Merge branch 'develop' into 4133-y24-120-bug-taken-link-error-when-cr…

…eating-sequencing-batches

.rubocop_todo.yml

@@ -691,7 +691,6 @@ RSpec/ExampleWording:
     - 'spec/heron/factories/sample_spec.rb'
     - 'spec/heron/factories/tube_rack_spec.rb'
     - 'spec/lib/accession/study_spec.rb'
-    - 'spec/models/parsers/cardinal_pbmc_count_parser_spec.rb'
     - 'spec/models/plate/quad_creator_spec.rb'
     - 'spec/models/qc_result/qc_result_factory_spec.rb'
     - 'spec/models/qcable_creator_spec.rb'

app/controllers/api/v2/request_metadata_controller.rb

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

@@ -4,7 +4,7 @@
 
 module Parsers
   ENCODINGS = %w[Windows-1252 iso-8859-1 utf-8 utf-16].freeze
-  PARSERS = [QuantParser, BioanalysisCsvParser, PlateReaderParser, CardinalPbmcCountParser].freeze
+  PARSERS = [QuantParser, BioanalysisCsvParser, PlateReaderParser, PbmcCountParser].freeze
 
   def self.parser_for(filename, content_type, content)
     return nil unless filename.downcase.end_with?('.csv') || content_type == 'text/csv'

app/models/parsers/cardinal_pbmc_count_parser.rb → app/models/parsers/pbmc_count_parser.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 module Parsers
-  # A parser for the cardinal pipeline qc file
-  class CardinalPbmcCountParser
+  # A parser for the cardinal and scrna pipeline qc files
+  class PbmcCountParser
     class_attribute :assay_type, :assay_version
 
     HEADERS = [
@@ -20,7 +20,7 @@ class CardinalPbmcCountParser
       'Errors:'
     ].freeze
 
-    self.assay_type = 'Cardinal_PBMC_Count'
+    self.assay_type = 'PBMC_Count'
     self.assay_version = 'v1.0'
 
     def self.parses?(content)
@@ -38,8 +38,9 @@ def rows
     end
 
     # 0 - well name
-    # 2 - cell count
+    # 2 - live cell count
     # 4 - viability
+    # 9 - total cell count
     def qc_data
       @qc_data ||=
         {}.tap do |qc_data|
@@ -67,6 +68,7 @@ def each_well_and_parameters(&block)
     def qc_metrics_hash(row)
       {}.tap do |hash|
         hash[:live_cell_count] = Unit.new(row[2], 'cells')
+        hash[:total_cell_count] = Unit.new(row[9], 'cells')
         viability = row[4]
         hash[:viability] = Unit.new(viability) unless viability == 'NaN'
       end

app/models/pbmc_pooling_customer_request.rb

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+# A class for customer requests that need the extra metadata fields used for PBMC pooling calculations
+class PbmcPoolingCustomerRequest < CustomerRequest
+  has_metadata as: Request do
+    custom_attribute(:number_of_samples_per_pool, integer: true, required: false, default: nil)
+    custom_attribute(:cells_per_chip_well, integer: true, required: false, default: nil)
+  end
+end

