Merge branch 'develop' into y24-475-bug-improve-integration-suite-uat…

…-actions-error-message

.rubocop_todo.yml

@@ -297,6 +297,7 @@ Metrics/AbcSize:
     - 'app/controllers/api/v2/transfers_controller.rb'
     - 'app/jobs/export_pool_xp_to_traction_job.rb'
     - 'app/sample_manifest_excel/sample_manifest_excel/manifest_type_list.rb'
+    - 'spec/models/bulk_submission_scrna_spec.rb'
 
 # Offense count: 1
 # Configuration parameters: CountComments, Max, CountAsOne.
@@ -856,6 +857,7 @@ RSpec/LetSetup:
     - 'spec/models/transfer_request_collection_spec.rb'
     - 'spec/requests/api/v2/comments_spec.rb'
     - 'spec/requests/api/v2/plates_spec.rb'
+    - 'spec/models/bulk_submission_scrna_spec.rb'
 
 # Offense count: 40
 # Configuration parameters: EnforcedStyle.

Gemfile.lock

@@ -456,7 +456,7 @@ GEM
       rexml
     ruby-prof (1.7.1)
     ruby-progressbar (1.13.0)
-    ruby-units (4.0.3)
+    ruby-units (4.1.0)
     ruby-vips (2.2.1)
       ffi (~> 1.12)
     ruby2_keywords (0.0.5)

app/models/bulk_submission.rb

@@ -54,6 +54,15 @@ def initialize(attrs = {})
     self.encoding = attrs.fetch(:encoding, DEFAULT_ENCODING)
   end
 
+  # Returns the warnings collection for the BulkSubmission object.
+  # Initialises the warnings collection if it does not exist yet. The collection
+  # is used for showing informative warning messages to the user after the bulk
+  # submission has been processed successfully.
+  # @return [ActiveModel::Errors] the warnings collection
+  def warnings
+    @warnings ||= ActiveModel::Errors.new(self)
+  end
+
   include ManifestUtil
 
   # rubocop:todo Metrics/MethodLength
@@ -231,7 +240,7 @@ def process # rubocop:todo Metrics/CyclomaticComplexity
     'gigabases expected',
     'priority',
     'flowcell type',
-    'scrna core number of samples per pool',
+    'scrna core number of pools',
     'scrna core cells per chip well'
   ].freeze
 
@@ -312,6 +321,12 @@ def add_study_to_assets(assets, study)
     assets.map(&:samples).flatten.uniq.each { |sample| sample.studies << study unless sample.studies.include?(study) }
   end
 
+  # Assigns a value from the source object to the target object if the source value is present.
+  #
+  # @param [Hash] source_obj The source object containing the value to be assigned.
+  # @param [String, Symbol] source_key The key to look up the value in the source object.
+  # @param [Hash] target_obj The target object where the value will be assigned.
+  # @param [String, Symbol] target_key The key to assign the value in the target object.
   def assign_value_if_source_present(source_obj, source_key, target_obj, target_key)
     target_obj[target_key] = source_obj[source_key] if source_obj[source_key].present?
   end
@@ -329,7 +344,7 @@ def extract_request_options(details)
         ['gigabases expected', 'gigabases_expected'],
         ['primer panel', 'primer_panel_name'],
         ['flowcell type', 'requested_flowcell_type'],
-        ['scrna core number of samples per pool', 'number_of_samples_per_pool'],
+        ['scrna core number of pools', 'number_of_pools'],
         ['scrna core cells per chip well', 'cells_per_chip_well']
       ].each do |source_key, target_key|
         assign_value_if_source_present(details, source_key, request_options, target_key)

app/models/pbmc_pooling_customer_request.rb

@@ -3,7 +3,7 @@
 # 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)
+    custom_attribute(:number_of_pools, integer: true, required: false, default: nil)
   end
 end

app/models/study.rb

@@ -82,11 +82,28 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
     DATA_RELEASE_TIMING_IMMEDIATE,
     DATA_RELEASE_TIMING_DELAYED
   ].freeze
-  DATA_RELEASE_PREVENTION_REASONS = ['data validity', 'legal', 'replication of data subset'].freeze
 
