Class: Core::Io::Base

Inherits:

Object

• Object
• Core::Io::Base

Extended by:

Benchmarking, EagerLoadingBehaviour, JsonFormattingBehaviour, Logging

Defined in:

app/api/core/io/base.rb

Overview

Core class for API V1 IO, which effectively acts as a view layer. New IO should be placed in app/api/io/ and should inherit from Core::IO::Base. All IO are in the Io namespace.

Examples:

BaitLibrary

class Io::BaitLibrary < Core::Io::Base
  set_model_for_input(::BaitLibrary)
  set_json_root(:bait_library)
  define_attribute_and_json_mapping("
    bait_library_supplier.name  => supplier.name
           supplier_identifier  => supplier.identifier
                          name  => name
                target_species  => target.species
        bait_library_type.name  => bait_library_type
  ")
end

Direct Known Subclasses

Io::Aliquot, Io::Asset, Io::AssetAudit, Io::AssetGroup, Io::BaitLibrary, Io::BaitLibraryLayout, Io::BarcodePrinter, Io::Batch, Io::BulkTransfer, Io::Comment, Io::CustomMetadatumCollection, Io::ExtractionAttribute, Io::Labware, Io::LibraryEvent, Io::Lot, Io::LotType, Io::Order, Io::Pipeline, Io::Plate, Io::PlateConversion, Io::PlateCreation, Io::PlatePurpose, Io::PlateTemplate, Io::PooledPlateCreation, Io::Project, Io::Purpose, Io::QcDecision, Io::QcFile, Io::Qcable, Io::QcableCreator, Io::Receptacle, Io::ReferenceGenome, Io::Request, Io::RequestType, Io::Robot, Io::Sample, Io::SampleManifest, Io::Search, Io::SpecificTubeCreation, Io::Stamp, Io::StateChange, Io::Study, Io::Submission, Io::SubmissionPool, Io::SubmissionTemplate, Io::Supplier, Io::Tag2Layout, Io::Tag2LayoutTemplate, Io::TagGroup, Io::TagLayout, Io::TagLayoutTemplate, Io::Transfer, Io::Transfer::BetweenPlates, Io::Transfer::BetweenPlatesBySubmission, Io::Transfer::BetweenSpecificTubes, Io::Transfer::BetweenTubesBySubmission, Io::Transfer::FromPlateToSpecificTubes, Io::Transfer::FromPlateToSpecificTubesByPool, Io::Transfer::FromPlateToTube, Io::Transfer::FromPlateToTubeByMultiplex, Io::Transfer::FromPlateToTubeBySubmission, Io::TransferRequest, Io::TransferRequestCollection, Io::TransferTemplate, Io::Tube::Purpose, Io::TubeCreation, Io::TubeFromTubeCreation, Io::User, Io::VolumeUpdate, Io::Well, Io::WorkCompletion

Class Method Summary

• .map_parameters_to_attributes(*_args) ⇒ Object

Methods included from Logging

debug, error, info, low_level

Methods included from Benchmarking

benchmark, registered

Class Method Details

.map_parameters_to_attributes(*_args) ⇒ Object

# File 'app/api/core/io/base.rb', line 26

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