app/resources/api/v2/request_metadata_resource.rb

@@ -0,0 +1,48 @@
+# frozen_string_literal: true
+
+module Api
+  module V2
+    # @todo This documentation does not yet include a detailed description of what this resource represents.
+    # @todo This documentation does not yet include detailed descriptions for relationships, attributes and filters.
+    # @todo This documentation does not yet include any example usage of the API via cURL or similar.
+    #
+    # @note Access this resource via the `/api/v2/requests_metadata/` endpoint.
+    #
+    # Provides a JSON:API representation of {Request::Metadata}.
+    #
+    # For more information about JSON:API see the [JSON:API Specifications](https://jsonapi.org/format/)
+    # or look at the [JSONAPI::Resources](http://jsonapi-resources.com/) package for Sequencescape's implementation
+    # of the JSON:API standard.
+    class RequestMetadataResource < BaseResource
+      # NB. request_metadata has been added to config/initializers/inflections.rb to make this class name
+      # work otherwise it expects RequestMetadatumResource
+
+      # Sets add_model_hint true by default, this allows updates from Limber, otherwise get a
+      # 500 error as it looks for resource Api::V2::MetadatumResource
+      model_name 'Request::Metadata'
+
+      # Associations:
+      has_one :request
+
+      ###
+      # Attributes
+      ###
+
+      # @!attribute [r] number_of_samples_per_pool
+      #   @return [Int] the number_of_samples_per_pool.
+      attribute :number_of_samples_per_pool, readonly: true
+
+      # @!attribute [r] cells_per_chip_well
+      #   @return [Int] the cells_per_chip_well.
+      attribute :cells_per_chip_well, 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

@@ -31,6 +31,7 @@ class RequestResource < BaseResource
       has_one :primer_panel
       has_one :pre_capture_pool
       has_many :poly_metadata, as: :metadatable, class_name: 'PolyMetadatum'
+      has_one :request_metadata, class_name: 'RequestMetadata', foreign_key_on: :related
 
       # Attributes
       attribute :uuid, readonly: true

app/resources/api/v2/sample_metadata_resource.rb

@@ -15,6 +15,9 @@ module V2
     # or look at the [JSONAPI::Resources](http://jsonapi-resources.com/) package for Sequencescape's implementation
     # of the JSON:API standard.
     class SampleMetadataResource < BaseResource
+      # NB. sample_metadata has been added to config/initializers/inflections.rb to make this class name
+      # work otherwise it expects SampleMetadatumResource
+
       # Set add_model_hint true to allow updates from Limber, otherwise get a
       # 500 error as it looks for resource Api::V2::MetadatumResource
       model_name 'Sample::Metadata', add_model_hint: true

app/uat_actions/uat_actions/tube_submission.rb

@@ -31,6 +31,26 @@ class UatActions::TubeSubmission < UatActions
                include_blank: 'Using default library type...'
              }
 
+  form_field :number_of_samples_per_pool,
+             :number_field,
+             label: 'Number of samples per pool',
+             help:
+               'Optional field to set the number_of_samples_per_pool field on the ' \
+                 'submission request. Leave blank if not required.',
+             options: {
+               minimum: 0
+             }
+
+  form_field :cells_per_chip_well,
+             :number_field,
+             label: 'Cells per Chip Well',
+             help:
+               'Optional field to set the cells_per_chip_well field on the ' \
+                 'submission request. Leave blank if not required.',
+             options: {
+               minimum: 0
+             }
+
   validates :submission_template, presence: { message: 'could not be found' }
 
   # Returns a default copy of the UatAction which will be used to fill in the form
@@ -74,12 +94,21 @@ def perform
   # Fills the report with the information from the submission
   #
   # @return [Void]
+  # rubocop:disable Metrics/AbcSize
   def fill_report(order)
     report['tube_barcodes'] = assets.map(&:human_barcode)
     report['submission_id'] = order.submission.id
     report['library_type'] = order.request_options[:library_type] if order.request_options[:library_type].present?
+    report['number_of_samples_per_pool'] = order.request_options[:number_of_samples_per_pool] if order.request_options[
+      :number_of_samples_per_pool
+    ].present?
+    report['cells_per_chip_well'] = order.request_options[:cells_per_chip_well] if order.request_options[
+      :cells_per_chip_well
+    ].present?
   end
 
+  # rubocop:enable Metrics/AbcSize
+
   # Returns the submisssion template to use for the submission
   #
   # @return [SubmissionTemplate] The submission template to use
@@ -131,6 +160,8 @@ def default_request_options
   def custom_request_options
     options = {}
     options[:library_type] = library_type_name if library_type_name.present?
+    options[:number_of_samples_per_pool] = number_of_samples_per_pool.presence
+    options[:cells_per_chip_well] = cells_per_chip_well.presence
     options
   end
 

config/default_records/request_types/014_limber_scrna_core_cdna_prep_request_types.wip.yml → config/default_records/request_types/014_limber_scrna_core_cdna_prep_request_types.yml

