Module: Tasks::CherrypickHandler

Included in:
WorkflowsController
Defined in:
app/models/tasks/cherrypick_handler.rb

Overview

Handles the behaviour of CherrypickTask and included in WorkflowsController A Task used in cherrypick pipelines Performs the main bulk of cherrypick action. Although a lot of the options on this page are presented as part of the previous step, and get persisted on this page as hidden fields. This page shows a drag-drop plate layout which lets users set-up the way the plate will be picked. The target asset of each request will have its plate and map set accordingly. Well attributes are set to track picking volumes

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.included(base) ⇒ Object

rubocop:todo Metrics/ModuleLength


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# File 'app/models/tasks/cherrypick_handler.rb', line 6

def self.included(base)
  base.class_eval { include Cherrypick::Task::PickHelpers }
end

Instance Method Details

#do_cherrypick_task(_task, params) ⇒ Object

rubocop:todo Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/AbcSize


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# File 'app/models/tasks/cherrypick_handler.rb', line 99

def do_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexity
  plates = params[:plate]
  size = params[:plate_size]
  plate_type = params[:plate_type]

  # rubocop:todo Metrics/BlockLength
  ActiveRecord::Base.transaction do
    # Determine if there is a standard plate to use.
    partial_plate = nil
    plate_barcode = params[:plate_barcode]
    fluidigm_plate = params[:fluidigm_plate]
    partial_plate = Plate.find_from_barcode(fluidigm_plate.presence || plate_barcode)
    raise(Cherrypick::Error, "No plate with barcode #{plate_barcode}") if partial_plate.nil? && plate_barcode.present?

    # Ensure that we have a plate purpose for any plates we are creating
    plate_purpose = PlatePurpose.find(params[:plate_purpose_id])
    asset_shape_id = plate_purpose.asset_shape_id

    # Configure the cherrypicking action based on the parameters
    cherrypicker =
      case params[:cherrypick_action]
      when 'nano_grams_per_micro_litre'
        create_nano_grams_per_micro_litre_picker(params[:nano_grams_per_micro_litre])
      when 'nano_grams'
        create_nano_grams_picker(params[:nano_grams])
      when 'micro_litre'
        create_micro_litre_picker(params[:micro_litre])
      else
        raise StandardError, "Invalid cherrypicking type #{params[:cherrypick_action]}"
      end

    # We can preload the well locations so that we can do efficient lookup later.
    well_locations =
      Map
        .where_plate_size(partial_plate.try(:size) || size)
        .where_plate_shape(partial_plate.try(:asset_shape) || asset_shape_id)
        .in_row_major_order
        .index_by(&:description)

    # All of the requests we're going to be using should be part of the batch.  If they are not
    # then we have an error, so we can pre-map them for quick lookup.  We're going to pre-cache a
    # whole load of wells so that they can be retrieved quickly and easily.
    wells = Well.includes(:well_attribute).find(@batch.requests.map(&:target_asset_id)).index_by(&:id)
    request_and_well =
      @batch.requests.includes(:request_metadata).map { |r| [r.id.to_i, [r, wells[r.target_asset_id]]] }.to_h
    used_requests = []
    plates_and_wells = Hash.new { |h, k| h[k] = [] }
    plate_and_requests = Hash.new { |h, k| h[k] = [] }

    # If we overflow the plate we create a new one, even if we subsequently clear the fields.
    plates_with_samples = plates.reject { |_pid, rows| rows.values.map(&:values).flatten.all?(&:empty?) }

    if fluidigm_plate.present? && plates_with_samples.to_h.size > 1
      raise Cherrypick::Error, 'Sorry, You cannot pick to multiple fluidigm plates in one batch.'
    end

    plates_with_samples.each do |_id, plate_params|
      # The first time round this loop we'll either have a plate, from the partial_plate, or we'll
      # be needing to create a new one.
      plate = partial_plate
      if plate.nil?
        barcode_number = PlateBarcode.create.barcode
        barcode = { prefix: plate_purpose.prefix, number: barcode_number }
        plate =
          plate_purpose.create!(
            :do_not_create_wells,
            name: "Cherrypicked #{barcode_number}",
            size: size,
            sanger_barcode: barcode
          ) { |new_plate| new_plate.fluidigm_barcode = fluidigm_plate if fluidigm_plate.present? }
      end

      # Set the plate type, regardless of what it was.  This may change the standard plate.
      plate.plate_type = plate_type unless plate_type.nil?
      plate.save!

      plate_params.each do |row, row_params|
        row = row.to_i
        row_params.each do |col, request_id|
          next if request_id.blank?

          request, well =
            request_and_well[request_id.gsub('well_', '').to_i] ||
              raise(ActiveRecord::RecordNotFound, "Cannot find request #{request_id.inspect}")

          # NOTE: Performance enhancement here
          # This collects the wells together for the plate they should be on, and modifies
          # the values in the well data.  It *does not* save either of these, which means that
          # SELECT & INSERT/UPDATE are not interleaved, which affects the cache
          well.map = well_locations[plate.asset_shape.location_from_row_and_column(row, col.to_i + 1, plate.size)]
          cherrypicker.call(well, request)
          plates_and_wells[plate] << well
          plate_and_requests[plate] << request
          used_requests << request
        end
      end

