From 7f5b6b78712ca8a815b8400d64296e21773d80c5 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 12 Oct 2023 23:55:48 +0100
Subject: [PATCH 01/52] Added bed numbers to config

---
 config/robots.rb | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/config/robots.rb b/config/robots.rb
index 6d46be4b8..c63f66eeb 100644
--- a/config/robots.rb
+++ b/config/robots.rb
@@ -3061,4 +3061,27 @@
         }
       }
     )
+
+    # LRC Hamilton Star bed verification
+    # LRC PBMC Bank to LRC Bank Seq and LRC Bank Spare
+    custom_robot(
+      'hamilton-lrc-pbmc-bank-to-lrc-bank-seq-and-lrc-bank-spare',
+      name: 'Hamilton LRC PBMC Bank => LRC Bank Seq and LRC Bank Spare',
+      beds: {
+        bed(12).barcode => {
+          purpose: 'LRC PBMC Bank',
+          states: ['passed'],
+          label: 'Bed 12'
+        },
+        bed(15).barcode => {
+          purpose: 'LRC Bank Seq',
+          states: ['pending'],
+          label: 'Bed 15',
+        },
+        bed(14).barcode => {
+          purpose: 'LRC Bank Spare',
+          states: ['pending'],
+          label: 'Bed 14',
+        }
+      }
   end

From 6fb48d9409c6fa3ad9753fa12ac92e1ef2bfe4b9 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 12 Oct 2023 23:59:40 +0100
Subject: [PATCH 02/52] Fixed syntax in config

---
 config/robots.rb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/config/robots.rb b/config/robots.rb
index c63f66eeb..e24887680 100644
--- a/config/robots.rb
+++ b/config/robots.rb
@@ -3076,12 +3076,13 @@
         bed(15).barcode => {
           purpose: 'LRC Bank Seq',
           states: ['pending'],
-          label: 'Bed 15',
+          label: 'Bed 15'
         },
         bed(14).barcode => {
           purpose: 'LRC Bank Spare',
           states: ['pending'],
-          label: 'Bed 14',
+          label: 'Bed 14'
         }
       }
+    }
   end

From c739e896b1a2f0b26df9abad99ea6c00d81c41d0 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 13 Oct 2023 00:02:51 +0100
Subject: [PATCH 03/52] Fixed syntax in config 2

---
 config/robots.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/robots.rb b/config/robots.rb
index e24887680..b82f8b198 100644
--- a/config/robots.rb
+++ b/config/robots.rb
@@ -3084,5 +3084,5 @@
           label: 'Bed 14'
         }
       }
-    }
+    )
   end

From 220fcf2cc3026139e8c5b0b61bf8a8b4b4012ff8 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 16 Oct 2023 15:25:52 +0100
Subject: [PATCH 04/52] Removed the relationships section from plate to tube
 racks robot config

---
 config/robots.rb | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/config/robots.rb b/config/robots.rb
index b82f8b198..3b9ddac79 100644
--- a/config/robots.rb
+++ b/config/robots.rb
@@ -3076,12 +3076,16 @@
         bed(15).barcode => {
           purpose: 'LRC Bank Seq',
           states: ['pending'],
-          label: 'Bed 15'
+          label: 'Bed 15',
+          parent: bed(12).barcode,
+          target_state: 'passed'
         },
         bed(14).barcode => {
           purpose: 'LRC Bank Spare',
           states: ['pending'],
-          label: 'Bed 14'
+          label: 'Bed 14',
+          parent: bed(12).barcode,
+          target_state: 'passed'
         }
       }
     )

From 5ec11f913d516165e353df916feb95a56fc653e3 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Wed, 18 Oct 2023 17:39:54 +0100
Subject: [PATCH 05/52] Added relationships back as it allows specifying
 multiple children from parent

---
 config/robots.rb | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/config/robots.rb b/config/robots.rb
index 3b9ddac79..a67faeb7b 100644
--- a/config/robots.rb
+++ b/config/robots.rb
@@ -3077,16 +3077,24 @@
           purpose: 'LRC Bank Seq',
           states: ['pending'],
           label: 'Bed 15',
-          parent: bed(12).barcode,
           target_state: 'passed'
         },
         bed(14).barcode => {
           purpose: 'LRC Bank Spare',
           states: ['pending'],
           label: 'Bed 14',
-          parent: bed(12).barcode,
           target_state: 'passed'
         }
-      }
+      },
+      class: 'Robots::PlateToTubeRacksRobot',
+      relationships: [
+        {
+          'type' => 'LRC PBMBC Bank to LRC Bank Seq/Spare',
+          'options' => {
+            'parent' => bed(12).barcode,
+            'children' => [bed(15).barcode, bed(14).barcode]
+          }
+        }
+      ]
     )
   end

From 6c56bb39941aea28295275bc5efcead6fdf98c63 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Oct 2023 09:59:38 +0100
Subject: [PATCH 06/52] Fixed typo in robot config

---
 config/robots.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/robots.rb b/config/robots.rb
index a67faeb7b..8538acedb 100644
--- a/config/robots.rb
+++ b/config/robots.rb
@@ -3089,7 +3089,7 @@
       class: 'Robots::PlateToTubeRacksRobot',
       relationships: [
         {
-          'type' => 'LRC PBMBC Bank to LRC Bank Seq/Spare',
+          'type' => 'LRC PBMC Bank to LRC Bank Seq/Spare',
           'options' => {
             'parent' => bed(12).barcode,
             'children' => [bed(15).barcode, bed(14).barcode]

From 79faa2951d86b393f8cff07b86a609ced3137cf0 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Oct 2023 10:00:22 +0100
Subject: [PATCH 07/52] Adding tube rack wrapper to reuse existing validations

---
 .../robots/bed/plate_to_tube_racks_bed.rb     | 41 +++++++++++++++++++
 app/models/robots/bed/tube_rack_wrapper.rb    | 16 ++++++++
 .../robots/plate_to_tube_racks_robot.rb       | 36 ++++++++++++++++
 3 files changed, 93 insertions(+)
 create mode 100644 app/models/robots/bed/plate_to_tube_racks_bed.rb
 create mode 100644 app/models/robots/bed/tube_rack_wrapper.rb
 create mode 100644 app/models/robots/plate_to_tube_racks_robot.rb

diff --git a/app/models/robots/bed/plate_to_tube_racks_bed.rb b/app/models/robots/bed/plate_to_tube_racks_bed.rb
new file mode 100644
index 000000000..8cececd6b
--- /dev/null
+++ b/app/models/robots/bed/plate_to_tube_racks_bed.rb
@@ -0,0 +1,41 @@
+# frozen_string_literal: true
+
+module Robots::Bed
+  # Plate to tube racks robot beds
+  class PlateToTubeRacksBed < Robots::Bed::Base
+    # TODO: Do I need this accessor?
+    attr_accessor :parents
+
+    PLATE_INCLUDES = 'purpose,wells,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
+
+    def find_all_labware
+      Sequencescape::Api::V2::Plate.find_all({ barcode: @barcodes }, includes: PLATE_INCLUDES)
+    end
+
+    def load_labware_from_parents(parents)
+      return if labware.present?
+      @labware = parents.flat_map(&:child_labware).select { |labware| labware.barcode == barcode }
+    end
+
+    def child_labware
+      return [] if labware.nil?
+
+      @child_labware ||= child_labware_of_plate
+    end
+
+    def child_labware_of_plate
+      labware
+        .wells
+        .sort_by(&well_order)
+        .each_with_object([]) do |well, racks|
+          next if well.downstream_tubes.empty?
+
+          well.downstream_tubes.each do |tube|
+            barcode = tube.custom_metadatum_collection.metadata[:tube_rack_barcode]
+            rack = racks.detect { |rack| rack.barcode == barcode } || racks.push(TubeRackWrapper.new(barcode)).last
+            rack.tubes << tube
+          end
+        end
+    end
+  end
+end
diff --git a/app/models/robots/bed/tube_rack_wrapper.rb b/app/models/robots/bed/tube_rack_wrapper.rb
new file mode 100644
index 000000000..784c0426d
--- /dev/null
+++ b/app/models/robots/bed/tube_rack_wrapper.rb
@@ -0,0 +1,16 @@
+module Robots::Bed
+  # Tube rack info from tube metadata
+  class TubeRackWrapper
+    attr_accessor :barcode, :tubes
+    delegate :purpose_name, :state, :uuid, to: :first_tube, allow_nil: true
+
+    def initialize(barcode, tubes: [])
+      @barcode = barcode
+      @tubes = tubes
+    end
+
+    def first_tube
+      @tubes.first
+    end
+  end
+end
diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
new file mode 100644
index 000000000..58a2737c2
--- /dev/null
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -0,0 +1,36 @@
+# frozen_string_literal: true
+
+module Robots
+  class PlateToTubeRacksRobot < Robots::Robot
+    attr_writer :relationships
+
+    def bed_class
+      Robots::Bed::PlateToTubeRacksBed
+    end
+
+    def bed_labwares=(bed_labwares)
+      super
+      parents = beds.values.select { |bed| bed.labware && bed.child_labware }
+      beds.values.each { |bed| bed.load_labware_from_parents(parents) if bed.labware.blank? }
+    end
+
+    def valid_relationships # rubocop:todo Metrics/AbcSize
+      raise StandardError, "Relationships for #{name} are empty" if @relationships.empty?
+
+      @relationships.each_with_object({}) do |relationship, validations|
+        parent_bed = relationship.dig('options', 'parent')
+        child_beds = relationship.dig('options', 'children')
+
+        validations[parent_bed] = beds[parent_bed].child_labware.present?
+        error(beds[parent_bed], 'should not be empty.') if beds[parent_bed].empty?
+        error(beds[parent_bed], 'should have children.') if beds[parent_bed].child_labware.empty?
+
+        expected_children = beds[parent_bed].child_labware
+        expected_children.each_with_index do |expected_child, index|
+          child_bed = child_beds[index]
+          validations[child_bed] = check_labware_identity([expected_child], child_bed)
+        end
+      end
+    end
+  end
+end

From e10f3ba122292c69454b1e695e392716d5620625 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 22 Oct 2023 03:31:15 +0100
Subject: [PATCH 08/52] Fixed error message for created_with_robot metadata

---
 app/controllers/robots_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/controllers/robots_controller.rb b/app/controllers/robots_controller.rb
index bd716e6d8..c956f825b 100644
--- a/app/controllers/robots_controller.rb
+++ b/app/controllers/robots_controller.rb
@@ -34,7 +34,7 @@ def start # rubocop:todo Metrics/AbcSize
             .update!(created_with_robot: params[:robot_barcode])
         rescue Sequencescape::Api::ResourceNotFound
           respond_to do |format|
-            format.html { redirect_to robot_path(id: @robot.id), notice: "Plate #{plate_barcode} not found." }
+            format.html { redirect_to robot_path(id: @robot.id), notice: "Labware #{labware_barcode} not found." }
           end
         end
       end

From 5e0561b58d56c3574757cd012e819d28c07e2313 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 23 Oct 2023 10:21:01 +0100
Subject: [PATCH 09/52] Changes for bed verification with tube racks so far

---
 app/controllers/robots_controller.rb             | 10 +++++++---
 app/models/robots/bed/plate_to_tube_racks_bed.rb | 10 ++++++++--
 app/models/robots/bed/tube_rack_wrapper.rb       |  3 ++-
 app/models/robots/plate_to_tube_racks_robot.rb   |  6 ++++--
 4 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/app/controllers/robots_controller.rb b/app/controllers/robots_controller.rb
index c956f825b..cdfbef04e 100644
--- a/app/controllers/robots_controller.rb
+++ b/app/controllers/robots_controller.rb
@@ -29,9 +29,13 @@ def start # rubocop:todo Metrics/AbcSize
 
         labware_barcode = bed.labware.barcode.machine
         begin
-          LabwareMetadata
-            .new(api: api, user: current_user_uuid, barcode: labware_barcode)
-            .update!(created_with_robot: params[:robot_barcode])
+          if bed.respond_to?(:set_created_with_robot)
+            bed.set_created_with_robot(params[:robot_barcode])
+          else
+            LabwareMetadata
+              .new(api: api, user: current_user_uuid, barcode: labware_barcode)
+              .update!(created_with_robot: params[:robot_barcode])
+          end
         rescue Sequencescape::Api::ResourceNotFound
           respond_to do |format|
             format.html { redirect_to robot_path(id: @robot.id), notice: "Labware #{labware_barcode} not found." }
diff --git a/app/models/robots/bed/plate_to_tube_racks_bed.rb b/app/models/robots/bed/plate_to_tube_racks_bed.rb
index 8cececd6b..887b124e9 100644
--- a/app/models/robots/bed/plate_to_tube_racks_bed.rb
+++ b/app/models/robots/bed/plate_to_tube_racks_bed.rb
@@ -8,13 +8,15 @@ class PlateToTubeRacksBed < Robots::Bed::Base
 
     PLATE_INCLUDES = 'purpose,wells,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
 
+    def set_created_with_robot(robot_barcode); end
+
     def find_all_labware
       Sequencescape::Api::V2::Plate.find_all({ barcode: @barcodes }, includes: PLATE_INCLUDES)
     end
 
     def load_labware_from_parents(parents)
       return if labware.present?
-      @labware = parents.flat_map(&:child_labware).select { |labware| labware.barcode == barcode }
+      @labware = parents.flat_map(&:child_labware).select { |labware| labware.barcode.human == barcode }
     end
 
     def child_labware
@@ -32,7 +34,11 @@ def child_labware_of_plate
 
           well.downstream_tubes.each do |tube|
             barcode = tube.custom_metadatum_collection.metadata[:tube_rack_barcode]
-            rack = racks.detect { |rack| rack.barcode == barcode } || racks.push(TubeRackWrapper.new(barcode)).last
+            rack = racks.detect { |rack| rack.barcode.human == barcode }
+            if rack.nil?
+              labware_barcode = LabwareBarcode.new(human: barcode, machine: barcode)
+              rack = racks.push(TubeRackWrapper.new(labware_barcode)).last
+            end
             rack.tubes << tube
           end
         end
diff --git a/app/models/robots/bed/tube_rack_wrapper.rb b/app/models/robots/bed/tube_rack_wrapper.rb
index 784c0426d..34bd1b089 100644
--- a/app/models/robots/bed/tube_rack_wrapper.rb
+++ b/app/models/robots/bed/tube_rack_wrapper.rb
@@ -1,8 +1,9 @@
+# frozen_string_literal: true
 module Robots::Bed
   # Tube rack info from tube metadata
   class TubeRackWrapper
     attr_accessor :barcode, :tubes
-    delegate :purpose_name, :state, :uuid, to: :first_tube, allow_nil: true
+    delegate :purpose_name, :purpose, :human_barcode, :state, :uuid, to: :first_tube, allow_nil: true
 
     def initialize(barcode, tubes: [])
       @barcode = barcode
diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index 58a2737c2..d3f5a01e5 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -10,8 +10,10 @@ def bed_class
 
     def bed_labwares=(bed_labwares)
       super
-      parents = beds.values.select { |bed| bed.labware && bed.child_labware }
-      beds.values.each { |bed| bed.load_labware_from_parents(parents) if bed.labware.blank? }
+      parents = beds.values.select { |bed| bed.respond_to?(:labware) && bed.labware && bed.child_labware }
+      beds.each_value do |bed|
+        bed.load_labware_from_parents(parents) if bed.respond_to?(:labware) && bed.labware.blank?
+      end
     end
 
     def valid_relationships # rubocop:todo Metrics/AbcSize

From 918d0f2fa0b99d39059f9dc1451235ff4c11f684 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 26 Oct 2023 02:10:59 +0100
Subject: [PATCH 10/52] robot controller start action created_with_robot
 metadata

---
 app/controllers/robots_controller.rb          | 43 ++++++++++---------
 .../robots/{bed => }/tube_rack_wrapper.rb     |  0
 2 files changed, 23 insertions(+), 20 deletions(-)
 rename app/models/robots/{bed => }/tube_rack_wrapper.rb (100%)

diff --git a/app/controllers/robots_controller.rb b/app/controllers/robots_controller.rb
index cdfbef04e..f3ed8a2f3 100644
--- a/app/controllers/robots_controller.rb
+++ b/app/controllers/robots_controller.rb
@@ -23,26 +23,7 @@ def show
 
   def start # rubocop:todo Metrics/AbcSize
     @robot.perform_transfer(stripped_beds)
-    if params[:robot_barcode].present?
-      @robot.beds.each_value do |bed|
-        next unless bed.transitions? && bed.labware
-
-        labware_barcode = bed.labware.barcode.machine
-        begin
-          if bed.respond_to?(:set_created_with_robot)
-            bed.set_created_with_robot(params[:robot_barcode])
-          else
-            LabwareMetadata
-              .new(api: api, user: current_user_uuid, barcode: labware_barcode)
-              .update!(created_with_robot: params[:robot_barcode])
-          end
-        rescue Sequencescape::Api::ResourceNotFound
-          respond_to do |format|
-            format.html { redirect_to robot_path(id: @robot.id), notice: "Labware #{labware_barcode} not found." }
-          end
-        end
-      end
-    end
+    update_labware_metadata(params[:robot_barcode]) if params[:robot_barcode].present?
     respond_to { |format| format.html { redirect_to search_path, notice: "Robot #{@robot.name} has been started." } }
   rescue Robots::Bed::BedError => e
     # Our beds complained, nothing has happened.
@@ -51,6 +32,28 @@ def start # rubocop:todo Metrics/AbcSize
     end
   end
 
