Top Level Namespace

Defined Under Namespace

Modules: AASM, Accession, AccessionHelper, AccessionService, Accessionable, ActsAsDescriptable, Api, ApiTools, ApplicationHelper, ArrayWithFieldList, AssetsHelper, Attributable, AuthenticatedSystem, AuthenticatedTestHelper, BarcodePrintersHelper, BatchesHelper, BootstrapHelper, BulkSubmissionExcel, CarrierWave, Cherrypick, CherrypickFormHelper, Commentable, CommentsProxy, CompoundSampleHelper, ControlRequestTypeCreation, ControllerHelper, Core, CronScripts, CsvParserClient, DataRelease, DelayedJobsHelper, DelegateValidation, Deployed, DescriptorJavascriptHelper, Dev, EBICheck, EncodingDetector, Endpoints, EventfulRecord, FieldInfosHelper, FlashTruncation, FontawesomeHelper, HTTPClients, HasBehaviour, Heron, HistoriesHelper, IncludeTag, Informatics, Insdc, Io, LabWhereClient, LabelPrinter, LinefeedFix, ManifestUtil, Metadata, MethodBenchmarking, NestedValidation, Parsers, PhiX, PipelinesHelper, PlatePicks, PlatesHelper, Presenters, ProductHelpers, PrototypeReplacementHelper, RecordLoader, ReportFailsHelper, RequestClassDeprecator, RequestTypePurposeCreation, RequestTypesHelper, RequestsHelper, RetentionInstructionHelper, SampleAccessioning, SampleManifestExcel, SamplesHelper, SearchBehaviour, SequencescapeExcel, SequencingQcBatch, SharedBehaviour, SingleReceptacleLabware, Squishify, StandardNamedScopes, StateChanger, StudiesHelper, SubmissionSerializer, SubmissionsHelper, Swipecardable, TagSubstitutionHelper, Tasks, UiHelper, UnderRepWellCommentsToBroadcast, UsersHelper, Validateable, ValidationStateGuard, ViewsSchema, VolumeCheck, WorkflowsHelper, WorkingSetup Classes: Ability, AbilityAnalysis, AddSpikedInControlTask, AdminController, AdvancedSearchController, Aliquot, AliquotIndex, AliquotIndexer, ApiApplication, ApiV2Generator, ApplicationController, ApplicationRecord, Asset, AssetAudit, AssetAuditsController, AssetBarcode, AssetCreation, AssetGroup, AssetGroupAsset, AssetLink, AssetShape, AssetsController, AssignTagsTask, AssignTagsToTubesTask, AssignTubesToMultiplexedWellsTask, AutomatedOrder, BaitLibrary, BaitLibraryLayout, BaitLibraryType, Barcode, BarcodePrefix, BarcodePrinter, BarcodePrinterType, BarcodePrinterType1DTube, BarcodePrinterType384DoublePlate, BarcodePrinterType384Plate, BarcodePrinterType96Plate, BarcodePrintersController, BaseLoginProxy, Batch, BatchCreationValidator, BatchRequest, BatchesController, BindingKitBarcodeTask, BioscanControlLocationsController, BroadcastEvent, BudgetDivision, BulkSubmission, BulkSubmissionsController, BulkTransfer, CherrypickForFluidigmRequest, CherrypickForPulldownPipeline, CherrypickForPulldownRequest, CherrypickPipeline, CherrypickRequest, CherrypickTask, CherrypickingPipeline, Comment, CompoundAliquot, Control, ControlPlate, ControlRequest, CreateAssetRequest, CustomMetadatum, CustomMetadatumCollection, CustomText, CustomerRequest, DataReleaseStudyType, DbFile, DeploymentEnvironment, Descriptor, DilutionPlate, DilutionPlatePurpose, Document, DocumentsController, DriverFilesController, ElementAvitiSequencingPipeline, ElementAvitiSequencingRequest, ElementAvitiValidator, Equipment, ErrorsController, Event, EventFactory, EventSender, EventfulMailer, EventsController, ExportPoolXpToTractionJob, ExtendedValidator, ExternalLibraryCreationRequest, ExternalProperty, ExternalReleaseEvent, ExtractionAttribute, FacultySponsor, Failure, FieldInfo, FlexibleCherrypickPipeline, FlexibleSubmission, FlowcellType, FlowcellTypesRequestType, FluidigmFile, FluidigmTemplateTask, Fragment, GelDilutionPlate, GelsController, GenerateCreateAssetRequestsJob, GenotypingPipeline, GenotypingRequest, GetYourQcCompletedTubesHereController, Health, HealthController, HiSeqSequencingRequest, HomesController, HttpLoginProxy, Identifier, IllegalOperation, Implement, Item, LabEvent, LabSearchesController, Labware, LabwareController, LabwhereReception, LabwhereReceptionsController, Lane, Latin1Validator, LegacyPipeline, LibPoolNormTubeGenerator, LibraryCreationRequest, LibraryEvent, LibraryTube, LibraryType, LibraryTypesRequestType, LinearSubmission, LocationReport, LocationReportJob, LocationReportsController, Lot, LotType, Map, MbraveTagsCreator, Messenger, MessengerCreator, MessengersController, MiSeqSequencingRequest, MovieLengthTask, MultiplexedCherrypickingTask, MultiplexedLibraryCreationRequest, MultiplexedLibraryTube, NovaSeq6000PESequencingRequest, NovaseqxPeValidator, NullCustomMetadatumCollection, ObjectSpaceProfile, OligoEnumerator, Order, OrderCompatibilityValidator, OrderRole, OrdersController, PacBioLibraryTube, PacBioSamplePrepPipeline, PacBioSamplePrepRequest, PacBioSequencingPipeline, PacBioSequencingRequest, ParentsController, PbmcPoolingCustomerRequest, Permission, PhiXesController, PickList, PickListJob, PickListsController, PicoAssayPlate, PicoDilutionPlate, Pipeline, PipelineRequestInformationType, PipelinesController, PipelinesRequestType, Plate, PlateBarcode, PlateConversion, PlateCreation, PlateMapGeneration, PlateOwner, PlatePicksController, PlatePurpose, PlateSummariesController, PlateTemplate, PlateTemplateTask, PlateTemplatesController, PlateTransferTask, PlateType, PlateVolume, PlatesController, PlatesFromTubesController, PolyMetadatum, PolymorphicUploader, PooledCherrypickRequest, PooledPlateCreation, Pooling, PoolingsController, PreCapturePool, PrepKitBarcodeTask, PrimerPanel, Product, ProductCatalogue, ProductCriteria, ProductLine, ProductProductCatalogue, Program, ProgramsValidator, Project, ProjectManager, ProjectsController, PsdFormatter, PulldownMultiplexedLibraryCreationRequest, PulldownMultiplexedLibraryTube, Purpose, QcAssay, QcDecision, QcFile, QcFilesController, QcMetric, QcMetricRequest, QcReport, QcReportJob, QcReportsController, QcRequest, QcResult, QcResultFactory, QcTube, Qcable, QcableCreator, QcableLibraryPlatePurpose, QcablePlatePurpose, QcableTubePurpose, QuadStampController, RackedTube, ReRequestSubmission, Receptacle, ReceptaclesController, ReferenceGenome, ReferenceGenomesController, ReportFail, ReportFailsController, Request, RequestEvent, RequestFactory, RequestInformation, RequestInformationType, RequestLogger, RequestType, RequestsController, Robot, RobotProperty, RobotVerificationsController, Role, Sample, SampleAccessioningJob, SampleCompoundComponent, SampleLogisticsController, SampleManifest, SampleManifestAsset, SampleManifestUploadWithTagSequencesController, SamplePrepQcTask, SampleTube, SamplesController, SangerSampleId, Search, SearchesController, SequencingPipeline, SequencingRequest, SequenomQcPlate, SequenomQcPlatesController, SessionsController, SetDescriptorsTask, SingleRequestSubmission, SpecificTubeCreation, SpecificTubeRackCreation, SpikedBuffer, Stamp, StateChange, StockLibraryTube, StockMultiplexedLibraryTube, StockStamper, StockStampersController, StripCreationRequest, StripTube, StudiesController, Study, StudyReport, StudyReportJob, StudyReportsController, StudySample, StudyType, Submission, SubmissionBuilderJob, SubmissionPool, SubmissionTemplate, SubmissionTemplateRequestType, SubmissionsController, SubmittedAsset, Supplier, SystemRequest, Tag, Tag2Layout, Tag2LayoutTemplate, TagGroup, TagGroupsController, TagGroupsTask, TagLayout, TagLayoutTemplate, TagLayoutTemplatesController, TagSet, TagSetsController, TagSubstitution, TagSubstitutionsController, Task, TaxaController, TestInformatics, Transfer, TransferRequest, TransferRequestCollection, TransferRequestCollectionTransferRequest, TransferTemplate, Tube, TubeCreation, TubeFromPlateCreation, TubeFromTubeCreation, TubeRack, TubeRackStatus, TubeRackStatusesController, TubeRackSummariesController, UatActionGenerator, UatActions, UatActionsController, UltimaGlobal, UltimaSequencingPipeline, UltimaSequencingRequest, UltimaValidator, User, UsersController, Utf8mb3Validator, Uuid, UuidsController, ValidateSampleSheetTask, VolumeUpdate, Well, WellAttribute, WorkCompletion, WorkCompletionsSubmission, WorkOrder, WorkOrderType, Workflow, WorkflowsController, WorkingDilutionPlate, XmlLoginProxy

