Merge pull request #4596 from sanger/y24-475-bug-improve-integration-…

…suite-uat-actions-error-message

Y24-475 [PR] [BUG] Improve integration suite UAT actions error message

app/uat_actions/uat_actions/generate_plates.rb

@@ -1,11 +1,16 @@
 # frozen_string_literal: true
 
 # Will construct plates with well_count wells filled with samples
+# rubocop:disable Metrics/ClassLength
 class UatActions::GeneratePlates < UatActions
   self.title = 'Generate plate'
   self.description = 'Generate plates in the selected study.'
   self.category = :generating_samples
 
+  ERROR_WELL_COUNT_EXCEEDS_PLATE_SIZE = "Well count of %s exceeds the plate size of %s for the plate purpose '%s'."
+  ERROR_PLATE_PURPOSE_DOES_NOT_EXIST = "Plate purpose '%s' does not exist."
+  ERROR_STUDY_DOES_NOT_EXIST = 'Study %s does not exist.'
+
   form_field :plate_purpose_name,
              :select,
              label: 'Plate Purpose',
@@ -45,8 +50,27 @@ class UatActions::GeneratePlates < UatActions
              help: 'The order in which wells are laid out. Affects where empty wells are located.',
              select_options: %w[Column Row Random]
 
-  validate :well_count_smaller_than_plate_size
-  validates :number_of_samples_in_each_well, numericality: { greater_than: 0, only_integer: true, allow_blank: false }
+  validates :plate_purpose_name, presence: true
+  validates :plate_count, numericality: { greater_than: 0, smaller_than: 20, only_integer: true, allow_blank: false }
+  validates :well_count, numericality: { greater_than: 0, only_integer: true, allow_blank: false }
+  validates :number_of_samples_in_each_well,
+            numericality: {
+              greater_than: 0,
+              smaller_than: 20,
+              only_integer: true,
+              allow_blank: false
+            }
+  validates :study_name, presence: true
+  validates :well_layout,
+            presence: true,
+            inclusion: {
+              in: %w[Column Row Random],
+              message: 'must be Column, Row, or Random'
+            }
+
+  validate :validate_plate_purpose_exists
+  validate :validate_well_count_is_smaller_than_plate_size
+  validate :validate_study_exists
 
   def self.default
     new(
@@ -72,11 +96,38 @@ def perform
 
   private
 
-  def well_count_smaller_than_plate_size
-    return true if well_count.to_i <= plate_purpose.size
+  # Validates that the plate purpose exists for the selected plate purpose name.
+  #
+  # @return [void]
+  def validate_plate_purpose_exists
+    return if plate_purpose_name.blank?
+    return if PlatePurpose.exists?(name: plate_purpose_name)
+
+    message = format(ERROR_PLATE_PURPOSE_DOES_NOT_EXIST, plate_purpose_name)
+    errors.add(:plate_purpose_name, message)
+  end
+
+  # Validates that the well count is smaller than the plate size for the
+  # selected plate purpose.
+  #
+  # @return [void]
+  def validate_well_count_is_smaller_than_plate_size
+    return unless PlatePurpose.exists?(name: plate_purpose_name)
+    return if well_count.to_i <= plate_purpose.size
+
+    message = format(ERROR_WELL_COUNT_EXCEEDS_PLATE_SIZE, well_count, plate_purpose.size, plate_purpose.name)
+    errors.add(:well_count, message)
+  end
+
+  # Validates that the study exists for the selected study name.
+  #
+  # @return [void]
+  def validate_study_exists
+    return if study_name.blank?
+    return if Study.exists?(name: study_name)
 
-    errors.add(:well_count, "is larger than the size of a #{plate_purpose.name} (plate_purpose.size)")
-    false
+    message = format(ERROR_STUDY_DOES_NOT_EXIST, study_name)
+    errors.add(:study_name, message)
   end
 
