Class: Reception::ResourceFactory

Inherits:
Object
  • Object
show all
Extended by:
NestedValidation
Includes:
ActiveModel::Model
Defined in:
app/models/reception/resource_factory.rb

Overview

Acts on behalf of a Reception to construct all associated requests, as well as any necessary samples, plates, wells and tubes. In order to improve performance, the ResourceFactory implements caching of samples and library and data types. This allows up to retrieve all records in a single query upfront, avoiding N+1 query problems. It also ensures we can centralize the registration of new plates and tubes, making it easier to prevent registration of duplicate records.

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from NestedValidation

validates_nested

Instance Attribute Details

#reception ⇒ Object

Returns the value of attribute reception.



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# File 'app/models/reception/resource_factory.rb', line 15

def reception
  @reception
end

Instance Method Details

#compound_sample_tubes_attributes=(compound_sample_tubes_attributes) ⇒ Object

method to handle compound tubes attributes



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# File 'app/models/reception/resource_factory.rb', line 30

def compound_sample_tubes_attributes=(compound_sample_tubes_attributes)
  create_compound_tubes(compound_sample_tubes_attributes)
end

#construct_resources! ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 58

def construct_resources!
  requests.each(&:save!) # Note this also saves associated records we generate
  labware_status
end

#containers ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 46

def containers
  @containers ||= []
end

#create_compound_tubes(compound_tube_attributes) ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 100

def create_compound_tubes(compound_tube_attributes)
  compound_tube_attributes.each do |tube_attr|
    process_compound_tube(tube_attr)
  end
end

#create_plates(plates_attributes) ⇒ Object

Populates containers and requests from plates_attributes



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# File 'app/models/reception/resource_factory.rb', line 64

def create_plates(plates_attributes)
  plates_attributes.each do |plate_attr|
    # Gets the existing plate or creates a new one
    plate = find_or_create_labware(plate_attr[:barcode], Plate)
    containers << plate
    plate_attr[:wells_attributes].each do |well_attr|
      # Gets the existing well or creates a new one
      well = plate.wells.located_at(well_attr[:position])
      # If a well already exists with records, we want to add an error
      if well.existing_records.present?
        update_labware_status(plate.barcode, 'partial', "#{well.position} already has a sample")
        next
      end

      # Creates a request for the well
      create_request_for_container(well_attr, well)
    end
  end
end

#create_pool(pool_attributes) ⇒ Object

Creates a pool from pool_attributes and uses the imported libraries



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# File 'app/models/reception/resource_factory.rb', line 107

def create_pool(pool_attributes)
  return if pool_attributes.blank?

  # Currently only supports Ont
  @pool = Ont::Pool.new(pool_attributes)
  begin
    @pool.libraries = libraries
    update_labware_status(pool_attributes['barcode'], 'success', nil)
  rescue StandardError => e
    update_labware_status(pool_attributes['barcode'], 'failed', e.message)
  end
end

#create_tubes(tubes_attributes) ⇒ Object

Populates containers and requests from tubes_attributes



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# File 'app/models/reception/resource_factory.rb', line 85

def create_tubes(tubes_attributes)
  tubes_attributes.each do |tube_attr|
    # Gets the existing tube or creates a new one
    tube = find_or_create_labware(tube_attr[:barcode], Tube)
    # If a tube already exists with records, we want to add an error
    if tube.existing_records.present?
      update_labware_status(tube.barcode, 'failed', 'Tube already has a sample')
      next
    end

    # Creates a request for the tube
    create_request_for_container(tube_attr, tube)
  end
end

#data_type_for(attributes) ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 130

def data_type_for(attributes)
  data_type_cache.fetch(attributes[:data_type], nil)
end

#labware_status ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 54

def labware_status
  @labware_status ||= {}
end

#libraries ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 42

def libraries
  @libraries ||= []
end

#library_type_for(request_attributes) ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 120

def library_type_for(request_attributes)
  # Gets a library type from the cache or returns an unknown type
  library_type = request_attributes[:library_type]
  library_type_cache.fetch(
    library_type,
    UnknownLibraryType.new(library_type:,
                           permitted: library_type_cache.keys)
  )
end

#plates_attributes=(plates_attributes) ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 21

def plates_attributes=(plates_attributes)
  create_plates(plates_attributes)
end

#pool ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 38

def pool
  @pool ||= nil
end

#pool_attributes=(pool_attributes) ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 34

def pool_attributes=(pool_attributes)
  create_pool(pool_attributes)
end

#requests ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 50

def requests
  @requests ||= []
end

#sample_for(attributes) ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 134

def sample_for(attributes)
  # Used to reduce database queries.
  # It gets a sample from the cache, if it doesn't exist it searches the database
  # or creates a new one
  sample_cache[attributes[:external_id]] ||=
    Sample.find_by(external_id: attributes[:external_id]) || Sample.new(attributes)
end

#tubes_attributes=(tubes_attributes) ⇒ Object 



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# File 'app/models/reception/resource_factory.rb', line 25

def tubes_attributes=(tubes_attributes)
  create_tubes(tubes_attributes)
end