-  DATA_RELEASE_DELAY_FOR_OTHER = 'other'
-  DATA_RELEASE_DELAY_REASONS_STANDARD = ['phd study', DATA_RELEASE_DELAY_FOR_OTHER].freeze
-  DATA_RELEASE_DELAY_REASONS_ASSAY = ['phd study', 'assay of no other use', DATA_RELEASE_DELAY_FOR_OTHER].freeze
+  OLD_DATA_RELEASE_PREVENTION_REASONS = ['data validity', 'legal', 'replication of data subset'].freeze
+  DATA_RELEASE_PREVENTION_REASON_OTHER = 'Other (please specify)'
+  DATA_RELEASE_PREVENTION_REASONS = [
+    'Pilot or validation studies - DAC approval not required',
+    'Collaborators will share data in a research repository - DAC approval not required',
+    'Prevent harm (e.g sensitive studies or biosecurity) - DAC approval required',
+    'Protecting IP - DAC approval required',
+    DATA_RELEASE_PREVENTION_REASON_OTHER
+  ].freeze
+
+  OLD_DATA_RELEASE_DELAY_FOR_OTHER = 'other'
+  DATA_RELEASE_DELAY_FOR_OTHER = 'Other (please specify below)'
+  OLD_DATA_RELEASE_DELAY_REASONS = ['other', 'phd study'].freeze
+  DATA_RELEASE_DELAY_REASONS_STANDARD = [
+    'PhD study',
+    'Capacity building',
+    'Intellectual property protection',
+    'Additional time to make data FAIR',
+    DATA_RELEASE_DELAY_FOR_OTHER
+  ].freeze
+  DATA_RELEASE_DELAY_REASONS_ASSAY = ['assay of no other use'].freeze
 
   DATA_RELEASE_DELAY_PERIODS = ['3 months', '6 months', '9 months', '12 months', '18 months'].freeze
 
@@ -214,14 +231,15 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
     custom_attribute(
       :data_release_delay_reason,
       required: true,
-      in: DATA_RELEASE_DELAY_REASONS_ASSAY,
+      in: [*DATA_RELEASE_DELAY_REASONS_STANDARD, *DATA_RELEASE_DELAY_REASONS_ASSAY, *OLD_DATA_RELEASE_DELAY_REASONS],
       if: :delayed_release?
     )
+
     custom_attribute(:data_release_delay_period, required: true, in: DATA_RELEASE_DELAY_PERIODS, if: :delayed_release?)
     custom_attribute(:bam, default: true)
 
-    with_options(required: true, if: :delayed_for_other_reasons?) do
-      custom_attribute(:data_release_delay_other_comment)
+    with_options(if: :delayed_for_other_reasons?) do
+      custom_attribute(:data_release_delay_other_comment, required: true)
       custom_attribute(:data_release_delay_reason_comment)
     end
 
@@ -231,14 +249,19 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength
     custom_attribute(:ega_policy_accession_number)
     custom_attribute(:array_express_accession_number)
 
-    with_options(if: :delayed_for_long_time?, required: true) do
-      custom_attribute(:data_release_delay_approval, in: YES_OR_NO, default: NO)
-    end
-
-    with_options(if: :never_release?, required: true) do
-      custom_attribute(:data_release_prevention_reason, in: DATA_RELEASE_PREVENTION_REASONS)
-      custom_attribute(:data_release_prevention_approval, in: YES_OR_NO)
-      custom_attribute(:data_release_prevention_reason_comment)
+    with_options(if: :never_release?) do
+      custom_attribute(
+        :data_release_prevention_reason,
+        in: [*DATA_RELEASE_PREVENTION_REASONS, *OLD_DATA_RELEASE_PREVENTION_REASONS],
+        required: true
+      )
+      custom_attribute(
+        :data_release_prevention_other_comment,
+        required: true,
+        if: :data_release_prevention_reason_other?
+      )
+      custom_attribute(:data_release_prevention_reason_comment, required: true)
+      custom_attribute(:data_release_prevention_approval)
     end
 
     # NOTE: Additional validation in Study::Metadata Class to validate_presence_of :data_access_group, if: :managed
@@ -567,6 +590,33 @@ def poly_metadatum_by_key(key)
     poly_metadata.find { |pm| pm.key == key.to_s }
   end
 
+  # Helper method for edit dropdowns to support backwards compatibility with old options.
+  #
+  # @return [Array<String>] the list of options for the data release prevention reason dropdown
+  def data_release_prevention_options
+    additional_options = []
+    if OLD_DATA_RELEASE_PREVENTION_REASONS.include? study_metadata.data_release_prevention_reason
+      additional_options << study_metadata.data_release_prevention_reason
+    end
+
+    DATA_RELEASE_PREVENTION_REASONS + additional_options
+  end
+
+  # Helper method for edit dropdowns to support backwards compatibility with old options.
+  #
+  # @param [Boolean] assay_option - whether to include assay-specific options
+  # @return [Array<String>] the list of options for the data release delay reason dropdown
+  def data_release_delay_options(assay_option: false)
+    # If the current value is an old one, then we need to include it in the list of options
+    additional_options = []
+    if OLD_DATA_RELEASE_DELAY_REASONS.include? study_metadata.data_release_delay_reason
+      additional_options << study_metadata.data_release_delay_reason
+    end
+
+    additional_options.concat(DATA_RELEASE_DELAY_REASONS_ASSAY) if assay_option
+    DATA_RELEASE_DELAY_REASONS_STANDARD + additional_options
+  end
+
   private
 
