.html.erb │ ├── edit.html.erb │ ├── history.html.erb │ ├── index.html.erb │ ├── index.xml.builder │ ├── new.html.erb │ ├── reset_values_for_move.html.erb │ ├── review.html.erb │ ├── show.html.erb │ ├── show.xml.builder │ └── show_submissions.html.erb │ ├── sdb │ ├── home │ │ └── index.html.erb │ ├── sample_manifests │ │ ├── _pool.html.erb │ │ ├── _samples.html.erb │ │ ├── _side_links.html.erb │ │ ├── _upload.html.erb │ │ ├── export.html.erb │ │ ├── index.html.erb │ │ ├── new.html.erb │ │ └── show.html.erb │ └── suppliers │ │ ├── _edit_supplier.html.erb │ │ ├── edit.html.erb │ │ ├── index.html.erb │ │ ├── new.html.erb │ │ ├── sample_manifests.html.erb │ │ ├── show.html.erb │ │ └── studies.html.erb │ ├── searches │ ├── _search.html.erb │ ├── _show.html.erb │ ├── _study.html.erb │ ├── index.html.erb │ └── show │ │ ├── _asset.html.erb │ │ ├── _asset_group.html.erb │ │ ├── _barcode.html.erb │ │ ├── _labware.html.erb │ │ ├── _project.html.erb │ │ ├── _request.html.erb │ │ ├── _sample.html.erb │ │ ├── _study.html.erb │ │ ├── _submission.html.erb │ │ └── _supplier.html.erb │ ├── sequenom_qc_plates │ ├── _sequenom_plate_details_row.html.erb │ └── index.html.erb │ ├── sessions │ ├── login.html.erb │ ├── settings.html.erb │ └── signup.html.erb │ ├── shared │ ├── _actions.html.erb │ ├── _batch.html.erb │ ├── _batches.html.erb │ ├── _comment.html.erb │ ├── _comments.html.erb │ ├── _create_manifests_side_links.html.erb │ ├── _data_release_enforce.html.erb │ ├── _edit_fields.html.erb │ ├── _ethical_approval_upload.html.erb │ ├── _external_properties.html.erb │ ├── _financial_approval.html.erb │ ├── _footer.html.erb │ ├── _header.html.erb │ ├── _item.rhtml │ ├── _labware_to_print.html.erb │ ├── _long_read_warning.html.erb │ ├── _manifests.html.erb │ ├── _menu.html.erb │ ├── _plate_print.html.erb │ ├── _print.html.erb │ ├── _printer_list.html.erb │ ├── _progress_statistics_summary.html.erb │ ├── _project_listing.html.erb │ ├── _property.html.erb │ ├── _show_plate.html.erb │ ├── _sidebar.html.erb │ ├── _study_reports.html.erb │ ├── _suppliers_list.html.erb │ ├── _tab.html.erb │ ├── _tag_info.erb │ ├── _tags_list.html.erb │ ├── fields │ │ ├── _selection_edit.html.erb │ │ └── _text_edit.html.erb │ ├── metadata │ │ ├── _edit_document_field.html.erb │ │ ├── _edit_field.html.erb │ │ ├── _edit_value.html.erb │ │ ├── _file.html.erb │ │ ├── _plain_field.html.erb │ │ ├── _radio_field.html.erb │ │ ├── _related_fields.html.erb │ │ ├── edit │ │ │ ├── _lane.html.erb │ │ │ ├── _project.html.erb │ │ │ ├── _request.html.erb │ │ │ ├── _sample.html.erb │ │ │ └── _study.html.erb │ │ └── show │ │ │ ├── _project.html.erb │ │ │ ├── _request.html.erb │ │ │ ├── _sample.html.erb │ │ │ └── _study.html.erb │ └── submission.xml.builder │ ├── stock_assets │ └── new.html.erb │ ├── stock_stampers │ ├── create.html.erb │ └── new.html.erb │ ├── studies │ ├── _add_related_study.html.erb │ ├── _managed_study.html.erb │ ├── _role.html.erb │ ├── _roles.html.erb │ ├── _study.html.erb │ ├── _study_groups.html.erb │ ├── _study_list.html.erb │ ├── asset_groups │ │ ├── edit.html.erb │ │ ├── index.html.erb │ │ ├── new.html.erb │ │ ├── print.html.erb │ │ ├── printing.html.erb │ │ ├── search.html.erb │ │ └── show.html.erb │ ├── collaborators.html.erb │ ├── comments │ │ ├── _list.html.erb │ │ └── index.html.erb │ ├── edit.html.erb │ ├── events │ │ └── index.html.erb │ ├── index.html.erb │ ├── index.xml.builder │ ├── index_deprecated_xml.xml.builder │ ├── information │ │ ├── _accession_statuses.html.erb │ │ ├── _asset_progress.html.erb │ │ ├── _items.html.erb │ │ ├── _sample_progress.html.erb │ │ ├── _study_summary.html.erb │ │ ├── _submission_warning.html.erb │ │ ├── _summary.html.erb │ │ ├── _summary_for_request_type.html.erb │ │ ├── show.html.erb │ │ └── summary.html.erb │ ├── new.html.erb │ ├── plates │ │ ├── index.html.erb │ │ ├── show.html.erb │ │ ├── view_wells.html.erb │ │ └── wells │ │ │ ├── edit.html.erb │ │ │ ├── index.html.erb │ │ │ ├── new.html.erb │ │ │ └── show.html.erb │ ├── projects.html.erb │ ├── projects.xml.builder │ ├── properties.html.erb │ ├── sample_manifests.html.erb │ ├── samples │ │ └── index.html.erb │ ├── show.html.erb │ ├── show.xml.builder │ ├── state.html.erb │ ├── study_reports.html.erb │ └── suppliers.html.erb │ ├── study_reports │ └── index.html.erb │ ├── submissions │ ├── _list.html.erb │ ├── _order.html.erb │ ├── _order_errors.html.erb │ ├── _order_fields.html.erb │ ├── _orders.html.erb │ ├── _saved_order.html.erb │ ├── _study_assets.html.erb │ ├── _warnings.html.erb │ ├── edit.html.erb │ ├── index.html.erb │ ├── new.html.erb │ ├── show.html.erb │ └── study.html.erb │ ├── tag_groups │ ├── index.html.erb │ ├── new.html.erb │ └── show.html.erb │ ├── tag_layout_templates │ ├── index.html.erb │ ├── new.html.erb │ └── show.html.erb │ ├── tag_sets │ ├── index.html.erb │ ├── new.html.erb │ └── show.html.erb │ ├── tag_substitutions │ └── new.html.erb │ ├── tube_rack_statuses │ └── index.html.erb │ ├── tube_rack_summaries │ └── show.html.erb │ ├── uat_actions │ ├── _entry.html.erb │ ├── create.html.erb │ ├── form_fields │ │ └── _form_field.html.erb │ ├── index.html.erb │ └── show.html.erb │ ├── users │ ├── edit.html.erb │ ├── projects.html.erb │ ├── show.html.erb │ └── study_reports.html.erb │ └── workflows │ ├── _add_spiked_in_control.html.erb │ ├── _assign_plate_purpose.html.erb │ ├── _cherrypick_batches.html.erb │ ├── _cherrypick_by_amount.html.erb │ ├── _cherrypick_by_concentration.html.erb │ ├── _cherrypick_by_volume.html.erb │ ├── _cherrypick_strategies.html.erb │ ├── _descriptor.html.erb │ ├── _descriptors.html.erb │ ├── _direct_phi_x_fields.erb │ ├── _dna_qc_results.html.erb │ ├── _events.html.erb │ ├── _failed.html.erb │ ├── _filter_samples_batches.html.erb │ ├── _fluidigm_template_batches.html.erb │ ├── _indirect_phi_x_fields.erb │ ├── _next_stage_submit.html.erb │ ├── _plate.html.erb │ ├── _plate_template_batches.html.erb │ ├── _plate_transfer.html.erb │ ├── _qc_plate.html.erb │ ├── _requests_header.html.erb │ ├── _scratch_pad.html.erb │ ├── _select_tag_for_well.html.erb │ ├── _set_descriptors.html.erb │ ├── _sidebar.html.erb │ ├── released.html.erb │ └── stage.html.erb ├── bin ├── bundle ├── cucumber ├── knapsack_pro_cucumber ├── knapsack_pro_feature ├── knapsack_pro_rspec ├── rails ├── rake ├── setup ├── update ├── vite └── yarn ├── codecov.yml ├── compile-build ├── config.ru ├── config ├── accession │ └── tags.yml ├── aker.yml.example ├── application.rb ├── boot.rb ├── broker.yml ├── bulk_submission_excel │ ├── columns.yml │ ├── conditional_formattings.yml │ └── ranges.yml ├── cable.yml ├── config.rb ├── cucumber.yml ├── database.yml ├── default_records │ ├── asset_shapes │ │ └── default_records.yml │ ├── barcode_printer_types │ │ └── default_records.yml │ ├── descriptors │ │ ├── 002_element_aviti_descriptors.yml │ │ └── 003_ultima_descriptors.wip.yml │ ├── flowcell_types │ │ ├── 002_element_aviti_flowcell_types.yml │ │ └── default_records.yml │ ├── flowcell_types_request_types │ │ ├── 002_element_aviti_flowcell_types_request_types.yml │ │ └── default_records.yml │ ├── library_types │ │ ├── .about_library_types │ │ ├── 001_long_read.yml │ │ ├── 002_ultima_library_types.wip.yml │ │ └── default_records.yml │ ├── pipeline_request_information_types │ │ ├── 002_element_aviti_pipeline_request_information_types.yml │ │ ├── 003_ultima_pipeline_request_information_types.wip.yml │ │ └── default_records.yml │ ├── pipelines │ │ ├── 002_element_aviti_pipelines.yml │ │ ├── 003_ultima_pipelines.wip.yml │ │ └── default_records.yml │ ├── plate_creators │ │ └── 000_example.yml │ ├── plate_purposes │ │ ├── 001_extraction_plates.yml │ │ ├── 002_illumina_b_legacy_purposes.dev.yml │ │ ├── 003_illumina_c_legacy_purposes.dev.yml │ │ ├── 004_illumina_htp_legacy_purposes.dev.yml │ │ ├── 005_limber_purposes.yml │ │ ├── 006_heron_purposes.yml │ │ ├── 008_limber_lcm_dna_rna_seq.yml │ │ ├── 009_bioscan_purposes.yml │ │ ├── 010_deep_well_plates.yml │ │ ├── 011_scrna_core_cdna_prep_plate_purposes.yml │ │ ├── 012_anospp_plate_purposes.yml │ │ ├── 013_lcm_triomics_plate_purposes.yml │ │ ├── 014_bge.yml │ │ ├── 015_rna_stock_plate.yml │ │ └── 016_ultima_purposes.wip.yml │ ├── plate_types │ │ └── plate_types.yml │ ├── primer_panels │ │ └── primer_panels.dev.yml │ ├── product_catalogues │ │ ├── 001_cardinal_product_catalogues.yml │ │ ├── 002_targeted_nanoseq_product_catalogues.yml │ │ ├── 003_lcm_dna_rna_seq.yml │ │ ├── 