Class: PlatePurpose

Inherits:
Purpose show all
Includes:
Api::PlatePurposeIo::Extensions, Purpose::Relationship::Associations
Defined in:
app/models/plate_purpose.rb

Overview

Note:

JG: Generally I have been trying to eliminate as much of the purpose specific behaviour as possible, and have pushed the business logic outwards towards the pipeline applications themselves. This is to try and reduce the overall complexity or Sequencescape models, reduce coupling between Sequencescape and its clients, and to make behaviour of individual plates more predictable. This is intended to increase the flexibility and adaptability of the pipelines.

The standard Purpose class for plates. This defines the standard behaviour, and is the class used for the majority of PlatePurposes.

The Purpose of a piece of Labware describes its role in the lab. While most labware will retain a single purpose through their life cycle, it is possible for purpose to be changed. Ideally this should be performed with a PlateConversion to ensure proper tracking.

Historically Purpose has modified the behaviour of its corresponding Labware, with a number of methods, such as Plate#state delegating to Plate#plate_purpose. While this is still occasionally required, it tends to result in quite brittle, unflexible behaviour. More recently we have been trying to push these differences in business logic outwards. In this new approach the Pipeline handles differences in behaviour, and the purpose acts merely as a tag, which can be used to inform the pipeline how it may wish to proceed. This approach makes Labware far more interchangeable.

Information about which purpose classes are used, and their last activity can be generated by running: bundle exec rake report:purposes in the appropriate environment. (Probably production)

Defined Under Namespace

Classes: AdditionalInput, InitialPurpose, Input

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Api::PlatePurposeIo::Extensions

included, #json_root

Methods included from Purpose::Relationship::Associations

included

Methods inherited from Purpose

#barcode_type, #prefix=, #set_default_barcode_prefix, #source_plate, #source_plates, #source_purpose_name=, #target_class

Methods included from Uuid::Uuidable

included, #unsaved_uuid!, #uuid

Methods included from SharedBehaviour::Named

included

Methods inherited from ApplicationRecord

alias_association, convert_labware_to_receptacle_for, find_by_id_or_name, find_by_id_or_name!

Methods included from Squishify

extended

Class Method Details

.stock_plate_purpose ⇒ Object 



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# File 'app/models/plate_purpose.rb', line 90

def self.stock_plate_purpose
  PlatePurpose.create_with(
    stock_plate: true,
    cherrypickable_target: true,
    type: 'PlatePurpose::Input'
  ).find_or_create_by!(name: 'Stock Plate')
end

Instance Method Details

#asset_shape ⇒ Object 



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# File 'app/models/plate_purpose.rb', line 33

def asset_shape
  super || AssetShape.default
end

#attached?(_plate) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/plate_purpose.rb', line 124

def attached?(_plate)
  true
end

#cherrypick_completed(plate) ⇒ Object 



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# File 'app/models/plate_purpose.rb', line 40

def cherrypick_completed(plate)
  messenger_creators.each { |creator| creator.create!(plate) }
end

#cherrypick_in_rows? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/plate_purpose.rb', line 120

def cherrypick_in_rows?
  cherrypick_direction == 'row'
end

#child_plate_purposes ⇒ Object 



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# File 'app/models/plate_purpose.rb', line 128

def child_plate_purposes
  child_purposes.where_is_a(PlatePurpose)
end

#create!(*args, &block) ⇒ Object 



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# File 'app/models/plate_purpose.rb', line 102

def create!(*args, &block)
  attributes = args.extract_options!
  do_not_create_wells = args.first.present?
  attributes[:size] ||= size
  attributes[:purpose] = self

  # Delete these attributes if they exist as create! with barcode param is being deprecated in rails 6.1
  # Removed sanger_barcode attribute as its now generated by plate.create_with_barcode!
  #
  # 2022-04-20 10:04 - These attributes (barcode) are needed when the test creates a plate with a specific
  # barcode (and we dont want to access Baracoda in that case)
  attributes.delete(:barcode)
  attributes.delete(:barcode_prefix)
  target_class
    .create_with_barcode!(attributes, &block)
    .tap { |plate| plate.wells.construct! unless do_not_create_wells }
end

#input_plate=(is_input) ⇒ Object

Set the class to PlatePurpose::Input is set to true. Allows creation of the input plate purposes through the API without directly exposing our class names. Note: This could be moved to the V2 API resource when V1 is removed.

Parameters:

  • is_input (Bool) —

    Set to true to assign the sti type to PlatePurpose::Input



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# File 'app/models/plate_purpose.rb', line 63

def input_plate=(is_input)
  self.type = 'PlatePurpose::Input' if is_input
end

#plate_height ⇒ Object 



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# File 'app/models/plate_purpose.rb', line 44

def plate_height
  asset_shape.plate_height(size)
end

#plate_width ⇒ Object 



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# File 'app/models/plate_purpose.rb', line 48

def plate_width
  asset_shape.plate_width(size)
end

#pool_wells(wells) ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/models/plate_purpose.rb', line 67

def pool_wells(wells) # rubocop:todo Metrics/MethodLength
  _pool_wells(wells)
    .joins(
      # rubocop:todo Layout/LineLength
      'LEFT OUTER JOIN uuids AS pool_uuids ON pool_uuids.resource_type="Submission" AND pool_uuids.resource_id=submission_id'
      # rubocop:enable Layout/LineLength
    )
    .select('pool_uuids.external_id AS pool_uuid')
    .readonly(false)
    .tap do |wells_with_pool|
      if wells_with_pool.group_by(&:id).any? { |_, multiple_pools| multiple_pools.uniq.size > 1 }
        raise StandardError, 'Cannot deal with a well in multiple pools'
      end
    end
end

#size ⇒ Object 



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# File 'app/models/plate_purpose.rb', line 98

def size
  super || 96
end

#source_wells_for(stock_wells) ⇒ Object 



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# File 'app/models/plate_purpose.rb', line 132

def source_wells_for(stock_wells)
  stock_wells
end

#state_of(plate) ⇒ Object

The state of a plate is based on the transfer requests.



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# File 'app/models/plate_purpose.rb', line 53

def state_of(plate)
  plate.state_from(plate.transfer_requests)
end