Module: Cherrypick::VolumeByNanoGramsPerMicroLitre

Included in:
Well
Defined in:
app/models/cherrypick/volume_by_nano_grams_per_micro_litre.rb

Overview

Included in Well to provide calculations for cherrypicking

Instance Method Summary collapse

Instance Method Details

#volume_to_cherrypick_by_nano_grams_per_micro_litre(final_volume_desired, final_conc_desired, source_concentration, source_volume, robot_minimum_pick_vol = 0.0) ⇒ Float

Used in the cherrypicking process to calculate the relative volumes of source and buffer required to reach the target volume and concentration.

  • Ideally will aim for a target well containing volume final_volume_desired at concentration final_conc_desired

  • This will be made by combining material from the source well (well_attribute.picked_volume) and buffer (well_attribute.buffer_volume)

  • Maximum picked_volume is limited by the amount available (source_volume) and the amount you want in the target well (final_volume_desired)

  • If source_volume < final_volume_desired then buffer will be added to make up final_volume_desired even if it reduces the target concentration below final_conc_desired

rubocop:todo Metrics/MethodLength, Metrics/AbcSize

Parameters:

  • final_volume_desired (Float) —

    The volume to aim for in the target well (self)

  • final_conc_desired (Float) —

    The concentration to aim for in the target well (self)

  • source_concentration (Float) —

    The concentration (ng/ul) in the source well

  • source_volume (Float) —

    The volume (ul) in the source well (ie. the maximum pick)

  • robot_minimum_pick_vol (Float) (defaults to: 0.0) —

    (ul) the minimum volume the robot can pick (the robot software will reject requests to pick less than this)

Returns:

  • (Float) —

    The volume that we will instruct to robot to pick from the source well



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# File 'app/models/cherrypick/volume_by_nano_grams_per_micro_litre.rb', line 27

def volume_to_cherrypick_by_nano_grams_per_micro_litre(
  final_volume_desired,
  final_conc_desired,
  source_concentration,
  source_volume,
  robot_minimum_pick_vol = 0.0
)
  robot_minimum_pick_vol ||= 0

  check_inputs_to_volume_to_cherrypick_by_nano_grams_per_micro_litre!(
    final_volume_desired,
    final_conc_desired,
    source_concentration
  )

  # @note Here we appear to set the concentration based on the required concentration, regardless of whether we hit it
  # it or not. Checking if this behaviour is desired RT#719205
  well_attribute.concentration = final_conc_desired
  well_attribute.requested_volume = final_volume_desired

  # Similarly we set current volume based on required. This is only untrue in rare edge cases though
  # (When you have almost all your required volume from your source, then add more buffer than intended
  #  due to minimum robot picks)
  well_attribute.current_volume = final_volume_desired

  # The maximum picking volume is limited by the available source volume, and the final volume desired
  # in the source well.
  # It also cannot be less than the minimum picking volume required by the robot.
  max_pick_volume = [final_volume_desired, source_volume].compact.min
  max_pick_volume = [max_pick_volume, robot_minimum_pick_vol].max

  # calculate the volume of source that contains the amount of material we want in our target well
  # this will then be made up to the desired volume with buffer
  source_volume_needed =
    if source_concentration.zero?
      final_volume_desired # If we have no material, then transfer everything
    else
      (final_volume_desired * final_conc_desired) / source_concentration
    end

  # clamp applies maximum and minimum values to source_volume_needed
  source_volume_to_tell_robot_to_pick = source_volume_needed.clamp(robot_minimum_pick_vol..max_pick_volume)

  # If the available source volume is actually less than the robot minimum picking volume,
  # we note two things - the amount we tell the robot to pick (robot_minimum_pick_vol),
  # and the amount it will actually pick (source_volume)
  # We use the latter for the buffer calculation, to make sure we make the desired final volume.
  # See comments on RT https://rt.sanger.ac.uk/Ticket/Display.html?id=735176
  source_volume_it_will_actually_pick =
    source_volume < robot_minimum_pick_vol ? source_volume : source_volume_to_tell_robot_to_pick

  well_attribute.picked_volume = source_volume_to_tell_robot_to_pick
  well_attribute.buffer_volume =
    calculate_buffer_volume(final_volume_desired, source_volume_it_will_actually_pick, robot_minimum_pick_vol)
  well_attribute.robot_minimum_picking_volume = robot_minimum_pick_vol

  source_volume_to_tell_robot_to_pick
end