   def valid_ethically_approved?
@@ -601,7 +651,11 @@ def never_release?
     end
 
     def delayed_for_other_reasons?
-      data_release_delay_reason == DATA_RELEASE_DELAY_FOR_OTHER
+      [DATA_RELEASE_DELAY_FOR_OTHER, OLD_DATA_RELEASE_DELAY_FOR_OTHER].include?(data_release_delay_reason)
+    end
+
+    def data_release_prevention_reason_other?
+      data_release_prevention_reason == DATA_RELEASE_PREVENTION_REASON_OTHER
     end
 
     def delayed_for_long_time?

app/models/submission/scrna_core_cdna_prep_feasibility_calculator.rb

@@ -0,0 +1,70 @@
+# frozen_string_literal: true
+
+# This module provides methods for calculating the full allowance volume and the
+# final resuspension volume for scRNA core cDNA prep feasibility validations.
+module Submission::ScrnaCoreCdnaPrepFeasibilityCalculator
+  # This method calculates the full allowance volume (in microlitres) for the
+  # specified number of cells per chip well, which is typically specified in
+  # in a bulk submission per study and project. It uses the pooling settings
+  # from the scRNA config. It first calculates the chip loading volume for the
+  # given number of cells per chip well, and then the full allowance for that
+  # chip loading volume.
+  #
+  # @param number_of_cells_per_chip_well [Integer] the number of cells per chip well from the bulk submission
+  # @return [Float] the full allowance volume
+  def calculate_full_allowance(number_of_cells_per_chip_well)
+    # "Full allowance" = ( "Chip loading volume" * 2) + 25
+    # 2 is because this is for 2 runs
+    # 25 is 2 lots of 10ul for cell counting, and 5ul for wastage when transferring between labware
+    chip_loading_volume = calculate_chip_loading_volume(number_of_cells_per_chip_well)
+    (chip_loading_volume * scrna_config[:desired_number_of_runs]) +
+      (scrna_config[:desired_number_of_runs] * scrna_config[:volume_taken_for_cell_counting]) +
+      scrna_config[:wastage_volume]
+  end
+
+  # This method calculates the chip loading volume (in microlitres) for the
+  # specified number of cells per chip well, which is typically specified in
+  # in a bulk submission per study and project. It uses the pooling settings
+  # from the scRNA config.
+  #
+  # @param number_of_cells_per_chip_well [Integer] the number of cells per chip well from the bulk submission
+  # @return [Float] the chip loading volume
+  def calculate_chip_loading_volume(number_of_cells_per_chip_well)
+    # "Chip loading volume" = "Number of cells per chip well" / "Chip loading concentration"
+    number_of_cells_per_chip_well / scrna_config[:desired_chip_loading_concentration]
+  end
+
+  # This method calculates the resuspension volume (in microlitres) for the
+  # specified number of samples in a pool, which is typically taken as the
+  # number of samples in the smallest pool for a study and project. It uses the
+  # pooling settings from the scRNA config. It first calculates the total cells
+  # in 300ul for the given number of samples in the pool, and then the
+  # resuspension volume for that total cell count.
+  #
+  # @param count_of_samples_in_pool [Integer] the number of samples in the pool
+  # @return [Float] the resuspension volume
+  def calculate_resuspension_volume(count_of_samples_in_pool)
+    total_cells_in_300ul = calculate_total_cells_in_300ul(count_of_samples_in_pool)
+    total_cells_in_300ul / scrna_config[:desired_chip_loading_concentration]
+  end
+
+  # This method calculates the total cells in 300ul for the specified number of
+  # samples in a pool, which is typically taken as the number of samples in the
+  # smallest pool for a study and project. It uses the pooling settings from the
+  # scRNA config.
+  #
+  # @param count_of_samples_in_pool [Integer] the number of samples in the pool
+  # @return [Integer] the total cells in 300ul
+  def calculate_total_cells_in_300ul(count_of_samples_in_pool)
+    (count_of_samples_in_pool * scrna_config[:required_number_of_cells_per_sample_in_pool]) *
+      scrna_config[:wastage_factor]
+  end
+
+  private
+
+  # This method returns the scRNA config from the Rails application config.
+  # @return [Hash] the scRNA config
+  def scrna_config
+    Rails.application.config.scrna_config
+  end
+end