Merge pull request #1582 from sanger/1390-dpl-916-pbmc-donor-pooling-…

…create-plate

DPL-916 PBMC Donor Pooling create plate

app/models/concerns/labware_creators/donor_pooling_calculator.rb

@@ -0,0 +1,162 @@
+# frozen_string_literal: true
+
+# This module contains algorithms to allocate source wells into a target number of pools.
+module LabwareCreators::DonorPoolingCalculator
+  extend ActiveSupport::Concern
+
+  # Splits wells into groups by study and project. Wells are grouped based on the
+  # study and project of the first aliquot in each well (only one aliquot is
+  # expected per well). Returns an array of groups, where each group is an array
+  # of wells with the same study and project.
+  #
+  # If the input group is [w1, w2, w3, w4, w5, w6, w7, w8, w9]
+  # where w1, w2, w3, w4, w5, w6, w7, w8, and w9 are wells with (study_id, project_id),
+  #
+  # w1(1,1)
+  # w2(1,2)
+  # w3(1,3)
+  # w4(1,1)
+  # w5(1,2)
+  # w6(1,3)
+  # w7(1,1)
+  # w8(2,1)
+  # w9(2,2)
+  #
+  # the result will be:
+  # [[w1, w4, w7], [w2, w5], [w3, w6], [w8], [w9]]
+  #
+  # @param group [Array<Well>] The group of wells to be split.
+  # @return [Array<Array<Well>>] An array of well groups.
+  def split_single_group_by_study_and_project(group)
+    group.group_by { |well| [well.aliquots.first.study.id, well.aliquots.first.project.id] }.values
+  end
+
+  # Splits groups ensuring unique donor_ids within each group. Iterates over
+  # each group, creating subgroups with wells from a unique donor. The first
+  # occurrences of unique donor_ids are grouped, then the second occurrences,
+  # and so on. This prevents combining samples with the same donor_id. The
+  # result is flattened to a single array of subgroups.
+  #
+  # If the input groups are [[w1, w2, w3, w4], [w5, w6, w7], [w8, w9]]
+  # where w1, w2, w3, w4, w5, w6, w7, w8, and w9 are wells with (donor_id),
+  #
+  # w1(1)
+  # w2(2)
+  # w3(3)
+  # w4(1)
+  # w5(4)
+  # w6(4)
+  # w7(5)
+  # w8(6)
+  # w9(7)
+  #
+  # the result will be:
+  # [[w1, w2, w3], [w4], [w5, w7], [w6], [w8, w9]]
+  #
+  # Note that the input groups are not mixed. donor_ids are unique within each
+  # result subgroup.
+  #
+  # @param groups [Array<Array<Well>>] Array of well groups to be split.
+  # @return [Array<Array<Well>>] Array of subgroups split by donor ID.
+  def split_groups_by_unique_donor_ids(groups)
+    groups.flat_map { |group| split_single_group_by_unique_donor_ids(group) }
+  end
+
+  # Splits a single group of wells by donor_ids. This method is used by the
+  # 'split_groups_by_unique_donor_ids' method. It iteratively segregates wells with
+  # the first encountered instance of each unique donor_id into a separate
+  # subgroup. This process continues until there are no wells left in the
+  # original group. The result is a collection of subgroups, each containing
+  # wells from distinct donors.
+  #
+  # If the input group is [w1, w2, w3, w4, w5, w6, w7, w8, w9]