+  def update_labware_metadata(robot_barcode)
+    @robot.beds.each_value do |bed|
+      next unless bed.transitions? && bed.labware
+      labware_barcode = bed.labware.barcode.machine
+      if bed.respond_to?(:labware_created_with_robot)
+        bed.labware_created_with_robot(robot_barcode)
+      else
+        labware_created_with_robot(labware_barcode, robot_barcode)
+      end
+    rescue Sequencescape::Api::ResourceNotFound
+      respond_to do |format|
+        format.html { redirect_to robot_path(id: @robot.id), notice: "Labware #{labware_barcode} not found." }
+      end
+    end
+  end
+
+  def labware_created_with_robot(labware_barcode, robot_barcode)
+    LabwareMetadata
+      .new(api: api, user: current_user_uuid, barcode: labware_barcode)
+      .update!(created_with_robot: robot_barcode)
+  end
+
   def verify
     render(json: @robot.verify(robot_params))
   end
diff --git a/app/models/robots/bed/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
similarity index 100%
rename from app/models/robots/bed/tube_rack_wrapper.rb
rename to app/models/robots/tube_rack_wrapper.rb

From 775799d73bdd3356191b2a24216898f1da9debf2 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 26 Oct 2023 02:12:42 +0100
Subject: [PATCH 11/52] Robot finds labware for beds

---
 .../robots/bed/plate_to_tube_racks_bed.rb     | 41 +++++--------------
 1 file changed, 11 insertions(+), 30 deletions(-)

diff --git a/app/models/robots/bed/plate_to_tube_racks_bed.rb b/app/models/robots/bed/plate_to_tube_racks_bed.rb
index 887b124e9..3fddd151b 100644
--- a/app/models/robots/bed/plate_to_tube_racks_bed.rb
+++ b/app/models/robots/bed/plate_to_tube_racks_bed.rb
@@ -6,42 +6,23 @@ class PlateToTubeRacksBed < Robots::Bed::Base
     # TODO: Do I need this accessor?
     attr_accessor :parents
 
-    PLATE_INCLUDES = 'purpose,wells,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
-
-    def set_created_with_robot(robot_barcode); end
-
-    def find_all_labware
-      Sequencescape::Api::V2::Plate.find_all({ barcode: @barcodes }, includes: PLATE_INCLUDES)
-    end
-
-    def load_labware_from_parents(parents)
-      return if labware.present?
-      @labware = parents.flat_map(&:child_labware).select { |labware| labware.barcode.human == barcode }
+    def labware_created_with_robot(robot_barcode)
+      labware.tubes.each do |tube|
+        LabwareMetadata
+          .new(api: api, user: user_uuid, barcode: tube.barcode.machine)
+          .update!(created_with_robot: robot_barcode)
+      end
     end
 
     def child_labware
-      return [] if labware.nil?
+      return [] if labware.blank?
 
-      @child_labware ||= child_labware_of_plate
+      @child_labware ||= robot.child_labware(labware)
     end
 
-    def child_labware_of_plate
-      labware
-        .wells
-        .sort_by(&well_order)
-        .each_with_object([]) do |well, racks|
-          next if well.downstream_tubes.empty?
-
-          well.downstream_tubes.each do |tube|
-            barcode = tube.custom_metadatum_collection.metadata[:tube_rack_barcode]
-            rack = racks.detect { |rack| rack.barcode.human == barcode }
-            if rack.nil?
-              labware_barcode = LabwareBarcode.new(human: barcode, machine: barcode)
-              rack = racks.push(TubeRackWrapper.new(labware_barcode)).last
-            end
-            rack.tubes << tube
-          end
-        end
+    def load(barcodes)
+      @barcodes = Array(barcodes).filter_map(&:strip).uniq
+      @labware = @barcodes.present? ? robot.find_bed_labware(@barcodes) : []
     end
   end
 end

From cdf9d09049ce7d6a45cfded63996c2740859f2b5 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 26 Oct 2023 02:14:00 +0100
Subject: [PATCH 12/52] Initialise labware store in robot and find labware for
 beds

---
 .../robots/plate_to_tube_racks_robot.rb       | 70 +++++++++++++++++--
 1 file changed, 65 insertions(+), 5 deletions(-)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index d3f5a01e5..a279c53ad 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -4,16 +4,20 @@ module Robots
   class PlateToTubeRacksRobot < Robots::Robot
     attr_writer :relationships
 
+    PLATE_INCLUDES = 'purpose,wells,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
+
     def bed_class
       Robots::Bed::PlateToTubeRacksBed
     end
 
-    def bed_labwares=(bed_labwares)
+    def perform_transfer(bed_settings)
+      init_labware_store(bed_settings)
+      super
+    end
+
+    def verify(params)
+      init_labware_store(params[:bed_labwares])
       super
-      parents = beds.values.select { |bed| bed.respond_to?(:labware) && bed.labware && bed.child_labware }
-      beds.each_value do |bed|
-        bed.load_labware_from_parents(parents) if bed.respond_to?(:labware) && bed.labware.blank?
-      end
     end
 
     def valid_relationships # rubocop:todo Metrics/AbcSize
@@ -34,5 +38,61 @@ def valid_relationships # rubocop:todo Metrics/AbcSize
         end
       end
     end
+
+    def find_bed_labware(barcodes)
+      barcodes.filter_map { |barcode| labware_store[barcode] }
+    end
+
+    def child_labware(plate)
+      labware_store.values.select { |labware| labware.respond_to?(:parent) && labware.parent.uuid == plate.uuid }
+    end
+
+    def init_labware_store(bed_labwares)
+      return if labware_store.present?
+      stripped_barcodes(bed_labwares).each do |barcode|
+        plate = find_plate(barcode)
+        next if plate.blank?
+        add_plate_to_labware_store(plate)
+        add_tube_racks_to_labware_store(plate)
+      end
+    end
+
+    def stripped_barcodes(bed_labwares)
+      bed_labwares.values.flatten.filter_map(&:strip).uniq
+    end
+
+    def add_plate_to_labware_store(plate)
+      labware_store[plate.barcode.machine] = plate
+    end
+
+    def add_tube_racks_to_labware_store(plate)
+      find_tube_racks(plate).each { |rack| labware_store[rack.barcode.machine] = rack }
+    end
+
+    def labware_store
+      @labware_store ||= {}
+    end
+
+    def find_plate(barcode)
+      Sequencescape::Api::V2::Plate.find_all({ barcode: barcode }, includes: PLATE_INCLUDES).first
+    end
+
+    def find_tube_racks(plate)
+      plate
+        .wells
+        .sort_by(&well_order)
+        .each_with_object([]) do |well, racks|
+          next if well.downstream_tubes.empty?
+          well.downstream_tubes.each do |tube|
+            barcode = tube.custom_metadatum_collection.metadata[:tube_rack_barcode]
+            rack = racks.detect { |tube_rack| tube_rack.barcode.machine == barcode }
+            if rack.nil?
+              labware_barcode = LabwareBarcode.new(human: barcode, machine: barcode)
+              rack = racks.push(TubeRackWrapper.new(labware_barcode, plate)).last
+            end
+            rack.tubes << tube
+          end
+        end
+    end
   end
 end

From d96124d97759feeffa18028e5c1aa2d16b0082bb Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 26 Oct 2023 02:14:42 +0100
Subject: [PATCH 13/52] Added parent field to tube rack wrapper

---
 app/models/robots/tube_rack_wrapper.rb | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index 34bd1b089..165a4a3b5 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -1,12 +1,13 @@
 # frozen_string_literal: true
-module Robots::Bed
+module Robots
   # Tube rack info from tube metadata
   class TubeRackWrapper
-    attr_accessor :barcode, :tubes
+    attr_accessor :barcode, :parent, :tubes
     delegate :purpose_name, :purpose, :human_barcode, :state, :uuid, to: :first_tube, allow_nil: true
 
-    def initialize(barcode, tubes: [])
+    def initialize(barcode, parent, tubes: [])
       @barcode = barcode
+      @parent = parent
       @tubes = tubes
     end
 

From b9e55a1c91d60e3daa59ec56680444d4024acbb0 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 26 Oct 2023 18:26:12 +0100
Subject: [PATCH 14/52] Added code comments to plate to tube racks robot

---
 .../robots/plate_to_tube_racks_robot.rb       | 118 ++++++++++++++++--
 1 file changed, 110 insertions(+), 8 deletions(-)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index a279c53ad..d3301b7bd 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -1,20 +1,58 @@
 # frozen_string_literal: true
 
 module Robots
+  # This plate to tube racks robot takes one parent plate, and transfers it to
+  # its child tubes that are on multiple tube racks. The tube racks handled by
+  # this robot are not actual recorded labware. Their barcodes are extracted
+  # from the metadata of the tubes and they are accessed using wrapper objects.
+  # When robot controller calls the robot's verify or perform_transfer actions,
+  # the robot will first initialize its labware store with the plate and tube
+  # rack objects. The plate information comes from the Sequencescape API call,
+  # however the tube rack information comes from the metadata of the downstream
+  # tubes included in the same API response. Therefore, the bed verification of
+  # the tube racks depend on the verification of the plate.
+  #
+  # The destination tubes racks are distinguished by their barcodes. We assume
+  # that the tubes on the same tube rack have the same labware purpose. We also
+  # assume that there cannot be two tube racks with the tubes of the same
+  # labware purpose. For bed verification, only the etched barcode of the tube
+  # racks are scanned, not the individual tubes. The number of tube racks to be
+  # verified not only depends on the robot's configured relationships but also
+  # whether the plate has children with those purposes.
+  #
   class PlateToTubeRacksRobot < Robots::Robot
-    attr_writer :relationships
+    attr_writer :relationships # Hash from robot config into @relationships
 
+    # Option for including downstream tubes and metadata in Plate API response.
     PLATE_INCLUDES = 'purpose,wells,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
 
+    # Returns the bed class for this robot.
+    #
+    # @return [Class] the bed class
     def bed_class
       Robots::Bed::PlateToTubeRacksBed
     end
 
+    # Performs the transfer between plate and tube racks. This method is called
+    # by the robot controller when the user clicks the start robot button. The
+    # method first initializes the labware store with the plate and tube racks.
+    #
+    # @param [Hash] bed_settings bed_labwares hash from request parameters
+    # @return [void]
+    #
     def perform_transfer(bed_settings)
       init_labware_store(bed_settings)
       super
     end
 
+    # Performs the bed verification of plate and tube racks. This method is
+    # called by the robot controller when the user clicks the validate layout
+    # button.  The method first initializes the labware store with the plate
+    # and tube racks.
+    #
+    # @param [Hash] params request parameters
+    # @return [void]
+    #
     def verify(params)
       init_labware_store(params[:bed_labwares])
       super
@@ -39,14 +77,34 @@ def valid_relationships # rubocop:todo Metrics/AbcSize
       end
     end
 
+    # Returns an array of labware from the robot's labware store for barcodes.
+    # This method is called by the robot's beds when they need to find their
+    # labware. The labware returned can be Plate objects or labware-like
+    # wrapper objects for tube racks.
+    #
+    # @param [Array<String>] barcodes array of barcodes
+    # @return [Array<Plate, TubeRackWrapper>]
+    #
     def find_bed_labware(barcodes)
       barcodes.filter_map { |barcode| labware_store[barcode] }
     end
 
+    # Returns an array of child labware from the robot's labware store for
+    # the given Plate.
+    #
+    # @param [Plate] plate the parent plate
+    # @return [Array<TubeRackWrapper>] array of tube rack wrapper objects
+    #
     def child_labware(plate)
       labware_store.values.select { |labware| labware.respond_to?(:parent) && labware.parent.uuid == plate.uuid }
     end
 
+    # Prepares the labware store before handling robot actions. This method is
+    # called before the robot's bed verification and perform transfer actions.
+    #
+    # @param [Hash] bed_labwares hash from request parameters
+    # @return [void]
+    #
     def init_labware_store(bed_labwares)
       return if labware_store.present?
       stripped_barcodes(bed_labwares).each do |barcode|
@@ -57,42 +115,86 @@ def init_labware_store(bed_labwares)
       end
     end
 
+    # Returns an array of sanitised barcodes from the bed_labwares hash from
+    # request parameters.
+    #
+    # @param [Hash] bed_labwares hash from request parameters
+    # @return [Array<String>] array of barcodes
+    #
     def stripped_barcodes(bed_labwares)
       bed_labwares.values.flatten.filter_map(&:strip).uniq
     end
 
+    # Adds the plate to the robot's labware store.
+    #
+    # @param [Plate] plate the parent plate
+    # @return [void]
+    #
     def add_plate_to_labware_store(plate)
       labware_store[plate.barcode.machine] = plate
     end
 
+    # Adds the tube racks wrappers from plate includes to the labware store.
+    #
+    # @param [Plate] plate the parent plate
+    # @return [void]
+    #
     def add_tube_racks_to_labware_store(plate)
       find_tube_racks(plate).each { |rack| labware_store[rack.barcode.machine] = rack }
     end
 
+    # Returns the labware store. The hash is indexed by the labware barcode.
+    # The values are either Plate objects or labware-like wrapper objects for
+    # tube racks.
+    #
+    # @return [Hash<String, Labware>] the labware store
+    #
     def labware_store
       @labware_store ||= {}
     end
 
+    # Returns the Plate for the given barcode from the Sequencescape API.
+    # The call includes downstream tubes and their metadata as well.
+    #
+    # @param [String] barcode the barcode of the plate
+    # @return [Plate] the plate
+    #
     def find_plate(barcode)
       Sequencescape::Api::V2::Plate.find_all({ barcode: barcode }, includes: PLATE_INCLUDES).first
     end
 
+    # Returns an array of tube rack wrapper objects that from the downstream tubes
+    # of the given plate.
+    #
+    # @param [Plate] plate the parent plate
+    # @return [Array<TubeRackWrapper>] array of tube rack wrapper objects
+    #
     def find_tube_racks(plate)
       plate
         .wells
         .sort_by(&well_order)
         .each_with_object([]) do |well, racks|
-          next if well.downstream_tubes.empty?
+          next if well.downstream_tubes.blank?
           well.downstream_tubes.each do |tube|
             barcode = tube.custom_metadatum_collection.metadata[:tube_rack_barcode]
-            rack = racks.detect { |tube_rack| tube_rack.barcode.machine == barcode }
-            if rack.nil?
-              labware_barcode = LabwareBarcode.new(human: barcode, machine: barcode)
-              rack = racks.push(TubeRackWrapper.new(labware_barcode, plate)).last
-            end
-            rack.tubes << tube
+            find_or_create_tube_rack(racks, barcode, plate).tubes.push(tube)
           end
         end
     end
+
+    # Returns an existing or new tube rack wrapper object.
+    #
+    # @param [Array<TubeRackWrapper>] racks the tube racks found so far
+    # @param [String] barcode the barcode of the tube rack
+    # @param [Plate] plate the parent plate
+    #
+    # @return [TubeRackWrapper] the tube rack wrapper object
+    #
+    def find_or_create_tube_rack(racks, barcode, plate)
+      rack = racks.detect { |tube_rack| tube_rack.barcode.machine == barcode }
+      return rack if rack.present?
+      labware_barcode = LabwareBarcode.new(human: barcode, machine: barcode)
+      racks.push(TubeRackWrapper.new(labware_barcode, plate)).last
+    end
   end
 end

From 83b0ca2db42eb6c5f3cd7f459c16a095276a0ddc Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 26 Oct 2023 20:26:50 +0100
Subject: [PATCH 15/52] Removed parents attr_accessor from bed

---
 .../robots/bed/plate_to_tube_racks_bed.rb     | 24 +++++++++++++++----
 .../robots/plate_to_tube_racks_robot.rb       | 13 ++++++----
 app/models/robots/tube_rack_wrapper.rb        | 15 +++++++++++-
 3 files changed, 42 insertions(+), 10 deletions(-)

diff --git a/app/models/robots/bed/plate_to_tube_racks_bed.rb b/app/models/robots/bed/plate_to_tube_racks_bed.rb
index 3fddd151b..89c0881c7 100644
--- a/app/models/robots/bed/plate_to_tube_racks_bed.rb
+++ b/app/models/robots/bed/plate_to_tube_racks_bed.rb
@@ -1,11 +1,18 @@
 # frozen_string_literal: true
 
 module Robots::Bed
-  # Plate to tube racks robot beds
+  # This bed hosts the parent plate or a tube-rack. It uses the robot to find
+  # its labware and child labware. When it is used the source bed, it should
+  # host the Plate. When it is used as a destination bed, it should host a
+  # tube-rack wrapper.
   class PlateToTubeRacksBed < Robots::Bed::Base
-    # TODO: Do I need this accessor?
-    attr_accessor :parents
-
+    # Updates the metadata of the labware with the robot barcode.
+    # This method is called inside the robot controller's start action for
+    # tube-rack wrappers and it sets the created_with_robot metadata field.
+    #
+    # @param [String] robot_barcode the robot barcode
+    # @return [void]
+    #
     def labware_created_with_robot(robot_barcode)
       labware.tubes.each do |tube|
         LabwareMetadata
@@ -14,12 +21,21 @@ def labware_created_with_robot(robot_barcode)
       end
     end
 
+    # Returns an array of labware from the robot's labware store for barcodes.
+    #
+    # @return [Array<TubeRackWrapper>] child tube-rack wrappers
+    #
     def child_labware
       return [] if labware.blank?
 
