Merge branch '3936-dpl-969-support-for-chromium-chip-labware' into ua…

…t-26th-jan-24

app/controllers/api/v2/plate_purposes_controller.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Api
+  module V2
+    # Provides a JSON API controller for receptacle
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
+    class PlatePurposesController < JSONAPI::ResourceController
+      # By default JSONAPI::ResourceController provides most the standard
+      # behaviour, and in many cases this file may be left empty.
+    end
+  end
+end

app/models/map.rb

@@ -18,7 +18,19 @@ module Coordinate
     # TODO: These methods are only valid for standard plates. Moved them here to make that more explicit
     # (even if its not strictly appropriate) They could do with refactoring/removing.
 
-    PLATE_DIMENSIONS = Hash.new { |_h, _k| [] }.merge(96 => [12, 8], 384 => [24, 16])
+    # A hash representing the dimensions of different types of plates.
+    # The keys are the total number of wells in the plate, and the values are
+    # arrays, where the first element is the number of columns and the second
+    # element is the number of rows.
+    #
+    # @note
+    #   - 96 represents a 96-well plate, arranged in 12 columns and 8 rows.
+    #   - 384 represents a 384-well plate, arranged in 24 columns and 16 rows.
+    #   - 16 represents a 16-well Chromium Chip, which has 8 columns and 2 rows.
+    #     Although a 16-well Chromium Chip does not have 3:2 ratio to be a
+    #     standard plate, i.e. it has 4:1 ratio, the methods here still apply.
+    # @return [Hash{Integer => Array<Integer>}] the dimensions of the plates
+    PLATE_DIMENSIONS = Hash.new { |_h, _k| [] }.merge(96 => [12, 8], 384 => [24, 16], 16 => [8, 2])
 
     # Seems to expect row to be zero-indexed but column to be 1 indexed
     def self.location_from_row_and_column(row, column, _ = nil, __ = nil)
@@ -269,5 +281,6 @@ def walk_plate_in_row_major_order(size, asset_shape = nil)
         .order(:row_order)
         .each { |position| yield(position, position.row_order) }
     end
+    alias walk_plate_horizontally walk_plate_in_row_major_order
   end
 end

app/resources/api/v2/plate_purpose_resource.rb

@@ -0,0 +1,85 @@
+# frozen_string_literal: true
+
+module Api
+  module V2
+    # Provides a JSON API representation of PlatePurpose
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
+    class PlatePurposeResource < BaseResource
+      model_name 'PlatePurpose'
+
+      # This resource is similar to PurposeResource but it was created to
+      # migrate the registration of plate purposes done by the Limber rake
+      # task config:generate from API version 1 to API version 2.
+
+      # The following attributes are sent by Limber for a new plate purpose.
+
+      # @!attribute name
+      #  @return [String] the name of the plate purpose
+      attribute :name
+
+      # @!attribute stock_plate
+      #  @return [Boolean] whether the plates of this purpose are stock plates
+      attribute :stock_plate
+
+      # @!attribute cherrypickable_target
+      #  @return [Boolean] whether the plates of this purpose are cherrypickable
+      attribute :cherrypickable_target
+
+      # @!attribute input_plate
+      #  @return [Boolean] whether the plates of this purpose are input plates
+      attribute :input_plate
+
+      # @!attribute size
+      #  @return [Integer] the size of the plates of this purpose
+      attribute :size
+
+      # @!attribute asset_shape
+      #  @return [String] the name of the shape of the plates of this purpose
+      attribute :asset_shape
+
+      # The following attribute is required by Limber to store purposes.
+
+      # @!attribute [r] uuid
+      #  @return [String] the UUID of the plate purpose
+      attribute :uuid, readonly: true
+
+      # Sets the asset shape of the plate purpose by name if given.
+      # 'asset_shape' can be given via the Limber purpose configuration and
+      # defaults to 'Standard' if not provided. If the name is given and not
+      # found, an error is raised. Note that the name is case-sensitive.
+      #
+      # @param name [String] the name of the asset shape
+      # @return [void]
+      def asset_shape=(name)
+        @model.asset_shape = (AssetShape.find_by!(name: name) if name.present?) || AssetShape.default
+      end
+
+      # Returns the name of the asset shape of the plate purpose.
+      # The asset_shape association is not utilized in Limber. This method
+      # returns the name of the asset shape associated with the plate purpose.
+      #
+      # @return [String] the name of the asset shape
+      def asset_shape
+        @model.asset_shape.name
+      end
+
+      # Returns the input_plate attribute from the type of the plate purpose.
+      # This method is the counterpart to the model's attribute writer for
+      # input_plate. It performs the inverse operation, determining the value
+      # of input_plate attribute based on the model's type.
+      #
+      # @return [Boolean] whether the plate purpose is an input plate
+      def input_plate
+        @model.type == 'PlatePurpose::Input'
+      end
+
+      # Prevents updating existing plate purposes.
+      #
+      # @param _context [JSONAPI::Resource::Context] not used
+      # @return [Array<Symbol>] empty array
+      def updatable_fields(_context)
+        []
+      end
+    end
+  end
+end

