Merge pull request #4331 from sanger/y24-055-2

Y24-055 Take 2

Gemfile.lock

@@ -301,6 +301,8 @@ GEM
     nio4r (2.7.3)
     nokogiri (1.16.7-arm64-darwin)
       racc (~> 1.4)
+    nokogiri (1.16.7-x86_64-darwin)
+      racc (~> 1.4)
     nokogiri (1.16.7-x86_64-linux)
       racc (~> 1.4)
     parallel (1.24.0)
@@ -565,6 +567,7 @@ GEM
 PLATFORMS
   arm64-darwin
   arm64-darwin-23
+  x86_64-darwin-21
   x86_64-linux
 
 DEPENDENCIES

app/models/tag_set.rb

@@ -6,6 +6,9 @@
 class TagSet < ApplicationRecord
   # For dual index tags, tag_group is i7 oligos and tag2_group is i5 oligos
   belongs_to :tag_group, class_name: 'TagGroup', optional: false
+
+  # In order to support a unified access to dual and single index sets,
+  # it allows tag2_group to be null.
   belongs_to :tag2_group, class_name: 'TagGroup', optional: true
 
   # We can assume adapter_type is the same for both tag groups
@@ -15,7 +18,16 @@ class TagSet < ApplicationRecord
   validates :name, presence: true, uniqueness: true
   validate :tag_group_adapter_types_must_match
 
+  scope :dual_index, -> { where.not(tag2_group: nil) }
+  scope :visible,
+        -> { joins(:tag_group, :tag2_group).where(tag_group: { visible: true }, tag2_group: { visible: true }) }
+
+  # The scoping retrieves the visible tag sets and makes sure they are dual index.
+  scope :visible_dual_index, -> { dual_index.visible }
+
   # Dynamic method to determine the visibility of a tag_set based on the visibility of its tag_groups
+  # TagSet has a method to check if itself is visible by checking
+  # the visibility of both tag_group and (if not null) tag2_group.
   def visible
     tag_group.visible && (tag2_group.nil? || tag2_group.visible)
   end

app/sequencescape_excel/sequencescape_excel/specialised_field/dual_index_tag_set.rb

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+module SequencescapeExcel
+  module SpecialisedField
+    ##
+    # DualIndexTagSet
+    class DualIndexTagSet
+      include Base
+      include ValueRequired
+
+      validate :dual_index_tag_set
+
+      def tag_set_id
+        @tag_set_id ||= ::TagSet.dual_index.visible.find_by(name: value)&.id
+      end
+
+      private
+
+      # Check the Dual Index Tag Set with a visible tag_group and tag2_group exists here
+      # Check the TagSet/TagWell combination in DualIndexTagWell
+      def dual_index_tag_set
+        return if tag_set_id.present?
+
+        errors.add(:base, "could not find a visible dual index Tag Set with name '#{value}'.")
+      end
+    end
+  end
+end

app/sequencescape_excel/sequencescape_excel/specialised_field/dual_index_tag_well.rb