       @child_labware ||= robot.child_labware(labware)
     end
 
+    # Loads labware into this bed.
+    #
+    # @param [Array<String>] barcodes array containing the barcode of the labware
+    # @return [void]
+    #
     def load(barcodes)
       @barcodes = Array(barcodes).filter_map(&:strip).uniq
       @labware = @barcodes.present? ? robot.find_bed_labware(@barcodes) : []
diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index d3301b7bd..12121ba12 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -12,13 +12,14 @@ module Robots
   # tubes included in the same API response. Therefore, the bed verification of
   # the tube racks depend on the verification of the plate.
   #
-  # The destination tubes racks are distinguished by their barcodes. We assume
+  # The destination tube racks are distinguished by their barcodes. We assume
   # that the tubes on the same tube rack have the same labware purpose. We also
   # assume that there cannot be two tube racks with the tubes of the same
-  # labware purpose. For bed verification, only the etched barcode of the tube
-  # racks are scanned, not the individual tubes. The number of tube racks to be
-  # verified not only depends on the robot's configured relationships but also
-  # whether the plate has children with those purposes.
+  # labware purpose on the robot at the same time. For bed verification, only
+  # the etched barcode of the tube racks are scanned, not the individual tubes.
+  # The number of tube racks to be verified not only depends on the robot's
+  # configured relationships but also whether the plate has children with those
+  # purposes.
   #
   class PlateToTubeRacksRobot < Robots::Robot
     attr_writer :relationships # Hash from robot config into @relationships
@@ -115,6 +116,8 @@ def init_labware_store(bed_labwares)
       end
     end
 
+    private
+
     # Returns an array of sanitised barcodes from the bed_labwares hash from
     # request parameters.
     #
diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index 165a4a3b5..ed14a71a1 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -1,16 +1,29 @@
 # frozen_string_literal: true
 module Robots
-  # Tube rack info from tube metadata
+  # This wrapper class is for tube racks that are not actual recorded labware.
+  # The instances acts as a labware wrapper and provides access to the tubes.
+  # Labware methods are delegated to the first tube on the tube rack.
+  #
   class TubeRackWrapper
     attr_accessor :barcode, :parent, :tubes
     delegate :purpose_name, :purpose, :human_barcode, :state, :uuid, to: :first_tube, allow_nil: true
 
+    # Initializes a new instance of the class.
+    #
+    # @param [LabwareBarcode] barcode the barcode object of the tube rack
+    # @param [Plate] parent the parent plate
+    # @tubes [Array<Tube>] the tubes on the tube rack
+    #
     def initialize(barcode, parent, tubes: [])
       @barcode = barcode
       @parent = parent
       @tubes = tubes
     end
 
+    # Returns the first tube on the tube rack. This method used for delegating
+    # certain methods to make it behave like a like a labware object.
+    #
+    # @return [Tube] the first tube
     def first_tube
       @tubes.first
     end

From ddd94e49d4dc8f32cbc9f5eb8381f5c17049d4dd Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 26 Oct 2023 20:30:54 +0100
Subject: [PATCH 16/52] Updated bed code comments

---
 app/models/robots/bed/plate_to_tube_racks_bed.rb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/app/models/robots/bed/plate_to_tube_racks_bed.rb b/app/models/robots/bed/plate_to_tube_racks_bed.rb
index 89c0881c7..1c22fca72 100644
--- a/app/models/robots/bed/plate_to_tube_racks_bed.rb
+++ b/app/models/robots/bed/plate_to_tube_racks_bed.rb
@@ -2,9 +2,10 @@
 
 module Robots::Bed
   # This bed hosts the parent plate or a tube-rack. It uses the robot to find
-  # its labware and child labware. When it is used the source bed, it should
+  # its labware and child labware. When it is used as a source bed, it should
   # host the Plate. When it is used as a destination bed, it should host a
   # tube-rack wrapper.
+  #
   class PlateToTubeRacksBed < Robots::Bed::Base
     # Updates the metadata of the labware with the robot barcode.
     # This method is called inside the robot controller's start action for
@@ -31,7 +32,7 @@ def child_labware
       @child_labware ||= robot.child_labware(labware)
     end
 
-    # Loads labware into this bed.
+    # Loads labware into this bed from the robot's labware store.
     #
     # @param [Array<String>] barcodes array containing the barcode of the labware
     # @return [void]

From 3d7b17228ab72eecaa211cdde6c8db0dc58006bd Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 27 Oct 2023 20:14:17 +0100
Subject: [PATCH 17/52] Comment about using machine barcode for setting
 robot_barcode in metadata

---
 app/models/robots/bed/plate_to_tube_racks_bed.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/models/robots/bed/plate_to_tube_racks_bed.rb b/app/models/robots/bed/plate_to_tube_racks_bed.rb
index 1c22fca72..2a12dd16b 100644
--- a/app/models/robots/bed/plate_to_tube_racks_bed.rb
+++ b/app/models/robots/bed/plate_to_tube_racks_bed.rb
@@ -15,6 +15,7 @@ class PlateToTubeRacksBed < Robots::Bed::Base
     # @return [void]
     #
     def labware_created_with_robot(robot_barcode)
+      # RobotController uses machine barcode for initialising LabwareMetadata
       labware.tubes.each do |tube|
         LabwareMetadata
           .new(api: api, user: user_uuid, barcode: tube.barcode.machine)

From 1c5bdc64def249671890b85d2d77bb37a5a40d93 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 27 Oct 2023 20:15:23 +0100
Subject: [PATCH 18/52] Switched to human barcode for indexing

---
 app/models/robots/plate_to_tube_racks_robot.rb | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index 12121ba12..339e3e05e 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -52,14 +52,14 @@ def perform_transfer(bed_settings)
     # and tube racks.
     #
     # @param [Hash] params request parameters
-    # @return [void]
+    # @return [Report]
     #
     def verify(params)
       init_labware_store(params[:bed_labwares])
       super
     end
 
-    def valid_relationships # rubocop:todo Metrics/AbcSize
+    def valid_relationships
       raise StandardError, "Relationships for #{name} are empty" if @relationships.empty?
 
       @relationships.each_with_object({}) do |relationship, validations|
@@ -134,7 +134,7 @@ def stripped_barcodes(bed_labwares)
     # @return [void]
     #
     def add_plate_to_labware_store(plate)
-      labware_store[plate.barcode.machine] = plate
+      labware_store[plate.barcode.human] = plate
     end
 
     # Adds the tube racks wrappers from plate includes to the labware store.
@@ -143,7 +143,7 @@ def add_plate_to_labware_store(plate)
     # @return [void]
     #
     def add_tube_racks_to_labware_store(plate)
-      find_tube_racks(plate).each { |rack| labware_store[rack.barcode.machine] = rack }
+      find_tube_racks(plate).each { |rack| labware_store[rack.barcode.human] = rack }
     end
 
     # Returns the labware store. The hash is indexed by the labware barcode.
@@ -163,7 +163,7 @@ def labware_store
     # @return [Plate] the plate
     #
     def find_plate(barcode)
-      Sequencescape::Api::V2::Plate.find_all({ barcode: barcode }, includes: PLATE_INCLUDES).first
+      Sequencescape::Api::V2::Plate.find_all({ barcode: [barcode] }, includes: PLATE_INCLUDES).first
     end
 
     # Returns an array of tube rack wrapper objects that from the downstream tubes
@@ -194,7 +194,7 @@ def find_tube_racks(plate)
     # @return [TubeRackWrapper] the tube rack wrapper object
     #
     def find_or_create_tube_rack(racks, barcode, plate)
-      rack = racks.detect { |tube_rack| tube_rack.barcode.machine == barcode }
+      rack = racks.detect { |tube_rack| tube_rack.barcode.human == barcode }
       return rack if rack.present?
       labware_barcode = LabwareBarcode.new(human: barcode, machine: barcode)
       racks.push(TubeRackWrapper.new(labware_barcode, plate)).last

From fa6e2cbcdad8f375743c856eedc703d847337f87 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 27 Oct 2023 20:16:33 +0100
Subject: [PATCH 19/52] Delegate tube-rack wrapper attributes to the last tube

---
 app/models/robots/tube_rack_wrapper.rb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index ed14a71a1..9c21f83eb 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -6,7 +6,7 @@ module Robots
   #
   class TubeRackWrapper
     attr_accessor :barcode, :parent, :tubes
-    delegate :purpose_name, :purpose, :human_barcode, :state, :uuid, to: :first_tube, allow_nil: true
+    delegate :purpose_name, :purpose, :human_barcode, :state, :uuid, to: :last_tube, allow_nil: true
 
     # Initializes a new instance of the class.
     #
@@ -20,12 +20,12 @@ def initialize(barcode, parent, tubes: [])
       @tubes = tubes
     end
 
-    # Returns the first tube on the tube rack. This method used for delegating
+    # Returns the last tube on the tube rack. This method used for delegating
     # certain methods to make it behave like a like a labware object.
     #
-    # @return [Tube] the first tube
-    def first_tube
-      @tubes.first
+    # @return [Tube] the last tube
+    def last_tube
+      @tubes.last
     end
   end
 end

From d985cdb8c1875e125a280242336577d908b01c84 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 27 Oct 2023 20:17:28 +0100
Subject: [PATCH 20/52] Added test for a valid scanned layout

---
 .../robots/plate_to_tube_racks_robot_spec.rb  | 220 ++++++++++++++++++
 1 file changed, 220 insertions(+)
 create mode 100644 spec/models/robots/plate_to_tube_racks_robot_spec.rb

diff --git a/spec/models/robots/plate_to_tube_racks_robot_spec.rb b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
new file mode 100644
index 000000000..3c3ba767c
--- /dev/null
+++ b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
@@ -0,0 +1,220 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+RSpec.describe Robots::PlateToTubeRacksRobot, robot: true do
+  include FeatureHelpers # Include methods for stubbing Sequencescape API requests.
+  include RobotHelpers # Include methods for stubbing bed labware lookups.
+  has_a_working_api # Add a mock Sequencescape API to the test context.
+
+  describe '#verify' do
+    # The robot will receive the scanned layout as bed_labwares from request parameters
+    # and return a report object showing the validity of each bed and robot.
+    subject { robot.verify(bed_labwares: scanned_layout) }
+
+    # user_uuid
+    let(:user_uuid) { 'user_uuid' }
+
+    # tube rack barcodes
+    let(:tube_rack1_barcode) { 'TR00000001' }
+    let(:tube_rack2_barcode) { 'TR00000002' }
+
+    # tube metadata
+    let(:tube1_metadata) { { 'tube_rack_barcode' => tube_rack1_barcode, 'tube_rack_position' => 'A1' } }
+    let(:tube2_metadata) { { 'tube_rack_barcode' => tube_rack1_barcode, 'tube_rack_position' => 'B1' } }
+    let(:tube3_metadata) { { 'tube_rack_barcode' => tube_rack1_barcode, 'tube_rack_position' => 'C1' } }
+    let(:tube4_metadata) { { 'tube_rack_barcode' => tube_rack2_barcode, 'tube_rack_position' => 'A1' } }
+    let(:tube5_metadata) { { 'tube_rack_barcode' => tube_rack2_barcode, 'tube_rack_position' => 'B1' } }
+    let(:tube6_metadata) { { 'tube_rack_barcode' => tube_rack2_barcode, 'tube_rack_position' => 'C1' } }
+
+    # tube custom metadata collections
+    let(:tube1_custom_metadata) { create(:custom_metadatum_collection, metadata: tube1_metadata) }
+    let(:tube2_custom_metadata) { create(:custom_metadatum_collection, metadata: tube2_metadata) }
+    let(:tube3_custom_metadata) { create(:custom_metadatum_collection, metadata: tube3_metadata) }
+    let(:tube4_custom_metadata) { create(:custom_metadatum_collection, metadata: tube4_metadata) }
+    let(:tube5_custom_metadata) { create(:custom_metadatum_collection, metadata: tube5_metadata) }
+    let(:tube6_custom_metadata) { create(:custom_metadatum_collection, metadata: tube6_metadata) }
+
+    # tube uuids
+    let(:tube1_uuid) { 'tube1_uuid' }
+    let(:tube2_uuid) { 'tube2_uuid' }
+    let(:tube3_uuid) { 'tube3_uuid' }
+    let(:tube4_uuid) { 'tube4_uuid' }
+    let(:tube5_uuid) { 'tube5_uuid' }
+    let(:tube6_uuid) { 'tube6_uuid' }
+
+    # tube purpose uuids
+    let(:tube_purpose1_uuid) { 'tube_purpose1_uuid' }
+    let(:tube_purpose2_uuid) { 'tube_purpose2_uuid' }
+
+    # tube purpose names
+    let(:tube_purpose1_name) { 'tube_purpose1_name' }
+    let(:tube_purpose2_name) { 'tube_purpose2_name' }
+
+    # tube purposes
+    let(:tube_purpose1) { create(:v2_purpose, name: tube_purpose1_name, uuid: tube_purpose1_uuid) }
+    let(:tube_purpose2) { create(:v2_purpose, name: tube_purpose2_name, uuid: tube_purpose2_uuid) }
+
+    # tube states
+    let(:tube1_state) { 'pending' }
+    let(:tube2_state) { 'pending' }
+    let(:tube3_state) { 'pending' }
+    let(:tube4_state) { 'pending' }
+    let(:tube5_state) { 'pending' }
+    let(:tube6_state) { 'pending' }
+
+    # tubes
+    let(:tube1) do
+      create(
+        :v2_tube_with_metadata,
+        uuid: tube1_uuid,
+        barcode_prefix: 'FX',
+        barcode_number: 4,
+        custom_metadatum_collection: tube1_custom_metadata,
+        purpose: tube_purpose1,
+        state: tube1_state
+      )
+    end
+    let(:tube2) do
+      create(
+        :v2_tube_with_metadata,
+        uuid: tube2_uuid,
+        barcode_prefix: 'FX',
+        barcode_number: 5,
+        custom_metadatum_collection: tube2_custom_metadata,
+        purpose: tube_purpose1,
+        state: tube2_state
+      )
+    end
+    let(:tube3) do
+      create(
+        :v2_tube_with_metadata,
+        uuid: tube3_uuid,
+        barcode_prefix: 'FX',
+        barcode_number: 6,
+        custom_metadatum_collection: tube3_custom_metadata,
+        purpose: tube_purpose1,
+        state: tube3_state
+      )
+    end
+    let(:tube4) do
+      create(
+        :v2_tube_with_metadata,
+        uuid: tube4_uuid,
+        barcode_prefix: 'FX',
+        barcode_number: 7,
+        custom_metadatum_collection: tube4_custom_metadata,
+        purpose: tube_purpose2,
+        state: tube4_state
+      )
+    end
+    let(:tube5) do
+      create(
+        :v2_tube_with_metadata,
+        uuid: tube5_uuid,
+        barcode_prefix: 'FX',
+        barcode_number: 8,
+        custom_metadatum_collection: tube5_custom_metadata,
+        purpose: tube_purpose2,
+        state: tube5_state
+      )
+    end
+    let(:tube6) do
+      create(
+        :v2_tube_with_metadata,
+        uuid: tube6_uuid,
+        barcode_prefix: 'FX',
+        barcode_number: 9,
+        custom_metadatum_collection: tube6_custom_metadata,
+        purpose: tube_purpose2,
+        state: tube6_state
+      )
+    end
+
+    # wells
+    let(:well1) { create(:v2_well, location: 'A1', downstream_tubes: [tube1, tube4]) }
+    let(:well2) { create(:v2_well, location: 'B1', downstream_tubes: [tube2, tube5]) }
+    let(:well3) { create(:v2_well, location: 'C1', downstream_tubes: [tube3, tube6]) }
+
+    # plate purpose uuid
+    let(:plate_purpose_uuid) { 'plate_purpose_uuid' }
+
+    # plate purpose name
+    let(:plate_purpose_name) { 'plate_purpose' }
+
+    # plate purpose
+    let(:plate_purpose) { create(:v2_purpose, name: plate_purpose_name, uuid: plate_purpose_uuid) }
+
+    # plate uuid
+    let(:plate_uuid) { 'plate_uuid' }
+
+    # plate state
+    let(:plate_state) { 'passed' }
+
+    # plate
+    let(:plate) do
+      create(:v2_plate, wells: [well1, well2, well3], barcode_number: 3, purpose: plate_purpose, state: plate_state)
+    end
+
+    let(:bed1_barcode) { 'bed1_barcode' }
+    let(:bed2_barcode) { 'bed2_barcode' }
+    let(:bed3_barcode) { 'bed3_barcode' }
+
+    let(:robot_config) do
+      {
+        name: 'robot_name',
+        beds: {
+          bed1_barcode => {
+            purpose: plate_purpose_name,
+            states: ['passed'],
+            label: 'Bed 1'
+          },
+          bed2_barcode => {
+            purpose: tube_purpose1_name,
+            states: ['pending'],
+            label: 'Bed 2',
+            target_state: 'passed'
+          },
+          bed3_barcode => {
+            purpose: tube_purpose2_name,
+            states: ['pending'],
+            label: 'Bed 3',
+            target_state: 'passed'
+          }
+        },
+        relationships: [
+          {
+            'type' => 'relationship_type',
+            'options' => {
+              'parent' => bed1_barcode,
+              'children' => [bed2_barcode, bed3_barcode]
+            }
+          }
+        ]
+      }
+    end
+
+    let(:robot) { described_class.new(robot_config.merge(api: api, user_uuid: user_uuid)) }
+
+    before do
+      # Stub the robot requests to the Sequencescape API to look up labware by
+      # barcode. It returns the plate with its wells and downstream tubes.
+      includes = 'purpose,wells,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
+      bed_plate_lookup_with_barcode(plate.barcode.human, [plate], includes)
+      bed_plate_lookup_with_barcode(tube_rack1_barcode, [], includes)
+      bed_plate_lookup_with_barcode(tube_rack2_barcode, [], includes)
+    end
+
+    context 'with a valid scanned layout' do
+      let(:scanned_layout) do
+        {
+          bed1_barcode => [plate.human_barcode],
+          bed2_barcode => [tube_rack1_barcode],
+          bed3_barcode => [tube_rack2_barcode]
+        }
+      end
+
+      it { is_expected.to be_valid }
+    end
+  end
+end

