Merge branch 'dpl-977-update-tnano-export-file' into uat-19th-feb-24

app/models/labware_creators/pcr_cycles_binned_plate/csv_file/duplex_seq/row.rb

@@ -0,0 +1,69 @@
+# frozen_string_literal: true
+
+# Part of the Labware creator classes
+module LabwareCreators
+  require_dependency 'labware_creators/pcr_cycles_binned_plate/csv_file_for_duplex_seq'
+
+  module PcrCyclesBinnedPlate::CsvFile
+    #
+    # This version of the row is for the Duplex Seq pipeline.
+    #
+    class DuplexSeq::Row < RowBase
+      include ActiveModel::Validations
+
+      SUB_POOL_NOT_BLANK = 'has a value when Submit for Sequencing is N, it should be empty, in %s'
+      SUBMIT_FOR_SEQ_INVALID = 'is empty or has an unrecognised value (should be Y or N), in %s'
+      COVERAGE_MISSING = 'is missing but should be present when Submit for Sequencing is Y, in %s'
+      COVERAGE_NEGATIVE = 'is negative but should be a positive value, in %s'
+
+      attr_reader :submit_for_sequencing, :sub_pool, :coverage
+
+      validate :submit_for_sequencing_has_expected_value
+      validate :sub_pool_within_expected_range
+      validates :coverage,
+                presence: {
+                  message: ->(object, _data) { COVERAGE_MISSING % object }
+                },
+                numericality: {
+                  greater_than: 0,
+                  message: ->(object, _data) { COVERAGE_NEGATIVE % object }
+                },
+                unless: -> { empty? || !submit_for_sequencing? }
+
+      delegate :submit_for_sequencing_column, :sub_pool_column, :coverage_column, to: :header
+
+      def initialize_pipeline_specific_columns
+        @submit_for_sequencing_as_string = @row_data[submit_for_sequencing_column]&.strip&.upcase
+        @sub_pool = @row_data[sub_pool_column]&.strip&.to_i
+        @coverage = @row_data[coverage_column]&.strip&.to_i
+      end
+
+      def submit_for_sequencing?
+        @submit_for_sequencing ||= (@submit_for_sequencing_as_string == 'Y')
+      end
+
+      def submit_for_sequencing_has_expected_value
+        return if empty?
+
+        return if %w[Y N].include? @submit_for_sequencing_as_string
+
+        errors.add('submit_for_sequencing', format(SUBMIT_FOR_SEQ_INVALID, to_s))
+      end
+
+      def sub_pool_within_expected_range
+        return if empty?
+
+        # check the value is within range when we do expect a value to be present
+        if submit_for_sequencing?
+          in_range('sub_pool', sub_pool, @row_config.sub_pool_min, @row_config.sub_pool_max)
+        else
+          # expect sub-pool field to be blank, possible mistake by user if not
+          return if sub_pool.blank?
+
+          # sub-pool is NOT blank and should be
+          errors.add('sub_pool', format(SUB_POOL_NOT_BLANK, to_s))
+        end
+      end
+    end
+  end
+end

app/models/labware_creators/pcr_cycles_binned_plate/csv_file/duplex_seq/well_details_header.rb

@@ -0,0 +1,34 @@
+# frozen_string_literal: true
+
+# Part of the Labware creator classes
+module LabwareCreators
+  require_dependency 'labware_creators/pcr_cycles_binned_plate/csv_file_for_duplex_seq'
+
+  module PcrCyclesBinnedPlate::CsvFile
+    #
+    # Class WellDetailsHeader provides a simple wrapper for handling and validating
+    # the plate barcode header row from the customer csv file
+    #
+    class DuplexSeq::WellDetailsHeader < WellDetailsHeaderBase
+      # Return the index of the respective column.
+      attr_reader :submit_for_sequencing_column, :sub_pool_column, :coverage_column
+
+      SUBMIT_FOR_SEQUENCING_COLUMN = 'Submit for sequencing (Y/N)?'
+      SUB_POOL_COLUMN = 'Sub-Pool'
+      COVERAGE_COLUMN = 'Coverage'
+      NOT_FOUND = 'could not be found in: '
+
+      validates :submit_for_sequencing_column, presence: { message: ->(object, _data) { "#{NOT_FOUND}'#{object}'" } }
+      validates :sub_pool_column, presence: { message: ->(object, _data) { "#{NOT_FOUND}'#{object}'" } }
+      validates :coverage_column, presence: { message: ->(object, _data) { "#{NOT_FOUND}'#{object}'" } }
+
+      private
+
+      def initialize_pipeline_specific_columns
+        @submit_for_sequencing_column = index_of_header(SUBMIT_FOR_SEQUENCING_COLUMN)
+        @sub_pool_column = index_of_header(SUB_POOL_COLUMN)
+        @coverage_column = index_of_header(COVERAGE_COLUMN)
+      end
+    end
+  end
+end

app/models/labware_creators/pcr_cycles_binned_plate/csv_file/plate_barcode_header.rb

@@ -2,7 +2,7 @@
 
 # Part of the Labware creator classes
 module LabwareCreators
-  require_dependency 'labware_creators/custom_pooled_tubes/csv_file'
+  require_dependency 'labware_creators/pcr_cycles_binned_plate/csv_file_base'
 
   #
   # Class PlateBarcodeHeader provides a simple wrapper for handling and validating
@@ -22,9 +22,10 @@ class PcrCyclesBinnedPlate::CsvFile::PlateBarcodeHeader
     BARCODE_NOT_MATCHING =
       'The plate barcode in the file (%s) does not match the barcode of ' \
         'the plate being uploaded to (%s), please check you have the correct file.'
+    NOT_FOUND = 'could not be found in: '
 
-    validates :barcode_lbl_index, presence: { message: ->(object, _data) { "could not be found in: '#{object}'" } }
-    validates :plate_barcode, presence: { message: ->(object, _data) { "could not be found in: '#{object}'" } }
+    validates :barcode_lbl_index, presence: { message: ->(object, _data) { "#{NOT_FOUND}'#{object}'" } }
+    validates :plate_barcode, presence: { message: ->(object, _data) { "#{NOT_FOUND}'#{object}'" } }
     validate :plate_barcode_matches_parent?
 
     #