+  # where w1, w2, w3, w4, w5, w6, w7, w8, and w9 are wells with (donor_id),
+  #
+  # w1(1)
+  # w2(2)
+  # w3(3)
+  # w4(1)
+  # w5(2)
+  # w6(4)
+  # w7(5)
+  # w8(5)
+  # w9(5)
+  #
+  # the result will be:
+  # [[w1, w2, w3, w6, w7], [w4, w5, w8], [w9]]
+  #
+  # @param group [Array<Well>] The group of wells to split.
+  # @return [Array<Array<Well>>] An array of subgroups, each containing wells
+  #   from different donors.
+  def split_single_group_by_unique_donor_ids(group)
+    group = group.dup
+    output = []
+    wells_moved = 0
+    wells_total = group.size
+    while wells_moved < wells_total
+      subgroup = []
+      unique_donor_ids(group).each do |donor_id|
+        wells_moved += 1
+        index = group.index { |well| well.aliquots.first.sample.sample_metadata.donor_id == donor_id }
+        subgroup << group.delete_at(index)
+      end
+      output << subgroup
+    end
+    output
+  end
+
+  # Returns the unique donor_ids from a group of wells. Used by the
+  # 'split_single_group_by_unique_donor_ids' method.
+  #
+  # If the input group is [w1, w2, w3, w4, w5, w6, w7, w8, w9]
+  # where w1, w2, w3, w4, w5, w6, w7, w8, and w9 are wells with (donor_id),
+  #
+  # w1(1)
+  # w2(2)
+  # w3(3)
+  # w4(1)
+  # w5(2)
+  # w6(4)
+  # w7(5)
+  # w8(5)
+  # w9(5)
+  #
+  # the result will be:
+  # [1, 2, 3, 4, 5]
+  #
+  # @param group [Array<Well>] The group of wells from which to retrieve donor_ids.
+  # @return [Array<String>] An array of unique donor_ids.
+  def unique_donor_ids(group)
+    group.map { |well| well.aliquots.first.sample.sample_metadata.donor_id }.uniq
+  end
+
+  # Distributes samples across pools based on group sizes. It sorts the groups
+  # by size and splits the largest group into two until the number of groups
+  # equals the number of pools or until all groups have a size of 1. The input
+  # groups are the result of applying conditions, hence they cannot be mixed.
+  #
+  # If the request number of pools is 6 and the input groups are
+  # [[1, 2, 3], [4, 5], [6, 7, 8, 9]] where the numbers denote wells,
+  #
+  # the result will be:
+  # [[3], [1], [2], [4, 5], [6, 7], [8, 9]]
+  #
+  # for which the steps are:
+  # [[1, 2, 3], [4, 5], [6, 7, 8, 9]] -> 3 pools (input)
+  # [[4, 5], [6, 7], [8, 9], [1, 2, 3]] -> 4 pools
+  # [[3], [4, 5], [6, 7], [8, 9], [1, 2]] -> 5 pools
+  # [[3], [1], [2], [4, 5], [6, 7], [8, 9]] -> 6 pools (output)
+  #
+  # @param groups [Array<Array<Well>>] Array of well groups to be distributed.
+  # @return [Array<Array<Well>>] Array of distributed groups.
+  def distribute_groups_across_pools(groups, number_of_pools)
+    groups = groups.dup
+    groups.sort_by!(&:size)
+    while groups.any? && groups.last.size > 1 && groups.size < number_of_pools
+      largest = groups.pop # last
+      splits = largest.each_slice((largest.size / 2.0).ceil).to_a
+      groups.concat(splits).sort_by!(&:size)
+    end
+    groups
+  end
+end

