Merge branch 'dpl-976-modify-customer-file-handling' into dpl-977-upd…

…ate-tnano-export-file

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

@@ -0,0 +1,70 @@
+# 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 true if empty?
+
+        return true 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 true if empty?
+
+        # check the value is within range when we do expect a value to be present
+        if submit_for_sequencing?
+          return in_range?('sub_pool', sub_pool, @row_config.sub_pool_min, @row_config.sub_pool_max)
+        end
+
+        # expect sub-pool field to be blank, possible mistake by user if not
+        return true if sub_pool.blank?
+
+        # sub-pool is NOT blank and should be
+        errors.add('sub_pool', format(SUB_POOL_NOT_BLANK, to_s))
+        false
+      end
+    end
+  end
+end

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

@@ -0,0 +1,36 @@
+# 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::DuplexSeq
+    #
+    # Class WellDetailsHeader provides a simple wrapper for handling and validating
+    # the plate barcode header row from the customer csv file
+    #
+    class WellDetailsHeader < PcrCyclesBinnedPlate::CsvFile::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'
+
+      validates :submit_for_sequencing_column,
+                presence: {
+                  message: ->(object, _data) { "could not be found in: '#{object}'" }
+                }
+      validates :sub_pool_column, presence: { message: ->(object, _data) { "could not be found in: '#{object}'" } }
+      validates :coverage_column, presence: { message: ->(object, _data) { "could not be found in: '#{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/pcr_cycles_binned_plate/csv_file'
+  require_dependency 'labware_creators/pcr_cycles_binned_plate/csv_file_base'
 
   #
   # Class PlateBarcodeHeader provides a simple wrapper for handling and validating

app/models/labware_creators/pcr_cycles_binned_plate/csv_file/row_for_t_nano_seq.rb → app/models/labware_creators/pcr_cycles_binned_plate/csv_file/row_base.rb

@@ -2,17 +2,15 @@
 
 # Part of the Labware creator classes
 module LabwareCreators
-  require_dependency 'labware_creators/pcr_cycles_binned_plate/csv_file'
-
   #
-  # This version of the row is for the Targeted NanoSeq pipeline.
+  # Provides a simple wrapper for handling and validating individual CSV rows.
+  # Abstract class, extend for uses in specific pipelines.
   #
-  class PcrCyclesBinnedPlate::CsvFile::RowForTNanoSeq
+  class PcrCyclesBinnedPlate::CsvFile::RowBase
     include ActiveModel::Validations
 
     IN_RANGE = 'is empty or contains a value that is out of range (%s to %s), in %s'
     WELL_NOT_RECOGNISED = 'contains an invalid well name: %s'
-    HYB_PANEL_MISSING = 'is empty, in %s'
 
     attr_reader :header,
                 :well,
@@ -24,7 +22,6 @@ class PcrCyclesBinnedPlate::CsvFile::RowForTNanoSeq
                 :sample_volume,
                 :diluent_volume,
                 :pcr_cycles,
-                :hyb_panel,
                 :index
 
     validates :well,
@@ -37,7 +34,7 @@ class PcrCyclesBinnedPlate::CsvFile::RowForTNanoSeq
     validate :sample_volume_within_expected_range?
     validate :diluent_volume_within_expected_range?
     validate :pcr_cycles_within_expected_range?
-    validate :hyb_panel_is_present?
+
     delegate :well_column,
              :concentration_column,
              :sanger_sample_id_column,
@@ -47,10 +44,9 @@ class PcrCyclesBinnedPlate::CsvFile::RowForTNanoSeq
              :sample_volume_column,
              :diluent_volume_column,
              :pcr_cycles_column,
-             :hyb_panel_column,
              to: :header
 
-    # rubocop:disable Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/PerceivedComplexity
+    # rubocop:todo Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/PerceivedComplexity
     def initialize(row_config, header, index, row_data)
       @row_config = row_config
       @header = header
@@ -69,11 +65,16 @@ def initialize(row_config, header, index, row_data)
       @sample_volume = @row_data[sample_volume_column]&.strip&.to_f
       @diluent_volume = @row_data[diluent_volume_column]&.strip&.to_f
       @pcr_cycles = @row_data[pcr_cycles_column]&.strip&.to_i
-      @hyb_panel = @row_data[hyb_panel_column]&.strip
+
+      initialize_pipeline_specific_columns
     end
 
     # rubocop:enable Metrics/AbcSize,Metrics/CyclomaticComplexity,Metrics/PerceivedComplexity
 
+    def initialize_pipeline_specific_columns
+      raise '#initialize_pipeline_specific_columns must be implemented on subclasses'
+    end
+
     def to_s
       @well.present? ? "row #{index + 2} [#{@well}]" : "row #{index + 2}"
     end
@@ -99,19 +100,6 @@ def pcr_cycles_within_expected_range?
       in_range?('pcr_cycles', pcr_cycles, @row_config.pcr_cycles_min, @row_config.pcr_cycles_max)
     end
 
-    # Checks whether the Hyb Panel column is filled in
-    def hyb_panel_is_present?
-      return true if empty?
-
-      # TODO: can we validate the hyb panel value? Does not appear to be tracked in LIMS.
-      result = hyb_panel.present?
-      unless result
-        msg = format(HYB_PANEL_MISSING, to_s)
-        errors.add('hyb_panel', msg)
-      end
-      result
-    end
-
     # Checks whether a row value it within the specified range using min/max values
     # from the row config
     #