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
-
#do_cherrypick_task(_task, params) ⇒ Object
rubocop:todo Metrics/CyclomaticComplexity.
- #render_cherrypick_task(_task, params) ⇒ Object
- #setup_input_params_for_pass_through ⇒ Object
Class Method Details
.included(base) ⇒ Object
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# File 'app/models/tasks/cherrypick_handler.rb', line 6 def self.included(base) base.class_eval do include Cherrypick::Task::PickHelpers end end |
Instance Method Details
#do_cherrypick_task(_task, params) ⇒ Object
rubocop:todo Metrics/CyclomaticComplexity
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# File 'app/models/tasks/cherrypick_handler.rb', line 92 def do_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexity plates = params[:plate] size = params[:plate_size] plate_type = params[:plate_type] ActiveRecord::Base.transaction do # rubocop:todo Metrics/BlockLength # Determine if there is a standard plate to use. partial_plate = nil = params[:plate_barcode] fluidigm_plate = params[:fluidigm_plate] partial_plate = Plate.(fluidigm_plate.presence || ) raise(Cherrypick::Error, "No plate with barcode #{}") if partial_plate.nil? && .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' then create_nano_grams_per_micro_litre_picker(params[:nano_grams_per_micro_litre]) when 'nano_grams' then create_nano_grams_picker(params[:nano_grams]) when 'micro_litre' then 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 do |r| [r.id.to_i, [r, wells[r.target_asset_id]]] end.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? = PlateBarcode.create. = { prefix: plate_purpose.prefix, number: } plate = plate_purpose.create!(:do_not_create_wells, name: "Cherrypicked #{}", size: size, sanger_barcode: ) do |new_plate| new_plate. = fluidigm_plate if fluidigm_plate.present? end 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 do |source_plate| [source_plate.id, target_plate.id] end 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 end |
#render_cherrypick_task(_task, params) ⇒ Object
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# File 'app/models/tasks/cherrypick_handler.rb', line 12 def render_cherrypick_task(_task, params) 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.(@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.(@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
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# File 'app/models/tasks/cherrypick_handler.rb', line 71 def setup_input_params_for_pass_through @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 |