Constant Summary collapse

OrderTemplate =

SubmissionTemplate is really OrderTemplate, and the only place that actually cares is the API, so alias If we remove this, then we break our API endpoints. Some of which, at least at one point, actually had external users.

SubmissionTemplate

Instance Method Summary collapse

Instance Method Details

#error_message_header(object) ⇒ Object 



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# File 'app/helpers/application_helper.rb', line 391

def error_message_header(object)
  count = object.errors.full_messages.count
  model_name = object.class.to_s.tableize.tr('_', ' ').gsub(%r{/.*}, '').singularize
  is_plural = count > 1 ? 's' : ''
  header = "#{count} error#{is_plural} prohibited this #{model_name} from being saved"
  content_tag(:h2, header)
end

#error_messages_ul_html_safe(object) ⇒ Object 



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# File 'app/helpers/application_helper.rb', line 399

def error_messages_ul_html_safe(object)
  messages = object.errors.full_messages.map { |msg| content_tag(:li, ERB::Util.html_escape(msg)) }.join.html_safe
  content_tag(:ul, messages)
end

#extract_barcode(args, attributes) ⇒ Object

mutates 'attributes'



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# File 'app/models/tube.rb', line 112

def extract_barcode(args, attributes)
  barcode = args.first || attributes.delete(:barcode)
  prefix = attributes.delete(:barcode_prefix)&.prefix || default_prefix
  [barcode, prefix]
end

#handle_consent_withdrawal(cleaned_params, sample, user) ⇒ Object

If consent is being withdrawn and wasn't previously, set a couple of fields



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# File 'app/controllers/samples_controller.rb', line 256

def handle_consent_withdrawal(cleaned_params, sample, user)
  return unless (cleaned_params[:sample_metadata_attributes][:consent_withdrawn] == 'true') && !sample.consent_withdrawn

  cleaned_params[:date_of_consent_withdrawn] = DateTime.now
  cleaned_params[:user_id_of_consent_withdrawn] = user.id
end

#handle_page_update_failure(sample) ⇒ Object 



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# File 'app/controllers/samples_controller.rb', line 269

def handle_page_update_failure(sample)
  flash[:error] = 'Failed to update attributes for sample'
  flash[:warning] = sample.errors.full_messages if sample.errors.present?
  redirect_to edit_sample_path(sample)
end

#handle_page_update_success(sample) ⇒ Object 



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# File 'app/controllers/samples_controller.rb', line 263

def handle_page_update_success(sample)
  flash[:notice] = 'Sample details have been updated'
  flash[:warning] = sample.errors.full_messages if sample.errors.present?
  redirect_to sample_path(sample)
end

#render_error_messages(object) ⇒ Object

error_messages_for method was deprecated, however lots of the tests depend on the message format it was using. apidock.com/rails/ActionView/Helpers/ActiveRecordHelper/error_messages_for



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# File 'app/helpers/application_helper.rb', line 382

def render_error_messages(object)
  return if object.errors.count.zero?

  contents = +''
  contents << error_message_header(object)
  contents << error_messages_ul_html_safe(object)
  content_tag(:div, contents.html_safe)
end