From 6a994a7492520e78a5c2366841be562910710c62 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sat, 28 Oct 2023 01:22:31 +0100
Subject: [PATCH 21/52] Reduced method sizes for updating labware metadata

---
 app/controllers/robots_controller.rb | 37 ++++++++++++++++++++++------
 1 file changed, 29 insertions(+), 8 deletions(-)

diff --git a/app/controllers/robots_controller.rb b/app/controllers/robots_controller.rb
index f3ed8a2f3..d87016d83 100644
--- a/app/controllers/robots_controller.rb
+++ b/app/controllers/robots_controller.rb
@@ -23,7 +23,7 @@ def show
 
   def start # rubocop:todo Metrics/AbcSize
     @robot.perform_transfer(stripped_beds)
-    update_labware_metadata(params[:robot_barcode]) if params[:robot_barcode].present?
+    update_all_labware_metadata(params[:robot_barcode]) if params[:robot_barcode].present?
     respond_to { |format| format.html { redirect_to search_path, notice: "Robot #{@robot.name} has been started." } }
   rescue Robots::Bed::BedError => e
     # Our beds complained, nothing has happened.
@@ -32,22 +32,43 @@ def start # rubocop:todo Metrics/AbcSize
     end
   end
 
-  def update_labware_metadata(robot_barcode)
+  # Updates all bed labware metadata with robot barcode.
+  # Beds with no transitions and labware are ignored.
+  #
+  # @param [String] robot_barcode
+  # @raise [Sequencescape::Api::ResourceNotFound] if the labware cannot be found
+  #
+  def update_all_labware_metadata(robot_barcode)
     @robot.beds.each_value do |bed|
       next unless bed.transitions? && bed.labware
-      labware_barcode = bed.labware.barcode.machine
-      if bed.respond_to?(:labware_created_with_robot)
-        bed.labware_created_with_robot(robot_barcode)
-      else
-        labware_created_with_robot(labware_barcode, robot_barcode)
-      end
+      update_bed_labware_metadata(bed, robot_barcode)
     rescue Sequencescape::Api::ResourceNotFound
+      labware_barcode = bed.labware.barcode.machine
       respond_to do |format|
         format.html { redirect_to robot_path(id: @robot.id), notice: "Labware #{labware_barcode} not found." }
       end
     end
   end
 
+  # Updates bed labware metadata with robot barcode. If the bed has its own
+  # method for updating, use that, otherwise use the method of this controller.
+  #
+  # @param [String] labware_barcode
+  # @param [String] robot_barcode
+  # @raise [Sequencescape::Api::ResourceNotFound] if the labware cannot be found
+  #
+  def update_bed_labware_metadata(bed, robot_barcode)
+    return bed.labware_created_with_robot(robot_barcode) if bed.respond_to?(:labware_created_with_robot)
+    labware_barcode = bed.labware.barcode.machine
+    labware_created_with_robot(labware_barcode, robot_barcode)
+  end
+
+  # Updates labware metadata with robot barcode.
+  #
+  # @param [String] labware_barcode
+  # @param [String] robot_barcode
+  # @raise [Sequencescape::Api::ResourceNotFound] if the labware cannot be found
+  #
   def labware_created_with_robot(labware_barcode, robot_barcode)
     LabwareMetadata
       .new(api: api, user: current_user_uuid, barcode: labware_barcode)

From 0930176ef96425209b4e1175825db925b7ed75c2 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sat, 28 Oct 2023 01:24:06 +0100
Subject: [PATCH 22/52] Disabled valid_relationships rubocop metrics for now

---
 app/models/robots/plate_to_tube_racks_robot.rb | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index 339e3e05e..466bef5f9 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -59,6 +59,8 @@ def verify(params)
       super
     end
 
+    # rubocop:todo Metrics/AbcSize
+    # rubocop:todo Metrics/MethodLength
     def valid_relationships
       raise StandardError, "Relationships for #{name} are empty" if @relationships.empty?
 
@@ -78,6 +80,9 @@ def valid_relationships
       end
     end
 
+    # rubocop:enable Metrics/MethodLength
+    # rubocop:enable Metrics/AbcSize
+
     # Returns an array of labware from the robot's labware store for barcodes.
     # This method is called by the robot's beds when they need to find their
     # labware. The labware returned can be Plate objects or labware-like
@@ -180,7 +185,7 @@ def find_tube_racks(plate)
           next if well.downstream_tubes.blank?
           well.downstream_tubes.each do |tube|
             barcode = tube.custom_metadatum_collection.metadata[:tube_rack_barcode]
-            find_or_create_tube_rack(racks, barcode, plate).tubes.push(tube)
+            find_or_create_tube_rack(racks, barcode, plate).push(tube)
           end
         end
     end
@@ -190,7 +195,6 @@ def find_tube_racks(plate)
     # @param [Array<TubeRackWrapper>] racks the tube racks found so far
     # @param [String] barcode the barcode of the tube rack
     # @param [Plate] plate the parent plate
-    #
     # @return [TubeRackWrapper] the tube rack wrapper object
     #
     def find_or_create_tube_rack(racks, barcode, plate)

From 2581134b7f9276c2d05d5c8679404d2ecdf86fdf Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sat, 28 Oct 2023 01:25:12 +0100
Subject: [PATCH 23/52] Updated tube rack wrapper to handle duplicate tubes

---
 app/models/robots/tube_rack_wrapper.rb | 36 +++++++++++++++++++++++---
 1 file changed, 33 insertions(+), 3 deletions(-)

diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index 9c21f83eb..10cca93e3 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -6,7 +6,7 @@ module Robots
   #
   class TubeRackWrapper
     attr_accessor :barcode, :parent, :tubes
-    delegate :purpose_name, :purpose, :human_barcode, :state, :uuid, to: :last_tube, allow_nil: true
+    delegate :purpose_name, :purpose, :human_barcode, :state, :uuid, to: :last, allow_nil: true
 
     # Initializes a new instance of the class.
     #
@@ -17,15 +17,45 @@ class TubeRackWrapper
     def initialize(barcode, parent, tubes: [])
       @barcode = barcode
       @parent = parent
-      @tubes = tubes
+      @tubes = []
+      @tube_positions = {} # Keep track of tube positions for push performance
+      tubes.each { |tube| push(tube) } # Eliminate duplicate tubes by position
     end
 
     # Returns the last tube on the tube rack. This method used for delegating
     # certain methods to make it behave like a like a labware object.
     #
     # @return [Tube] the last tube
-    def last_tube
+    def last
       @tubes.last
     end
+
+    # Appends a tube to the tube rack. If there is an existing tube with the
+    # same position, the tube with the latest creation date is kept. The
+    # instance is returned for method chaining.
+    #
+    # @param [Tube] tube the tube to be added
+    # @return [TubeRackWrapper] the instance of the class
+    #
+    def push(tube)
+      index = @tube_positions[tube_rack_position(tube)]
+      if index.present?
+        @tubes[index] = tube if tube.created_at >= @tubes[index].created_at
+      else
+        @tubes.push(tube)
+        @tube_positions[tube_rack_position(tube)] = @tubes.length - 1
+      end
+    end
+
+    private
+
+    # Returns the tube rack position of a tube from its metadata
+    #
+    # @param [Tube] tube the tube
+    # @return [String] the tube rack position
+    #
+    def tube_rack_position(tube)
+      tube.custom_metadatum_collection.metadata[:tube_rack_position]
+    end
   end
 end

From ffdcdd5ffbbb9151f9d7bc969f1d87cc0d4c6f56 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 01:14:34 +0000
Subject: [PATCH 24/52] Renamed wrapper methods

---
 .../robots/plate_to_tube_racks_robot.rb       | 29 ++++++++++---------
 app/models/robots/tube_rack_wrapper.rb        | 14 ++++-----
 2 files changed, 23 insertions(+), 20 deletions(-)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index 466bef5f9..4d236a2cc 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -13,13 +13,16 @@ module Robots
   # the tube racks depend on the verification of the plate.
   #
   # The destination tube racks are distinguished by their barcodes. We assume
-  # that the tubes on the same tube rack have the same labware purpose. We also
-  # assume that there cannot be two tube racks with the tubes of the same
-  # labware purpose on the robot at the same time. For bed verification, only
-  # the etched barcode of the tube racks are scanned, not the individual tubes.
-  # The number of tube racks to be verified not only depends on the robot's
-  # configured relationships but also whether the plate has children with those
-  # purposes.
+  # that the tubes on the same tube rack have the same labware purpose. When
+  # multiple tubes of the same purpose and the same position are found, the
+  # latest tube is assumed to be on the tube rack and the other tubes are
+  # ignored. We also assume that there cannot be multiple tube racks with the
+  # tubes of the same labware purpose on the robot at the same time.
+  #
+  # For bed verification, only the etched barcode of the tube racks are scanned,
+  # not the individual tubes. The number of tube racks to be verified not only
+  # depends on the robot's configured relationships but also whether the plate
+  # has children with those purposes.
   #
   class PlateToTubeRacksRobot < Robots::Robot
     attr_writer :relationships # Hash from robot config into @relationships
@@ -38,11 +41,11 @@ def bed_class
     # by the robot controller when the user clicks the start robot button. The
     # method first initializes the labware store with the plate and tube racks.
     #
-    # @param [Hash] bed_settings bed_labwares hash from request parameters
+    # @param [Hash] bed_labwares the bed_labwares hash from request parameters
     # @return [void]
     #
-    def perform_transfer(bed_settings)
-      init_labware_store(bed_settings)
+    def perform_transfer(bed_labwares)
+      init_labware_store(bed_labwares)
       super
     end
 
@@ -105,6 +108,8 @@ def child_labware(plate)
       labware_store.values.select { |labware| labware.respond_to?(:parent) && labware.parent.uuid == plate.uuid }
     end
 
+    private
+
     # Prepares the labware store before handling robot actions. This method is
     # called before the robot's bed verification and perform transfer actions.
     #
@@ -121,8 +126,6 @@ def init_labware_store(bed_labwares)
       end
     end
 
-    private
-
     # Returns an array of sanitised barcodes from the bed_labwares hash from
     # request parameters.
     #
@@ -185,7 +188,7 @@ def find_tube_racks(plate)
           next if well.downstream_tubes.blank?
           well.downstream_tubes.each do |tube|
             barcode = tube.custom_metadatum_collection.metadata[:tube_rack_barcode]
-            find_or_create_tube_rack(racks, barcode, plate).push(tube)
+            find_or_create_tube_rack(racks, barcode, plate).push_tube(tube)
           end
         end
     end
diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index 10cca93e3..bf93bc069 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -6,7 +6,7 @@ module Robots
   #
   class TubeRackWrapper
     attr_accessor :barcode, :parent, :tubes
-    delegate :purpose_name, :purpose, :human_barcode, :state, :uuid, to: :last, allow_nil: true
+    delegate :purpose_name, :purpose, :human_barcode, :state, :uuid, to: :last_tube, allow_nil: true
 
     # Initializes a new instance of the class.
     #
@@ -26,18 +26,18 @@ def initialize(barcode, parent, tubes: [])
     # certain methods to make it behave like a like a labware object.
     #
     # @return [Tube] the last tube
-    def last
+    def last_tube
       @tubes.last
     end
 
-    # Appends a tube to the tube rack. If there is an existing tube with the
-    # same position, the tube with the latest creation date is kept. The
-    # instance is returned for method chaining.
+    # Appends a tube to the tube rack or replaces an existing tube. If there
+    # is an existing tube with the same position, the tube with the latest
+    # creation date is kept.
     #
     # @param [Tube] tube the tube to be added
-    # @return [TubeRackWrapper] the instance of the class
+    # @return [Void]
     #
-    def push(tube)
+    def push_tube(tube)
       index = @tube_positions[tube_rack_position(tube)]
       if index.present?
         @tubes[index] = tube if tube.created_at >= @tubes[index].created_at

From ad670128860d6b5c989d91216de75af1425a9205 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 01:15:07 +0000
Subject: [PATCH 25/52] Added initial test for contingency-only bed
 verification

---
 .../robots/plate_to_tube_racks_robot_spec.rb  | 37 ++++++++++++++-----
 1 file changed, 28 insertions(+), 9 deletions(-)

diff --git a/spec/models/robots/plate_to_tube_racks_robot_spec.rb b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
index 3c3ba767c..9865c8bda 100644
--- a/spec/models/robots/plate_to_tube_racks_robot_spec.rb
+++ b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
@@ -197,7 +197,7 @@
     let(:robot) { described_class.new(robot_config.merge(api: api, user_uuid: user_uuid)) }
 
     before do
-      # Stub the robot requests to the Sequencescape API to look up labware by
+      # Stub robot requests to the Sequencescape API to look up plate by
       # barcode. It returns the plate with its wells and downstream tubes.
       includes = 'purpose,wells,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
       bed_plate_lookup_with_barcode(plate.barcode.human, [plate], includes)
@@ -205,16 +205,35 @@
       bed_plate_lookup_with_barcode(tube_rack2_barcode, [], includes)
     end
 
-    context 'with a valid scanned layout' do
-      let(:scanned_layout) do
-        {
-          bed1_barcode => [plate.human_barcode],
-          bed2_barcode => [tube_rack1_barcode],
-          bed3_barcode => [tube_rack2_barcode]
-        }
+    context 'with two destination purposes' do
+      # Parent plate has two child tube-racks. We validate parent bed and two child beds.
+      context 'with a valid scanned layout' do
+        let(:scanned_layout) do
+          {
+            bed1_barcode => [plate.human_barcode],
+            bed2_barcode => [tube_rack1_barcode],
+            bed3_barcode => [tube_rack2_barcode]
+          }
+        end
+
+        it { is_expected.to be_valid }
       end
+    end
 
-      it { is_expected.to be_valid }
+    context 'with one destination purpose' do
+      # Parent plate has only one child tube-rack. We validate parent bed and one child bed.
+      # wells
+      let(:well1) { create(:v2_well, location: 'A1', downstream_tubes: [tube4]) }
+      let(:well2) { create(:v2_well, location: 'B1', downstream_tubes: [tube5]) }
+      let(:well3) { create(:v2_well, location: 'C1', downstream_tubes: [tube6]) }
+
+      context 'with a valid scanned layout' do
+        let(:scanned_layout) { { bed1_barcode => [plate.human_barcode], bed2_barcode => [tube_rack1_barcode] } }
+
+        it 'test' do
+          is_expected.to be_valid
+        end
+      end
     end
   end
 end

From c68f0bb69426a2e6b0a0cd8675820125954d7788 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 15:15:45 +0000
Subject: [PATCH 26/52] Prepare robot for contingency-only verification

---
 .../robots/plate_to_tube_racks_robot.rb       | 74 ++++++++++++++++---
 1 file changed, 65 insertions(+), 9 deletions(-)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index 4d236a2cc..0a185fc6d 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -38,32 +38,29 @@ def bed_class
     end
 
     # Performs the transfer between plate and tube racks. This method is called
-    # by the robot controller when the user clicks the start robot button. The
-    # method first initializes the labware store with the plate and tube racks.
+    # by the robot controller when the user clicks the start robot button.
     #
     # @param [Hash] bed_labwares the bed_labwares hash from request parameters
     # @return [void]
     #
     def perform_transfer(bed_labwares)
-      init_labware_store(bed_labwares)
+      prepare_robot(bed_labwares)
       super
     end
 
     # Performs the bed verification of plate and tube racks. This method is
     # called by the robot controller when the user clicks the validate layout
-    # button.  The method first initializes the labware store with the plate
-    # and tube racks.
+    # button.
     #
     # @param [Hash] params request parameters
     # @return [Report]
     #
     def verify(params)
-      init_labware_store(params[:bed_labwares])
+      prepare_robot(params[:bed_labwares])
       super
     end
 
     # rubocop:todo Metrics/AbcSize
-    # rubocop:todo Metrics/MethodLength
     def valid_relationships
       raise StandardError, "Relationships for #{name} are empty" if @relationships.empty?
 
