Class: LabwareCreators::PcrCyclesBinnedPlateForTNanoSeq

Inherits:
PcrCyclesBinnedPlateBase show all
Defined in:
app/models/labware_creators/pcr_cycles_binned_plate_for_t_nano_seq.rb

Overview

This version of the class is specific to the Targeted NanoSeq pipeline.

Constant Summary collapse

CUSTOMER_FILENAME = 
'targeted_nano_seq_customer_file.csv'

Instance Method Summary collapse

Constructor Details

This class inherits a constructor from LabwareCreators::Base

Instance Method Details

#after_transfer! ⇒ Object

rubocop:disable Metrics/AbcSize



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# File 'app/models/labware_creators/pcr_cycles_binned_plate_for_t_nano_seq.rb', line 11

def after_transfer!
  # called as part of the 'super' call in the 'save' method
  # retrieve child plate through v2 api, using uuid got through v1 api
  child_v2_plate = Sequencescape::Api::V2.plate_with_custom_includes(CHILD_PLATE_INCLUDES, uuid: child.uuid)

  # cycle through the child wells and for each get the related request and write some metadata
  # to it based on the details in the customer file
  child_wells_by_location = child_v2_plate.wells.index_by(&:location)

  well_details.each do |parent_location, details|
    child_well_location = transfer_hash[parent_location]['dest_locn']
    child_well = child_wells_by_location[child_well_location]

    # NB. this seems to return an array of requests via the api but a single request in tests
    request = Array(child_well.aliquots.first.request).first

    if request.blank?
      raise StandardError, "Unable to identify request for child plate well at location #{child_well_location}"
    end

    # create hash containing the key value pairs we want to store as metadata on the request
    request_metadata = {
      'original_plate_barcode' => parent.human_barcode,
      'original_well_id' => parent_location,
      'concentration_nm' => details['concentration'].to_s,
      'input_amount_available' => details['input_amount_available'].to_s,
      'input_amount_desired' => details['input_amount_desired'].to_s,
      'sample_volume' => details['sample_volume'].to_s,
      'diluent_volume' => details['diluent_volume'].to_s,
      'pcr_cycles' => details['pcr_cycles'].to_s,
      'hyb_panel' => details['hyb_panel']
    }
    create_or_update_request_metadata(request, request_metadata, child_well_location)
  end
end

#create_or_update_request_metadata(request, request_metadata, child_well_location) ⇒ Object

Cycles through a hash of key value pairs and creates a new metadatum or updates the existing one for each metadata field to be stored against the request object. NB. makes assumption that metadata from previous iterations can be safely overwritten



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# File 'app/models/labware_creators/pcr_cycles_binned_plate_for_t_nano_seq.rb', line 52

def create_or_update_request_metadata(request, request_metadata, child_well_location)
  request_metadata.each do |metadata_key, metadata_value|
    existing_metadata_v2 = find_existing_metadata(metadata_key, request.id)

    if existing_metadata_v2.present?
      update_existing_metadata(existing_metadata_v2, metadata_value, metadata_key, child_well_location)
    else
      create_new_metadata(metadata_key, metadata_value, request, child_well_location)
    end
  end
end