      # At this point we can consider ourselves finished with the partial plate
      partial_plate = nil
    end

    # Attach the wells into their plate for maximum efficiency.
    plates_and_wells.each do |plate, plate_wells|
      plate_wells.each do |w|
        w.well_attribute.save!
        w.save!
      end
      plate.wells << plate_wells
    end

    links =
      plate_and_requests.flat_map do |target_plate, requests|
        Plate.with_requests(requests).map { |source_plate| [source_plate.id, target_plate.id] }
      end.uniq

    @batch.lab_events.create(
      description: 'Cherrypick Layout Set',
      message: 'Layout set',
      user_id: current_user.id,
      descriptors: {
        'robot_id' => params[:robot_id]
      }
    )

    AssetLink::BuilderJob.create(links)

    # Now pass each of the requests we used and ditch any there weren't back into the inbox.
    used_requests.map(&:pass!)
    (@batch.requests - used_requests).each(&:recycle_from_batch!)
  end

  # rubocop:enable Metrics/BlockLength
  [true, 'Layout set']
end

#render_cherrypick_task(_task, params) ⇒ Object

rubocop:todo Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/AbcSize


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# File 'app/models/tasks/cherrypick_handler.rb', line 11

def render_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexity
  if flash[:error].present?
    redirect_to action: 'stage', batch_id: @batch.id, workflow_id: @workflow.id, id: (@stage - 1).to_s
    return
  end

  plate_template = PlateTemplate.find(params[:plate_template]['0'].to_i) if params[:plate_template].present?
  if plate_template.nil?
    flash[:error] = 'Please select a template'
    redirect_to action: 'stage', batch_id: @batch.id, workflow_id: @workflow.id, id: (@stage - 1).to_s
    return
  end

  control_plate_id = params[:Control][:plate_id] if params[:Control]
  @control_plate = Plate.find(control_plate_id) if control_plate_id.present?

  setup_input_params_for_pass_through

  @batch = Batch.includes(:requests, :pipeline, :lab_events).find(params[:batch_id])
  @requests = @batch.ordered_requests

  @plate = nil
  @plate_barcode = params[:existing_plate]
  @fluidigm_plate = params[:fluidigm_plate]

  if @plate_barcode.present?
    @plate = Plate.find_from_barcode(@plate_barcode)
    if @plate.nil?
      flash[:error] = 'Invalid plate barcode'
      redirect_to action: 'stage', batch_id: @batch.id, workflow_id: @workflow.id, id: (@stage - 1).to_s
      return
    end
  elsif @fluidigm_plate.present?
    if @fluidigm_plate.size > 10
      flash[:error] = 'Invalid fluidigm barcode'
      redirect_to action: 'stage', batch_id: @batch.id, workflow_id: @workflow.id, id: (@stage - 1).to_s
      return
    end
    @plate = Plate.find_from_barcode(@fluidigm_barcode)
  end

  @plate_purpose = PlatePurpose.find(params[:plate_purpose_id])
  flash.now[:warning] = I18n.t('cherrypick.picking_by_row') if @plate_purpose.cherrypick_in_rows?

  @workflow = Workflow.includes(:tasks).find(params[:workflow_id])
  @map_info =
    if @spreadsheet_layout
      @spreadsheet_layout
    elsif @plate.present?
      @task.pick_onto_partial_plate(@requests, plate_template, @robot, @plate, @control_plate, self)
    else
      @task.pick_new_plate(@requests, plate_template, @robot, @plate_purpose, @control_plate, self)
    end
  @plates = @map_info[0]
  @source_plate_ids = @map_info[1]

  @plate_cols = @plate.try(:width) || @plate_purpose.plate_width
  @plate_rows = @plate.try(:height) || @plate_purpose.plate_height
end

#setup_input_params_for_pass_through ⇒ Object

rubocop:todo Metrics/MethodLength


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# File 'app/models/tasks/cherrypick_handler.rb', line 74

def setup_input_params_for_pass_through # rubocop:todo Metrics/AbcSize
  @robot_id = params[:robot_id]
  @robot = Robot.find(@robot_id)
  @plate_type = params[:plate_type]
  if params[:nano_grams_per_micro_litre]
    @nano_grams_per_micro_litre_volume_required = params[:nano_grams_per_micro_litre][:volume_required]
    @nano_grams_per_micro_litre_concentration_required = params[:nano_grams_per_micro_litre][:concentration_required]
    @nano_grams_per_micro_litre_robot_minimum_picking_volume =
      params[:nano_grams_per_micro_litre][:robot_minimum_picking_volume]
  end
  if params[:nano_grams]
    @nano_grams_minimum_volume = params[:nano_grams][:minimum_volume]
    @nano_grams_maximum_volume = params[:nano_grams][:maximum_volume]
    @nano_grams_total_nano_grams = params[:nano_grams][:total_nano_grams]
    @nano_grams_robot_minimum_picking_volume = params[:nano_grams][:robot_minimum_picking_volume]
  end
  @micro_litre_volume_required = params[:micro_litre][:volume_required] if params[:micro_litre]
  @cherrypick_action = params[:cherrypick][:action]
  @plate_purpose_id = params[:plate_purpose_id]
  @fluidigm_barcode = params[:fluidigm_plate]
end