@@ -83,7 +80,6 @@ def valid_relationships
       end
     end
 
-    # rubocop:enable Metrics/MethodLength
     # rubocop:enable Metrics/AbcSize
 
     # Returns an array of labware from the robot's labware store for barcodes.
@@ -110,13 +106,22 @@ def child_labware(plate)
 
     private
 
+    # Prepares the robot before handling actions.
+    #
+    # @param [Hash] bed_labwares hash from request parameters
+    # @return [void]
+    def prepare_robot(bed_labwares)
+      prepare_labware_store(bed_labwares)
+      prepare_beds
+    end
+
     # Prepares the labware store before handling robot actions. This method is
     # called before the robot's bed verification and perform transfer actions.
     #
     # @param [Hash] bed_labwares hash from request parameters
     # @return [void]
     #
-    def init_labware_store(bed_labwares)
+    def prepare_labware_store(bed_labwares)
       return if labware_store.present?
       stripped_barcodes(bed_labwares).each do |barcode|
         plate = find_plate(barcode)
@@ -126,6 +131,57 @@ def init_labware_store(bed_labwares)
       end
     end
 
+    # Prepares the beds before handling robot actions. This method is called
+    # after preparing the labware store and before assigning bed_labwares
+    # request parameter to beds. It is simply modifying the config loaded
+    # into the robot (beds and relationships).
+    #
+    # There are two reasons we need to prepare the beds. 1) If parent labware
+    # cannot be found, we cannot find the child labware, hence we cannot
+    # validate child beds separately. The bed verification will fail because of
+    # the parent bed in this case. 2) If the parent labware can be found, but
+    # the parent does not have a child labware of one of the purposes, we should
+    # not validate the bed for that purpose. The bed verification will continue
+    # with the expected labware.
+    #
+    # This method relies on the bed_labwares specified in request parameters,
+    # that were already recorded by the prepare_labware_store method. We
+    # override the bed configuration based on availability of labware here.
+    #
+    # NB. The child labware are tube-rack wrapper objects, not actual labware.
+    # The information about tube-racks for are found using the metadata of the
+    # downstream tubes, included in the Sequencescape API response.
+    #
+    # @ return [void]
+    #
+    def prepare_beds
+      @relationships.each do |relationship|
+        relationship_children = relationship.dig('options', 'children')
+        labware_store_purposes = labware_store.values.map(&:purpose_name)
+
+        bed_barcodes_to_remove =
+          relationship_children.select { |barcode| labware_store_purposes.exclude?(beds[barcode].purpose) }
+
+        delete_beds(bed_barcodes_to_remove, relationship_children)
+      end
+    end
+
+    # Deletes the beds and their relationships from the robot's configuration.
+    # This method is called by the prepare_beds method after finding which
+    # beds should not be verified. For scRNA, this means either we need to
+    # verify the parent bed first as it has a problem, or we have to remove
+    # the sequencing tube-rack from the robot's config as the parent has only
+    # contingency-only tube rack to be verified.
+    #
+    # @param [Array<String>] barcodes array of barcodes to be removed
+    # @param [Array<String>] relationship_children array of child barcodes
+    # @return [void]
+    #
+    def delete_beds(barcodes, relationship_children)
+      beds.delete_if { |barcode, _bed| barcodes.include?(barcode) }
+      relationship_children.delete_if { |barcode| barcodes.include?(barcode) }
+    end
+
     # Returns an array of sanitised barcodes from the bed_labwares hash from
     # request parameters.
     #

From 0ae1fbe0bc81b82e1df2e00e028cd20ef42e5a75 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 15:17:34 +0000
Subject: [PATCH 27/52] Added test for a contingency-only valid scanned layout

---
 spec/models/robots/plate_to_tube_racks_robot_spec.rb | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/spec/models/robots/plate_to_tube_racks_robot_spec.rb b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
index 9865c8bda..aca9424ad 100644
--- a/spec/models/robots/plate_to_tube_racks_robot_spec.rb
+++ b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
@@ -206,7 +206,8 @@
     end
 
     context 'with two destination purposes' do
-      # Parent plate has two child tube-racks. We validate parent bed and two child beds.
+      # Parent plate has two child tube-racks. We validate parent bed (bed1)
+      # and two child beds (bed2 and bed3).
       context 'with a valid scanned layout' do
         let(:scanned_layout) do
           {
@@ -221,18 +222,17 @@
     end
 
     context 'with one destination purpose' do
-      # Parent plate has only one child tube-rack. We validate parent bed and one child bed.
+      # Parent plate has only one child tube-rack. We validate parent bed
+      # (bed1) and one child bed (bed3).
       # wells
       let(:well1) { create(:v2_well, location: 'A1', downstream_tubes: [tube4]) }
       let(:well2) { create(:v2_well, location: 'B1', downstream_tubes: [tube5]) }
       let(:well3) { create(:v2_well, location: 'C1', downstream_tubes: [tube6]) }
 
       context 'with a valid scanned layout' do
-        let(:scanned_layout) { { bed1_barcode => [plate.human_barcode], bed2_barcode => [tube_rack1_barcode] } }
+        let(:scanned_layout) { { bed1_barcode => [plate.human_barcode], bed3_barcode => [tube_rack2_barcode] } }
 
-        it 'test' do
-          is_expected.to be_valid
-        end
+        it { is_expected.to be_valid }
       end
     end
   end

From 4b7bd86fb21955feed91c157de8ff4ba90fe7a7f Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 15:43:29 +0000
Subject: [PATCH 28/52] Added test for a plate on an unknown bed

---
 .../robots/plate_to_tube_racks_robot_spec.rb  | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/spec/models/robots/plate_to_tube_racks_robot_spec.rb b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
index aca9424ad..305e36778 100644
--- a/spec/models/robots/plate_to_tube_racks_robot_spec.rb
+++ b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
@@ -219,6 +219,31 @@
 
         it { is_expected.to be_valid }
       end
+
+      context 'with plate on an unknown bed' do
+        # Plate is on a bed we are not supposed to use for any labware.
+        let(:bed_barcode) { 'unknown_bed_barcode' }
+        let(:scanned_layout) do
+          {
+            bed_barcode => [plate.human_barcode],
+            bed2_barcode => [tube_rack1_barcode],
+            bed3_barcode => [tube_rack2_barcode]
+          }
+        end
+
+        it { is_expected.not_to be_valid }
+
+        it 'has error messages' do
+          errors = [
+            "#{bed_barcode} does not appear to be a valid bed barcode.",
+            "Bed 1: should not be empty.",
+            "Bed 1: should have children."
+          ]
+          errors.each do |error|
+            expect(subject.message).to include(error)
+          end
+        end
+      end
     end
 
     context 'with one destination purpose' do

From 53f8f8f5026cc660a30ab0e42ceeddfee272f2e4 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 15:50:25 +0000
Subject: [PATCH 29/52] Added test for a child tube-rack missing

---
 .../robots/plate_to_tube_racks_robot_spec.rb  | 24 ++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/spec/models/robots/plate_to_tube_racks_robot_spec.rb b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
index 305e36778..58f5208f6 100644
--- a/spec/models/robots/plate_to_tube_racks_robot_spec.rb
+++ b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
@@ -239,11 +239,29 @@
             "Bed 1: should not be empty.",
             "Bed 1: should have children."
           ]
-          errors.each do |error|
-            expect(subject.message).to include(error)
-          end
+          errors.each { |error| expect(subject.message).to include(error) }
         end
       end
+
+      context 'with a child tube-rack missing' do
+        # We forgot to scan one of the child tube-racks.
+        let(:scanned_layout) do
+          {
+            bed1_barcode => [plate.human_barcode],
+            bed2_barcode => [tube_rack1_barcode],
+          }
+        end
+        it { is_expected.not_to be_valid }
+
+        it 'has error messages' do
+          errors = [
+            "Bed 3: Was expected to contain labware barcode FX9G but nothing was scanned (empty)."
+          ]
+          errors.each { |error| expect(subject.message).to include(error) }
+        end
+
+      end
+
     end
 
     context 'with one destination purpose' do

From 1022ba7f6ca58d487750c7ff67ca417d5b5c9f3f Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 16:14:53 +0000
Subject: [PATCH 30/52] Fixed incorrect tube-rack barcode in error message

---
 app/models/robots/tube_rack_wrapper.rb               | 10 +++++++++-
 spec/models/robots/plate_to_tube_racks_robot_spec.rb | 11 ++++++-----
 2 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index bf93bc069..fc1f18c0c 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -6,7 +6,7 @@ module Robots
   #
   class TubeRackWrapper
     attr_accessor :barcode, :parent, :tubes
-    delegate :purpose_name, :purpose, :human_barcode, :state, :uuid, to: :last_tube, allow_nil: true
+    delegate :purpose_name, :purpose, :state, :uuid, to: :last_tube, allow_nil: true
 
     # Initializes a new instance of the class.
     #
@@ -47,6 +47,14 @@ def push_tube(tube)
       end
     end
 
+    # Returns the human readable barcode of the tube rack.
+    #
+    # @return [String] the human readable barcode
+    #
+    def human_barcode
+      barcode.human
+    end
+
     private
 
     # Returns the tube rack position of a tube from its metadata
diff --git a/spec/models/robots/plate_to_tube_racks_robot_spec.rb b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
index 58f5208f6..0439f4c27 100644
--- a/spec/models/robots/plate_to_tube_racks_robot_spec.rb
+++ b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
@@ -233,7 +233,7 @@
 
         it { is_expected.not_to be_valid }
 
-        it 'has error messages' do
+        it 'has correct messages' do
           errors = [
             "#{bed_barcode} does not appear to be a valid bed barcode.",
             "Bed 1: should not be empty.",
@@ -244,7 +244,7 @@
       end
 
       context 'with a child tube-rack missing' do
-        # We forgot to scan one of the child tube-racks.
+        # We forgot to scan the second tube-rack.
         let(:scanned_layout) do
           {
             bed1_barcode => [plate.human_barcode],
@@ -253,15 +253,16 @@
         end
         it { is_expected.not_to be_valid }
 
-        it 'has error messages' do
+        it 'has correct messages' do
           errors = [
-            "Bed 3: Was expected to contain labware barcode FX9G but nothing was scanned (empty)."
+            "Bed 3: Was expected to contain labware barcode #{tube_rack2_barcode} but nothing was scanned (empty)."
           ]
           errors.each { |error| expect(subject.message).to include(error) }
         end
-
       end
 
+
+
     end
 
     context 'with one destination purpose' do

From d3527e9c83bfdc112627ac04ca77123994d4aec2 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 16:15:33 +0000
Subject: [PATCH 31/52] Added test for all child tube-racks missing

---
 .../robots/plate_to_tube_racks_robot_spec.rb     | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/spec/models/robots/plate_to_tube_racks_robot_spec.rb b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
index 0439f4c27..f19f61ada 100644
--- a/spec/models/robots/plate_to_tube_racks_robot_spec.rb
+++ b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
@@ -261,7 +261,23 @@
         end
       end
 
+     context 'with all child tube-racks missing' do
+        # We forgot to scan all tube-racks.
+        let(:scanned_layout) do
+          {
+            bed1_barcode => [plate.human_barcode]
+          }
+        end
+         it { is_expected.not_to be_valid }
 
+        it 'has correct messages' do
+          errors = [
+            "Bed 2: Was expected to contain labware barcode #{tube_rack1_barcode} but nothing was scanned (empty).",
+            "Bed 3: Was expected to contain labware barcode #{tube_rack2_barcode} but nothing was scanned (empty)."
+          ]
+          errors.each { |error| expect(subject.message).to include(error) }
+        end
+      end
 
     end
 

From 07d948c4fb9b809bb815379c96d94921ea47f45a Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 16:25:45 +0000
Subject: [PATCH 32/52] Added test for a tube-rack on an unknown bed

---
 .../robots/plate_to_tube_racks_robot_spec.rb  | 44 ++++++++++++-------
 1 file changed, 28 insertions(+), 16 deletions(-)

diff --git a/spec/models/robots/plate_to_tube_racks_robot_spec.rb b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
index f19f61ada..e297c4f84 100644
--- a/spec/models/robots/plate_to_tube_racks_robot_spec.rb
+++ b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
@@ -222,10 +222,10 @@
 
       context 'with plate on an unknown bed' do
         # Plate is on a bed we are not supposed to use for any labware.
-        let(:bed_barcode) { 'unknown_bed_barcode' }
+        let(:unknown_bed_barcode) { 'unknown_bed_barcode' }
         let(:scanned_layout) do
           {
-            bed_barcode => [plate.human_barcode],
+            unknown_bed_barcode => [plate.human_barcode],
             bed2_barcode => [tube_rack1_barcode],
             bed3_barcode => [tube_rack2_barcode]
           }
@@ -235,9 +235,9 @@
 
         it 'has correct messages' do
           errors = [
-            "#{bed_barcode} does not appear to be a valid bed barcode.",
-            "Bed 1: should not be empty.",
-            "Bed 1: should have children."
+            "#{unknown_bed_barcode} does not appear to be a valid bed barcode.",
+            'Bed 1: should not be empty.',
+            'Bed 1: should have children.'
           ]
           errors.each { |error| expect(subject.message).to include(error) }
         end
@@ -245,12 +245,7 @@
 
       context 'with a child tube-rack missing' do
         # We forgot to scan the second tube-rack.
-        let(:scanned_layout) do
-          {
-            bed1_barcode => [plate.human_barcode],
-            bed2_barcode => [tube_rack1_barcode],
-          }
-        end
+        let(:scanned_layout) { { bed1_barcode => [plate.human_barcode], bed2_barcode => [tube_rack1_barcode] } }
         it { is_expected.not_to be_valid }
 
         it 'has correct messages' do
@@ -261,24 +256,41 @@
         end
       end
 
-     context 'with all child tube-racks missing' do
+      context 'with all child tube-racks missing' do
         # We forgot to scan all tube-racks.
+        let(:scanned_layout) { { bed1_barcode => [plate.human_barcode] } }
+        it { is_expected.not_to be_valid }
+
+        it 'has correct messages' do
+          errors = [
+            "Bed 2: Was expected to contain labware barcode #{tube_rack1_barcode} but nothing was scanned (empty).",
+            "Bed 3: Was expected to contain labware barcode #{tube_rack2_barcode} but nothing was scanned (empty)."
+          ]
+          errors.each { |error| expect(subject.message).to include(error) }
+        end
+      end
+
+      context 'with a tube-rack on an unknown bed' do
+        # The second tube-rack is on a bed we are not supposed to use for any labware.
+        let(:unknown_bed_barcode) { 'unknown_bed_barcode' }
         let(:scanned_layout) do
           {
-            bed1_barcode => [plate.human_barcode]
+            bed1_barcode => [plate.human_barcode],
+            bed2_barcode => [tube_rack1_barcode],
+            unknown_bed_barcode => [tube_rack2_barcode]
           }
         end
-         it { is_expected.not_to be_valid }
+
+        it { is_expected.not_to be_valid }
 
         it 'has correct messages' do
           errors = [
-            "Bed 2: Was expected to contain labware barcode #{tube_rack1_barcode} but nothing was scanned (empty).",
+            "#{unknown_bed_barcode} does not appear to be a valid bed barcode.",
             "Bed 3: Was expected to contain labware barcode #{tube_rack2_barcode} but nothing was scanned (empty)."
           ]
           errors.each { |error| expect(subject.message).to include(error) }
         end
       end
-
     end
 
     context 'with one destination purpose' do

From ac3cfa4edb7d5d3a27b736b266de65d1d5cebe92 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 23:34:07 +0000
Subject: [PATCH 33/52] Added state transition for all tubes of the tube-rack
 on the bed

