Class: LabwareCreators::PooledWellsBySampleInGroups

Inherits:
Base
  • Object
show all
Includes:
SupportParent::PlateOnly
Defined in:
app/models/labware_creators/pooled_wells_by_sample_in_groups.rb

Overview

This labware creator pools PBMC isolations with the same samples in pairs (or configured number of source wells) per destination before cell counting to reduce the number runs on Celleca (cell counting). The robot transfer is done from LRC Blood Bank to LRC PBMC Bank plate. Only the wells with passed state will be transferred to the destination plate. The destination wells are compressed to top left by column on the plate.

Instance Method Summary collapse

Constructor Details

This class inherits a constructor from LabwareCreators::Base

Instance Method Details

#build_pools ⇒ Object

List of pools to be created; index is the destination pool number; each pool is a list of source wells



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 41

def build_pools
  parent_wells_for_pooling
    .group_by { |well| well.aliquots.first.sample.uuid }
    .flat_map { |_uuid, wells| wells.each_slice(number_of_source_wells).to_a }
end

#get_well_for_plate_location(plate, well_location) ⇒ Object

Well object at well location on plate



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 66

def get_well_for_plate_location(plate, well_location)
  plate.wells.detect { |well| well.location == well_location }
end

#labware_wells ⇒ Object

List of passed wells of the parent labware in column order. Used by well filter.



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 26

def labware_wells
  source_plate.wells_in_columns.select(&:passed?)
end

#number_of_source_wells ⇒ Object

Number of source wells with the same sample to be pooled.



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 16

def number_of_source_wells
  @number_of_source_wells ||= purpose_config.dig(:creator_class, :args, :number_of_source_wells)
end

#parent ⇒ Object Originally defined in module SupportParent::PlateOnly

#parent_wells_for_pooling ⇒ Object

List of filtered wells for pooling.



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 36

def parent_wells_for_pooling
  well_filter.filtered.map(&:first)
end

#pools ⇒ Object

List of pools built from passed wells from parent plate



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 48

def pools
  @pools ||= build_pools
end

#request_hash(source_well, dest_plate, additional_parameters) ⇒ Object

Attributes for transfer request from source_well to dest_plate



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 71

def request_hash(source_well, dest_plate, additional_parameters)
  dest_location = transfer_hash[source_well.location][:dest_locn]
  {
    'source_asset' => source_well.uuid,
    'target_asset' => get_well_for_plate_location(dest_plate, dest_location)&.uuid,
    'merge_equivalent_aliquots' => true
  }.merge(additional_parameters)
end

#source_plate ⇒ Object

Parent plate using SS v2 API



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 31

def source_plate
  @source_plate ||= Sequencescape::Api::V2::Plate.find_by(uuid: parent.uuid)
end

#transfer_hash ⇒ Object

Object mapping source wells to destination wells for transfers



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 53

def transfer_hash
  result = {}
  pools.each_with_index do |pool, index|
    dest_location = WellHelpers.well_at_column_index(index)
    pool.each do |source_well|
      source_location = source_well.location
      result[source_location] = { dest_locn: dest_location }
    end
  end
  result
end

#transfer_material_from_parent!(dest_uuid) ⇒ Object

Send the transfer request to SS



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 88

def transfer_material_from_parent!(dest_uuid)
  dest_plate = Sequencescape::Api::V2::Plate.find_by(uuid: dest_uuid)
  api.transfer_request_collection.create!(
    user: user_uuid,
    transfer_requests: transfer_request_attributes(dest_plate)
  )
  true
end

#transfer_request_attributes(dest_plate) ⇒ Object

List of objects mapping source wells to destination wells



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 81

def transfer_request_attributes(dest_plate)
  well_filter.filtered.filter_map do |source_well, additional_parameters|
    request_hash(source_well, dest_plate, additional_parameters)
  end
end

#well_filter ⇒ Object

Well filter with this object as the creator



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# File 'app/models/labware_creators/pooled_wells_by_sample_in_groups.rb', line 21

def well_filter
  @well_filter ||= WellFilter.new(creator: self)
end