@@ -8,7 +8,7 @@ limber_scrna_core_cdna_prep_gem_x_5p:
   name: scRNA Core cDNA Prep GEM-X 5p
   asset_type: SampleTube
   order: 1
-  request_class_name: CustomerRequest
+  request_class_name: PbmcPoolingCustomerRequest
   for_multiplexing: false
   billable: true
   product_line_name: Short Read

config/initializers/inflections.rb

@@ -11,7 +11,9 @@
 #   inflect.uncountable %w( fish sheep )
 # end
 
-ActiveSupport::Inflector.inflections(:en) { |inflect| inflect.uncountable %w[health sample_metadata labware] }
+ActiveSupport::Inflector.inflections(:en) do |inflect|
+  inflect.uncountable %w[health sample_metadata request_metadata labware]
+end
 
 # These inflection rules are supported but not enabled by default:
 # ActiveSupport::Inflector.inflections(:en) do |inflect|

config/locales/metadata/en.yml

@@ -58,6 +58,12 @@ en:
         requested_flowcell_type:
           label: Flowcell type
 
+        number_of_samples_per_pool:
+          label: Number of samples per pool
+
+        cells_per_chip_well:
+          label: Cells per chip well
+
     library_creation_request:
       <<: *REQUEST
     sequencing_request:

config/routes.rb

@@ -43,6 +43,7 @@
       jsonapi_resources :qcables
       jsonapi_resources :racked_tubes
       jsonapi_resources :receptacles
+      jsonapi_resources :request_metadata
       jsonapi_resources :request_types
       jsonapi_resources :requests
       jsonapi_resources :samples

db/migrate/20240917133813_addsc_rna_fields_to_request_metadata.rb

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+class AddscRnaFieldsToRequestMetadata < ActiveRecord::Migration[6.1]
+  def change
+    add_column :request_metadata, :number_of_samples_per_pool, :integer, null: true
+    add_column :request_metadata, :cells_per_chip_well, :integer, null: true
+  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: 2024_09_12_000109) do
+ActiveRecord::Schema.define(version: 2024_09_17_133813) do
 
   create_table "aliquot_indices", id: :integer, charset: "utf8mb4", collation: "utf8mb4_unicode_ci", options: "ENGINE=InnoDB ROW_FORMAT=DYNAMIC", force: :cascade do |t|
     t.integer "aliquot_id", null: false
@@ -1175,6 +1175,8 @@
     t.string "data_type"
     t.integer "primer_panel_id"
     t.string "requested_flowcell_type"
+    t.integer "number_of_samples_per_pool"
+    t.integer "cells_per_chip_well"
     t.index ["request_id"], name: "index_request_metadata_on_request_id"
   end
 

lib/tasks/populate_number_of_samples_per_pool.rake

@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+# Run the rake task with the following command:
+# bundle exec rake number_of_samples_per_pool:populate[20,1]
+# The rake task will populate the number of samples per pool column in the request_metadata table
+# for a given submission ID.
+namespace :number_of_samples_per_pool do
+  desc 'Populate number of samples per pool column in request_metadata table for a given submission ID'
+
+  task :populate, %i[samples_per_pool submission_id] => :environment do |_, args|
+    args.with_defaults(samples_per_pool: nil, submission_id: nil)
+
+    raise StandardError, 'Number of samples per pool is missing' if args[:samples_per_pool].nil?
+    raise StandardError, 'Submission ID is missing' if args[:submission_id].nil?
+
+    puts "Populating number of samples per pool column with #{args[:samples_per_pool]}
+        in request_metadata table for submission: #{args[:submission_id]}..."
+
+    ActiveRecord::Base.transaction do
+      saved_count = 0
+      Request::Metadata
+        .joins(:request)
+        .where(requests: { submission_id: args[:submission_id] })
+        .find_each(batch_size: 50) do |request_metadata|
+          puts "Processing request_metadata #{request_metadata.id}..."
+          saved_count = process_request_metadata(request_metadata, saved_count, args[:samples_per_pool])
+        end
+    end
+  end
+
+  def process_request_metadata(request_metadata, saved_count, samples_per_pool)
+    request_metadata.number_of_samples_per_pool = samples_per_pool
+    begin
+      request_metadata.save!
+      saved_count += 1
+    rescue ActiveRecord::ActiveRecordError, StandardError => e
+      puts "Error processing request_metadata #{request_metadata.id}: #{e.message}"
+      raise e
+    end
+    saved_count
+  end
+end