---
 .../robots/bed/plate_to_tube_racks_bed.rb     | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/app/models/robots/bed/plate_to_tube_racks_bed.rb b/app/models/robots/bed/plate_to_tube_racks_bed.rb
index 2a12dd16b..6c8cd05e3 100644
--- a/app/models/robots/bed/plate_to_tube_racks_bed.rb
+++ b/app/models/robots/bed/plate_to_tube_racks_bed.rb
@@ -42,5 +42,25 @@ def load(barcodes)
       @barcodes = Array(barcodes).filter_map(&:strip).uniq
       @labware = @barcodes.present? ? robot.find_bed_labware(@barcodes) : []
     end
+
+    # Changes the state of the labware to the target state. It will change the
+    # state of all tubes of the tube-rack on this bed.
+    #
+    # @return [void]
+    #
+    def transition
+      return if target_state.nil? || labware.nil? # We have nothing to do
+
+      labware.tubes.each { |tube| change_tube_state(tube) }
+    end
+
+    # Changes the state of one tube to the target state. This method is called
+    # by the transition method.
+    #
+    # @param [Tube] tube the tube
+    def change_tube_state(tube)
+      state_changer = StateChangers.lookup_for(tube.purpose.uuid)
+      state_changer.new(api, tube.uuid, user_uuid).move_to!(target_state, "Robot #{robot.name} started")
+    end
   end
 end

From 8e4168469bf33f97608af897a13aae24fae00d3b Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 23:35:41 +0000
Subject: [PATCH 34/52] Subclass SplittingRobot for validating relationships

---
 .../robots/plate_to_tube_racks_robot.rb       | 24 +------------------
 1 file changed, 1 insertion(+), 23 deletions(-)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index 0a185fc6d..24d8d4ca7 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -24,7 +24,7 @@ module Robots
   # depends on the robot's configured relationships but also whether the plate
   # has children with those purposes.
   #
-  class PlateToTubeRacksRobot < Robots::Robot
+  class PlateToTubeRacksRobot < Robots::SplittingRobot
     attr_writer :relationships # Hash from robot config into @relationships
 
     # Option for including downstream tubes and metadata in Plate API response.
@@ -60,28 +60,6 @@ def verify(params)
       super
     end
 
-    # rubocop:todo Metrics/AbcSize
-    def valid_relationships
-      raise StandardError, "Relationships for #{name} are empty" if @relationships.empty?
-
-      @relationships.each_with_object({}) do |relationship, validations|
-        parent_bed = relationship.dig('options', 'parent')
-        child_beds = relationship.dig('options', 'children')
-
-        validations[parent_bed] = beds[parent_bed].child_labware.present?
-        error(beds[parent_bed], 'should not be empty.') if beds[parent_bed].empty?
-        error(beds[parent_bed], 'should have children.') if beds[parent_bed].child_labware.empty?
-
-        expected_children = beds[parent_bed].child_labware
-        expected_children.each_with_index do |expected_child, index|
-          child_bed = child_beds[index]
-          validations[child_bed] = check_labware_identity([expected_child], child_bed)
-        end
-      end
-    end
-
-    # rubocop:enable Metrics/AbcSize
-
     # Returns an array of labware from the robot's labware store for barcodes.
     # This method is called by the robot's beds when they need to find their
     # labware. The labware returned can be Plate objects or labware-like

From 140ebe6f69bc81e5df55f3e255a69f55b86e430f Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Sun, 29 Oct 2023 23:37:44 +0000
Subject: [PATCH 35/52] Added test for state changing for all tubes of
 tube-racks

---
 .../robots/plate_to_tube_racks_robot_spec.rb  | 475 ++++++++++--------
 1 file changed, 278 insertions(+), 197 deletions(-)

diff --git a/spec/models/robots/plate_to_tube_racks_robot_spec.rb b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
index e297c4f84..25aa43bf2 100644
--- a/spec/models/robots/plate_to_tube_racks_robot_spec.rb
+++ b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
@@ -7,216 +7,227 @@
   include RobotHelpers # Include methods for stubbing bed labware lookups.
   has_a_working_api # Add a mock Sequencescape API to the test context.
 
-  describe '#verify' do
-    # The robot will receive the scanned layout as bed_labwares from request parameters
-    # and return a report object showing the validity of each bed and robot.
-    subject { robot.verify(bed_labwares: scanned_layout) }
-
-    # user_uuid
-    let(:user_uuid) { 'user_uuid' }
-
-    # tube rack barcodes
-    let(:tube_rack1_barcode) { 'TR00000001' }
-    let(:tube_rack2_barcode) { 'TR00000002' }
-
-    # tube metadata
-    let(:tube1_metadata) { { 'tube_rack_barcode' => tube_rack1_barcode, 'tube_rack_position' => 'A1' } }
-    let(:tube2_metadata) { { 'tube_rack_barcode' => tube_rack1_barcode, 'tube_rack_position' => 'B1' } }
-    let(:tube3_metadata) { { 'tube_rack_barcode' => tube_rack1_barcode, 'tube_rack_position' => 'C1' } }
-    let(:tube4_metadata) { { 'tube_rack_barcode' => tube_rack2_barcode, 'tube_rack_position' => 'A1' } }
-    let(:tube5_metadata) { { 'tube_rack_barcode' => tube_rack2_barcode, 'tube_rack_position' => 'B1' } }
-    let(:tube6_metadata) { { 'tube_rack_barcode' => tube_rack2_barcode, 'tube_rack_position' => 'C1' } }
-
-    # tube custom metadata collections
-    let(:tube1_custom_metadata) { create(:custom_metadatum_collection, metadata: tube1_metadata) }
-    let(:tube2_custom_metadata) { create(:custom_metadatum_collection, metadata: tube2_metadata) }
-    let(:tube3_custom_metadata) { create(:custom_metadatum_collection, metadata: tube3_metadata) }
-    let(:tube4_custom_metadata) { create(:custom_metadatum_collection, metadata: tube4_metadata) }
-    let(:tube5_custom_metadata) { create(:custom_metadatum_collection, metadata: tube5_metadata) }
-    let(:tube6_custom_metadata) { create(:custom_metadatum_collection, metadata: tube6_metadata) }
-
-    # tube uuids
-    let(:tube1_uuid) { 'tube1_uuid' }
-    let(:tube2_uuid) { 'tube2_uuid' }
-    let(:tube3_uuid) { 'tube3_uuid' }
-    let(:tube4_uuid) { 'tube4_uuid' }
-    let(:tube5_uuid) { 'tube5_uuid' }
-    let(:tube6_uuid) { 'tube6_uuid' }
-
-    # tube purpose uuids
-    let(:tube_purpose1_uuid) { 'tube_purpose1_uuid' }
-    let(:tube_purpose2_uuid) { 'tube_purpose2_uuid' }
-
-    # tube purpose names
-    let(:tube_purpose1_name) { 'tube_purpose1_name' }
-    let(:tube_purpose2_name) { 'tube_purpose2_name' }
-
-    # tube purposes
-    let(:tube_purpose1) { create(:v2_purpose, name: tube_purpose1_name, uuid: tube_purpose1_uuid) }
-    let(:tube_purpose2) { create(:v2_purpose, name: tube_purpose2_name, uuid: tube_purpose2_uuid) }
-
-    # tube states
-    let(:tube1_state) { 'pending' }
-    let(:tube2_state) { 'pending' }
-    let(:tube3_state) { 'pending' }
-    let(:tube4_state) { 'pending' }
-    let(:tube5_state) { 'pending' }
-    let(:tube6_state) { 'pending' }
-
-    # tubes
-    let(:tube1) do
-      create(
-        :v2_tube_with_metadata,
-        uuid: tube1_uuid,
-        barcode_prefix: 'FX',
-        barcode_number: 4,
-        custom_metadatum_collection: tube1_custom_metadata,
-        purpose: tube_purpose1,
-        state: tube1_state
-      )
-    end
-    let(:tube2) do
-      create(
-        :v2_tube_with_metadata,
-        uuid: tube2_uuid,
-        barcode_prefix: 'FX',
-        barcode_number: 5,
-        custom_metadatum_collection: tube2_custom_metadata,
-        purpose: tube_purpose1,
-        state: tube2_state
-      )
-    end
-    let(:tube3) do
-      create(
-        :v2_tube_with_metadata,
-        uuid: tube3_uuid,
-        barcode_prefix: 'FX',
-        barcode_number: 6,
-        custom_metadatum_collection: tube3_custom_metadata,
-        purpose: tube_purpose1,
-        state: tube3_state
-      )
-    end
-    let(:tube4) do
-      create(
-        :v2_tube_with_metadata,
-        uuid: tube4_uuid,
-        barcode_prefix: 'FX',
-        barcode_number: 7,
-        custom_metadatum_collection: tube4_custom_metadata,
-        purpose: tube_purpose2,
-        state: tube4_state
-      )
-    end
-    let(:tube5) do
-      create(
-        :v2_tube_with_metadata,
-        uuid: tube5_uuid,
-        barcode_prefix: 'FX',
-        barcode_number: 8,
-        custom_metadatum_collection: tube5_custom_metadata,
-        purpose: tube_purpose2,
-        state: tube5_state
-      )
-    end
-    let(:tube6) do
-      create(
-        :v2_tube_with_metadata,
-        uuid: tube6_uuid,
-        barcode_prefix: 'FX',
-        barcode_number: 9,
-        custom_metadatum_collection: tube6_custom_metadata,
-        purpose: tube_purpose2,
-        state: tube6_state
-      )
-    end
+  # user_uuid
+  let(:user_uuid) { 'user_uuid' }
+
+  # tube rack barcodes
+  let(:tube_rack1_barcode) { 'TR00000001' }
+  let(:tube_rack2_barcode) { 'TR00000002' }
+
+  # tube metadata
+  let(:tube1_metadata) { { 'tube_rack_barcode' => tube_rack1_barcode, 'tube_rack_position' => 'A1' } }
+  let(:tube2_metadata) { { 'tube_rack_barcode' => tube_rack1_barcode, 'tube_rack_position' => 'B1' } }
+  let(:tube3_metadata) { { 'tube_rack_barcode' => tube_rack1_barcode, 'tube_rack_position' => 'C1' } }
+  let(:tube4_metadata) { { 'tube_rack_barcode' => tube_rack2_barcode, 'tube_rack_position' => 'A1' } }
+  let(:tube5_metadata) { { 'tube_rack_barcode' => tube_rack2_barcode, 'tube_rack_position' => 'B1' } }
+  let(:tube6_metadata) { { 'tube_rack_barcode' => tube_rack2_barcode, 'tube_rack_position' => 'C1' } }
+
+  # tube custom metadata collections
+  let(:tube1_custom_metadata) { create(:custom_metadatum_collection, metadata: tube1_metadata) }
+  let(:tube2_custom_metadata) { create(:custom_metadatum_collection, metadata: tube2_metadata) }
+  let(:tube3_custom_metadata) { create(:custom_metadatum_collection, metadata: tube3_metadata) }
+  let(:tube4_custom_metadata) { create(:custom_metadatum_collection, metadata: tube4_metadata) }
+  let(:tube5_custom_metadata) { create(:custom_metadatum_collection, metadata: tube5_metadata) }
+  let(:tube6_custom_metadata) { create(:custom_metadatum_collection, metadata: tube6_metadata) }
+
+  # tube uuids
+  let(:tube1_uuid) { 'tube1_uuid' }
+  let(:tube2_uuid) { 'tube2_uuid' }
+  let(:tube3_uuid) { 'tube3_uuid' }
+  let(:tube4_uuid) { 'tube4_uuid' }
+  let(:tube5_uuid) { 'tube5_uuid' }
+  let(:tube6_uuid) { 'tube6_uuid' }
+
+  let(:tube_uuids) { [tube1_uuid, tube2_uuid, tube3_uuid, tube4_uuid, tube5_uuid, tube6_uuid] }
+
+  # tube purpose uuids
+  let(:tube_purpose1_uuid) { 'tube_purpose1_uuid' }
+  let(:tube_purpose2_uuid) { 'tube_purpose2_uuid' }
+
+  # tube purpose names
+  let(:tube_purpose1_name) { 'tube_purpose1_name' }
+  let(:tube_purpose2_name) { 'tube_purpose2_name' }
+
+  # tube purposes
+  let(:tube_purpose1) { create(:v2_purpose, name: tube_purpose1_name, uuid: tube_purpose1_uuid) }
+  let(:tube_purpose2) { create(:v2_purpose, name: tube_purpose2_name, uuid: tube_purpose2_uuid) }
+
+  # tube states
+  let(:tube1_state) { 'pending' }
+  let(:tube2_state) { 'pending' }
+  let(:tube3_state) { 'pending' }
+  let(:tube4_state) { 'pending' }
+  let(:tube5_state) { 'pending' }
+  let(:tube6_state) { 'pending' }
+
+  # tubes
+  let(:tube1) do
+    create(
+      :v2_tube_with_metadata,
+      uuid: tube1_uuid,
+      barcode_prefix: 'FX',
+      barcode_number: 4,
+      custom_metadatum_collection: tube1_custom_metadata,
+      purpose: tube_purpose1,
+      state: tube1_state
+    )
+  end
+  let(:tube2) do
+    create(
+      :v2_tube_with_metadata,
+      uuid: tube2_uuid,
+      barcode_prefix: 'FX',
+      barcode_number: 5,
+      custom_metadatum_collection: tube2_custom_metadata,
+      purpose: tube_purpose1,
+      state: tube2_state
+    )
+  end
+  let(:tube3) do
+    create(
+      :v2_tube_with_metadata,
+      uuid: tube3_uuid,
+      barcode_prefix: 'FX',
+      barcode_number: 6,
+      custom_metadatum_collection: tube3_custom_metadata,
+      purpose: tube_purpose1,
+      state: tube3_state
+    )
+  end
+  let(:tube4) do
+    create(
+      :v2_tube_with_metadata,
+      uuid: tube4_uuid,
+      barcode_prefix: 'FX',
+      barcode_number: 7,
+      custom_metadatum_collection: tube4_custom_metadata,
+      purpose: tube_purpose2,
+      state: tube4_state
+    )
+  end
+  let(:tube5) do
+    create(
+      :v2_tube_with_metadata,
+      uuid: tube5_uuid,
+      barcode_prefix: 'FX',
+      barcode_number: 8,
+      custom_metadatum_collection: tube5_custom_metadata,
+      purpose: tube_purpose2,
+      state: tube5_state
+    )
+  end
+  let(:tube6) do
+    create(
+      :v2_tube_with_metadata,
+      uuid: tube6_uuid,
+      barcode_prefix: 'FX',
+      barcode_number: 9,
+      custom_metadatum_collection: tube6_custom_metadata,
+      purpose: tube_purpose2,
+      state: tube6_state
+    )
+  end
 
-    # wells
-    let(:well1) { create(:v2_well, location: 'A1', downstream_tubes: [tube1, tube4]) }
-    let(:well2) { create(:v2_well, location: 'B1', downstream_tubes: [tube2, tube5]) }
-    let(:well3) { create(:v2_well, location: 'C1', downstream_tubes: [tube3, tube6]) }
+  # wells
+  let(:well1) { create(:v2_well, location: 'A1', downstream_tubes: [tube1, tube4]) }
+  let(:well2) { create(:v2_well, location: 'B1', downstream_tubes: [tube2, tube5]) }
+  let(:well3) { create(:v2_well, location: 'C1', downstream_tubes: [tube3, tube6]) }
 