   # Ensures number of samples per occupied well is at least 1
@@ -171,3 +222,4 @@ def plate_purpose
     Purpose.find_by!(name: plate_purpose_name)
   end
 end
+# rubocop:enable Metrics/ClassLength

app/uat_actions/uat_actions/generate_sample_manifest.rb

@@ -6,6 +6,8 @@ class UatActions::GenerateSampleManifest < UatActions
   self.description = 'Generate sample manifest with the provided information.'
   self.category = :generating_samples
 
+  ERROR_TUBE_PURPOSE_DOES_NOT_EXIST = "Tube purpose '%s' does not exist."
+
   form_field :study_name,
              :select,
              label: 'Study Name',
@@ -41,6 +43,9 @@ class UatActions::GenerateSampleManifest < UatActions
 
   form_field :with_samples, :check_box, help: 'Create new samples for recipients?', label: 'With Samples?'
 
+  validates :tube_purpose_name, presence: true
+  validate :validate_tube_purpose_exists
+
   def self.default
     new(
       study_name: UatActions::StaticRecords.study.name,
@@ -59,6 +64,17 @@ def perform
     true
   end
 
+  # Validates that the tube purpose exists for the selected tube purpose name.
+  #
+  # @return [void]
+  def validate_tube_purpose_exists
+    return if tube_purpose_name.blank? # Already validated by presence
+    return if Tube::Purpose.exists?(name: tube_purpose_name)
+
+    message = format(ERROR_TUBE_PURPOSE_DOES_NOT_EXIST, tube_purpose_name)
+    errors.add(:tube_purpose_name, message)
+  end
+
   def create_sample_manifest
     SampleManifest.create!(study:, supplier:, asset_type:, count:, purpose:)
   end

app/uat_actions/uat_actions/test_submission.rb

@@ -11,6 +11,12 @@ class UatActions::TestSubmission < UatActions # rubocop:todo Metrics/ClassLength
       'This may produce odd results for some pipelines.'
   self.category = :setup_and_test
 
+  ERROR_SUBMISSION_TEMPLATE_DOES_NOT_EXIST = "Submission template '%s' does not exist."
+  ERROR_PLATE_DOES_NOT_EXIST = 'Plate with barcode %s does not exist.'
+  ERROR_PLATE_PURPOSE_DOES_NOT_EXIST = "Plate purpose '%s' does not exist."
+  ERROR_LIBRARY_TYPE_DOES_NOT_EXIST = "Library type '%s' does not exist."
+  ERROR_PRIMER_PANEL_DOES_NOT_EXIST = "Primer panel '%s' does not exist."
+
   # Form fields
   form_field :submission_template_name,
              :select,
@@ -95,6 +101,12 @@ class UatActions::TestSubmission < UatActions # rubocop:todo Metrics/ClassLength
   validates :number_of_samples_in_each_well, numericality: { greater_than: 0, only_integer: true, allow_blank: true }
   validates :number_of_wells_to_submit, numericality: { greater_than: 0, only_integer: true, allow_blank: true }
 
+  validate :validate_submission_template_exists
+  validate :validate_plate_exists
+  validate :validate_plate_purpose_exists
+  validate :validate_library_type_exists
+  validate :validate_primer_panel_exists
+
   #
   # Returns a default copy of the UatAction which will be used to fill in the form
   #
@@ -145,6 +157,71 @@ def perform # rubocop:todo Metrics/AbcSize
 
