added validations in csv file for duplicate well coordinates and tube…

… barcodes, and for multiple rack barcodes

app/models/labware_creators/plate_split_to_tube_racks/csv_file.rb

@@ -23,6 +23,9 @@ class PlateSplitToTubeRacks::CsvFile
 
     validate :correctly_parsed?
     validates_nested :tube_rack_scan, if: :correctly_formatted?
+    validate :check_for_rack_barcodes_the_same, if: :correctly_formatted?
+    validate :check_no_duplicate_well_coordinates, if: :correctly_formatted?
+    validate :check_no_duplicate_tube_barcodes, if: :correctly_formatted?
 
     NO_TUBE_TEXTS = ['NO READ', 'NOSCAN'].freeze
 
@@ -97,6 +100,33 @@ def correctly_formatted?
       correctly_parsed?
     end
 
+    def check_for_rack_barcodes_the_same
+      tube_rack_barcodes = tube_rack_scan.group_by(&:tube_rack_barcode).keys
+
+      return unless tube_rack_barcodes.size > 1
+
+      barcodes_str = tube_rack_barcodes.join(',')
+      errors.add(:base, "Should not contain different rack barcodes (#{barcodes_str})")
+    end
+
+    def check_no_duplicate_well_coordinates
+      duplicated_well_coordinates =
+        tube_rack_scan.group_by(&:tube_position).select { |_position, tubes| tubes.size > 1 }.keys.join(',')
+
+      return if duplicated_well_coordinates.empty?
+
+      errors.add(:base, "Contains duplicate well coordinates (#{duplicated_well_coordinates})")
+    end
+
+    def check_no_duplicate_tube_barcodes
+      duplicated_tube_barcodes =
+        tube_rack_scan.group_by(&:tube_barcode).select { |_tube_barcode, tubes| tubes.size > 1 }.keys.join(',')
+
+      return if duplicated_tube_barcodes.empty?
+
+      errors.add(:base, "Contains duplicate tube barcodes (#{duplicated_tube_barcodes})")
+    end
+
     # Generates a hash of position details based on the tube rack scan data in the CSV file.
     #
     # @return [Hash] A hash of position details, where the keys are positions and the values

spec/fixtures/files/plate_split_to_tube_racks/tube_rack_scan_with_different_rack_barcodes.csv

@@ -0,0 +1,16 @@
+FX12345678, A1, AB10000001
+FX12345678, B1, AB10000002
+FX12345678, C1, AB10000003
+FX12345678, D1, AB10000004
+FX12345678, E1, AB10000005
+FX12345678, F1, AB10000006
+FX12345678, G1, AB10000007
+FX12345678, H1, AB10000008
+FX23838838, A2, AB10000009
+FX12345678, B2, AB10000010
+FX12345678, C2, AB10000011
+FX12345678, D2, AB10000012
+FX12345678, E2, AB10000013
+FX12345678, F2, AB10000014
+FX12345678, G2, AB10000015
+FX12345678, H2, AB10000016

spec/fixtures/files/plate_split_to_tube_racks/tube_rack_scan_with_duplicate_tubes.csv

@@ -0,0 +1,16 @@
+FX12345678, A1, AB10000001
+FX12345678, B1, AB10000002
+FX12345678, C1, AB10000003
+FX12345678, D1, AB10000004
+FX12345678, E1, AB10000005
+FX12345678, F1, AB10000006
+FX12345678, G1, AB10000007
+FX12345678, H1, AB10000008
+FX12345678, A2, AB10000009
+FX12345678, B2, AB10000009
+FX12345678, C2, AB10000011
+FX12345678, D2, AB10000011
+FX12345678, E2, AB10000013
+FX12345678, F2, AB10000014
+FX12345678, G2, AB10000015
+FX12345678, H2, AB10000016

spec/fixtures/files/plate_split_to_tube_racks/tube_rack_scan_with_duplicate_well_positions.csv

@@ -0,0 +1,16 @@
+FX12345678, A1, AB10000001
+FX12345678, B1, AB10000002
+FX12345678, C1, AB10000003
+FX12345678, D1, AB10000004
+FX12345678, E1, AB10000005
+FX12345678, F1, AB10000006
+FX12345678, G1, AB10000007
+FX12345678, H1, AB10000008
+FX12345678, A2, AB10000009
+FX12345678, A2, AB10000010
+FX12345678, C2, AB10000011
+FX12345678, D2, AB10000012
+FX12345678, E2, AB10000013
+FX12345678, E2, AB10000014
+FX12345678, G2, AB10000015
+FX12345678, H2, AB10000016

spec/models/labware_creators/plate_split_to_tube_racks/csv_file_spec.rb

@@ -300,4 +300,69 @@
       end
     end
   end
+
+  # there should be only one rack barcode in the file and it should be the same for all rows
+  context 'A file with inconsistant rack barcodes' do
+    let(:file) do
+      fixture_file_upload(
+        'spec/fixtures/files/plate_split_to_tube_racks/tube_rack_scan_with_different_rack_barcodes.csv',
+        'sequencescape/qc_file'
+      )
+    end
+
+    describe '#valid?' do
+      it 'should be invalid' do
+        expect(subject.valid?).to be false
+      end
+
+      it 'reports the errors' do
+        subject.valid?
+        expect(subject.errors.full_messages).to include(
+          'Should not contain different rack barcodes (FX12345678,FX23838838)'
+        )
+      end
+    end
+  end
+
+  # the same well position should not appear more than once in the file
+  context 'A file with duplicated well positions' do
+    let(:file) do
+      fixture_file_upload(
+        'spec/fixtures/files/plate_split_to_tube_racks/tube_rack_scan_with_duplicate_well_positions.csv',
+        'sequencescape/qc_file'
+      )
+    end
+
+    describe '#valid?' do
+      it 'should be invalid' do
+        expect(subject.valid?).to be false
+      end
+
+      it 'reports the errors' do
+        subject.valid?
+        expect(subject.errors.full_messages).to include('Contains duplicate well coordinates (A2,E2)')
+      end
+    end
+  end
+
+  # the same tube barcode should not appear more than once in the file
+  context 'A file with duplicated tube barcodes' do
+    let(:file) do
+      fixture_file_upload(
+        'spec/fixtures/files/plate_split_to_tube_racks/tube_rack_scan_with_duplicate_tubes.csv',
+        'sequencescape/qc_file'
+      )
+    end
+
+    describe '#valid?' do
+      it 'should be invalid' do
+        expect(subject.valid?).to be false
+      end
+
+      it 'reports the errors' do
+        subject.valid?
+        expect(subject.errors.full_messages).to include('Contains duplicate tube barcodes (AB10000009,AB10000011)')
+      end
+    end
+  end
 end