-    # plate purpose uuid
-    let(:plate_purpose_uuid) { 'plate_purpose_uuid' }
+  # plate purpose uuid
+  let(:plate_purpose_uuid) { 'plate_purpose_uuid' }
 
-    # plate purpose name
-    let(:plate_purpose_name) { 'plate_purpose' }
+  # plate purpose name
+  let(:plate_purpose_name) { 'plate_purpose_name' }
 
-    # plate purpose
-    let(:plate_purpose) { create(:v2_purpose, name: plate_purpose_name, uuid: plate_purpose_uuid) }
+  # plate purpose
+  let(:plate_purpose) { create(:v2_purpose, name: plate_purpose_name, uuid: plate_purpose_uuid) }
 
-    # plate uuid
-    let(:plate_uuid) { 'plate_uuid' }
+  # plate uuid
+  let(:plate_uuid) { 'plate_uuid' }
 
-    # plate state
-    let(:plate_state) { 'passed' }
+  # plate state
+  let(:plate_state) { 'passed' }
 
-    # plate
-    let(:plate) do
-      create(:v2_plate, wells: [well1, well2, well3], barcode_number: 3, purpose: plate_purpose, state: plate_state)
-    end
+  # plate
+  let(:plate) do
+    create(:v2_plate, wells: [well1, well2, well3], barcode_number: 3, purpose: plate_purpose, state: plate_state)
+  end
 
-    let(:bed1_barcode) { 'bed1_barcode' }
-    let(:bed2_barcode) { 'bed2_barcode' }
-    let(:bed3_barcode) { 'bed3_barcode' }
-
-    let(:robot_config) do
-      {
-        name: 'robot_name',
-        beds: {
-          bed1_barcode => {
-            purpose: plate_purpose_name,
-            states: ['passed'],
-            label: 'Bed 1'
-          },
-          bed2_barcode => {
-            purpose: tube_purpose1_name,
-            states: ['pending'],
-            label: 'Bed 2',
-            target_state: 'passed'
-          },
-          bed3_barcode => {
-            purpose: tube_purpose2_name,
-            states: ['pending'],
-            label: 'Bed 3',
-            target_state: 'passed'
-          }
+  # bed barcodes
+  let(:bed1_barcode) { 'bed1_barcode' }
+  let(:bed2_barcode) { 'bed2_barcode' }
+  let(:bed3_barcode) { 'bed3_barcode' }
+
+  # bed purposes: same as plate and tube-rack purposes by default
+  let(:config_plate_purpose) { 'plate_purpose_name' }
+  let(:config_tube_purpose1) { 'tube_purpose1_name' }
+  let(:config_tube_purpose2) { 'tube_purpose2_name' }
+
+  let(:robot_name) { 'robot_name' }
+
+  let(:robot_config) do
+    {
+      :name => robot_name,
+      :beds => {
+        bed1_barcode => {
+          purpose: config_plate_purpose,
+          states: ['passed'],
+          label: 'Bed 1'
         },
-        relationships: [
-          {
-            'type' => 'relationship_type',
-            'options' => {
-              'parent' => bed1_barcode,
-              'children' => [bed2_barcode, bed3_barcode]
-            }
+        bed2_barcode => {
+          purpose: config_tube_purpose1,
+          states: ['pending'],
+          label: 'Bed 2',
+          target_state: 'passed'
+        },
+        bed3_barcode => {
+          purpose: config_tube_purpose2,
+          states: ['pending'],
+          label: 'Bed 3',
+          target_state: 'passed'
+        }
+      },
+      'class' => 'Robots::PlateToTubeRacksRobot',
+      :relationships => [
+        {
+          'type' => 'relationship_type',
+          'options' => {
+            'parent' => bed1_barcode,
+            'children' => [bed2_barcode, bed3_barcode]
           }
-        ]
-      }
-    end
+        }
+      ]
+    }
+  end
 
-    let(:robot) { described_class.new(robot_config.merge(api: api, user_uuid: user_uuid)) }
+  let(:robot) { described_class.new(robot_config.merge(api: api, user_uuid: user_uuid)) }
 
-    before do
-      # Stub robot requests to the Sequencescape API to look up plate by
-      # barcode. It returns the plate with its wells and downstream tubes.
-      includes = 'purpose,wells,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
-      bed_plate_lookup_with_barcode(plate.barcode.human, [plate], includes)
-      bed_plate_lookup_with_barcode(tube_rack1_barcode, [], includes)
-      bed_plate_lookup_with_barcode(tube_rack2_barcode, [], includes)
-    end
+  let(:scanned_layout) do
+    {
+      bed1_barcode => [plate.human_barcode],
+      bed2_barcode => [tube_rack1_barcode],
+      bed3_barcode => [tube_rack2_barcode]
+    }
+  end
+
+  before do
+    # Stub robot requests to the Sequencescape API to look up plate by
+    # barcode. It returns the plate with its wells and downstream tubes.
+    includes = 'purpose,wells,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
+    bed_plate_lookup_with_barcode(plate.barcode.human, [plate], includes)
+    bed_plate_lookup_with_barcode(tube_rack1_barcode, [], includes)
+    bed_plate_lookup_with_barcode(tube_rack2_barcode, [], includes)
+  end
+
+  describe '#verify' do
+    # The robot will receive the scanned layout as bed_labwares from request parameters
+    # and return a report object showing the validity of each bed and robot.
+    subject { robot.verify(bed_labwares: scanned_layout) }
 
     context 'with two destination purposes' do
       # Parent plate has two child tube-racks. We validate parent bed (bed1)
       # and two child beds (bed2 and bed3).
       context 'with a valid scanned layout' do
-        let(:scanned_layout) do
-          {
-            bed1_barcode => [plate.human_barcode],
-            bed2_barcode => [tube_rack1_barcode],
-            bed3_barcode => [tube_rack2_barcode]
-          }
-        end
-
         it { is_expected.to be_valid }
       end
 
@@ -233,7 +244,7 @@
 
         it { is_expected.not_to be_valid }
 
-        it 'has correct messages' do
+        it 'has correct error messages' do
           errors = [
             "#{unknown_bed_barcode} does not appear to be a valid bed barcode.",
             'Bed 1: should not be empty.',
@@ -243,12 +254,31 @@
         end
       end
 
+      context 'with a plate missing' do
+        # We forgot to scan the plate.
+        let(:scanned_layout) { { bed2_barcode => [tube_rack1_barcode], bed3_barcode => [tube_rack2_barcode] } }
+        it { is_expected.not_to be_valid }
+
+        it 'has correct error messages' do
+          # The following errors are expected because we could not find the
+          # plate, we do not know anything about the tube-racks, and we had to
+          # remove the beds from the robot.
+          errors = [
+            'Bed 1: should not be empty.',
+            'Bed 1: should have children.',
+            "#{bed2_barcode} does not appear to be a valid bed barcode.",
+            "#{bed3_barcode} does not appear to be a valid bed barcode."
+          ]
+          errors.each { |error| expect(subject.message).to include(error) }
+        end
+      end
+
       context 'with a child tube-rack missing' do
         # We forgot to scan the second tube-rack.
         let(:scanned_layout) { { bed1_barcode => [plate.human_barcode], bed2_barcode => [tube_rack1_barcode] } }
         it { is_expected.not_to be_valid }
 
-        it 'has correct messages' do
+        it 'has correct error messages' do
           errors = [
             "Bed 3: Was expected to contain labware barcode #{tube_rack2_barcode} but nothing was scanned (empty)."
           ]
@@ -261,7 +291,7 @@
         let(:scanned_layout) { { bed1_barcode => [plate.human_barcode] } }
         it { is_expected.not_to be_valid }
 
-        it 'has correct messages' do
+        it 'has correct error messages' do
           errors = [
             "Bed 2: Was expected to contain labware barcode #{tube_rack1_barcode} but nothing was scanned (empty).",
             "Bed 3: Was expected to contain labware barcode #{tube_rack2_barcode} but nothing was scanned (empty)."
@@ -283,7 +313,7 @@
 
         it { is_expected.not_to be_valid }
 
-        it 'has correct messages' do
+        it 'has correct error messages' do
           errors = [
             "#{unknown_bed_barcode} does not appear to be a valid bed barcode.",
             "Bed 3: Was expected to contain labware barcode #{tube_rack2_barcode} but nothing was scanned (empty)."
@@ -291,6 +321,21 @@
           errors.each { |error| expect(subject.message).to include(error) }
         end
       end
+
+      context 'with a plate that has an incorrect purpose' do
+        # The plate has a purpose that does not match the bed purpose.
+        let(:plate_purpose_name) { 'incorrect_purpose' }
+
+        it { is_expected.not_to be_valid }
+
+        it 'has correct error messages' do
+          errors = [
+            "Bed 1 - Labware #{plate.barcode.human} is a #{plate_purpose_name} " \
+              "not a #{config_plate_purpose} labware."
+          ]
+          errors.each { |error| expect(subject.message).to include(error) }
+        end
+      end
     end
 
     context 'with one destination purpose' do
@@ -308,4 +353,40 @@
       end
     end
   end
+
+  describe '#perform_transfer' do
+    let(:state_change_requests) do
+      tube_uuids.map do |tube_uuid|
+        stub_api_post(
+          'state_changes',
+          payload: {
+            state_change: {
+              target_state: 'passed',
+              reason: "Robot #{robot_name} started",
+              customer_accepts_responsibility: false,
+              target: tube_uuid,
+              user: user_uuid,
+              contents: nil
+            }
+          },
+          body: json(:state_change, target_state: 'passed')
+        )
+      end
+    end
+
+    before do
+      # Create purpose configs in Settings for state changers.
+      create(:purpose_config, uuid: plate_purpose_uuid, name: plate_purpose_name)
+      create(:purpose_config, uuid: tube_purpose1_uuid, name: tube_purpose1_name)
+      create(:purpose_config, uuid: tube_purpose2_uuid, name: tube_purpose2_name)
+
+      # Stub state change requests to the Sequencescape API; one for each tube on tube-racks.
+      state_change_requests
+    end
+
+    it 'performs transfers for all tubes on the tube-racks' do
+      robot.perform_transfer(scanned_layout)
+      expect(state_change_requests[0]).to have_been_requested
+    end
+  end
 end

From da6942ee915a1b05f24d85a0d2724f1e410dc788 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 00:32:21 +0000
Subject: [PATCH 36/52] Added well_order to get wells by coordinate

---
 app/models/robots/plate_to_tube_racks_robot.rb | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index 24d8d4ca7..9dff2640c 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -30,6 +30,14 @@ class PlateToTubeRacksRobot < Robots::SplittingRobot
     # Option for including downstream tubes and metadata in Plate API response.
     PLATE_INCLUDES = 'purpose,wells,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
 
+    # Returns the well order for getting wells from the plate.
+    #
+    # @return [Symbol] the well order
+    #
+    def well_order
+      :coordinate
+    end
+
     # Returns the bed class for this robot.
     #
     # @return [Class] the bed class

From 9a8f1ce77bcd65804bfb33751060b348bdc866cc Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:43:43 +0000
Subject: [PATCH 37/52] Updated param description in code comments

Co-authored-by: KatyTaylor <kt17@sanger.ac.uk>
---
 app/models/robots/plate_to_tube_racks_robot.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index 9dff2640c..86feaff6a 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -48,7 +48,7 @@ def bed_class
     # Performs the transfer between plate and tube racks. This method is called
     # by the robot controller when the user clicks the start robot button.
     #
-    # @param [Hash] bed_labwares the bed_labwares hash from request parameters
+    # @param [Hash] bed_labwares the bed_labwares hash from request parameters (from user scanning labware into beds)
     # @return [void]
     #
     def perform_transfer(bed_labwares)

From 879e774f2b25bb14707c90e6a459117505cc2d28 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 13:16:09 +0000
Subject: [PATCH 38/52] Fixed pushing the tubes supplied as an argument

---
 app/models/robots/tube_rack_wrapper.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index fc1f18c0c..ae0245c03 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -19,7 +19,7 @@ def initialize(barcode, parent, tubes: [])
       @parent = parent
       @tubes = []
       @tube_positions = {} # Keep track of tube positions for push performance
-      tubes.each { |tube| push(tube) } # Eliminate duplicate tubes by position
+      tubes.each { |tube| push_tube(tube) } # Eliminate duplicate tubes by position
     end
 
     # Returns the last tube on the tube rack. This method used for delegating

From 6e6c8ac01508d9394e04f5f9a28ce9e17a54b093 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:36:24 +0000
Subject: [PATCH 39/52] Updated code comments of robots controller

---
 app/controllers/robots_controller.rb | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/app/controllers/robots_controller.rb b/app/controllers/robots_controller.rb
index d87016d83..9c51bacce 100644
--- a/app/controllers/robots_controller.rb
+++ b/app/controllers/robots_controller.rb
@@ -32,8 +32,10 @@ def start # rubocop:todo Metrics/AbcSize
     end
   end
 
-  # Updates all bed labware metadata with robot barcode.
-  # Beds with no transitions and labware are ignored.
+  # Saves the scanned robot barcode against all the target labware involved in
+  # this bed verification (using the 'labware metadata' model). Beds that are
+  # not involved in this bed verification (no 'transitions', and no labware
+  # scanned into them) are ignored.
   #
   # @param [String] robot_barcode
   # @raise [Sequencescape::Api::ResourceNotFound] if the labware cannot be found

From ae2a08a48f91aa63c1590a9406bcc2f4f206e3cd Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:39:56 +0000
Subject: [PATCH 40/52] Updated more code comments of robots controller

---
 app/controllers/robots_controller.rb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/app/controllers/robots_controller.rb b/app/controllers/robots_controller.rb
index 9c51bacce..f972ab792 100644
--- a/app/controllers/robots_controller.rb
+++ b/app/controllers/robots_controller.rb
@@ -52,8 +52,9 @@ def update_all_labware_metadata(robot_barcode)
     end
   end
 
-  # Updates bed labware metadata with robot barcode. If the bed has its own
-  # method for updating, use that, otherwise use the method of this controller.
+  # Saves the scanned robot barcode against the labware scanned into this bed
+  # (using the 'labware metadata' model). If the bed has its own method for
+  # updating, use that, otherwise use the method of this controller.
   #
   # @param [String] labware_barcode
   # @param [String] robot_barcode

From 7b80d7c765a54501c25f791189b6ebbdb9d65e9b Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:41:01 +0000
Subject: [PATCH 41/52] Removed type from robot config relationships

---
 config/robots.rb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/config/robots.rb b/config/robots.rb
index 8538acedb..5dafdaa35 100644
--- a/config/robots.rb
+++ b/config/robots.rb
@@ -3089,7 +3089,6 @@
       class: 'Robots::PlateToTubeRacksRobot',
       relationships: [
         {
-          'type' => 'LRC PBMC Bank to LRC Bank Seq/Spare',
           'options' => {
             'parent' => bed(12).barcode,
             'children' => [bed(15).barcode, bed(14).barcode]

From be3e7bc6e9e3fdca141f263300f21448f4ae5270 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:48:29 +0000
Subject: [PATCH 42/52] Update app/models/robots/tube_rack_wrapper.rb

Co-authored-by: KatyTaylor <kt17@sanger.ac.uk>
---
 app/models/robots/tube_rack_wrapper.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index ae0245c03..b10c8dbbe 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -22,7 +22,7 @@ def initialize(barcode, parent, tubes: [])
       tubes.each { |tube| push_tube(tube) } # Eliminate duplicate tubes by position
     end
 
-    # Returns the last tube on the tube rack. This method used for delegating
+    # Returns the last tube on the tube rack. This method is used for delegating
     # certain methods to make it behave like a like a labware object.
     #
     # @return [Tube] the last tube

From e8363942345b081fe7df8fd42d040607acaf55cb Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:48:57 +0000
Subject: [PATCH 43/52] Update app/models/robots/plate_to_tube_racks_robot.rb

Co-authored-by: KatyTaylor <kt17@sanger.ac.uk>
---
 app/models/robots/plate_to_tube_racks_robot.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index 86feaff6a..d24d3cf01 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -154,7 +154,7 @@ def prepare_beds
 
     # Deletes the beds and their relationships from the robot's configuration.
     # This method is called by the prepare_beds method after finding which
-    # beds should not be verified. For scRNA, this means either we need to
+    # beds should not be verified. For the scRNA Core pipeline, this means either we need to
     # verify the parent bed first as it has a problem, or we have to remove
     # the sequencing tube-rack from the robot's config as the parent has only
     # contingency-only tube rack to be verified.