app/models/concerns/labware_creators/donor_pooling_validator.rb

@@ -0,0 +1,130 @@
+# frozen_string_literal: true
+
+# This module contains validations for donor pooling.
+module LabwareCreators::DonorPoolingValidator
+  extend ActiveSupport::Concern
+
+  included do
+    validate :source_barcodes_must_be_entered
+    validate :source_barcodes_must_be_different
+    validate :source_plates_must_exist
+    validate :wells_with_aliquots_must_have_donor_id
+    validate :number_of_pools_must_not_exceed_configured
+  end
+
+  SOURCE_BARCODES_MUST_BE_ENTERED = 'At least one source plate must be scanned.'
+
+  SOURCE_BARCODES_MUST_BE_DIFFERENT = 'You must not scan the same barcode more than once.'
+
+  SOURCE_PLATES_MUST_EXIST =
+    'Source plates not found: %s. ' \
+      'Please check you scanned the correct source plates. '
+
+  NUMBER_OF_POOLS_MUST_NOT_EXCEED_CONFIGURED =
+    'The calculated number of pools (%s) is higher than the number of pools ' \
+      '(%s) configured. This is due to constraints such as: ' \
+      '* samples with different Studies or Projects cannot be combined ' \
+      '* multiple samples from the same donor cannot be combined. ' \
+      'Please check you have scanned the correct set of source plates.'
+
+  WELLS_WITH_ALIQUOTS_MUST_HAVE_DONOR_ID =
+    'All samples must have the donor_id specified. ' \
+      'Wells missing donor_id (on sample metadata): %s'
+
+  # Validates that at least one source barcode has been entered. If no barcodes
+  # are entered, an error is added to the :source_barcodes attribute.
+  #
+  # @return [void]
+  def source_barcodes_must_be_entered
+    return if minimal_barcodes.size >= 1
+
+    errors.add(:source_barcodes, SOURCE_BARCODES_MUST_BE_ENTERED)
+  end
+
+  # Validates that all source barcodes are unique. If any barcodes are
+  # duplicated, an error is added to the :source_barcodes attribute.
+  #
+  # @return [void]
+  def source_barcodes_must_be_different
+    return if minimal_barcodes.size == minimal_barcodes.uniq.size
+
+    errors.add(:source_barcodes, SOURCE_BARCODES_MUST_BE_DIFFERENT)
+  end
+
+  # Validates that all source plates corresponding to the minimal barcodes exist.
+  # If the number of source plates does not match the number of minimal barcodes,
+  # an error is added to the :source_plates attribute.
+  #
+  # @return [void]
+  def source_plates_must_exist
+    return if source_plates.size == minimal_barcodes.size
+
+    formatted_string = (minimal_barcodes - source_plates.map(&:human_barcode)).join(', ')
+
+    errors.add(:source_plates, format(SOURCE_PLATES_MUST_EXIST, formatted_string))
+  end
+
+  # Validates that the number of calculated pools does not exceed the configured
+  # number of pools. If the number of calculated pools is greater, an error is
+  # added to the :source_plates attribute.
+  #
+  # @return [void]
+  def number_of_pools_must_not_exceed_configured
+    # Don't add this error if there are already errors about missing donor_ids.
+    invalid_wells_hash = locations_with_missing_donor_id
+    return if invalid_wells_hash.any?
+
+    return if pools.size <= number_of_pools
+
+    errors.add(:source_plates, format(NUMBER_OF_POOLS_MUST_NOT_EXCEED_CONFIGURED, pools.size, number_of_pools))
+  end
+
+  # Validates that all wells with aliquots must have a donor_id.
+  # It uses the locations_with_missing_donor_id method to find any wells that are
+  # missing a donor_id. If any such wells are found, it adds an error message to
+  # the source_plates attribute, formatted with the barcodes of the plates and
+  # the wells that are missing a donor_id.
+  #
+  # @return [void]
+  def wells_with_aliquots_must_have_donor_id
+    invalid_wells_hash = locations_with_missing_donor_id
+    return if invalid_wells_hash.empty?
+
+    formatted_string = invalid_wells_hash.map { |barcode, locations| "#{barcode}: #{locations.join(', ')}" }.join(' ')
+    errors.add(:source_plates, format(WELLS_WITH_ALIQUOTS_MUST_HAVE_DONOR_ID, formatted_string))
+  end
+
+  private
+
+  # Checks each source well for pooling for missing donor_id. Returns a hash
+  # with keys as the barcodes of source plates and values as arrays of well
+  # locations with missing donor_id. If a plate has no wells with missing
+  # donor_id, it is not included in the returned hash. This method is used by
+  # the wells_with_aliquots_must_have_donor_id method to generate an error
+  # message.
+  #
+  # @return [Hash] A hash mapping source plate barcodes to arrays of invalid
+  #   well locations.
+  def locations_with_missing_donor_id
+    # source_wells_for_pooling contains filtered wells from source plates
+    invalid_wells = source_wells_for_pooling.select { |well| missing_donor_id?(well) }
+    invalid_wells.each_with_object({}) do |well, hash|
+      plate_barcode = source_wells_to_plates[well].human_barcode # find the plate barcode
+      hash[plate_barcode] ||= []
+      hash[plate_barcode] << well.location
+    end
+  end
+
+  # Checks if a well is missing a donor_id. If there is an aliquot, it checks
+  # if the associated sample_metadata has a donor_id. If the donor_id is
+  # missing, it returns true. Otherwise, it returns false.
+  #
+  # @param well [Well] The well to check.
+  # @return [Boolean] True if the well is missing a donor_id, false otherwise.
+  def missing_donor_id?(well)
+    aliquot = well.aliquots&.first
+    return false unless aliquot
+
+    (aliquot.sample.sample_metadata.donor_id || '').to_s.strip.blank?
+  end
+end