   private
 
+  # Validates that the submission template exists for the specified submission
+  # template name.
+  #
+  # @return [void]
+  def validate_submission_template_exists
+    return if submission_template_name.blank? # already validated by presence
+    return if SubmissionTemplate.exists?(name: submission_template_name)
+
+    message = format(ERROR_SUBMISSION_TEMPLATE_DOES_NOT_EXIST, submission_template_name)
+    errors.add(:submission_template_name, message)
+  end
+
+  # Validates that the plate exists for the specified plate barcode. It is
+  # is skipped if no barcode is provided, because a new plate is generated.
+  #
+  # @return [void]
+  def validate_plate_exists
+    return if plate_barcode.blank? # an appropriate plate will be generated
+    return if Plate.find_by_barcode(plate_barcode.strip).present?
+
+    message = format(ERROR_PLATE_DOES_NOT_EXIST, plate_barcode)
+    errors.add(:plate_barcode, message)
+  end
+
+  # Validates that the plate purpose exists for the specified plate purpose
+  # name. It will be skipped if a barcode specified. It will be also skipped
+  # when no purpose is provided because an appropriate purpose will be used when
+  # generating a new plate.
+  #
+  # @return [void]
+  def validate_plate_purpose_exists
+    return if plate_barcode.present? # takes precedence over plate purpose
+    return if plate_purpose_name.blank? # an appropriate purpose will be used
+    return if PlatePurpose.exists?(name: plate_purpose_name)
+
+    message = format(ERROR_PLATE_PURPOSE_DOES_NOT_EXIST, plate_purpose_name)
+    errors.add(:plate_purpose_name, message)
+  end
+
+  # Validates that the library type exists for the specified library type name.
+  # It is skipped if no library type name is provided because the first library
+  # type found will be used.
+  #
+  # return [void]
+  def validate_library_type_exists
+    return if library_type_name.blank? # first library type found will be used
+    return if LibraryType.exists?(name: library_type_name)
+
+    message = format(ERROR_LIBRARY_TYPE_DOES_NOT_EXIST, library_type_name)
+    errors.add(:library_type_name, message)
+  end
+
+  # Validates that the primer panel exists for the specified primer panel name.
+  # It is skipped if no primer panel name is provided because it is not
+  # applicable for the current submission template.
+  #
+  # return [void]
+  def validate_primer_panel_exists
+    return if primer_panel_name.blank? # not applicable for the template
+    return if PrimerPanel.exists?(name: primer_panel_name)
+
+    message = format(ERROR_PRIMER_PANEL_DOES_NOT_EXIST, primer_panel_name)
+    errors.add(:primer_panel_name, message)
+  end
+
   def submission_template
     @submission_template = SubmissionTemplate.find_by(name: submission_template_name)
   end

app/uat_actions/uat_actions/tube_submission.rb

@@ -3,11 +3,16 @@
 # This UAT Action will generates a basic submission for tubes. Initially, it
 # has been designed for generating scRNA Core Donor Pooling and cDNA Prep
 # submissions on LRC Bank Seq/Spare tubes.
+# rubocop:disable Metrics/ClassLength
 class UatActions::TubeSubmission < UatActions
   self.title = 'Tube submission'
   self.description = 'Generates a basic submission for tubes.'
   self.category = :setup_and_test
 
+  ERROR_SUBMISSION_TEMPLATE_DOES_NOT_EXIST = "Submission template '%s' does not exist."
+  ERROR_TUBES_DO_NOT_EXIST = 'Tubes with barcodes do not exist: %s'
+  ERROR_LIBRARY_TYPE_DOES_NOT_EXIST = "Library type '%s' does not exist."
+
   form_field :submission_template_name,
              :select,
              label: 'Submission Template',
@@ -56,6 +61,11 @@ class UatActions::TubeSubmission < UatActions
              }
 
   validates :submission_template, presence: { message: 'could not be found' }
+  validates :tube_barcodes, presence: true
+
+  validate :validate_submission_template_exists
+  validate :validate_tubes_exist
+  validate :validate_library_type_exists
 
   # Returns a default copy of the UatAction which will be used to fill in the form
   #
@@ -95,6 +105,46 @@ def perform
     true
   end
 