004_bioscan_product_catalogue.yml │ │ ├── 004_wgs.yml │ │ ├── 006_deep_well_stamping.yml │ │ ├── 007_novaseqx_product_catalogue.yml │ │ ├── 008_lcmb_product_catalogue.yml │ │ ├── 009_scrna_core_cell_extraction_product_catalogues.yml │ │ ├── 010_rvi_bait_capture_library_catalogue.yml │ │ ├── 011_scrna_core_catalogue.yml │ │ ├── 012_anospp_catalogue.yml │ │ ├── 013_lcm_triomics_catalogue.yml │ │ └── 020_bge.yml │ ├── request_information_types │ │ ├── 002_element_aviti_request_information_types.yml │ │ ├── 003_ultima_request_information_types.wip.yml │ │ └── default_records.yml │ ├── request_type_validators │ │ ├── 002_element_aviti_request_type_validators.yml │ │ └── default_records.yml │ ├── request_types │ │ ├── .about_request_types │ │ ├── 003_illumina_c_legacy_request_types.dev.yml │ │ ├── 004_limber_high_throughput.yml │ │ ├── 005_limber_bespoke.yml │ │ ├── 006_limber_cardinal.yml │ │ ├── 007_limber_lcm_dna_rna_seq.yml │ │ ├── 008_sequencing.yml │ │ ├── 009_bioscan_request_types.yml │ │ ├── 010_deep_well_stamping.yml │ │ ├── 011_novaseqx_sequencing.yml │ │ ├── 012_limber_scrna_core_cell_extraction.yml │ │ ├── 013_limber_rvi_bait_capture_library.yml │ │ ├── 014_limber_scrna_core_cdna_prep_request_types.yml │ │ ├── 015_limber_anospp_request_types.yml │ │ ├── 015_limber_scrna_core_library_prep_request_types.yml │ │ ├── 015_targeted_nanoseq_request_types.yml │ │ ├── 018_limber_lcm_triomics_request_types.yml │ │ ├── 019_limber_high_throughput_hic.yml │ │ ├── 020_limber_high_throughput_bge.yml │ │ ├── 021_element_aviti_sequencing_request_types.yml │ │ ├── 022_limber_scrna_core_pooling_norm_tubes.yml │ │ ├── 023_limber_kinnex_prep.yml │ │ ├── 023_limber_rvig_bait_capture_library.yml │ │ ├── 024_ultima_request_types.wip.yml │ │ └── cherrypicking.yml │ ├── robot_properties │ │ └── robot_properties.yml │ ├── robots │ │ └── robots.yml │ ├── submission_templates │ │ ├── 001_cardinal_submission_templates.yml │ │ ├── 002_targeted_nanoseq_submission_templates.yml │ │ ├── 003_lcm_dna_rna_seq.yml │ │ ├── 004_novaseq.yml │ │ ├── 005_bioscan_submission_templates.yml │ │ ├── 006_deep_well_stamping.yml │ │ ├── 007_novaseqx_sequencing.yml │ │ ├── 008_lcmb_submission_templates.yml │ │ ├── 009_scrna_core_cell_extraction_submission_templates.yml │ │ ├── 010_rvi_bait_capture_library_submission_templates.yml │ │ ├── 011_scrna_core_cdna_prep_submission_templates.yml │ │ ├── 012_anospp_submission_templates.yml │ │ ├── 012_scrna_core_library_prep_submission_templates.yml │ │ ├── 014_lcm_triomics_submission_templates.yml │ │ ├── 015_novaseqx_hic_sequencing.yml │ │ ├── 015_rnaf_submission_templates.yml │ │ ├── 016_bge.yml │ │ ├── 017_element_aviti_sequencing_submission_templates.yml │ │ ├── 018_kinnex_prep_submission_templates.yml │ │ ├── 018_rvig_bait_capture_library_submission_templates.yml │ │ ├── 019_ultima_submission_templates.wip.yml │ │ └── README.md │ ├── tag_group_adapter_types │ │ └── adapter_types.yml │ ├── tag_groups │ │ ├── 003_chromium.yml │ │ ├── 004_chromium_dual_index.yml │ │ ├── 004_chromium_single_index.yml │ │ ├── 005_ultima.yml │ │ ├── limber.dev.yml │ │ └── original.yml │ ├── tag_layout_templates │ │ ├── limber.dev.yml │ │ └── ultima.yml │ ├── tag_sets │ │ ├── 001_chromium_dual_index_tag_sets.yml │ │ ├── 001_chromium_single_index_tag_sets.yml │ │ └── 001_tag_sets_for_tag_groups.yml │ ├── tasks │ │ ├── 002_element_aviti_tasks.yml │ │ └── 003_ultima_tasks.wip.yml │ ├── transfer_templates │ │ └── bioscan_transfer_templates.yml │ ├── tube_purposes │ │ ├── 002_illumina_b_legacy_purposes.dev.yml │ │ ├── 003_illumina_c_legacy_purposes.dev.yml │ │ ├── 004_illumina_htp_legacy_purposes.dev.yml │ │ ├── 005_cardinal_tube_purposes.yml │ │ ├── 005_limber_purposes.yml │ │ ├── 007_scrna_core_cell_extraction_tube_purposes.yml │ │ ├── 008_scrna_core_cdna_prep_tube_purposes.yml │ │ ├── 009_bge_tube_purposes.yml │ │ └── 010_ultima_tube_purposes.wip.yml │ ├── tube_rack_purposes │ │ ├── 000_basic_purposes.yml │ │ └── 000_heron_purposes.yml │ └── ultima_globals │ │ └── 001_initial_ultima_globals.yml ├── ena_requirement_fields.yml ├── environment.rb ├── environments │ ├── cucumber.rb │ ├── development.rb │ ├── production.rb │ ├── profile.rb │ └── test.rb ├── failure_reasons.yml ├── feature_flags.yml ├── initializers │ ├── accession.rb │ ├── active_record_validations.rb │ ├── animations.rb │ ├── api_routing.rb │ ├── api_tools.rb │ ├── application_controller_renderer.rb │ ├── backtrace_silencers.rb │ ├── bulk_submission_excel.rb │ ├── content_security_policy.rb │ ├── cookies_serializer.rb │ ├── delayed_job_config.rb │ ├── deprecators.rb │ ├── failure_reasons.rb │ ├── filter_parameter_logging.rb │ ├── flipper.rb │ ├── formtastic.rb │ ├── function_overrides.rb │ ├── i18n.rb │ ├── inflections.rb │ ├── informatics.rb │ ├── jsonapi_resources.rb │ ├── label_printer_initializer.rb │ ├── load_config.rb │ ├── method_benchmarking.rb │ ├── mime_types.rb │ ├── new_framework_defaults_5_2.rb │ ├── new_framework_defaults_6_0.rb │ ├── new_framework_defaults_6_1.rb │ ├── new_rails_defaults.rb │ ├── patch_json_api_resource.rb │ ├── permissions_policy.rb │ ├── phi_x.rb │ ├── plates.rb │ ├── plates_from_tubes.rb │ ├── process_locale_files_with_erb.rb │ ├── psych.rb │ ├── rack_flooding_support.rb │ ├── rails_rack_metal_fix.rb │ ├── release.rb │ ├── ruby_net_http_proxy_hack.rb │ ├── sample_manifest_excel.rb │ ├── schema_dumper.rb │ ├── scrna_config.rb │ ├── session_store.rb │ ├── time_formats.rb │ ├── tube_racks_config.rb │ ├── unit.rb │ ├── versionstrings.rb │ └── wrap_parameters.rb ├── locales │ ├── en.yml │ └── metadata │ │ └── en.yml ├── messaging.rb ├── phi_x.yml ├── puma.rb ├── routes.rb ├── sample_manifest_excel │ ├── columns.yml │ ├── conditional_formattings.yml │ ├── manifest_types.yml │ └── ranges.yml ├── schedule.rb ├── services.yml ├── storage.yml ├── vite.json ├── vite.rb ├── warren.yml ├── warren_consumers.yml └── web.xml ├── data ├── avro_schema_cache │ └── .gitignore ├── ena_sample_checklists │ ├── .gitignore │ └── ERC000011.xml ├── example_ega_xml │ ├── experiment_set.xml │ ├── receipt.xml │ ├── run_set.xml │ ├── sample_set.xml │ ├── study_set.xml │ └── submission.xml ├── sample_information-2.xls ├── sample_information.xls └── sample_manifest.csv ├── db ├── migrate │ ├── 20250102154835_rename_column_number_of_samples_per_pool_to_number_of_pools.rb │ ├── 20250113154650_update_sample_public_name_for_rvi_program.rb │ ├── 20250114135342_add_data_release_prevention_other_comment_to_study_metadata.rb │ ├── 20250123105050_migrate_sample_metadata_for_invalid_insdc_country_of_origin.rb │ ├── 20250214120128_add_allowance_bands_to_request_metadata.rb │ ├── 20250220100453_remove_column_from_sample_metadata.rb │ ├── 20250326144346_add_element_aviti_pipeline_to_request_metadata.rb │ ├── 20250513112148_change_flipper_gates_value_to_text.rb │ ├── 20250514132842_add_ebi_requirement_fields_to_study_metadata.rb │ ├── 20250515133642_add_data_release_timing_publication_relevant_fields.rb │ ├── 20250818125034_add_active_to_lot_types.rb │ ├── 20250818131035_add_ultima_pipeline_to_request_metadata.rb │ ├── 20251030152601_create_accession_sample_statuses.rb │ └── 20251120204342_create_ultima_globals.rb ├── schema.rb ├── seeds.rb ├── seeds │ ├── 0000_api_applications.rb │ ├── 0000_plate_shapes_and_maps.rb │ ├── 0000_products.rb │ ├── 0000_request_types.rb │ ├── 0001_snp_plate_purposes.rb │ ├── 0001_tube_purposes.rb │ ├── 0001_workflows.rb │ ├── 0002_plate_purposes.rb │ ├── 0009_project_managers.rb │ ├── 0010_budget_division.rb │ ├── 0011_study_type.rb │ ├── 0012_data_release_study_type.rb │ ├── 0013_reference_genome.rb │ ├── 0015_custom_text_seeds.rb │ ├── 0015_tags.rb │ ├── 0015_transfer_templates.rb │ ├── 0016_tag_layout_templates.rb │ ├── 0017_bait_libraries.rb │ ├── 0018_standard_samples.rb │ ├── 0019_plate_creators.rb │ ├── 0090_lot_types.rb │ ├── 1000_illumina_b_workflow.rb │ ├── 2000_illumina_c_workflows.rb │ ├── 3000_library_types_setup.rb │ ├── 9996_searches.rb │ ├── 9997_qc_request_types.rb │ ├── 9998_submission_templates.rb │ ├── 9999_dev_only.rb │ └── 9999_tag_qc_setup.rb └── views_schema.rb ├── docker-compose-dev.yml ├── docker-compose.override.yml ├── docker-compose.yml ├── docs ├── about_docs.md ├── api_v1.md ├── api_v2.md ├── associated_applications.md ├── images │ └── plate.jpg ├── statement_of_truth.md ├── the_complex_matter_of_owning_work.md └── volume-uses.mermaid ├── entrypoint.sh ├── eslint.config.js ├── features ├── 