[ux] Add genders to internal accessioning validations

app/models/sample.rb

@@ -27,6 +27,7 @@ class Current < ActiveSupport::CurrentAttributes
 
   GC_CONTENTS = ['Neutral', 'High AT', 'High GC'].freeze
   GENDERS = ['Male', 'Female', 'Mixed', 'Hermaphrodite', 'Unknown', 'Not Applicable'].freeze
+  EGA_GENDERS = %w[Female Male Unknown].freeze
   DNA_SOURCES = [
     'Genomic',
     'Whole Genome Amplified',
@@ -194,6 +195,8 @@ class Current < ActiveSupport::CurrentAttributes
 
     with_options(on: :EGA) do
       validates :gender, presence: { message: 'is required' }
+      one_of_ega_genders = EGA_GENDERS.to_sentence(last_word_connector: ' or ', two_words_connector: ' or ')
+      validates :gender, inclusion: { in: EGA_GENDERS, message: "must be #{one_of_ega_genders}" }
       validates :phenotype, presence: { message: 'is required' }
       validates :donor_id, presence: { message: 'is required' }
     end

lib/accession/sample.rb

@@ -113,9 +113,8 @@ def check_required_fields
       # EBI will still perform its own validation on submission.
       return if Flipper.enabled?(:y25_714_skip_accessioning_tag_validation)
 
-      unless tags.meets_service_requirements?(service, standard_tags)
-        errors.add(:sample, "does not have the required metadata: #{tags.missing.sort.to_sentence.dasherize}.")
-      end
+      check_tags
+      check_samples
     end
 
     def check_studies
@@ -125,5 +124,15 @@ def check_studies
         errors.add(:sample, 'can only be accessioned if linked to a releasable, accessioned study.')
       end
     end
+
+    def check_tags
+      unless tags.meets_service_requirements?(service, standard_tags)
+        errors.add(:sample, "does not have the required metadata: #{tags.missing.sort.to_sentence.dasherize}.")
+      end
+    end
+
+    def check_samples
+      sample.errors.full_messages.each { |msg| errors.add(:sample, msg) } unless sample.valid?(service.provider)
+    end
   end
 end

spec/lib/accession/sample_spec.rb

@@ -90,6 +90,55 @@ def find_value_at_tag(xml_received, tag_name)
         expect(described_class.new(tag_list, sample)).not_to be_valid
       end
 
+      it 'can have a gender of Female' do
+        sample.sample_metadata.gender = 'Female'
+        expect(described_class.new(tag_list, sample)).to be_valid
+      end
+
+      it 'cannot have a leading space in gender' do
+        sample.sample_metadata.gender = ' Female'
+        expect(described_class.new(tag_list, sample)).not_to be_valid
+      end
+
+      it 'cannot have a trailing space in gender' do
+        sample.sample_metadata.gender = 'Female '
+        expect(described_class.new(tag_list, sample)).not_to be_valid
+      end
+
+      it 'can have a gender of Male' do
+        sample.sample_metadata.gender = 'Male'
+        expect(described_class.new(tag_list, sample)).to be_valid
+      end
+
+      it 'can have a gender of Unknown' do
+        sample.sample_metadata.gender = 'Unknown'
+        expect(described_class.new(tag_list, sample)).to be_valid
+      end
+
+      it 'cannot have a gender of Mixed' do
+        sample.sample_metadata.gender = 'Mixed'
+        expect(described_class.new(tag_list, sample)).not_to be_valid
+      end
+
+      it 'cannot have a gender of Hermaphrodite' do
+        sample.sample_metadata.gender = 'Hermaphrodite'
+        expect(described_class.new(tag_list, sample)).not_to be_valid
+      end
+
+      it 'cannot have a gender of Not Applicable' do
+        sample.sample_metadata.gender = 'Not Applicable'
+        expect(described_class.new(tag_list, sample)).not_to be_valid
+      end
+
+      it 'provides a clear error message about valid gender options' do
+        sample.sample_metadata.gender = 'Invalid Gender'
+        accession_sample = described_class.new(tag_list, sample)
+        accession_sample.validate
+        expect(accession_sample.errors.full_messages.join).to include(
+          'Sample metadata gender must be Female, Male or Unknown'
+        )
+      end
+
       it 'is required to define phenotype' do
         sample.sample_metadata.phenotype = nil
         expect(described_class.new(tag_list, sample)).not_to be_valid

spec/lib/accession/submission_spec.rb

@@ -55,7 +55,7 @@
       allow(described_class).to receive(:client).and_return(mock_client)
     end
 
-    context 'when th sample has not yet been accessioned' do
+    context 'when the sample has not yet been accessioned' do
       context 'when the submission is successful' do
         let(:accession_number) { 'EGA00001000240' }
         let(:mock_client) do