From cc5deb64bc03117b21dabee9526922fd62dfe788 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:58:10 +0000
Subject: [PATCH 44/52] Update app/models/robots/tube_rack_wrapper.rb

Co-authored-by: KatyTaylor <kt17@sanger.ac.uk>
---
 app/models/robots/tube_rack_wrapper.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index b10c8dbbe..6863b592e 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 module Robots
   # This wrapper class is for tube racks that are not actual recorded labware.
-  # The instances acts as a labware wrapper and provides access to the tubes.
+  # The instance acts as a labware wrapper and provides access to the tubes.
   # Labware methods are delegated to the first tube on the tube rack.
   #
   class TubeRackWrapper

From 1a6ba664c4498ca84fd0c41518ae3fa9293455ec Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:58:50 +0000
Subject: [PATCH 45/52] Update app/models/robots/tube_rack_wrapper.rb

Co-authored-by: KatyTaylor <kt17@sanger.ac.uk>
---
 app/models/robots/tube_rack_wrapper.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index 6863b592e..68aacfd3e 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -23,7 +23,7 @@ def initialize(barcode, parent, tubes: [])
     end
 
     # Returns the last tube on the tube rack. This method is used for delegating
-    # certain methods to make it behave like a like a labware object.
+    # certain methods to make it behave like a labware object.
     #
     # @return [Tube] the last tube
     def last_tube

From 28f7c672473856f75948750f0fa0380ebff1c420 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:59:14 +0000
Subject: [PATCH 46/52] Update app/models/robots/tube_rack_wrapper.rb

Co-authored-by: KatyTaylor <kt17@sanger.ac.uk>
---
 app/models/robots/tube_rack_wrapper.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index 68aacfd3e..17e31fd8b 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -2,7 +2,7 @@
 module Robots
   # This wrapper class is for tube racks that are not actual recorded labware.
   # The instance acts as a labware wrapper and provides access to the tubes.
-  # Labware methods are delegated to the first tube on the tube rack.
+  # Labware methods are delegated to the last tube on the tube rack.
   #
   class TubeRackWrapper
     attr_accessor :barcode, :parent, :tubes

From 5e83c039afb5362173b8376ce3b6653615472f21 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:47:18 +0000
Subject: [PATCH 47/52] Removed typo from code comment

---
 app/models/robots/plate_to_tube_racks_robot.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index d24d3cf01..5a7255b5c 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -135,7 +135,7 @@ def prepare_labware_store(bed_labwares)
     # override the bed configuration based on availability of labware here.
     #
     # NB. The child labware are tube-rack wrapper objects, not actual labware.
-    # The information about tube-racks for are found using the metadata of the
+    # The information about tube-racks are found using the metadata of the
     # downstream tubes, included in the Sequencescape API response.
     #
     # @ return [void]

From f7a67f270dd3059d3a360e5c79d5b833a4901cfe Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:56:54 +0000
Subject: [PATCH 48/52] Prettier

---
 config/robots.rb | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/config/robots.rb b/config/robots.rb
index 5dafdaa35..e8429d14e 100644
--- a/config/robots.rb
+++ b/config/robots.rb
@@ -3088,12 +3088,7 @@
       },
       class: 'Robots::PlateToTubeRacksRobot',
       relationships: [
-        {
-          'options' => {
-            'parent' => bed(12).barcode,
-            'children' => [bed(15).barcode, bed(14).barcode]
-          }
-        }
+        { 'options' => { 'parent' => bed(12).barcode, 'children' => [bed(15).barcode, bed(14).barcode] } }
       ]
     )
   end

From ba21795d81780d4854925cc4a0611ef38db04f6e Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Mon, 30 Oct 2023 23:57:23 +0000
Subject: [PATCH 49/52] Renamed find_or_create_tube_rack to
 find_or_create_tube_rack_wrapper

---
 app/models/robots/plate_to_tube_racks_robot.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index 5a7255b5c..7fb4b63c6 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -230,7 +230,7 @@ def find_tube_racks(plate)
           next if well.downstream_tubes.blank?
           well.downstream_tubes.each do |tube|
             barcode = tube.custom_metadatum_collection.metadata[:tube_rack_barcode]
-            find_or_create_tube_rack(racks, barcode, plate).push_tube(tube)
+            find_or_create_tube_rack_wrapper(racks, barcode, plate).push_tube(tube)
           end
         end
     end
@@ -242,7 +242,7 @@ def find_tube_racks(plate)
     # @param [Plate] plate the parent plate
     # @return [TubeRackWrapper] the tube rack wrapper object
     #
-    def find_or_create_tube_rack(racks, barcode, plate)
+    def find_or_create_tube_rack_wrapper(racks, barcode, plate)
       rack = racks.detect { |tube_rack| tube_rack.barcode.human == barcode }
       return rack if rack.present?
       labware_barcode = LabwareBarcode.new(human: barcode, machine: barcode)

From bc03b3b8f2fc3bf753cebbf9a3276a096a47f87b Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Tue, 31 Oct 2023 01:00:21 +0000
Subject: [PATCH 50/52] Updated comments about @tube_positions

---
 app/models/robots/tube_rack_wrapper.rb | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index 17e31fd8b..61360b7e8 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -18,7 +18,10 @@ def initialize(barcode, parent, tubes: [])
       @barcode = barcode
       @parent = parent
       @tubes = []
-      @tube_positions = {} # Keep track of tube positions for push performance
+
+      # Keep track of tube positions, tube coordinate on rack => index in
+      # @tubes array, e.g. 'C1' => 0 .
+      @tube_positions = {}
       tubes.each { |tube| push_tube(tube) } # Eliminate duplicate tubes by position
     end
 

From 62636bbc328527a4fd2e6d4eaa8c2444d954bae5 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 2 Nov 2023 00:17:42 +0000
Subject: [PATCH 51/52] Updated transfer test to check the state change on all
 tubes

---
 spec/models/robots/plate_to_tube_racks_robot_spec.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/spec/models/robots/plate_to_tube_racks_robot_spec.rb b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
index 25aa43bf2..a86d3603a 100644
--- a/spec/models/robots/plate_to_tube_racks_robot_spec.rb
+++ b/spec/models/robots/plate_to_tube_racks_robot_spec.rb
@@ -386,7 +386,9 @@
 
     it 'performs transfers for all tubes on the tube-racks' do
       robot.perform_transfer(scanned_layout)
+
       expect(state_change_requests[0]).to have_been_requested
+      tube_uuids.each_with_index { |_tube_uuid, index| expect(state_change_requests[index]).to have_been_requested }
     end
   end
 end

From aa5787cc61c5c382da22e10d1cd9cf7815e2bb2d Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 3 Nov 2023 10:30:16 +0000
Subject: [PATCH 52/52] Fixed the order of tag data for Yard @param tags

---
 app/controllers/robots_controller.rb          | 10 +++---
 .../robots/bed/plate_to_tube_racks_bed.rb     |  6 ++--
 .../robots/plate_to_tube_racks_robot.rb       | 32 +++++++++----------
 app/models/robots/tube_rack_wrapper.rb        | 10 +++---
 4 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/app/controllers/robots_controller.rb b/app/controllers/robots_controller.rb
index f972ab792..32f8e32bd 100644
--- a/app/controllers/robots_controller.rb
+++ b/app/controllers/robots_controller.rb
@@ -37,7 +37,7 @@ def start # rubocop:todo Metrics/AbcSize
   # not involved in this bed verification (no 'transitions', and no labware
   # scanned into them) are ignored.
   #
-  # @param [String] robot_barcode
+  # @param robot_barcode [String] the robot barcode scanned
   # @raise [Sequencescape::Api::ResourceNotFound] if the labware cannot be found
   #
   def update_all_labware_metadata(robot_barcode)
@@ -56,8 +56,8 @@ def update_all_labware_metadata(robot_barcode)
   # (using the 'labware metadata' model). If the bed has its own method for
   # updating, use that, otherwise use the method of this controller.
   #
-  # @param [String] labware_barcode
-  # @param [String] robot_barcode
+  # @param labware_barcode [String] the barcode of the labware on the bed
+  # @param robot_barcode [String] the robot barcode scanned
   # @raise [Sequencescape::Api::ResourceNotFound] if the labware cannot be found
   #
   def update_bed_labware_metadata(bed, robot_barcode)
@@ -68,8 +68,8 @@ def update_bed_labware_metadata(bed, robot_barcode)
 
   # Updates labware metadata with robot barcode.
   #
-  # @param [String] labware_barcode
-  # @param [String] robot_barcode
+  # @param labware_barcode [String] the barcode of the labware on the bed
+  # @param robot_barcode [String] the robot barcode scanned
   # @raise [Sequencescape::Api::ResourceNotFound] if the labware cannot be found
   #
   def labware_created_with_robot(labware_barcode, robot_barcode)
diff --git a/app/models/robots/bed/plate_to_tube_racks_bed.rb b/app/models/robots/bed/plate_to_tube_racks_bed.rb
index 6c8cd05e3..01617e757 100644
--- a/app/models/robots/bed/plate_to_tube_racks_bed.rb
+++ b/app/models/robots/bed/plate_to_tube_racks_bed.rb
@@ -11,7 +11,7 @@ class PlateToTubeRacksBed < Robots::Bed::Base
     # This method is called inside the robot controller's start action for
     # tube-rack wrappers and it sets the created_with_robot metadata field.
     #
-    # @param [String] robot_barcode the robot barcode
+    # @param robot_barcode [String] the robot barcode
     # @return [void]
     #
     def labware_created_with_robot(robot_barcode)
@@ -35,7 +35,7 @@ def child_labware
 
     # Loads labware into this bed from the robot's labware store.
     #
-    # @param [Array<String>] barcodes array containing the barcode of the labware
+    # @param barcodes [Array<String>] array containing the barcode of the labware
     # @return [void]
     #
     def load(barcodes)
@@ -57,7 +57,7 @@ def transition
     # Changes the state of one tube to the target state. This method is called
     # by the transition method.
     #
-    # @param [Tube] tube the tube
+    # @param tube [Tube] the tube for which the state should be changed
     def change_tube_state(tube)
       state_changer = StateChangers.lookup_for(tube.purpose.uuid)
       state_changer.new(api, tube.uuid, user_uuid).move_to!(target_state, "Robot #{robot.name} started")
diff --git a/app/models/robots/plate_to_tube_racks_robot.rb b/app/models/robots/plate_to_tube_racks_robot.rb
index 7fb4b63c6..9f00bc6a8 100644
--- a/app/models/robots/plate_to_tube_racks_robot.rb
+++ b/app/models/robots/plate_to_tube_racks_robot.rb
@@ -48,7 +48,7 @@ def bed_class
     # Performs the transfer between plate and tube racks. This method is called
     # by the robot controller when the user clicks the start robot button.
     #
-    # @param [Hash] bed_labwares the bed_labwares hash from request parameters (from user scanning labware into beds)
+    # @param bed_labwares [Hash] the bed_labwares hash from request parameters (from user scanning labware into beds)
     # @return [void]
     #
     def perform_transfer(bed_labwares)
@@ -60,7 +60,7 @@ def perform_transfer(bed_labwares)
     # called by the robot controller when the user clicks the validate layout
     # button.
     #
-    # @param [Hash] params request parameters
+    # @param params [Hash] request parameters
     # @return [Report]
     #
     def verify(params)
@@ -73,7 +73,7 @@ def verify(params)
     # labware. The labware returned can be Plate objects or labware-like
     # wrapper objects for tube racks.
     #
-    # @param [Array<String>] barcodes array of barcodes
+    # @param barcodes [Array<String>] array of barcodes
     # @return [Array<Plate, TubeRackWrapper>]
     #
     def find_bed_labware(barcodes)
@@ -83,7 +83,7 @@ def find_bed_labware(barcodes)
     # Returns an array of child labware from the robot's labware store for
     # the given Plate.
     #
-    # @param [Plate] plate the parent plate
+    # @param plate [Plate] the parent plate
     # @return [Array<TubeRackWrapper>] array of tube rack wrapper objects
     #
     def child_labware(plate)
@@ -94,7 +94,7 @@ def child_labware(plate)
 
     # Prepares the robot before handling actions.
     #
-    # @param [Hash] bed_labwares hash from request parameters
+    # @param bed_labwares [Hash] the hash from request parameters
     # @return [void]
     def prepare_robot(bed_labwares)
       prepare_labware_store(bed_labwares)
@@ -104,7 +104,7 @@ def prepare_robot(bed_labwares)
     # Prepares the labware store before handling robot actions. This method is
     # called before the robot's bed verification and perform transfer actions.
     #
-    # @param [Hash] bed_labwares hash from request parameters
+    # @param bed_labwares [Hash] the hash from request parameters
     # @return [void]
     #
     def prepare_labware_store(bed_labwares)
@@ -159,8 +159,8 @@ def prepare_beds
     # the sequencing tube-rack from the robot's config as the parent has only
     # contingency-only tube rack to be verified.
     #
-    # @param [Array<String>] barcodes array of barcodes to be removed
-    # @param [Array<String>] relationship_children array of child barcodes
+    # @param barcodes [Array<String>] array of barcodes to be removed
+    # @param relationship_children [Array<String>] array of child barcodes
     # @return [void]
     #
     def delete_beds(barcodes, relationship_children)
@@ -171,7 +171,7 @@ def delete_beds(barcodes, relationship_children)
     # Returns an array of sanitised barcodes from the bed_labwares hash from
     # request parameters.
     #
-    # @param [Hash] bed_labwares hash from request parameters
+    # @param bed_labwares [Hash] the hash from request parameters
     # @return [Array<String>] array of barcodes
     #
     def stripped_barcodes(bed_labwares)
@@ -180,7 +180,7 @@ def stripped_barcodes(bed_labwares)
 
     # Adds the plate to the robot's labware store.
     #
-    # @param [Plate] plate the parent plate
+    # @param plate [Plate] the parent plate
     # @return [void]
     #
     def add_plate_to_labware_store(plate)
@@ -189,7 +189,7 @@ def add_plate_to_labware_store(plate)
 
     # Adds the tube racks wrappers from plate includes to the labware store.
     #
-    # @param [Plate] plate the parent plate
+    # @param plate [Plate] the parent plate
     # @return [void]
     #
     def add_tube_racks_to_labware_store(plate)
@@ -209,7 +209,7 @@ def labware_store
     # Returns the Plate for the given barcode from the Sequencescape API.
     # The call includes downstream tubes and their metadata as well.
     #
-    # @param [String] barcode the barcode of the plate
+    # @param barcode [String] the barcode of the plate
     # @return [Plate] the plate
     #
     def find_plate(barcode)
@@ -219,7 +219,7 @@ def find_plate(barcode)
     # Returns an array of tube rack wrapper objects that from the downstream tubes
     # of the given plate.
     #
-    # @param [Plate] plate the parent plate
+    # @param plate [Plate] the parent plate
     # @return [Array<TubeRackWrapper>] array of tube rack wrapper objects
     #
     def find_tube_racks(plate)
@@ -237,9 +237,9 @@ def find_tube_racks(plate)
 
     # Returns an existing or new tube rack wrapper object.
     #
-    # @param [Array<TubeRackWrapper>] racks the tube racks found so far
-    # @param [String] barcode the barcode of the tube rack
-    # @param [Plate] plate the parent plate
+    # @param racks [Array<TubeRackWrapper>] the tube racks found so far
+    # @param barcode[String] the barcode of the tube rack
+    # @param plate [Plate] the parent plate
     # @return [TubeRackWrapper] the tube rack wrapper object
     #
     def find_or_create_tube_rack_wrapper(racks, barcode, plate)
diff --git a/app/models/robots/tube_rack_wrapper.rb b/app/models/robots/tube_rack_wrapper.rb
index 61360b7e8..a63445220 100644
--- a/app/models/robots/tube_rack_wrapper.rb
+++ b/app/models/robots/tube_rack_wrapper.rb
@@ -10,9 +10,9 @@ class TubeRackWrapper
 
     # Initializes a new instance of the class.
     #
-    # @param [LabwareBarcode] barcode the barcode object of the tube rack
-    # @param [Plate] parent the parent plate
-    # @tubes [Array<Tube>] the tubes on the tube rack
+    # @param barcode [LabwareBarcode] the barcode object of the tube rack
+    # @param parent [Plate] the parent plate
+    # @param tubes [Array<Tube>] the tubes on the tube rack
     #
     def initialize(barcode, parent, tubes: [])
       @barcode = barcode
@@ -37,7 +37,7 @@ def last_tube
     # is an existing tube with the same position, the tube with the latest
     # creation date is kept.
     #
-    # @param [Tube] tube the tube to be added
+    # @param tube [Tube] the tube to be added
     # @return [Void]
     #
     def push_tube(tube)
@@ -62,7 +62,7 @@ def human_barcode
 
     # Returns the tube rack position of a tube from its metadata
     #
-    # @param [Tube] tube the tube
+    # @param tube [Tube] the tube
     # @return [String] the tube rack position
     #
     def tube_rack_position(tube)