10071597_change_request_type_on_request.feature ├── 10076399_bug_cluster_formation_not_display_volume_and_read_lengths.feature ├── 11803383_bug_NPG_batch_state_released.feature ├── 3550676_search_functionality.feature ├── 3673146_tables_with_multiple_criteria.feature ├── 4696931_move_samples_from_plates_to_tubes.feature ├── 53788839_pre_cap_pool_test.feature ├── 5393882_spiked_in_control.feature ├── 5976844_add_question_on_study_for_ethical_approvals.feature ├── 6040471_truncate_sample_name_barcode.feature ├── 641709_create_duplicate_SE_pipeline_with_no_controls.feature ├── administration │ ├── 11184645_faculty_sponsor_management.feature │ ├── 13325113_information_box.feature │ ├── 26913815_add_bait_library_editor_to_admin_view.feature │ ├── 71118369_reference_genome_admin_interface.feature │ ├── admin_barcode_printer.feature │ ├── custom_text_administration.feature │ ├── plate_purpose.feature │ ├── robots.feature │ └── study_administration.feature ├── api │ ├── asset_groups.feature │ ├── barcode_printers.feature │ ├── batches.feature │ ├── bulk_transfers.feature │ ├── custom_metadatum_collections.feature │ ├── illumina_b │ │ ├── bottom_of_the_pipeline.feature │ │ ├── stock_plate_state.feature │ │ └── top_of_the_pipeline.feature │ ├── index_tag_layout_templates.feature │ ├── library_creation_requests.feature │ ├── library_events.feature │ ├── multiplexed_library_creation_requests.feature │ ├── npg │ │ └── 11438075_request_xml_exception_on_nil_study.feature │ ├── object_service.feature │ ├── order_templates.feature │ ├── pipelines.feature │ ├── plate_creations.feature │ ├── projects.feature │ ├── pulldown │ │ ├── bait_library_assignment.feature │ │ ├── bottom_of_the_pipeline.feature │ │ ├── custom_pooling.feature │ │ └── submissions.feature │ ├── qc_files.feature.IGNORE │ ├── reference_genomes.feature │ ├── requests.feature │ ├── sample_manifests │ │ ├── mx_library_tubes.feature │ │ ├── plates.feature │ │ ├── sample_tubes.feature │ │ └── updating_through_manifest.feature │ ├── sample_tubes.feature │ ├── samples.feature │ ├── searches.feature │ ├── searches │ │ ├── find_asset_by_barcode.feature │ │ ├── find_deprecated.feature │ │ ├── find_lot_by_batch_id.feature │ │ ├── find_lot_by_lot_number.feature │ │ ├── find_outstanding_illumina_b_pre_pcr.feature │ │ ├── find_plates_for_user.feature │ │ ├── find_project_study_sample_by_name.feature │ │ ├── find_qcables_by_barcode.feature │ │ ├── find_robots_by_barcode.feature │ │ ├── find_source_assets_by_destination_asset_barcode.feature │ │ ├── find_user_by_login.feature │ │ └── find_user_by_swipcard_code.feature │ ├── sequencing_requests.feature │ ├── studies.feature │ ├── suppliers.feature │ ├── tag_layout_templates.feature │ ├── tag_layouts.feature │ ├── tag_qc │ │ ├── lot_types.feature │ │ ├── lots.feature │ │ ├── plate_conversion.feature │ │ ├── qc_decision.feature │ │ ├── qcable_order.feature │ │ ├── robots.feature │ │ ├── stamps.feature │ │ └── state_change.feature │ ├── transfer_templates.feature │ ├── transfers.feature │ ├── uk10k │ │ ├── full_work_through.feature │ │ ├── orders.feature │ │ └── submissions.feature │ ├── users.feature │ ├── users │ │ └── swipecard_code.feature │ ├── uuid_lookup_service.feature │ └── volume_updates.feature ├── batch │ ├── 6223975_releasing_batch.feature │ ├── 6679401_batch_request_recycling_broken.feature │ ├── 6679401_batch_request_reset_behaviour.feature │ ├── print_label_cluster_info_bug.feature │ └── show_created_at_date.feature ├── create_plates.feature ├── data_release │ ├── 11233725_external_release_failure_reasons.feature │ ├── 12400603_update_accession.feature │ ├── 4491710_ega_integration.feature │ ├── 8487329_array_express_accession_number.feature │ └── 8487329_ega_dac_integration.feature ├── pipelines_navigation.feature ├── plain │ ├── 5004860_change_decision_by_request.feature │ ├── 5197615_external_release_flag.feature │ ├── 5413994_request_editing_using_legacy_properties.feature │ └── 5486734_npg_xml_interface_broken.feature ├── projects │ ├── project.feature │ └── project_creation.feature ├── sample_manifest │ ├── 8828501_order_plate_barcodes_in_manifest.feature │ ├── full_sample_manifest.feature │ ├── mx_library_tube_manifest.feature │ ├── sample_manifest.feature │ ├── sample_tube_manifest.feature │ └── supplier.feature ├── samples │ ├── 6110751_correct_volume_unit_for_samples.feature │ ├── samples.feature │ ├── workflow_filtering_views.feature │ └── xml_interface.feature ├── slf │ ├── 5397621_slf_roles.feature │ ├── 5997026_print_if_buffer_is_required.feature │ ├── gel_qc.feature │ └── robot_verification.feature ├── ss507_library_type_in_batch_worksheet.feature ├── step_definitions │ ├── .gitkeep │ └── .keep ├── studies │ ├── 4295391_study_xml_needs_to_be_reverted_to_old_version.feature │ ├── 5393080_nil_document_details.feature │ ├── 5528168_delayed_studies_causing_errors.feature │ ├── 5549125_add_OTHER_study_type_to_EBI.feature │ ├── 5859843_create_study_owner_bug.feature │ ├── 7125863_bug_on_sample_duplicated_studies.feature │ ├── 8447221_data_release_help_text.feature │ ├── accession_number.feature │ ├── data_release_timings.feature │ ├── listing_by_type.feature │ ├── release_agreement.feature │ ├── study_report.feature │ ├── study_state.feature │ └── user_group.feature ├── submission │ ├── 20530077_weird_submission_link_behaviour.feature │ ├── 27012705_prevent_inactive_projects_from_being_selected_at_submission.feature │ ├── 8628145_show_submissions_being_built_as_such.feature │ ├── bulk_submission_from_tubes.feature │ ├── csv │ │ ├── 1_deprecated_rows.csv │ │ ├── 1_invalid_rows.csv │ │ ├── 1_tube_submission.csv │ │ ├── 1_valid_1_invalid.csv │ │ ├── 1_valid_rows.csv │ │ ├── 2_invalid_rows.csv │ │ ├── 2_valid_rows.csv │ │ ├── bad_header.csv │ │ ├── invalid_cp1252_rows.csv │ │ ├── invalid_utf8_rows.csv │ │ ├── jr16_test.csv │ │ ├── no_rows.csv │ │ ├── template_test.csv │ │ ├── with_conflicting_submissions.csv │ │ ├── with_empty_column.csv │ │ ├── with_headerless_column.csv │ │ ├── with_moved_header.csv │ │ ├── with_multiple_libary_types.csv │ │ └── wrong_file_type.rb │ ├── multiple_orders.feature │ └── submission_order_roles.feature └── support │ ├── accession_service.rb │ ├── api.rb │ ├── barcode_service.rb │ ├── capybara.rb │ ├── capybara_failure_logger.rb │ ├── capybara_timeout_patch.rb │ ├── cucumber_failures.rb │ ├── cucumber_github_formatter.rb │ ├── env.rb │ ├── factory_bot.rb │ ├── helpers.rb │ ├── knapsack.rb │ ├── minitest.rb │ ├── mocha.rb │ ├── parameter_types.rb │ ├── paths.rb │ ├── simplecov.rb │ ├── step_definitions │ ├── .gitkeep │ ├── 10071597_change_request_type_on_request_steps.rb │ ├── 11438075_request_xml_exception_on_nil_study_steps.rb │ ├── 11803383_bug_NPG_batch_state_released_steps.rb │ ├── 20530077_weird_submission_link_behaviour.rb │ ├── 25387227_transfer_requests_request_type.rb │ ├── 269135815_add_bait_library_editor_to_admin_view.rb │ ├── 27012705_prevent_inactive_projects_from_being_selected_at_submission.rb │ ├── 35177179_updating_released_samples_steps.rb │ ├── 3550676_search_functionality_steps.rb │ ├── 3673146_tables_with_multiple_criteria_steps.rb │ ├── 3871492_links_from_study_workflow_view_steps.rb │ ├── 3958121_sample_update_filters_properties_steps.rb │ ├── 4491710_ega_integration_steps.rb │ ├── 4560014_refactoring_properties_descriptors_etc_to_table_columns_steps.rb │ ├── 4642667_pulldown_plate_creation_steps.rb │ ├── 4759010_bug_on_reset_batches_steps.rb │ ├── 49061511_qc_file_steps.rb │ ├── 5004860_change_decision_by_request_steps.rb │ ├── 5070230_requesting_additional_hiseq_sequencing_steps.rb │ ├── 5158172_gel_hide_blank_wells_steps.rb │ ├── 5197615_external_release_flag_steps.rb │ ├── 53788839_pre_cap_pool.rb │ ├── 5393080_nil_document_details_steps.rb │ ├── 5393882_spiked_in_control_steps.rb │ ├── 5397680_sequenome_plate_details_steps.rb │ ├── 5486734_npg_xml_interface_broken_steps.rb │ ├── 5781572_external_data_release_interactions_steps.rb │ ├── 6040471_truncate_sample_name_barcode_steps.rb │ ├── 6048016_correct_bug_qc_state_scannedintolab_steps.rb │ ├── 6218053_display_concentration_inbox_pipeline_steps.rb │ ├── 641709_create_duplicate_SE_pipeline_with_no_controls_steps.rb │ ├── 65192392_tag_qc_steps.rb │ ├── 6679401_batch_request_recycling_broken_steps.rb │ ├── 7119309_pulldown_cherrypick_pipeline_steps.rb │ ├── 7125863_bug_on_sample_duplicated_studies_steps.rb │ ├── 8966997_events_on_plates_steps.rb │ ├── 9216107_study_reports_failing_steps.rb │ ├── aliquot_steps.rb │ ├── api_steps.rb │ ├── asset_group_steps.rb │ ├── asset_steps.rb │ ├── authentication_steps.rb │ ├── bait_library_steps.rb │ ├── barcode_steps.rb │ ├── batch_steps.rb │ ├── bulk_submission_steps.rb │ ├── contact_steps.rb │ ├── custom_metadatum_collection_steps.rb │ ├── custom_text_steps.rb │ ├── debug_steps.rb │ ├── delayed_job_steps.rb │ ├── display_submitted_at_inbox_pipeline_steps.rb │ ├── event_steps.rb │ ├── general_view_steps.rb │ ├── genotyping_steps.rb │ ├── multiplexed_inbox_steps.rb │ ├── order_steps.rb │ ├── pipeline_steps.rb │ ├── plate_creation_steps.rb │ ├── plate_steps.rb │ ├── project_steps.rb │ ├── pulldown_steps.rb │ ├── reference_genome_steps.rb │ ├── request_steps.rb │ ├── robot_verification_steps.rb │ ├── role_steps.rb │ ├── sample_manifest_steps.rb │ ├── sample_metadata_steps.rb │ ├── samples_steps.rb │ ├── study_report_steps.rb │ ├── study_steps.rb │ ├── submission_steps.rb │ ├── tag_layout_steps.rb │ ├── time_travel_steps.rb │ ├── transfer_steps.rb │ ├── tube_steps.rb │ ├── user_steps.rb │ ├── uuid_steps.rb │ ├── various_object_construction_steps.rb │ ├── web_form_steps.rb │ ├── web_steps.rb │ ├── workflow_steps.rb │ └── xml_steps.rb │ ├── timecop.rb │ ├── uuid_store.rb │ ├── webmock.rb │ └── well_range.rb ├── knapsack_cucumber_report.json ├── knapsack_rspec_report.json ├── lefthook.yml ├── lib ├── ability_analysis.rb ├── ability_analysis │ └── spec_generator.rb ├── accession.rb ├── accession │ ├── accessionable.rb │ ├── configuration.rb │ ├── contact.rb │ ├── core_extensions.rb │ ├── sample.rb │ ├── service.rb │ ├── submission.rb │ ├── tag.rb │ └── tag_list.rb ├── acts_as_descriptable.rb ├── api_tools.rb ├── authenticated_system.rb ├── authenticated_test_helper.rb ├── control_request_type_creation.rb ├── cron_scripts │ └── import_fluidigm_data.rb ├── csv_parser_client.rb ├── deployed.rb ├── deployment_environment.rb ├── dev │ └── plate_barcode │ │ └── cache_barcodes.rb ├── encoding_detector.rb ├── event_factory.rb ├── eventful_mailer.rb ├── eventful_record.rb ├── generators │ ├── api_v2 │ │ ├── USAGE │ │ ├── api_v2_generator.rb │ │ └── templates │ │ │ ├── app │ │ │ ├── controllers │ │ │ │ └── api │ │ │ │ │ └── v2 │ │ │ │ │ └── %underscores%_controller.rb.tt │ │ │ └── resources │ │ │ │ └── api │ │ │ │ └── v2 │ │ │ │ └── %underscore%_resource.rb.tt │ │ │ └── spec │ │ │ ├── requests │ │ │ └── api │ │ │ │ └── v2 │ │ │ │ └── %underscores%_spec.rb.tt │ │ │ └── resources │ │ │ └── api │ │ │ └── v2 │ │ │ └── %underscore%_resource_spec.rb.tt │ └── uat_action │ │ ├── USAGE │ │ ├── templates │ │ ├── app │ │ │ └── uat_actions │ │ │ │ └── uat_actions │ │ │ │ └── %underscore%.rb.tt │ │ └── spec │ │ │ └── uat_actions │ │ │ └── %underscore%_spec.rb.tt │ │ └── uat_action_generator.rb ├── has_behaviour.rb ├── http_clients │ ├── accessioning_v1_client.rb │ ├── base_client.rb │ └── ena_taxa_client.rb ├── informatics.rb ├── informatics │ ├── LICENSE │ ├── MIT-LICENSE │ ├── README │ ├── Rakefile │ ├── lib │ │ ├── informatics.rb │ │ ├── informatics │ │ │ ├── application.rb │ │ │ ├── controller_helper.rb │ │ │ ├── globals.rb │ │ │ ├── support │ │ │ │ └── options.rb │ │ │ └── view │ │ │ │ ├── menu │ │ │ │ ├── item.rb │ │ │ │ └── list.rb │ │ │ │ └── tabs │ │ │ │ ├── item.rb │ │ │ │ └── list.rb │ │ ├── platform.rb │ │ └── tasks │ │ │ └── informatics_tasks.rake │ ├── test │ │ ├── helpers │ │ │ └── authentication_helper.rb │ │ └── test_informatics.rb │ └── views │ │ └── platform │ │ ├── _item.html.erb │ │ └── _tab.html.erb ├── insdc │ └── import_countries.rb ├── lab_where_client.rb ├── label_printer.rb ├── label_printer │ ├── label │ │ ├── asset_plate.rb │ │ ├── asset_plate_double.rb │ │ ├── asset_redirect.rb │ │ ├── asset_tube.rb │ │ ├── base_plate.rb │ │ ├── base_plate_double.rb │ │ ├── base_tube.rb │ │ ├── batch_plate.rb │ │ ├── batch_plate_amp.rb │ │ ├── batch_plate_double.rb │ │ ├── batch_plates.rb │ │ ├── batch_redirect.rb │ │ ├── batch_tube.rb │ │ ├── multiple_double_labels.rb │ │ ├── multiple_labels.rb │ │ ├── multiplexed_tube.rb │ │ ├── plate_creator.rb │ │ ├── plate_to_tubes.rb │ │ ├── robot_beds.rb │ │ ├── sample_manifest_multiplex.rb │ │ ├── sample_manifest_plate.rb │ │ ├── sample_manifest_plate_double.rb │ │ ├── sample_manifest_redirect.rb │ │ ├── sample_manifest_tube.rb │ │ └── swipecard.rb │ ├── pmb_client.rb │ └── print_job.rb ├── limber │ └── helper.rb ├── linefeed_fix.rb ├── manifest_util.rb ├── mbrave_tags_creator.rb ├── method_benchmarking.rb ├── migration_extensions │ ├── db_table_archiver.rb │ └── encoding_changes.rb ├── nested_validation.rb ├── object_space_profile.rb ├── oligo_enumerator.rb ├── plate_map_generation.rb ├── product_helpers.rb ├── psd_formatter.rb ├── record_loader │ ├── application_record_loader.rb │ ├── asset_shape_loader.rb │ ├── barcode_printer_type_loader.rb │ ├── descriptor_loader.rb │ ├── flowcell_type_loader.rb │ ├── flowcell_type_request_type_loader.rb │ ├── library_type_loader.rb │ ├── pipeline_loader.rb │ ├── pipeline_request_information_type_loader.rb │ ├── plate_creator_loader.rb │ ├── plate_purpose_loader.rb │ ├── plate_type_loader.rb │ ├── primer_panel_loader.rb │ ├── product_catalogue_loader.rb │ ├── request_information_type_loader.rb │ ├── request_type_loader.rb │ ├── request_type_validators_loader.rb │ ├── robot_loader.rb │ ├── robot_property_loader.rb │ ├── submission_template_loader.rb │ ├── tag_group_adapter_type_loader.rb │ ├── tag_group_loader.rb │ ├── tag_layout_templates_loader.rb │ ├── tag_set_loader.rb │ ├── task_loader.rb │ ├── transfer_template_loader.rb │ ├── tube_purpose_loader.rb │ ├── tube_rack_purpose_loader.rb │ ├── ultima_global_loader.rb │ └── workflow_loader.rb ├── request_class_deprecator.rb ├── request_type_purpose_creation.rb ├── sequencing_qc_batch.rb ├── submission_serializer.rb ├── tasks │ ├── README.md │ ├── add_heron_product.rake │ ├── add_missing_asset_audit_records.rake │ ├── add_templates_and_printers_to_pmb.rake │ ├── add_traction_records.rake │ ├── application.rake │ ├── assign_compound_sample_supplier_name.rake │ ├── benchmark_plate_creation.rake │ ├── benchmark_plate_transfer.rake │ ├── carrierwave_cleanup.rake │ ├── create_mbrave_tags.rake │ ├── cucumber.rake │ ├── devour.rake │ ├── generate_primer_panel_templates.rake │ ├── hic_library_types.rake │ ├── insdc │ │ └── import_countries.rake │ ├── jsorm.rake │ ├── limber.rake │ ├── limber_dev.rake │ ├── rebroadcast_pac_bio_multiple_requests_run.rake │ ├── record_loader.rake │ ├── record_loader │ │ ├── asset_shape.rake │ │ ├── barcode_printer_type.rake │ │ ├── descriptor.rake │ │ ├── flowcell_type.rake │ │ ├── flowcell_type_request_type.rake │ │ ├── library_type.rake │ │ ├── pipeline.rake │ │ ├── pipeline_request_information_type.rake │ │ ├── plate_creator.rake │ │ ├── plate_purpose.rake │ │ ├── plate_type.rake │ │ ├── primer_panel.rake │ │ ├── product_catalogue.rake │ │ ├── request_information_type.rake │ │ ├── request_type.rake │ │ ├── request_type_validators.rake │ │ ├── robot.rake │ │ ├── robot_property.rake │ │ ├── submission_template.rake │ │ ├── tag_group.rake │ │ ├── tag_group_adapter_type.rake │ │ ├── tag_layout_templates.rake │ │ ├── tag_set.rake │ │ ├── task.rake │ │ ├── transfer_template.rake │ │ ├── tube_purpose.rake │ │ ├── tube_rack_purpose.rake │ │ └── ultima_globals.rake │ ├── register_auto_imported_samples_as_stock.rake │ ├── remove_deprecated_purposes.rake │ ├── report.rake │ ├── retention_instructions.rake │ ├── sample_manifest_excel_tests.rake │ ├── sequencing.rake │ ├── support │ │ ├── add_stock_rna_plate_to_working_dilution_parents.rake │ │ ├── remove_duplicate_asset_links.rake │ │ └── update_library_types.rake │ ├── test.rake │ ├── views_schema.rake │ └── working_setup.rake ├── templates │ └── erb │ │ └── scaffold │ │ └── _form.html.erb ├── validateable.rb ├── views_schema.rb ├── volume_check.rb └── working_setup │ └── standard_seeder.rb ├── log └── .gitkeep ├── package.json ├── postcss.config.cjs ├── public ├── .htaccess ├── apple-icon-development.png ├── apple-icon-staging.png ├── apple-icon-training.png ├── apple-icon.png ├── blank_iframe.html ├── docs │ └── api_docs.pdf ├── error-pages.css ├── favicon-development.ico ├── favicon-staging.ico ├── favicon-training.ico ├── favicon.ico └── robots.txt ├── script ├── autospec ├── console ├── cucumber ├── dbconsole ├── delayed_job ├── performance │ ├── benchmarker │ ├── profiler │ └── request ├── plugin ├── poller ├── process │ ├── inspector │ ├── reaper │ └── spawner ├── rails ├── spec ├── support │ ├── .rubocop.yml │ ├── .rubocop_todo.yml │ └── sample_move.rb ├── tools │ └── receptacle-request-graph └── worker ├── spec ├── api │ ├── .about_api_spec │ ├── api_root_spec.rb │ ├── asset_audit_spec.rb │ ├── core │ │ └── logging_spec.rb │ ├── dilution_plate_purpose_spec.rb │ ├── extraction_attributes_spec.rb │ ├── labware_spec.rb │ ├── multiplexed_library_tube_spec.rb │ ├── plate_purpose_spec.rb │ ├── plate_spec.rb │ ├── qcable_creator_spec.rb │ ├── receptacle_spec.rb │ ├── request_types_spec.rb │ ├── shared_examples.rb │ ├── specific_tube_creation_spec.rb │ ├── state_change_spec.rb │ ├── submission_pool_spec.rb │ ├── tag_layout_template_spec.rb │ ├── transfer_request_collection_spec.rb │ ├── tube_creation_spec.rb │ ├── tube_purpose_spec.rb │ ├── well_spec.rb │ └── work_completion_spec.rb ├── bulk_submission_excel │ ├── bulk_submission_excel_spec.rb │ ├── configuration_spec.rb │ ├── data_worksheet_spec.rb │ └── download_spec.rb ├── controllers │ ├── admin │ │ ├── abilities_controller_spec.rb │ │ └── primer_panels_controller_spec.rb │ ├── api │ │ └── v2 │ │ │ ├── bioscan │ │ │ └── export_pool_xp_to_traction_controller_spec.rb │ │ │ ├── concerns │ │ │ └── api_key_authenticatable_spec.rb │ │ │ ├── heron │ │ │ ├── plates_controller_spec.rb │ │ │ └── tube_racks_controller_spec.rb │ │ │ └── poly_metadata_controller_spec.rb │ ├── aviti_sample_sheet │ │ └── sample_sheet_generator_spec.rb │ ├── batches_controller_spec.rb │ ├── bioscan_control_locations_controller_spec.rb │ ├── bulk_submission_excel │ │ └── downloads_controller_spec.rb │ ├── concerns │ │ ├── api │ │ │ └── v2 │ │ │ │ └── disable_destroy_action_spec.rb │ │ ├── flash_truncation_spec.rb │ │ └── plate_picks │ │ │ └── batches_json_spec.rb │ ├── driver_files_controller_spec.rb │ ├── errors_controller_spec.rb │ ├── lab_searches_controller_spec.rb │ ├── labwhere_receptions_controller_spec.rb │ ├── messengers_controller_spec.rb │ ├── npg_actions │ │ └── assets_controller_spec.rb │ ├── parents_controller_spec.rb │ ├── phi_x │ │ ├── spiked_buffers_controller_spec.rb │ │ └── stocks_controller_spec.rb │ ├── phi_xes_controller_spec.rb │ ├── receptacles_controller_spec.rb │ ├── report_fails_controller_spec.rb │ ├── robot_verifications_controller_spec.rb │ ├── sample_manifest_controller_spec.rb │ ├── sample_manifest_upload_with_tag_sequences_controller_spec.rb │ ├── samples_controller_spec.rb │ ├── searches_controller_spec.rb │ ├── sequenom_qc_plates_controller_spec.rb │ ├── sessions_controller_spec.rb │ ├── studies │ │ └── information_controller_spec.rb │ ├── studies_controller_spec.rb │ ├── submissions_controller_spec.rb │ ├── tag_sets_controller_spec.rb │ ├── taxa_controller_spec.rb │ ├── tube_rack_summaries_controller_spec.rb │ └── ultima_sample_sheet │ │ └── sample_sheet_generator_spec.rb ├── data │ ├── accession │ │ └── tags.yml │ ├── asset_audits │ │ ├── bad_format.csv │ │ ├── invalid_message.csv │ │ ├── missing_column.csv │ │ ├── missing_header.csv │ │ └── valid_data.csv │ ├── beckman │ │ ├── pooled_cherrypick.csv │ │ └── standard_cherrypick.csv │ ├── bulk_submission_excel │ │ ├── columns.yml │ │ ├── conditional_formattings.yml │ │ └── ranges.yml │ ├── hamilton │ │ ├── pooled_cherrypick.csv │ │ └── standard_cherrypick.csv │ ├── parsers │ │ ├── pbmc_count.csv │ │ ├── pbmc_count_blank_rows.csv │ │ └── pbmc_count_no_cells.csv │ ├── record_loader │ │ ├── application_record_loader │ │ │ └── example.wip.yml │ │ ├── barcode_printer_types │ │ │ └── barcode_printers_basic.yml │ │ ├── descriptors │ │ │ └── descriptors_basic.yml │ │ ├── flowcell_types │ │ │ └── two_entry_example.yml │ │ ├── flowcell_types_request_types │ │ │ └── two_entry_example.yml │ │ ├── library_types │ │ │ ├── library_types_basic.yml │ │ │ └── two_entry_example.yml │ │ ├── pipeline_request_information_types │ │ │ └── two_entry_example.yml │ │ ├── pipelines │ │ │ └── two_entry_example.yml │ │ ├── plate_creators │ │ │ ├── 000_example.yml │ │ │ ├── 001_example.yml │ │ │ └── 002_example.yml │ │ ├── plate_purposes │ │ │ ├── 000_example.yml │ │ │ ├── 002_example.yml │ │ │ ├── 003_shape4x1.yml │ │ │ ├── 004_shape8x1.yml │ │ │ └── plate_purposes_basic.yml │ │ ├── plate_types │ │ │ └── plate_types_basic.yml │ │ ├── primer_panels │ │ │ └── primer_panels_basic.yml │ │ ├── product_catalogues │ │ │ └── two_catalogues.yml │ │ ├── request_information_types │ │ │ └── two_entry_example.yml │ │ ├── request_type_validators │ │ │ └── two_entry_example.yml │ │ ├── request_types │ │ │ ├── request_types_basic.yml │ │ │ └── request_types_updated.yml │ │ ├── robot_properties │ │ │ └── robot_properties_example.yml │ │ ├── robots │ │ │ └── robots_example.yml │ │ ├── submission_templates │ │ │ └── two_submission_templates.yml │ │ ├── tag_group_adapter_types │ │ │ └── tag_group_adapter_types_basic.yml │ │ ├── tag_groups │ │ │ └── tag_groups_basic.yml │ │ ├── tag_layout_templates │ │ │ └── tag_layout_template_basic.yml │ │ ├── tag_sets │ │ │ └── tag_sets_basic.yml │ │ ├── tasks │ │ │ └── tasks_basic.yml │ │ ├── transfer_templates │ │ │ └── example_transfer_templates.yml │ │ ├── tube_purposes │ │ │ └── basic_tube_purposes.yml │ │ └── tube_rack_purposes │ │ │ └── two_tube_racks.yml │ ├── sample_manifest_excel │ │ ├── columns.yml │ │ ├── conditional_formattings.yml │ │ ├── extract │ │ │ ├── columns.yml │ │ │ ├── conditional_formattings.yml │ │ │ ├── manifest_types.yml │ │ │ └── ranges.yml │ │ ├── manifest_types.yml │ │ └── ranges.yml │ ├── submission │ │ ├── 1_valid_rows.csv │ │ ├── 2_valid_sc_submissions.csv │ │ ├── novaseqx_bulk_submission.csv │ │ ├── pcr_cycles.csv │ │ ├── primer_panels.csv │ │ ├── scRNA_bulk_submission.csv │ │ ├── scRNA_bulk_submission_tube.csv │ │ ├── scRNA_bulk_submission_tube_invalid.csv │ │ ├── scRNA_bulk_submission_tube_invalid_greater.csv │ │ ├── scrna_additional_validations_invalid_cells_per_chip_well.csv │ │ ├── scrna_additional_validations_invalid_samples_per_pool.csv │ │ ├── scrna_additional_validations_valid.csv │ │ ├── template_for_bulk_submission.csv │ │ ├── with_lowercase_library_type.csv │ │ └── with_unknown_library_type.csv │ ├── tecan │ │ └── stock_stamper.gwl │ └── tecan_v3 │ │ ├── case_1.gwl │ │ ├── case_2.gwl │ │ ├── case_3.gwl │ │ ├── case_4.gwl │ │ ├── case_5.gwl │ │ ├── case_6.gwl │ │ ├── case_7.gwl │ │ └── case_9.gwl ├── factories │ ├── accession │ │ ├── samples.rb │ │ ├── services.rb │ │ ├── status.rb │ │ ├── submissions.rb │ │ ├── tag_lists.rb │ │ └── tags.rb │ ├── aliquots.rb │ ├── api_applications.rb │ ├── asset_audits.rb │ ├── asset_groups.rb │ ├── asset_shape_factories.rb │ ├── bait_library_layout_factories.rb │ ├── barcode_factories.rb │ ├── barcode_printers.rb │ ├── batch_factories.rb │ ├── broadcast_event_factories.rb │ ├── bulk_transfers.rb │ ├── comments.rb │ ├── custom_metadatum_collection_factories.rb │ ├── custom_metadatum_factories.rb │ ├── custom_texts.rb │ ├── events.rb │ ├── fragments.rb │ ├── insdc_country_factories.rb │ ├── lanes.rb │ ├── lib_pcr_xp_factories.rb │ ├── messengers.rb │ ├── phix_factories.rb │ ├── pick_lists.rb │ ├── pipelines_factories.rb │ ├── plate_barcode_factories.rb │ ├── plate_conversion_factories.rb │ ├── plate_creation_factories.rb │ ├── plate_factories.rb │ ├── plate_type.rb │ ├── poly_metadata_factories.rb │ ├── pooled_plate_creation.rb │ ├── pooled_requests.rb │ ├── pre_capture_pools.rb │ ├── primer_panel_factories.rb │ ├── product_and_catalogue_factories.rb │ ├── programs.rb │ ├── project_metadata.rb │ ├── projects.rb │ ├── pulldown_factories.rb │ ├── purpose_factories.rb │ ├── qc_assays_factories.rb │ ├── qc_file.rb │ ├── qc_report_factories.rb │ ├── qc_results.rb │ ├── racked_tube.rb │ ├── receptacles.rb │ ├── reference_genomes.rb │ ├── request_event_factories.rb │ ├── request_factories.rb │ ├── request_metadata.rb │ ├── request_type_factories.rb │ ├── robot_factories.rb │ ├── roles.rb │ ├── sample_manifest_excel │ │ ├── column_lists.rb │ │ ├── columns.rb │ │ ├── conditional_formattings.rb │ │ ├── range_lists.rb │ │ ├── ranges.rb │ │ ├── sample_manifest_assets.rb │ │ ├── test_download_plates.rb │ │ ├── test_download_tubes.rb │ │ ├── test_download_tubes_in_rack.rb │ │ └── validations.rb │ ├── sample_manifest_factories.rb │ ├── sample_metadata.rb │ ├── samples.rb │ ├── sanger_sample_id.rb │ ├── searches.rb │ ├── sequences.rb │ ├── shared_traits.rb │ ├── specific_tube_creation.rb │ ├── specific_tube_rack_creation.rb │ ├── study_factories.rb │ ├── study_metadata_factories.rb │ ├── study_reports.rb │ ├── submission_factories.rb │ ├── submission_pool.rb │ ├── tag2_layout_factories.rb │ ├── tag_group_factories.rb │ ├── tag_qc_factories.rb │ ├── tag_set_factories.rb │ ├── tasks.rb │ ├── transfer_request_collections.rb │ ├── transfer_requests.rb │ ├── transfers.rb │ ├── tube_factories.rb │ ├── tube_from_plate_creation.rb │ ├── tube_from_tube_creation.rb │ ├── tube_rack.rb │ ├── ultima_globals.rb │ ├── user_factories.rb │ ├── volume_update.rb │ ├── well_factories.rb │ ├── work_completions_factories.rb │ └── work_order_factories.rb ├── features │ ├── admin │ │ ├── add_a_primer_panel_spec.rb │ │ ├── add_a_printer_spec.rb │ │ └── changing_user_roles_spec.rb │ ├── asset_information_spec.rb │ ├── assets │ │ ├── asset_submission_spec.rb │ │ ├── show_plate_spec.rb │ │ └── upload_and_retrieve_qc_file_spec.rb │ ├── batches │ │ ├── failing_requests_spec.rb │ │ └── sort_requests_spec.rb │ ├── contact_us_spec.rb │ ├── create_printer_spec.rb │ ├── creating_a_quad_stamp_spec.rb │ ├── generate_a_bulk_submission_template_spec.rb │ ├── gpl207_bug_incorrect_submission_id_on_transfer_spec.rb │ ├── lab_view_spec.rb │ ├── labware │ │ ├── looking_up_labware_history_spec.rb │ │ └── retention_instruction_spec.rb │ ├── labware_information_spec.rb │ ├── labwhere_reception_spec.rb │ ├── location_reports │ │ └── location_reports_spec.rb │ ├── patient_consent_withdrawl_spec.rb │ ├── perform_a_tag_substitution_spec.rb │ ├── pipelines │ │ ├── cherrypick │ │ │ ├── cherrypick_for_fluidigm_pipeline_micro_litre_spec.rb │ │ │ └── cherrypick_pipeline_spec.rb │ │ ├── creating_an_empty_batch_spec.rb │ │ ├── sequencing │ │ │ ├── following_a_sequencing_pipeline_spec.rb │ │ │ └── following_a_sequencing_pipeline_with_compound_sample_creation_spec.rb │ │ └── viewing_request_comments_spec.rb │ ├── plate_qc_display_spec.rb │ ├── pooling_spec.rb │ ├── receptacle_information_spec.rb │ ├── retrospective_failure_spec.rb │ ├── sample_logistics │ │ └── lab │ │ │ └── stock_stamping_spec.rb │ ├── sample_manifests │ │ ├── create_manifest_spec.rb │ │ ├── track_sample_manifest_updates_spec.rb │ │ └── uploader_for_manifests_with_tag_sequences_spec.rb │ ├── samples │ │ ├── sample_accession_errors_spec.rb │ │ └── sample_edit_spec.rb │ ├── shared_examples │ │ ├── cherrypicking.rb │ │ └── sequencing.rb │ ├── starting_transfers_on_repools_starts_repools_spec.rb │ ├── studies │ │ ├── accession_all_samples_spec.rb │ │ ├── change_study_roles_spec.rb │ │ ├── create_study_spec.rb │ │ ├── edit_study_spec.rb │ │ ├── manage_study_spec.rb │ │ ├── qc_reports_spec.rb │ │ ├── view_study_properties_spec.rb │ │ └── view_study_request_links_spec.rb │ ├── submissions │ │ └── bulk_submissions_spec.rb │ ├── tag_group_spec.rb │ ├── tag_layout_template_spec.rb │ └── tag_set_spec.rb ├── helpers │ ├── application_helper_spec.rb │ ├── assets_helper_spec.rb │ ├── batches_helper_spec.rb │ ├── bootstrap_helper_spec.rb │ ├── compound_sample_helper_spec.rb │ ├── delayed_jobs_helper_spec.rb │ ├── report_fails_helper_spec.rb │ └── retention_instruction_helper_spec.rb ├── insdc │ └── import_countries_spec.rb ├── jobs │ ├── export_pool_xp_to_traction_job_spec.rb │ └── sample_accessioning_job_spec.rb ├── lib │ ├── ability_analysis_spec.rb │ ├── accession │ │ ├── accessionable_spec.rb │ │ ├── configuration_spec.rb │ │ ├── contact_spec.rb │ │ ├── sample_spec.rb │ │ ├── service_spec.rb │ │ ├── study_spec.rb │ │ ├── submission_spec.rb │ │ ├── tag_list_spec.rb │ │ └── tag_spec.rb │ ├── add_missing_asset_audit_records_spec.rb │ ├── deployed_spec.rb │ ├── dev │ │ └── plate_barcode │ │ │ └── cache_barcodes_spec.rb │ ├── encoding_detector_spec.rb │ ├── http_clients │ │ ├── accessioning_v1_client_spec.rb │ │ ├── base_client_spec.rb │ │ └── ena_taxa_client_spec.rb │ ├── lab_where_client_spec.rb │ ├── label_printer │ │ ├── asset_labels_spec.rb │ │ ├── asset_redirect_spec.rb │ │ ├── batch_plate_amp_spec.rb │ │ ├── batch_plate_spec.rb │ │ ├── batch_tube_spec.rb │ │ ├── sample_manifest_plate_double_spec.rb │ │ └── swipecard_spec.rb │ ├── limber │ │ └── helper_spec.rb │ ├── mbrave_tags_creator_spec.rb │ ├── method_benchmarking_spec.rb │ ├── migration_extensions │ │ └── encoding_changes_spec.rb │ ├── mock_parser.rb │ ├── psd_formatter_spec.rb │ ├── record_loader │ │ ├── application_record_loader_spec.rb │ │ ├── barcode_printer_type_loader_spec.rb │ │ ├── descriptor_loader_spec.rb │ │ ├── flowcell_type_loader_spec.rb │ │ ├── flowcell_type_request_type_loader_spec.rb │ │ ├── library_type_loader_spec.rb │ │ ├── pipeline_loader_spec.rb │ │ ├── pipeline_request_information_type_loader_spec.rb │ │ ├── plate_creator_loader_spec.rb │ │ ├── plate_purpose_loader_spec.rb │ │ ├── plate_type_loader_spec.rb │ │ ├── primer_panel_loader_spec.rb │ │ ├── product_catalogue_loader_spec.rb │ │ ├── request_information_type_loader_spec.rb │ │ ├── request_type_loader_spec.rb │ │ ├── robot_loader_spec.rb │ │ ├── robot_property_loader_spec.rb │ │ ├── submission_template_loader_spec.rb │ │ ├── tag_group_adapter_type_loader_spec.rb │ │ ├── tag_group_loader_spec.rb │ │ ├── tag_layout_templates_loader_spec.rb │ │ ├── tag_set_loader_spec.rb │ │ ├── task_loader_spec.rb │ │ ├── transfer_template_loader_spec.rb │ │ ├── tube_purpose_loader_spec.rb │ │ └── tube_rack_purpose_loader_spec.rb │ └── retention_instructions_spec.rb ├── models │ ├── ability_spec.rb │ ├── accession │ │ └── sample_status_spec.rb │ ├── aliquot_spec.rb │ ├── api │ │ ├── aliquot_io_spec.rb │ │ ├── asset_link_io_spec.rb │ │ ├── batch_io_spec.rb │ │ ├── batch_request_io_spec.rb │ │ ├── lane_io_spec.rb │ │ ├── library_tube_io_spec.rb │ │ ├── messages │ │ │ ├── flowcell_io_spec.rb │ │ │ ├── pac_bio_run_io_spec.rb │ │ │ ├── pac_bio_run_with_tag2_io_spec.rb │ │ │ ├── qc_result_io_spec.rb │ │ │ ├── useq_wafer_io_spec.rb │ │ │ └── well_stock_resource_io_spec.rb │ │ ├── multiplexed_library_tube_io_spec.rb │ │ ├── order_io_spec.rb │ │ ├── pac_bio_library_tube_io_spec.rb │ │ ├── plate_io_spec.rb │ │ ├── plate_purpose_io_spec.rb │ │ ├── project_io_spec.rb │ │ ├── pulldown_multiplexed_library_tube_io_spec.rb │ │ ├── reference_genome_io_spec.rb │ │ ├── request_io_spec.rb │ │ ├── sample_io_spec.rb │ │ ├── sample_tube_io_spec.rb │ │ ├── study_io_spec.rb │ │ ├── study_sample_io_spec.rb │ │ ├── submission_io_spec.rb │ │ ├── tag_io_spec.rb │ │ └── well_io_spec.rb │ ├── asset_links_create_edge_spec.rb │ ├── asset_spec.rb │ ├── bait_library_type_spec.rb │ ├── barcode │ │ └── format_handlers_spec.rb │ ├── barcode_printer_spec.rb │ ├── barcode_spec.rb │ ├── batch_spec.rb │ ├── broadcast_event │ │ ├── broadcast_event_spec.rb │ │ ├── helpers │ │ │ └── external_subjects_spec.rb │ │ ├── lab_event_spec.rb │ │ ├── library_complete_spec.rb │ │ ├── plate_cherrypicked_spec.rb │ │ ├── pool_released_spec.rb │ │ ├── qc_assay_spec.rb │ │ └── sequencing_complete_spec.rb │ ├── bulk_submission_spec.rb │ ├── cherrypick_request_spec.rb │ ├── cherrypick_task │ │ └── control_locator_spec.rb │ ├── comment_spec.rb │ ├── element_aviti_sequencing_pipeline_spec.rb │ ├── element_aviti_sequencing_request_spec.rb │ ├── external_release_event_spec.rb │ ├── flowcell_type_spec.rb │ ├── heron │ │ └── factories │ │ │ ├── concerns │ │ │ ├── contents_spec.rb │ │ │ └── eventful_spec.rb │ │ │ ├── event_spec.rb │ │ │ ├── plate_from_rack_spec.rb │ │ │ ├── plate_spec.rb │ │ │ ├── sample_spec.rb │ │ │ ├── tube_rack_spec.rb │ │ │ ├── tube_rack_status_spec.rb │ │ │ └── tube_spec.rb │ ├── illumina_htp │ │ ├── initial_stock_tube_purpose_spec.rb │ │ └── requests │ │ │ ├── gbs_request_spec.rb │ │ │ ├── heron_request_spec.rb │ │ │ └── heron_tailed_request_spec.rb │ ├── insdc │ │ └── country_spec.rb │ ├── lab_event_spec.rb │ ├── labware_spec.rb │ ├── labwhere_reception_spec.rb │ ├── lane_spec.rb │ ├── library_type_spec.rb │ ├── linear_submission_spec.rb │ ├── location_report_form_spec.rb │ ├── location_report_spec.rb │ ├── lot_type_spec.rb │ ├── map_spec.rb │ ├── orders │ │ ├── automated_order_spec.rb │ │ ├── order_spec.rb │ │ └── shared_order_specs.rb │ ├── parsers │ │ └── pbmc_count_parser_spec.rb │ ├── parsers_spec.rb │ ├── phi_x │ │ ├── spiked_buffer_spec.rb │ │ └── stock_spec.rb │ ├── pick_list_spec.rb │ ├── plate │ │ ├── quad_creator_spec.rb │ │ └── sample_tube_factory_spec.rb │ ├── plate_barcode_spec.rb │ ├── plate_purpose │ │ └── input_spec.rb │ ├── plate_purpose_spec.rb │ ├── plate_spec.rb │ ├── plate_type_spec.rb │ ├── plate_volume_spec.rb │ ├── poly_metadatum_spec.rb │ ├── pooling_spec.rb │ ├── presenters │ │ └── batch_submenu_presenter_spec.rb │ ├── primer_panel_spec.rb │ ├── pulldown │ │ ├── requests │ │ │ └── isc_library_request_spec.rb │ │ └── requests_spec.rb │ ├── qc_report_spec.rb │ ├── qc_result │ │ ├── qc_result_factory_spec.rb │ │ └── qc_result_spec.rb │ ├── qcable_creator_spec.rb │ ├── qcable_spec.rb │ ├── racked_tube_spec.rb │ ├── receptacle │ │ └── downstream_aliquots_removal_spec.rb │ ├── receptacle_spec.rb │ ├── report_fail_spec.rb │ ├── request │ │ ├── sample_compound_aliquot_transfer_spec.rb │ │ ├── statistics │ │ │ └── counter_spec.rb │ │ └── traction │ │ │ └── grid_ion_spec.rb │ ├── request_event_spec.rb │ ├── request_information_type_spec.rb │ ├── request_spec.rb │ ├── request_type │ │ └── validator │ │ │ └── library_type_validator_spec.rb │ ├── request_type_spec.rb │ ├── robot │ │ ├── generator │ │ │ ├── beckman_spec.rb │ │ │ ├── hamilton_spec.rb │ │ │ ├── tecan_spec.rb │ │ │ └── tecan_v3_spec.rb │ │ ├── pick_data_spec.rb │ │ ├── pick_hash_tester_helper.rb │ │ └── verification │ │ │ ├── source_dest_beds_spec.rb │ │ │ └── source_dest_control_beds_spec.rb │ ├── robot_spec.rb │ ├── sample │ │ └── metadata_spec.rb │ ├── sample_compound_component_spec.rb │ ├── sample_manifest │ │ ├── generator_spec.rb │ │ └── uploader_spec.rb │ ├── sample_manifest_spec.rb │ ├── sample_spec.rb │ ├── scrna_core_cdna_prep_feasibility_validator_spec.rb │ ├── sequencing_request_spec.rb │ ├── specific_tube_creations_spec.rb │ ├── specific_tube_rack_creation_spec.rb │ ├── state_changer │ │ ├── initial_stock_tube_spec.rb │ │ ├── input_plate_spec.rb │ │ ├── mx_tube_spec.rb │ │ ├── qcable_labware_spec.rb │ │ ├── qcable_library_plate_spec.rb │ │ ├── standard_plate_spec.rb │ │ ├── stock_tube_spec.rb │ │ └── tube_rack_spec.rb │ ├── std_library_request_spec.rb │ ├── stock_stamper_spec.rb │ ├── study_spec.rb │ ├── submission │ │ ├── scrna_core_cdna_prep_feasibility_calcuator_spec.rb │ │ └── submission_creator_spec.rb │ ├── submission_spec.rb │ ├── tag2_layout_spec.rb │ ├── tag2_layout_template_spec.rb │ ├── tag_group │ │ └── adapter_type_spec.rb │ ├── tag_group_form_object_spec.rb │ ├── tag_group_spec.rb │ ├── tag_layout_spec.rb │ ├── tag_layout_template_spec.rb │ ├── tag_set_spec.rb │ ├── tag_substitutions_spec.rb │ ├── tasks │ │ ├── cherrypick_task_spec.rb │ │ ├── plate_template_task_spec.rb │ │ └── set_descriptors_handler │ │ │ └── handler_spec.rb │ ├── transfer │ │ ├── between_plates_spec.rb │ │ └── from_plate_to_tube_spec.rb │ ├── transfer_request_collection_spec.rb │ ├── transfer_request_spec.rb │ ├── tube_from_plate_creation_spec.rb │ ├── tube_purpose_spec.rb │ ├── tube_rack_spec.rb │ ├── tube_spec.rb │ ├── ultima_sequencing_pipeline_spec.rb │ ├── ultima_sequencing_request_spec.rb │ ├── user_spec.rb │ ├── well_attribute_spec.rb │ ├── well_spec.rb │ ├── work_completion_spec.rb │ ├── work_order_spec.rb │ ├── work_order_type_spec.rb │ └── working_dilution_plate_spec.rb ├── rails_helper.rb ├── requests │ ├── api │ │ └── v2 │ │ │ ├── aliquots_spec.rb │ │ │ ├── asset_audits_spec.rb │ │ │ ├── bait_library_layouts_spec.rb │ │ │ ├── barcode_printers_spec.rb │ │ │ ├── bulk_transfers_spec.rb │ │ │ ├── comments_spec.rb │ │ │ ├── custom_metadatum_collections_spec.rb │ │ │ ├── heron │ │ │ ├── plates_spec.rb │ │ │ └── tube_racks_spec.rb │ │ │ ├── labware_spec.rb │ │ │ ├── lanes_spec.rb │ │ │ ├── lot_types_spec.rb │ │ │ ├── lots_spec.rb │ │ │ ├── orders_spec.rb │ │ │ ├── pick_lists_spec.rb │ │ │ ├── plate_controller_spec.rb │ │ │ ├── plate_conversions_spec.rb │ │ │ ├── plate_creations_spec.rb │ │ │ ├── plate_purposes_spec.rb │ │ │ ├── plate_templates_spec.rb │ │ │ ├── plates_spec.rb │ │ │ ├── poly_metadata_spec.rb │ │ │ ├── pooled_plate_creations_spec.rb │ │ │ ├── pre_capture_pools_spec.rb │ │ │ ├── primer_panels_spec.rb │ │ │ ├── purposes_spec.rb │ │ │ ├── qc_assays_spec.rb │ │ │ ├── qc_files_spec.rb │ │ │ ├── qc_results_spec.rb │ │ │ ├── qcables_spec.rb │ │ │ ├── receptacles_spec.rb │ │ │ ├── request_types_spec.rb │ │ │ ├── requests_spec.rb │ │ │ ├── sample_metadata_spec.rb │ │ │ ├── shared_behaviour │ │ │ └── labware_shared_behaviour_spec.rb │ │ │ ├── shared_examples │ │ │ ├── api_key_authenticatable.rb │ │ │ └── requests.rb │ │ │ ├── specific_tube_creations_spec.rb │ │ │ ├── specific_tube_rack_creations_spec.rb │ │ │ ├── state_changes_spec.rb │ │ │ ├── studies_spec.rb │ │ │ ├── submission_pools_spec.rb │ │ │ ├── submission_templates_spec.rb │ │ │ ├── submissions_spec.rb │ │ │ ├── tag_groups_spec.rb │ │ │ ├── tag_layout_templates_spec.rb │ │ │ ├── tag_layouts_spec.rb │ │ │ ├── tag_sets_spec.rb │ │ │ ├── transfer_request_collections_spec.rb │ │ │ ├── transfer_requests_spec.rb │ │ │ ├── transfer_templates_spec.rb │ │ │ ├── transfers_spec.rb │ │ │ ├── tube_from_tube_creations_spec.rb │ │ │ ├── tube_purposes_spec.rb │ │ │ ├── tube_rack_purposes_spec.rb │ │ │ ├── tube_racks_spec.rb │ │ │ ├── tubes_spec.rb │ │ │ ├── users_spec.rb │ │ │ ├── volume_update_spec.rb │ │ │ ├── wells_spec.rb │ │ │ ├── work_completions_spec.rb │ │ │ └── work_orders_spec.rb │ ├── pick_lists_request_spec.rb │ ├── plate_picks_request_spec.rb │ ├── qc_files_spec.rb │ └── users_request_spec.rb ├── resources │ └── api │ │ └── v2 │ │ ├── aliquot_resource_spec.rb │ │ ├── bait_library_layout_resource_spec.rb │ │ ├── barcode_printer_resource_spec.rb │ │ ├── bulk_transfer_resource_spec.rb │ │ ├── comment_resource_spec.rb │ │ ├── custom_metadatum_collection_resource_spec.rb │ │ ├── faculty_sponsor_spec.rb │ │ ├── labware_resource_spec.rb │ │ ├── lane_resource_spec.rb │ │ ├── lot_resource_spec.rb │ │ ├── lot_type_resource_spec.rb │ │ ├── order_resource_spec.rb │ │ ├── pick_list_resource_spec.rb │ │ ├── plate_conversion_resource_spec.rb │ │ ├── plate_creation_resource_spec.rb │ │ ├── plate_purpose_resource_spec.rb │ │ ├── plate_resource_spec.rb │ │ ├── plate_template_resource_spec.rb │ │ ├── poly_metadatum_resource_spec.rb │ │ ├── pooled_plate_creation_resource_spec.rb │ │ ├── pre_capture_pool_resource_spec.rb │ │ ├── primer_panel_resource_spec.rb │ │ ├── project_resource_spec.rb │ │ ├── purpose_resource_spec.rb │ │ ├── qc_file_resource_spec.rb │ │ ├── qcable_creator_resource_spec.rb │ │ ├── qcable_resource_spec.rb │ │ ├── receptacle_resource_spec.rb │ │ ├── request_resource_spec.rb │ │ ├── request_type_resource_spec.rb │ │ ├── sample_metadata_resource_spec.rb │ │ ├── sample_resource_spec.rb │ │ ├── shared_examples │ │ ├── labware.rb │ │ └── receptacle.rb │ │ ├── specific_tube_creation_resource_spec.rb │ │ ├── specific_tube_rack_creation_resource_spec.rb │ │ ├── state_change_resource_spec.rb │ │ ├── study_metadata_resource_spec.rb │ │ ├── study_resource_spec.rb │ │ ├── submission_pool_resource_spec.rb │ │ ├── submission_resource_spec.rb │ │ ├── submission_template_resource_spec.rb │ │ ├── tag_group_resource_spec.rb │ │ ├── tag_layout_resource_spec.rb │ │ ├── tag_layout_template_resource_spec.rb │ │ ├── tag_resource_spec.rb │ │ ├── tag_set_resource_spec.rb │ │ ├── transfer_request_collection_resource_spec.rb │ │ ├── transfer_request_resource_spec.rb │ │ ├── transfer_resource_spec.rb │ │ ├── transfer_template_resource_spec.rb │ │ ├── tube_from_plate_creation_resource_spec.rb │ │ ├── tube_from_tube_creation_resource_spec.rb │ │ ├── tube_purpose_resource_spec.rb │ │ ├── tube_rack_purpose_resource_spec.rb │ │ ├── tube_rack_resource_spec.rb │ │ ├── tube_resource_spec.rb │ │ ├── user_resource_spec.rb │ │ ├── well_resource_spec.rb │ │ ├── work_completion_resource_spec.rb │ │ └── work_order_resource_spec.rb ├── sample_manifest_excel │ ├── configuration_spec.rb │ ├── download_spec.rb │ ├── manifest_type_list_spec.rb │ ├── sample_manifest_excel_spec.rb │ ├── tags_spec.rb │ ├── test_download_spec.rb │ ├── upload │ │ ├── data_spec.rb │ │ ├── processor_spec.rb │ │ ├── row_spec.rb │ │ ├── rows_spec.rb │ │ └── upload_spec.rb │ └── worksheet_spec.rb ├── sequencescape_excel │ ├── cell_spec.rb │ ├── column_list_spec.rb │ ├── column_spec.rb │ ├── conditional_formatting_default_list_spec.rb │ ├── conditional_formatting_default_spec.rb │ ├── conditional_formatting_list_spec.rb │ ├── conditional_formatting_spec.rb │ ├── configuration_spec.rb │ ├── formula_spec.rb │ ├── list_spec.rb │ ├── range_list_spec.rb │ ├── range_spec.rb │ ├── specialised_field_spec.rb │ ├── validation_spec.rb │ └── worksheet_spec.rb ├── shared_contexts │ ├── .about_shared_contexts │ ├── it_requires_login.rb │ ├── limber_shared_context.rb │ └── shared_io_examples.rb ├── spec_helper.rb ├── support │ ├── accession_v1_client_helper.rb │ ├── api_helper.rb │ ├── api_v2_helper.rb │ ├── api_v2_resource_matchers.rb │ ├── barcode_helper.rb │ ├── download_helper.rb │ ├── fetch_table.rb │ ├── lab_where_client_helper.rb │ ├── mock_accession.rb │ ├── table_helper.rb │ └── user_login.rb ├── tasks │ ├── assing_compound_sample_supplier_name_spec.rb │ ├── create_mbrave_tags_spec.rb │ └── support │ │ └── add_stock_rna_plate_to_working_dilution_parents_spec.rb ├── uat_actions │ ├── generate_fluidx_barcodes_spec.rb │ ├── generate_plate_concentrations_spec.rb │ ├── generate_plate_volumes_spec.rb │ ├── generate_plates_spec.rb │ ├── generate_primer_panel_spec.rb │ ├── generate_project_spec.rb │ ├── generate_qc_results_spec.rb │ ├── generate_sample_manifest_spec.rb │ ├── generate_spiked_buffer_tube_spec.rb │ ├── generate_study_spec.rb │ ├── generate_supplier_spec.rb │ ├── generate_tag_group_spec.rb │ ├── generate_tag_layout_template_spec.rb │ ├── generate_tag_set_spec.rb │ ├── generate_tagged_plates_spec.rb │ ├── generate_tube_racks_spec.rb │ ├── generate_tubes_spec.rb │ ├── integration_suite_tools_spec.rb │ ├── plate_information_spec.rb │ ├── shared │ │ ├── study_helper_spec.rb │ │ └── supplier_helper_spec.rb │ ├── static_records_spec.rb │ ├── test_submission_spec.rb │ ├── tube_submission_spec.rb │ ├── uat_actions_spec.rb │ └── update_state_of_requests_in_labware_spec.rb ├── validators │ ├── element_aviti_validator_spec.rb │ ├── latin1_validator_spec.rb │ ├── novaseqx_pe_validator_spec.rb │ ├── novaseqx_read_length_validator_spec.rb │ ├── ultima_validator_spec.rb │ └── utf8mb3_validator_spec.rb └── views │ ├── batches │ ├── print_amp_plate_labels_spec.rb │ └── print_labels_spec.rb │ ├── labware │ ├── retention_instruction_spec.rb │ ├── show_chromium_chip_spec.rb │ └── show_html_erb_spec.rb │ ├── report_fails │ └── index_html_erb_spec.rb │ ├── samples │ ├── edit_html_erb_spec.rb │ ├── index_html_erb_spec.rb │ └── show_html_erb_spec.rb │ └── tube_rack_summaries │ └── show_html_erb_spec.rb ├── test ├── controllers │ ├── admin_controller_test.rb │ ├── admin_programs_controller_test.rb │ ├── admin_projects_controller_test.rb │ ├── admin_roles_controller_test.rb │ ├── admin_studies_controller_test.rb │ ├── admin_users_controller_test.rb │ ├── api │ │ └── submissions_controller.rb │ ├── authentication_controller_test.rb │ ├── batches_controller_test.rb │ ├── events_controller_test.rb │ ├── get_your_qc_completed_tubes_here_controller_test.rb │ ├── labware_controller_test.rb │ ├── pipelines_controller_test.rb │ ├── plate_summaries_controller_test.rb │ ├── plate_template_controller_test.rb │ ├── plates_controller_test.rb │ ├── plates_from_tubes_controller_test.rb │ ├── projects_controller_test.rb │ ├── qc_files_controller_test.rb │ ├── qc_reports_controller_test.rb │ ├── receptacles_controller_test.rb │ ├── requests_comments_controller_test.rb │ ├── requests_controller_test.rb │ ├── robots_controller_test.rb │ ├── roles_users_controller_test.rb │ ├── sample_manifests_controller_test.rb │ ├── samples_comments_controller_test.rb │ ├── samples_controller_test.rb │ ├── sessions_controller_test.rb │ ├── studies_asset_groups_controller_test.rb │ ├── studies_comments_controller_test.rb │ ├── studies_controller_test.rb │ ├── studies_events_controller_test.rb │ ├── studies_sample_controller_test.rb │ ├── users_controller_test.rb │ └── workflows_controller_test.rb ├── data │ ├── 190_tube_sample_info.xls │ ├── bad.csv │ ├── bioanalysis_qc_results-with-error.csv │ ├── bioanalysis_qc_results.csv │ ├── blah.fasta │ ├── complete_quant_test.csv │ ├── example_file.txt │ ├── fluidigm.csv │ ├── full_manifest.csv │ ├── invalid_quant_test.csv │ ├── invalid_sample_manifest.csv │ ├── invalid_tube_sample_manifest.csv │ ├── manifests │ │ ├── mismatched_plate.csv │ │ └── mismatched_wells.csv │ ├── multiplexed_di_library_manifest.csv │ ├── multiplexed_library_manifest.csv │ ├── plate_reader_parsing_Zebrafish_example.csv │ ├── plate_volume │ │ ├── SQPD-111.csv │ │ ├── SQPD-1234567.csv │ │ └── SQPD-222.csv │ ├── qc_report.csv │ ├── quant_test.csv │ ├── quant_test_example.csv │ ├── sample_manifest.csv │ ├── sample_manifest_a_accessions.csv │ ├── sample_manifest_b_accessions.csv │ ├── sample_manifest_no_accessions.csv │ ├── sample_manifest_reference_genomes.csv │ ├── tecan │ │ ├── DN12345U.gwl │ │ ├── original.gwl │ │ └── pooled_cherrypick.gwl │ ├── test_blank_wells.csv │ ├── test_blank_wells_with_no_blanks.csv │ ├── test_blank_wells_with_no_blanks_new_data.csv │ ├── test_dna_sources_invalid.csv │ ├── test_dna_sources_valid.csv │ ├── test_no_vol_conc.csv │ ├── tube_sample_manifest.csv │ ├── updated_multiplexed_library_manifest.csv │ ├── very_small_file │ └── xsd │ │ ├── SRA.common.xsd │ │ └── SRA.sample.xsd ├── factories │ ├── location_report_factories.rb │ └── product_lines.rb ├── fixtures │ ├── approval_mailer │ │ ├── approved │ │ ├── on_hold │ │ └── rejected │ └── programs.yml ├── functional │ ├── external_validator_test.rb │ └── pre_cap_groups_test.rb ├── lib │ ├── label_printer │ │ ├── batch_tube_test.rb │ │ ├── labels_multiplication_test.rb │ │ ├── plate_creator_test.rb │ │ ├── plate_to_tube_test.rb │ │ ├── pmb_client_test.rb │ │ ├── print_job_test.rb │ │ ├── sample_manifest_multiplex_test.rb │ │ ├── sample_manifest_plate_test.rb │ │ ├── sample_manifest_tube_test.rb │ │ ├── shared_tests.rb │ │ └── swipecard_test.rb │ └── linefeed_fix_test.rb ├── performance │ ├── homepage_test.rb │ ├── plate_creation_test.rb │ ├── state_change_test.rb │ ├── transfer_request_collection_test.rb │ ├── work_completion_tubes_test.rb │ └── work_completions_test.rb ├── sample_information.xls ├── shoulda_macros │ ├── sanger_macros.rb │ └── sanger_macros │ │ └── resource_test.rb ├── test_helper.rb └── unit │ ├── accession_service_test.rb │ ├── aliquot_indexer_test.rb │ ├── aliquot_receptacle_test.rb │ ├── api │ └── core │ │ └── io │ │ ├── json │ │ ├── grammar_test.rb │ │ └── stream_test.rb │ │ └── json_output_test.rb │ ├── api_application_test.rb │ ├── asset_group_test.rb │ ├── asset_link_test.rb │ ├── asset_shape_test.rb │ ├── barcode_printer_test.rb │ ├── barcode_test.rb │ ├── batch_test.rb │ ├── cherrypick_task_test.rb │ ├── control_test.rb │ ├── custom_metadatum_collection_test.rb │ ├── custom_metadatum_test.rb │ ├── data_release_test.rb │ ├── descriptor_test.rb │ ├── event_factory_test.rb │ ├── event_test.rb │ ├── eventful_entry_test.rb │ ├── failure_test.rb │ ├── flexible_submission_test.rb │ ├── fluidigm_file_test.rb │ ├── fluidigm_plate_test.rb │ ├── fragment_test.rb │ ├── illumina_b │ └── request_validation.rb │ ├── import_fluidigm_data_test.rb │ ├── item_test.rb │ ├── lab_interface │ └── workflow_test.rb │ ├── lib_pool_norm_tube_generator_test.rb │ ├── library_tube_test.rb │ ├── map_test.rb │ ├── messaging │ ├── hash_generation_test.rb │ ├── messenger_creator_test.rb │ └── messenger_test.rb │ ├── multiplexed_library_tube_test.rb │ ├── parsers │ ├── bioanalysis_csv_parser_test.rb │ ├── plate_reader_parser_test.rb │ └── quant_parser_test.rb │ ├── permission_test.rb │ ├── phix_spiked_buffer_test.rb │ ├── pipeline_test.rb │ ├── plate_creator_test.rb │ ├── plate_owner_test.rb │ ├── plate_template_test.rb │ ├── plate_test.rb │ ├── product_catalogue │ └── library_driven_test.rb │ ├── product_catalogue_test.rb │ ├── product_criteria │ ├── advanced_test.rb │ └── basic_test.rb │ ├── product_criteria_test.rb │ ├── product_test.rb │ ├── program_test.rb │ ├── project_test.rb │ ├── purpose_test.rb │ ├── qc_file_test.rb │ ├── qc_metric_test.rb │ ├── qc_report_file_test.rb │ ├── qc_report_presenter_test.rb │ ├── qc_report_test.rb │ ├── report_contracts_test.rb │ ├── request_factory_test.rb │ ├── request_test.rb │ ├── request_type_test.rb │ ├── sample_test.rb │ ├── sample_tube_test.rb │ ├── sequencing_pipeline_test.rb │ ├── sequencing_qc_batch_test.rb │ ├── stock_library_tube_test.rb │ ├── stock_multiplexed_library_tube_test.rb │ ├── studies_helper_test.rb │ ├── study_sample_test.rb │ ├── submission_template_test.rb │ ├── tag_qc │ ├── lot_test.rb │ ├── plate_conversion_test.rb │ ├── qc_decision_test.rb │ ├── qcable_library_plate_purpose_test.rb │ ├── qcable_statemachine_checks.rb │ ├── qcable_statemachine_test.rb │ ├── qcable_test.rb │ └── stamp_test.rb │ ├── task_test.rb │ ├── task_test_base.rb │ ├── tasks │ └── plate_transfer_task_test.rb │ ├── transfer_templates │ 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