@@ -0,0 +1,76 @@
+# frozen_string_literal: true
+
+module SequencescapeExcel
+  module SpecialisedField
+    ##
+    # DualIndexTagWell
+    class DualIndexTagWell
+      include Base
+      include ValueRequired
+
+      # ValueToUpcase converts the `value` to uppercase
+      # For exqmple the `value` used in the well_index method would be 'A1' instead of 'a1'
+      # This is important because the description_to_vertical_plate_position method
+      # returns a different value for 'A1' vs 'a1', where the upcase version is correct
+      include ValueToUpcase
+
+      attr_accessor :sf_dual_index_tag_set
+
+      validates :well_index, presence: { message: 'is not valid' }
+      validates :tag, presence: { message: 'does not have associated i7 tag' }, if: :well_index
+      validates :tag2, presence: { message: 'does not have associated i5 tag' }, if: :well_index
+
+      PLATE_SIZE = 96
+
+      def update(_attributes = {})
+        return unless valid?
+
+        raise StandardError, 'Tag aliquot mismatch' unless asset.aliquots.one?
+
+        # For dual index tags, tag is a i7 oligo and tag2 is a i5 oligo
+        asset.aliquots.first.update(tag: tag, tag2: tag2)
+      end
+
+      def link(other_fields)
+        self.sf_dual_index_tag_set = other_fields[SequencescapeExcel::SpecialisedField::DualIndexTagSet]
+      end
+
+      # From the validation in DualIndexTagSet, we know this tag set is a valid dual index tag set
+      # with a visible tag group and visible tag2 group
+      def dual_index_tag_set
+        @dual_index_tag_set = TagSet.find(sf_dual_index_tag_set.tag_set_id) if sf_dual_index_tag_set&.tag_set_id
+      end
+
+      def tag_group_id
+        @tag_group_id ||= ::TagGroup.find_by(id: dual_index_tag_set.tag_group_id, visible: true).id
+      end
+
+      def tag2_group_id
+        @tag2_group_id ||= ::TagGroup.find_by(id: dual_index_tag_set.tag2_group_id, visible: true).id
+      end
+
+      private
+
+      # This assumes that the tags within a tag group for dual index tags are listed in 'column' order,
+      # i.e. the first tag is the one in the first column, the second tag is the one in the second column, etc.
+      # therefore description_to_vertical_plate_position is used to get the correct map_id
+      # A1 --> 1
+      # B1 --> 2
+      # ...
+      # H12 --> 96
+      def well_index
+        @well_index = Map::Coordinate.description_to_vertical_plate_position(value, PLATE_SIZE)
+      end
+
+      # i7 tag
+      def tag
+        Tag.find_by(tag_group_id: tag_group_id, map_id: well_index)
+      end
+
+      # i5 tag
+      def tag2
+        Tag.find_by(tag_group_id: tag2_group_id, map_id: well_index)
+      end
+    end
+  end
+end

app/sequencescape_excel/sequencescape_excel/specialised_field/value_to_upcase.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module SequencescapeExcel
+  module SpecialisedField
+    ##
+    # ValueToUpcase
+    module ValueToUpcase
+      def value=(value)
+        @value = value.upcase if value.present?
+      end
+    end
+  end
+end

config/sample_manifest_excel/columns.yml

@@ -153,7 +153,7 @@ chromium_tag_well:
       showErrorMessage: true
       errorStyle: :stop
       errorTitle: "Tag well"
-      error: "Tag Index must a well."
+      error: "Tag Index must be a well."
   conditional_formattings:
     empty_cell:
     is_number:
@@ -202,6 +202,43 @@ library_type_long_read:
   conditional_formattings:
     empty_cell:
     is_error:
+dual_index_tag_set:
+  heading: TAG PLATE NAME
+  unlocked: true
+  validation:
+    options:
+      type: :list
+      formula1: "$A$1:$A$2"
+      allowBlank: false
+      showInputMessage: true
+      promptTitle: "Dual Index Tag Plate Name"
+      prompt: "Input the name of a valid dual index tag plate."
+    range_name: :dual_index_tag_sets
+  conditional_formattings:
+    empty_cell:
+dual_index_tag_well:
+  heading: DUAL INDEX TAG WELL
+  unlocked: true
+  validation:
+    options:
+      type: :textLength
+      operator: :lessThanOrEqual
+      formula1: "3"
+      allowBlank: false
+      showInputMessage: true
+      promptTitle: "Dual Index Tag well"
+      prompt: "The name of the well, eg. A1 which supplied the dual index tag"
+      showErrorMessage: true
+      errorStyle: :stop
+      errorTitle: "Dual index tag well"
+      error: "Dual Index Tag must be a well."
+  conditional_formattings:
+    empty_cell:
+    is_number:
+    len:
+      formula:
+        operator: ">"
+        operand: 3
 reference_genome:
   heading: REFERENCE GENOME
   unlocked: true
@@ -461,7 +498,7 @@ dna_source:
     empty_cell:
     is_error:
 date_of_sample_collection:
-  heading: DATE OF SAMPLE COLLECTION (YYY-MM-DD)
+  heading: DATE OF SAMPLE COLLECTION (YYYY-MM-DD)
   unlocked: true
   validation:
     options:

