Top Level Namespace

Defined Under Namespace

Modules: AASM, Accession, AccessionHelper, AccessionService, Accessionable, ActsAsDescriptable, Admin, Api, ApiTools, ApplicationHelper, ArrayWithFieldList, AssetsHelper, Attributable, AuthenticatedSystem, AuthenticatedTestHelper, BarcodePrintersHelper, BatchesHelper, BootstrapHelper, BulkSubmissionExcel, CarrierWave, Cherrypick, CherrypickFormHelper, Commentable, CommentsProxy, CompoundSampleHelper, ControlRequestTypeCreation, ControllerHelper, CronScripts, CsvParserClient, DataRelease, DelayedJobsHelper, DelegateValidation, Deployed, DescriptorJavascriptHelper, Dev, EBICheck, EncodingDetector, EventfulRecord, FieldInfosHelper, FlashTruncation, FontawesomeHelper, HTTPClients, HasBehaviour, HasPolyMetadata, Heron, HistoriesHelper, IncludeTag, Informatics, Insdc, LabWhereClient, LabelPrinter, LinefeedFix, ManifestUtil, Metadata, MethodBenchmarking, NestedValidation, Parsers, PhiX, PipelinesHelper, PlatesHelper, Presenters, ProductHelpers, PrototypeReplacementHelper, RecordLoader, RemoteLinkPaginationHelper, 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, Warren, 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, ContentSecurityPolicyReportsController, 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, 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, NotificationJob, NovaSeq6000PESequencingRequest, NovaseqxPeValidator, NullCustomMetadatumCollection, ObjectSpaceProfile, OligoEnumerator, Order, OrderCompatibilityValidator, OrderRole, OrdersController, PacBioLibraryTube, PacBioSamplePrepPipeline, PacBioSamplePrepRequest, PacBioSequencingPipeline, PacBioSequencingRequest, ParentsController, PbmcPoolingCustomerRequest, Permission, PhiXesController, PicoAssayPlate, PicoDilutionPlate, Pipeline, PipelineRequestInformationType, PipelinesController, PipelinesRequestType, Plate, PlateBarcode, PlateConversion, PlateCreation, PlateMapGeneration, PlateOwner, PlatePurpose, PlateSummariesController, PlateTemplate, PlateTemplateTask, PlateTemplatesController, PlateTransferTask, PlateType, PlateVolume, PlatesController, PlatesFromTubesController, PolyMetadatum, PolymorphicUploader, PooledCherrypickRequest, PooledPlateCreation, Pooling, PoolingSourcePlatePurpose, 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, UltimaApplication, UltimaConversionRequest, UltimaGlobal, UltimaPreset, UltimaPrimer, UltimaSequencingPipeline, UltimaSequencingRequest, UltimaUG200SequencingPipeline, UltimaUG200SequencingRequest, UltimaUG200Validator, 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 390

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#error_messages_ul_html_safe(object) ⇒ Object 



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# File 'app/helpers/application_helper.rb', line 398

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#extract_barcode(args, attributes) ⇒ Object

mutates 'attributes'



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# File 'app/models/tube.rb', line 111

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 261

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#handle_page_update_failure(sample) ⇒ Object 



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# File 'app/controllers/samples_controller.rb', line 274

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end

#handle_page_update_success(sample) ⇒ Object 



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# File 'app/controllers/samples_controller.rb', line 268

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
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. https://apidock.com/rails/ActionView/Helpers/ActiveRecordHelper/error_messages_for



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# File 'app/helpers/application_helper.rb', line 381

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end