Revert "Revert "DPL-960- Bioscan input plate state changes""

app/models/plate_purpose/input_started.rb

@@ -0,0 +1,36 @@
+# frozen_string_literal: true
+
+# Input Plate purposes are the initial stock plates passing into
+# external piplines. They have special behaviour governing their state.
+# This essentially makes sure that all non-empty wells on a plate have requests
+# out of them. This is intended to ensure that submissions have been
+# correctly built before a plate has processed.
+#
+# - Input plates are progressed when all sample containing wells have requests out of them
+#
+# This version of the input class sets the state as started rather than passed.
+class PlatePurpose::InputStarted < PlatePurpose::Input
+  self.state_changer = StateChanger::InputStartedPlate
+
+  UNREADY_STATE = 'pending'
+  PREP_STATE = 'started'
+  READY_STATE = 'passed'
+
+  private
+
+  # The state of the plate is determined by the state of the wells
+  # In this version we add an extra state PREP_STATE
+  def calculate_state_of_plate(wells_states)
+    unique_states = wells_states.uniq
+    return UNREADY_STATE if unique_states.include?(:unready)
+
+    case unique_states.sort
+    when ['failed'], %w[cancelled failed]
+      'failed'
+    when ['cancelled']
+      'cancelled'
+    else
+      unique_states.all?('pending') ? PREP_STATE : READY_STATE
+    end
+  end
+end

app/models/receptacle.rb

@@ -7,7 +7,7 @@
 class Receptacle < Asset # rubocop:todo Metrics/ClassLength
   include Uuid::Uuidable
   include Commentable
-  include Transfer::State
+  include Transfer::State::ReceptacleState
   include Aliquot::Remover
   include StudyReport::AssetDetails
   include Receptacle::DownstreamAliquotsRemoval::Mixin

app/models/state_changer/input_started_plate.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+module StateChanger
+  # This adds an additional started state to input plates, which is used
+  # by the input_started plate purpose.
+  class InputStartedPlate < InputPlate
+    # Target state of labware to state of associated requests.
+    # All other transitions will be ignored.
+    self.map_target_state_to_associated_request_state = { 'failed' => 'failed', 'passed' => 'started' }
+
+    private
+
+    def associated_requests
+      receptacles.flat_map(&:requests_as_source)
+    end
+
+    def _receptacles
+      labware.wells.includes(:requests_as_source)
+    end
+
+    def transfer_requests
+      # We don't want to update any transfer requests
+      []
+    end
+  end
+end

app/models/transfer/state.rb

@@ -30,6 +30,45 @@ def state_from(state_requests)
     ALL_STATES.detect { |s| unique_states.include?(s) } || default_state || 'unknown'
   end
 
+  # This transfer state is specific to receptacles
+  # Added so can specifically check the state on certain types of input plates
+  # and return a default state of passed to allow well failing.
+  module ReceptacleState
+    # We have to include this specifically because it does not implicitly include the
+    # methods from the Transfer::State module.
+    include Transfer::State
+
+    def default_state
+      # Well state was 'unknown' without this change for our input plate because input
+      # plates do not have any transfer requests.
+      # This check was added specifically for the Bioscan pipeline, where the users wish to be able to fail
+      # wells at this point in the pipeline, and we need wells to be in state 'passed' for well failing to
+      # be allowed.
+      return 'passed' if input_started_plate_with_aliquots?
+
+      nil
+    end
+
+    private
+
+    def input_started_plate_with_aliquots?
+      # Had to add labware and purpose checks here as many tests seem to fail otherwise, probably
+      # due to incomplete factory test data setup (e.g. Well with no Plate, Tube with no purpose)
+      # which should not happen in reality.
+      return false unless labware&.purpose
+
+      labware_of_input_started_type? && labware_in_valid_state? && aliquots.present?
+    end
+
+    def labware_of_input_started_type?
+      labware.purpose.type == 'PlatePurpose::InputStarted'
+    end
+
+    def labware_in_valid_state?
+      %w[started passed].include?(labware.state)
+    end
+  end
+
   # Plate specific behaviour
   module PlateState
     def self.included(base) # rubocop:todo Metrics/MethodLength

config/default_records/plate_purposes/009_bioscan_purposes.yml

@@ -9,7 +9,7 @@
 # This is the insects in ethanol plate for the start of the Lysate pipeline
 # It is the original source plate that has come in from the suppliers around the UK.
 LILYS-96 Stock:
-  type: PlatePurpose::Input
+  type: PlatePurpose::InputStarted
   stock_plate: true
   cherrypickable_target: false
 # This is the lysed material plate, ready for the Library prep pipeline. These plates