config/sample_manifest_excel/manifest_types.yml

@@ -127,7 +127,7 @@ plate_rnachip:
     - :sample_ebi_accession_number
     - :donor_id
 plate_library:
-  heading: "Library Plate"
+  heading: "Library Plate - custom tags"
   asset_type: "library_plate"
   columns:
     - :sanger_plate_id
@@ -184,6 +184,63 @@ plate_library:
     - :sample_ebi_accession_number
     - :donor_id
     - :primer_panel
+plate_dual_index_tag_library:
+  heading: "Library Plate - dual index tag plate"
+  asset_type: "library_plate"
+  columns:
+    - :sanger_plate_id
+    - :well
+    - :sanger_sample_id
+    - :supplier_name
+    - :dual_index_tag_set
+    - :dual_index_tag_well
+    - :reference_genome
+    - :library_type
+    - :insert_size_from
+    - :insert_size_to
+    - :cohort
+    - :volume
+    - :concentration
+    - :gender
+    - :country_of_origin
+    - :geographical_region
+    - :ethnicity
+    - :dna_source
+    - :date_of_sample_collection
+    - :date_of_sample_extraction
+    - :sample_extraction_method
+    - :sample_purified
+    - :purification_method
+    - :concentration_determined_by
+    - :sample_storage_conditions
+    - :mother
+    - :father
+    - :sibling
+    - :gc_content
+    - :sample_public_name
+    - :sample_taxon_id
+    - :sample_common_name
+    - :sample_description
+    - :sample_strain_att
+    - :sample_type
+    - :genotype
+    - :phenotype
+    - :age
+    - :developmental_stage
+    - :cell_type
+    - :disease_state
+    - :compound
+    - :dose
+    - :immunoprecipitate
+    - :growth_condition
+    - :rnai
+    - :organism_part
+    - :time_point
+    - :treatment
+    - :subject
+    - :disease
+    - :sample_ebi_accession_number
+    - :donor_id
 plate_chromium_library:
   heading: "Chromium Library Plate"
   asset_type: "library_plate"

config/sample_manifest_excel/ranges.yml

@@ -61,6 +61,10 @@ chromium_tag_groups:
   identifier: :name
   scope: :chromium
   scope_on: TagGroup
+dual_index_tag_sets:
+  identifier: :name
+  scope: :visible_dual_index
+  scope_on: TagSet
 gc_content:
   options:
     - "Neutral"

spec/data/sample_manifest_excel/columns.yml

@@ -168,6 +168,43 @@ library_type:
   conditional_formattings:
     empty_cell:
     is_error:
+dual_index_tag_set:
+  heading: TAG PLATE NAME
+  unlocked: true
+  validation:
+    options:
+      type: :list
+      formula1: "$A$1:$A$2"
+      allowBlank: false
+      showInputMessage: true
+      promptTitle: "Dual Index Tag Plate Name"
+      prompt: "Input the name of a valid dual index tag plate."
+    range_name: :dual_index_tag_sets
+  conditional_formattings:
+    empty_cell:
+dual_index_tag_well:
+  heading: DUAL INDEX TAG WELL
+  unlocked: true
+  validation:
+    options:
+      type: :textLength
+      operator: :lessThanOrEqual
+      formula1: "3"
+      allowBlank: false
+      showInputMessage: true
+      promptTitle: "Dual Index Tag well"
+      prompt: "The name of the well, eg. A1, which is supplied in the dual index tag plate"
+      showErrorMessage: true
+      errorStyle: :stop
+      errorTitle: "Dual index tag well"
+      error: "Dual Index Tag must be a well."
+  conditional_formattings:
+    empty_cell:
+    is_number:
+    len:
+      formula:
+        operator: ">"
+        operand: 3
 reference_genome:
   heading: REFERENCE GENOME
   unlocked: true