Merge pull request #4010 from sanger/develop

Develop into master

.release-version

@@ -1 +1 @@
-14.30.0
+14.31.0

Gemfile.lock

@@ -281,7 +281,7 @@ GEM
     net-smtp (0.4.0)
       net-protocol
     netrc (0.11.0)
-    nio4r (2.5.9)
+    nio4r (2.7.0)
     nokogiri (1.15.4)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
@@ -298,7 +298,7 @@ GEM
     pry-rails (0.3.9)
       pry (>= 0.10.4)
     public_suffix (5.0.4)
-    puma (6.4.0)
+    puma (6.4.2)
       nio4r (~> 2.0)
     racc (1.7.3)
     rack (2.2.8)

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/controllers/api/v2/poly_metadata_controller.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module Api
+  module V2
+    # Provides a JSON API controller for PolyMetadatum
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
+    class PolyMetadataController < 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/location_report.rb

@@ -89,7 +89,7 @@ def generate!
 
     ActiveRecord::Base.transaction do
       Tempfile.open(filename) do |tempfile|
-        generate_report_rows { |fields| tempfile << CSV.generate_line(fields, csv_options) }
+        generate_report_rows { |fields| tempfile << CSV.generate_line(fields, **csv_options) }
         tempfile.rewind
         update!(report: tempfile)
       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/models/poly_metadatum.rb

@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+#
+# A polymetadatum is a key value pair store. It is set up such that it can be
+# associated with multiple different models (ie. a polymorphic relationship).
+#
+# It can be linked to any model that has the reverse association set up.
+# i.e. add this association line to the model:
+# has_many :poly_metadata, as: :metadatable, dependent: :destroy
+# and this line to the v2 api resource (if api access needed):
+# has_many :poly_metadata, as: :metadatable, class_name: 'PolyMetadatum'
+#
+# See Request model and associated api v2 resource for an example of how to use this.
+#
+class PolyMetadatum < ApplicationRecord
+  # Associations
+  belongs_to :metadatable, polymorphic: true, optional: false
+
+  # Validations
+  validates :key, presence: true # otherwise nil is a valid key
+  validates :value, presence: true
+
+  # Currently we allow the same key to be used for different metadatable objects,
+  # but it has to be unique for each metadatable object and is case insensitive.
+  # This is to allow the same key to be used for different models, e.g. a request
+  # and a sample might both have metadata called 'somename', but the same model cannot
+  # have two metadata called 'somename' and 'SOMENAME'.
+  # A metadatable has both a type and an id, so the combination key is unique.
+  # metadatable_type is the class name of the model, e.g. 'Request'
+  # metadatable_id is the database id of the model instance
+  validates :key, uniqueness: { scope: %i[metadatable_type metadatable_id], case_sensitive: false }
+
+  # Methods
+  def to_h
+    { key => value }
+  end
+end

app/models/request.rb

@@ -87,6 +87,9 @@ def date_for_state(state)
   # reflect the final product of a request.
   has_many :related_aliquots, class_name: 'Aliquot', inverse_of: :request
 
+  # Can have many key value pairs of metadata
+  has_many :poly_metadata, as: :metadatable, dependent: :destroy
+
   delegate :flowcell, to: :batch, allow_nil: true
   delegate :for_multiplexing?, to: :request_type
 

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

app/resources/api/v2/poly_metadatum_resource.rb

@@ -0,0 +1,32 @@
+# frozen_string_literal: true
+
+module Api
+  module V2
+    # Provides a JSON API representation of PolyMetadatum
+    # See: http://jsonapi-resources.com/ for JSONAPI::Resource documentation
+    class PolyMetadatumResource < BaseResource
+      # Constants...
+
+      # immutable # uncomment to make the resource immutable
+
+      # model_name / model_hint if required
+
+      # Associations:
+      has_one :metadatable, polymorphic: true
+
+      # Attributes
+      attribute :key
+      attribute :value
+      attribute :created_at, readonly: true
+      attribute :updated_at, readonly: true
+
+      # Filters
+
+      # Custom methods
+      # These shouldn't be used for business logic, and a more about
+      # I/O and isolating implementation details.
+
+      # Class method overrides
+    end
+  end
+end

app/resources/api/v2/request_resource.rb

@@ -23,6 +23,7 @@ class RequestResource < BaseResource
       has_one :request_type, always_include_linkage_data: true
       has_one :primer_panel
       has_one :pre_capture_pool
+      has_many :poly_metadata, as: :metadatable, class_name: 'PolyMetadatum'
 
       # Attributes
       attribute :uuid, readonly: true

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

@@ -28,8 +28,10 @@
       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
       jsonapi_resources :pre_capture_pools
       jsonapi_resources :primer_panels
       jsonapi_resources :projects
@@ -284,6 +286,7 @@
 
   resources :requests do
     resources :comments, controller: 'requests/comments'
+    resources :poly_metadata, controller: 'requests/poly_metadata'
 
     member do
       get :history

db/migrate/20231204163029_create_poly_metadata.rb

@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+#
+# Add polymorphic metadata table to flexibly hold key value pairs
+class CreatePolyMetadata < ActiveRecord::Migration[6.0]
+  def change
+    create_table :poly_metadata do |t|
+      t.string :key, null: false
+      t.string :value, null: false
+      t.references :metadatable, polymorphic: true, null: false
+
+      t.timestamps
+    end
+  end
+end

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 2023_05_12_102847) do
+ActiveRecord::Schema.define(version: 2023_12_04_163029) do
 
   create_table "aliquot_indices", id: :integer, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci ROW_FORMAT=DYNAMIC", force: :cascade do |t|
     t.integer "aliquot_id", null: false
@@ -865,6 +865,16 @@
     t.index ["uploaded_file_name"], name: "index_plate_volumes_on_uploaded_file_name"
   end
 
+  create_table "poly_metadata", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci", force: :cascade do |t|
+    t.string "key", null: false
+    t.string "value", null: false
+    t.string "metadatable_type", null: false
+    t.bigint "metadatable_id", null: false
+    t.datetime "created_at", precision: 6, null: false
+    t.datetime "updated_at", precision: 6, null: false
+    t.index ["metadatable_type", "metadatable_id"], name: "index_poly_metadata_on_metadatable_type_and_metadatable_id"
+  end
+
   create_table "pooling_methods", id: :integer, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci ROW_FORMAT=DYNAMIC", force: :cascade do |t|
     t.string "pooling_behaviour", limit: 50, null: false
     t.text "pooling_options", size: :medium

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]