config/default_records/asset_shapes/default_records.yml

@@ -0,0 +1,65 @@
+# This file contains the AssetShape and associated Map records to be created in
+# deployment environments by RecordLoader. The loading is triggered by the
+# "post_deploy" task. The records are checked against the database by their
+# names. If the records already exist, they are not created. AssetShape records
+# are created in the "asset_shapes" table, and Map records are created in the
+# "maps" table. Each section in this file starts with the name of the AssetShape
+# record. The "horizontal_ratio" and "vertical_ratio" options are used to define
+# the plate's shape. These options represent the simplest form of the ratio
+# between the number of columns and rows (i.e. width / height). Specifically,
+# "horizontal_ratio" corresponds to the number of columns (numerator), and
+# "vertical_ratio" corresponds to the number of rows (denominator). For
+# instance, a "Standard" 96-well plate has a horizontal ratio of 3 and a
+# vertical ratio of 2 because it has 12 columns (1 to 12) and 8 rows (A to H).
+# The "sizes" option defines different plate sizes with that shape, for example,
+# 96 and 384. Each size determines the number of Map records to be created for
+# that shape and size. The "description_strategy" option defines the nested
+# module in the Map model that is used for handling positions, rows, columns,
+# and wells in plate geometry. AssetShapeLoader uses PlateMapGeneration to
+# create records in the database. Each "Well" on a "Plate" is associated with a
+# "Map".
+#
+# When configuring a "Purpose", both "asset_shape" and "size" need to be
+# specified in that configuration in order to use the correct labware. If not
+# specified, they will default to Standard and 96 respectively. For example,
+# LRC HT 5p Chip:
+#   :asset_shape: ChromiumChip
+#   :size: 16
+#
+# The information in this file is duplicated in a couple of places in the
+# codebase. When the local development environment is "setup" or "reset", a
+# database "seed" is executed. This results in using the maps hash in
+# PlateMapGeneration. The same hash is used when the RSpec before suite hook
+# calls PlateMapGeneration to create records in the local test environment.
+# Plate sizes and number of rows and columns are also defined separately in
+# a hash in the Map model, which is used by the nested Coordinate module.
+---
+Standard:
+  horizontal_ratio: 3
+  vertical_ratio: 2
+  description_strategy: Coordinate
+  sizes: [96, 384]
+
+Fluidigm96:
+  horizontal_ratio: 3
+  vertical_ratio: 8
+  description_strategy: Sequential
+  sizes: [96]
+
+Fluidigm192:
+  horizontal_ratio: 3
+  vertical_ratio: 4
+  description_strategy: Sequential
+  sizes: [192]
+
+StripTubeColumn:
+  horizontal_ratio: 1,
+  vertical_ratio: 8,
+  description_strategy: Sequential
+  sizes: [8]
+
+ChromiumChip:
+  horizontal_ratio: 4
+  vertical_ratio: 1
+  description_strategy: Coordinate
+  sizes: [16]

config/routes.rb

@@ -28,6 +28,7 @@
       jsonapi_resources :lot_types
       jsonapi_resources :lots
       jsonapi_resources :orders
+      jsonapi_resources :plate_purposes
       jsonapi_resources :plate_templates
       jsonapi_resources :plates
       jsonapi_resources :poly_metadata

features/support/step_definitions/7119309_pulldown_cherrypick_pipeline_steps.rb

@@ -38,7 +38,8 @@
 Given(/^I have a plate "([^"]*)" with the following wells:$/) do |plate_barcode, well_details|
   plate = FactoryBot.create :plate, barcode: plate_barcode
   well_details.hashes.each do |well_detail|
-    well = Well.create!(map: Map.find_by(description: well_detail[:well_location], asset_size: 96), plate: plate)
+    well =
+      Well.create!(map: Map.find_by(description: well_detail[:well_location], asset_size: plate.size), plate: plate)
     well.well_attribute.update!(
       concentration: well_detail[:measured_concentration],
       measured_volume: well_detail[:measured_volume]