+  # Validates that the submission template exists for the specified submission
+  # template name.
+  #
+  # @return [void]
+  def validate_submission_template_exists
+    return if submission_template_name.blank? # already validated by presence
+    return if SubmissionTemplate.exists?(name: submission_template_name)
+
+    message = format(ERROR_SUBMISSION_TEMPLATE_DOES_NOT_EXIST, submission_template_name)
+    errors.add(:submission_template_name, message)
+  end
+
+  # Validates that the tubes exist for the specified barcodes.
+  #
+  # @return [void]
+  def validate_tubes_exist
+    return if tube_barcodes.blank? # already validated by presence
+    barcodes =
+      tube_barcodes
+        .gsub(/(\\[trfvn])+/, ' ')
+        .split
+        .select do |barcode|
+          Tube.find_by_barcode(barcode).blank? # not found
+        end
+
+    message = format(ERROR_TUBES_DO_NOT_EXIST, barcodes.join(', '))
+    errors.add(:tube_barcodes, message)
+  end
+
+  # Validates that the library type exists for the specified library type name.
+  #
+  # return [void]
+  def validate_library_type_exists
+    return if library_type_name.blank? # optional
+    return if LibraryType.exists?(name: library_type_name)
+
+    message = format(ERROR_LIBRARY_TYPE_DOES_NOT_EXIST, library_type_name)
+    errors.add(:library_type_name, message)
+  end
+
   # Fills the report with the information from the submission
   #
   # @return [Void]
@@ -191,3 +241,4 @@ def user
     UatActions::StaticRecords.user
   end
 end
+# rubocop:enable Metrics/ClassLength

spec/uat_actions/generate_plates_spec.rb

@@ -83,4 +83,83 @@
   it 'returns a default' do
     expect(described_class.default).to be_a described_class
   end
+
+  describe '#valid?' do
+    let(:uat_action) { described_class.new(parameters) }
+
+    describe '#validate_plate_purpose_exists' do
+      let(:parameters) { { plate_purpose_name: } }
+      let(:error_message) { format(described_class::ERROR_PLATE_PURPOSE_DOES_NOT_EXIST, plate_purpose_name) }
+
+      context 'when the plate purpose does not exist' do
+        let(:plate_purpose_name) { 'Invalid Plate Purpose' }
+
+        it 'adds the error message' do
+          expect(uat_action.valid?).to be false
+          expect(uat_action.errors[:plate_purpose_name]).to include(error_message)
+        end
+      end
+
+      context 'when the plate purpose exists' do
+        let(:plate) { create(:plate) }
+        let(:plate_purpose_name) { plate.purpose.name }
+
+        it 'does not add the error message' do
+          uat_action.valid? # run validations
+          expect(uat_action.errors[:plate_purpose_name]).not_to include(error_message)
+        end
+      end
+    end
+
+    describe '#validate_well_count_is_smaller_than_plate_size' do
+      let(:parameters) { { plate_purpose_name:, well_count: } }
+      let(:plate) { create(:plate, size: 96) }
+      let(:plate_purpose_name) { plate.purpose.name }
+      let(:error_message) do
+        format(described_class::ERROR_WELL_COUNT_EXCEEDS_PLATE_SIZE, well_count, plate.size, plate_purpose_name)
+      end
+
+      context 'when the well count exceeds the plate size' do
+        let(:well_count) { plate.size + 1 }
+
+        it 'adds the error message' do
+          expect(uat_action.valid?).to be false
+          expect(uat_action.errors[:well_count]).to include(error_message)
+        end
+      end
+
+      context 'when the well count is equal to the plate size' do
+        let(:well_count) { plate.size }
+
+        it 'does not add the error message' do
+          uat_action.valid? # run validations
+          expect(uat_action.errors[:well_count]).not_to include(error_message)
+        end
+      end
+    end
+
+    describe '#validate_study_exists' do
+      let(:parameters) { { study_name: } }
+      let(:error_message) { format(described_class::ERROR_STUDY_DOES_NOT_EXIST, study_name) }
+
+      context 'when the study exists' do
+        let(:study) { create(:study) }
+        let(:study_name) { study.name }
+
+        it 'does not add the error message' do
+          uat_action.valid? # run validations
+          expect(uat_action.errors[:study_name]).not_to include(error_message)
+        end
+      end
+
+      context 'when the study does not exist' do
+        let(:study_name) { 'Invalid Study' }
+
+        it 'adds the error message' do
+          expect(uat_action.valid?).to be false
+          expect(uat_action.errors[:study_name]).to include(error_message)
+        end
+      end
+    end
+  end
 end