spec/bulk_submission_excel/download_spec.rb

@@ -30,7 +30,7 @@
   let(:columns) { configuration.columns.all.dup }
   let(:ranges) { configuration.ranges.dup }
   let(:assets) { create(:plate_with_untagged_wells).wells }
-  let(:submission_template) { create :libray_and_sequencing_template }
+  let(:submission_template) { create :library_and_sequencing_template }
 
   after { File.delete(test_file) if File.exist?(test_file) }
 

spec/factories/request_type_factories.rb

@@ -35,6 +35,10 @@
       request_class { CustomerRequest }
     end
 
+    factory :pbmc_pooling_customer_request_type do
+      request_class { PbmcPoolingCustomerRequest }
+    end
+
     factory :cherrypick_request_type do
       request_class { CherrypickRequest }
       asset_type { 'Well' }

spec/factories/submission_factories.rb

@@ -30,17 +30,21 @@
       transient { request_types { [create(:library_request_type)] } }
     end
 
-    factory :libray_and_sequencing_template do
+    factory :library_and_sequencing_template do
       transient { request_types { [create(:library_request_type), create(:sequencing_request_type)] } }
     end
 
-    factory :heron_libray_and_sequencing_template do
+    factory :heron_library_and_sequencing_template do
       transient { request_types { [create(:heron_request_type), create(:sequencing_request_type)] } }
     end
 
-    factory :isc_libray_and_sequencing_template do
+    factory :isc_library_and_sequencing_template do
       transient { request_types { [create(:isc_library_request_type), create(:sequencing_request_type)] } }
     end
+
+    factory :pbmc_pooling_submission_template do
+      transient { request_types { [create(:pbmc_pooling_customer_request_type)] } }
+    end
   end
 
   factory :order do

spec/features/generate_a_bulk_submission_template_spec.rb

@@ -9,7 +9,7 @@
   # We only use two wells of out partial plate in our submission. However we are generating 13
   # to ensure we are only using the specified well. The other two will be ignored.
   let!(:partial_plate) { create(:plate_with_untagged_wells, well_count: 13) }
-  let!(:submission_template) { create :libray_and_sequencing_template }
+  let!(:submission_template) { create :library_and_sequencing_template }
 
   let(:iso_date) { Time.current.utc.strftime('%Y%m%d') }
   let(:filename) { "#{plate.human_barcode}_to_#{partial_plate.human_barcode}_#{iso_date}_#{user.login}.xlsx" }
@@ -37,7 +37,7 @@
   end
 
   context 'with a primer panel submission' do
-    let!(:submission_template) { create :heron_libray_and_sequencing_template }
+    let!(:submission_template) { create :heron_library_and_sequencing_template }
     let!(:primer_panel) { create :primer_panel }
 
     it 'populates the primer panel column' do
@@ -58,7 +58,7 @@
   end
 
   context 'with a bait_library submission' do
-    let!(:submission_template) { create :isc_libray_and_sequencing_template }
+    let!(:submission_template) { create :isc_library_and_sequencing_template }
     let!(:bait_library) { create :bait_library }
 
     it 'populates the primer panel column' do