features/support/step_definitions/plate_steps.rb

@@ -111,7 +111,7 @@
 Given /^well "([^"]*)" is holded by plate "([^"]*)"$/ do |well_uuid, plate_uuid|
   well = Uuid.find_by(external_id: well_uuid).resource
   plate = Uuid.find_by(external_id: plate_uuid).resource
-  well.update!(plate: plate, map: Map.find_by(description: 'A1'))
+  well.update!(plate: plate, map: Map.find_by(description: 'A1', asset_size: plate.size))
   Plate.find(plate_id).primary_barcode.update!(barcode: 'DN1S')
 end
 
@@ -213,7 +213,8 @@
   # plate = FactoryBot.create :plate, :barcode => plate_barcode
   plate = Uuid.find_by(external_id: uuid).resource
   well_details.hashes.each do |well_detail|
-    well = Well.create!(map: Map.find_by(description: well_detail[:well_location], asset_size: 96), plate: plate)
+    well =
+      Well.create!(map: Map.find_by(description: well_detail[:well_location], asset_size: plate.size), plate: plate)
     well.well_attribute.update!(
       concentration: well_detail[:measured_concentration],
       measured_volume: well_detail[:measured_volume]

lib/plate_map_generation.rb

@@ -22,7 +22,8 @@ def self.maps
         vertical_ratio: 8,
         description_strategy: 'Sequential',
         sizes: [8]
-      }
+      },
+      { name: 'ChromiumChip', horizontal_ratio: 4, vertical_ratio: 1, description_strategy: 'Coordinate', sizes: [16] }
     ]
   end
 

lib/record_loader/asset_shape_loader.rb

@@ -0,0 +1,33 @@
+# frozen_string_literal: true
+
+# RecordLoader handles automatic population and updating of database records
+# across different environments
+# @see https://rubydoc.info/github/sanger/record_loader/
+module RecordLoader
+  # Creates the specified asset shapes if they are not present
+  class AssetShapeLoader < ApplicationRecordLoader
+    config_folder 'asset_shapes'
+
+    # Creates an AssetShape record with the given name and options. If a record
+    # with the same name already exists, it is skipped. If not, a new one is
+    # created. For each size specified in the options, Map records are generated
+    # up to that size, unless they already exist.
+    #
+    # @param name [String] the name of the AssetShape record
+    # @param options [Hash] the options to be used for creating the record
+    # @option options [Integer] :horizontal_ratio the numerator in the simplest form of the plate width/height ratio
+    # @option options [Integer] :vertical_ratio the denominator in the simplest form of the plate width/height ratio
+    # @option options [String] :description_strategy The strategy for describing the plate
+    # @option options [Array<Integer>] :sizes The sizes of the plates to generate Maps for
+    def create_or_update!(name, options)
+      config = { name: name }.merge(options.symbolize_keys)
+
+      # PlateMapGeneration expects a non-namespaced constant for
+      # description_strategy. It adds "Map::" prefix to refer to a nested
+      # module in the Map class. We remove this prefix in case it is given
+      # in the records file.
+      config[:description_strategy] = config[:description_strategy].delete_prefix('Map::')
+      PlateMapGeneration.new(**config).save!
+    end
+  end
+end

lib/record_loader/plate_purpose_loader.rb

@@ -27,6 +27,7 @@ def create_purpose(name, config)
       creator = config.delete('plate_creator')
       config['barcode_printer_type'] = barcode_printer_type(config.delete('barcode_printer_type'))
       config['name'] = name
+      config['asset_shape'] = AssetShape.find_by(name: config.delete('asset_shape')) || AssetShape.default
       purpose = PlatePurpose.create!(config)
       build_creator(purpose, creator) if creator
     end

lib/tasks/record_loader/asset_shape.rake

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+namespace :record_loader do
+  desc 'Automatically generate AssetShapes and Maps through AssetShapesLoader'
+  task asset_shape: :environment do
+    RecordLoader::AssetShapeLoader.new.create!
+  end
+end
+
+# Automatically run this record loader as part of record_loader:all
+# Remove this line if the task should only run when invoked explicitly
+task 'record_loader:all' => 'record_loader:asset_shape'

spec/controllers/submissions_controller_spec.rb

@@ -17,12 +17,25 @@
 
       session[:user] = @user
 
+      # We need to specify the details of the map while using Map.find_by
+      # to avoid picking up another map with the same description. As of
+      # the current records, the 'description' and 'asset_size' attributes
+      # can uniquely identify a map; asset_shape is added for completeness.
+      @asset_shape = AssetShape.default
+      @asset_size = 96
+
       @plate = build :plate, barcode: 'SQPD-123456'
       %w[A1 A2 A3 B1 B2 B3 C1 C2 C3].each do |location|
-        well = build :well_with_sample_and_without_plate, map: Map.find_by(description: location)
+        well =
+          build :well_with_sample_and_without_plate,
+                map: Map.find_by(description: location, asset_shape: @asset_shape, asset_size: @asset_size)
         @plate.wells << well
       end
-      build(:well, map: Map.find_by(description: 'C5'), plate: @plate)
+      build(
+        :well,
+        map: Map.find_by(description: 'C5', asset_shape: @asset_shape, asset_size: @asset_size),
+        plate: @plate
+      )
       @plate.save
       @study = create :study, name: 'A study'
       @project = create :project, name: 'A project'
@@ -142,7 +155,10 @@
       context 'with a more recent plate' do
         before do
           @new_plate = create :plate, plate_purpose: @plate.purpose
-          @well = create :well, map: Map.find_by(description: 'A1'), plate: @new_plate
+          @well =
+            create :well,
+                   map: Map.find_by(description: 'A1', asset_shape: @asset_shape, asset_size: @asset_size),
+                   plate: @new_plate
           create(:aliquot, sample: Sample.find_by(name: @samples.first), receptacle: @well)
           post(
             :create,
@@ -184,7 +200,9 @@
         @order_count = Order.count
         @wd_plate = create :working_dilution_plate
         %w[A1 A2 A3 B1 B2 B3 C1 C2 C3].each do |location|
-          well = create :empty_well, map: Map.find_by(description: location)
+          well =
+            create :empty_well,
+                   map: Map.find_by(description: location, asset_shape: @asset_shape, asset_size: @asset_size)
           well.aliquots.create(sample: @plate.wells.located_at(location).first.aliquots.first.sample)
           @wd_plate.wells << well
         end

spec/data/record_loader/plate_purposes/003_chromium_chip.yml

@@ -0,0 +1,6 @@
+---
+ChromiumChip Plate:
+  asset_shape: ChromiumChip
+  cherrypickable_target: false
+  target_type: plate
+  size: 16

spec/factories/purpose_factories.rb

@@ -65,6 +65,11 @@
       size { 192 }
       asset_shape factory: %i[fluidigm_192_shape]
     end
+
+    factory :chromium_chip_purpose do
+      size { 16 }
+      asset_shape { AssetShape.find_by(name: 'ChromiumChip') }
+    end
   end
 
   factory :dilution_plate_purpose do

spec/lib/record_loader/plate_purpose_loader_spec.rb

@@ -61,4 +61,18 @@ def a_new_record_loader
       expect(the_creator.parent_plate_purposes).to eq(PlatePurpose.where(name: 'Stock Plate'))
     end
   end
+
+  context 'with ChromimumChip Plate purpose' do
+    let(:selected_files) { '003_chromium_chip' }
+    let(:purpose_name) { 'ChromiumChip Plate' }
+
+    before { record_loader.create! }
+
+    it 'creates a plate purpose' do
+      expect(Purpose.where(name: purpose_name).count).to eq(1)
+      purpose = Purpose.where(name: purpose_name).first
+      expect(purpose.asset_shape).to eq(AssetShape.find_by(name: 'ChromiumChip'))
+      expect(purpose.size).to eq(16)
+    end
+  end
 end

spec/models/api/messages/well_stock_resource_io_spec.rb

@@ -14,7 +14,7 @@
   let(:plate_barcode) { build(:plate_barcode) }
   let(:well) do
     create :well,
-           map: Map.find_by!(description: 'A1'),
+           map: Map.find_by!(description: 'A1', asset_shape: AssetShape.default, asset_size: 96),
            plate: create(:plate, barcode: plate_barcode.barcode),
            well_attribute: create(:complete_well_attribute)
   end