Fix functional tests about the isa json exporter

lib/isa_exporter.rb

@@ -184,9 +184,14 @@ def convert_assays(assay_stream)
       return unless assay_stream.can_view?(@current_user)
       return unless child_assays.all? { |a| a.can_view?(@current_user) }
 
+      child_assays.map do |ca|
+        unless ca.sample_type.present?
+          raise "No Sample type was found in Assay '#{ca.id} - #{ca.title}'," \
+                " part of Assay Stream '#{assay_stream.id - assay_stream.title}'"
+        end
+      end
+
       all_sample_types = child_assays.map(&:sample_type).compact
-      # first_assay = assays.detect { |s| s.position.zero? }
-      # raise 'No assay could be found!' unless first_assay
 
       stream_name = "assays_#{child_assays.pluck(:id).join('_')}"
       assay_comments = convert_assay_comments(assay_stream)
@@ -745,7 +750,7 @@ def random_string(len)
     end
 
     def get_derived_from_type(sample_type)
-      raise 'There is no sample!' if sample_type.samples.length == 0
+      raise "There are no samples in '#{sample_type.title}'!" if sample_type.samples.blank?
 
       prev_sample_type = sample_type.samples[0]&.linked_samples[0]&.sample_type
       return nil if prev_sample_type.blank?

test/factories/assays.rb

@@ -14,7 +14,7 @@
   end
 
   factory(:assay_stream_class, class: AssayClass) do
-    title { 'Assay Stream' }
+    title { I18n.t('assays.assay_stream') }
     key { 'ASS' }
     description { "An assay stream class description" }
   end
@@ -115,7 +115,7 @@
     description { 'A holder assay holding multiple child assays' }
     association :assay_class, factory: :assay_stream_class
     after(:build) do |assay|
-      assay.study = FactoryBot.create(:isa_json_compliant_study)
+      assay.study ||= FactoryBot.create(:isa_json_compliant_study, contributor: assay.contributor)
     end
   end
 

test/functional/investigations_controller_test.rb

@@ -911,16 +911,22 @@ def test_title
                           contributor: other_user.person)
 
       # Create a 'private' assay in an assay stream
-      assay_1_stream_1_sample_type = FactoryBot.create(:isa_assay_material_sample_type, linked_sample_type: sample_collection_sample_type, template_id: FactoryBot.create(:isa_assay_material_template).id)
-      assay_1_stream_1 = FactoryBot.create(:assay, position: 0, sample_type: assay_1_stream_1_sample_type, study: accessible_study, contributor: current_user.person)
-      assay_2_stream_1_sample_type = FactoryBot.create(:isa_assay_data_file_sample_type, linked_sample_type: assay_1_stream_1_sample_type, template_id: FactoryBot.create(:isa_assay_data_file_template).id)
-      assay_2_stream_1 = FactoryBot.create(:assay, position:1, sample_type: assay_2_stream_1_sample_type, study: accessible_study, contributor: other_user.person)
+      stream_1 = FactoryBot.create(:assay_stream, title: 'Assay Stream 1', study: accessible_study, contributor: other_user.person)
+      assert_equal(stream_1.study, accessible_study)
+      assert(stream_1.is_assay_stream?)
+      assay_1_stream_1_sample_type = FactoryBot.create(:isa_assay_material_sample_type, contributor: other_user.person, linked_sample_type: sample_collection_sample_type, template_id: FactoryBot.create(:isa_assay_material_template).id)
+      assay_1_stream_1 = FactoryBot.create(:assay, position: 1, sample_type: assay_1_stream_1_sample_type, study: accessible_study, contributor: other_user.person, assay_stream_id: stream_1.id)
+      assay_2_stream_1_sample_type = FactoryBot.create(:isa_assay_data_file_sample_type, contributor: other_user.person, linked_sample_type: assay_1_stream_1_sample_type, template_id: FactoryBot.create(:isa_assay_data_file_template).id)
+      assay_2_stream_1 = FactoryBot.create(:assay, position: 2, sample_type: assay_2_stream_1_sample_type, study: accessible_study, contributor: other_user.person, assay_stream_id: stream_1.id)
 
       # Create an assay stream with all assays visible
-      assay_1_stream_2_sample_type = FactoryBot.create(:isa_assay_material_sample_type, linked_sample_type: sample_collection_sample_type, template_id: FactoryBot.create(:isa_assay_material_template).id)
-      assay_1_stream_2 = FactoryBot.create(:assay, position: 0, sample_type: assay_1_stream_2_sample_type, study: accessible_study, contributor: current_user.person)
-      assay_2_stream_2_sample_type = FactoryBot.create(:isa_assay_data_file_sample_type, linked_sample_type: assay_1_stream_2_sample_type, template_id: FactoryBot.create(:isa_assay_data_file_template).id)
-      assay_2_stream_2 = FactoryBot.create(:assay, position:1, sample_type: assay_2_stream_2_sample_type, study: accessible_study, contributor: current_user.person)
+      stream_2 = FactoryBot.create(:assay_stream, title: 'Assay Stream 2', study: accessible_study, contributor: current_user.person)
+      assert_equal(stream_2.study, accessible_study)
+      assert(stream_2.is_assay_stream?)
+      assay_1_stream_2_sample_type = FactoryBot.create(:isa_assay_material_sample_type, contributor: current_user.person, linked_sample_type: sample_collection_sample_type, template_id: FactoryBot.create(:isa_assay_material_template).id)
+      assay_1_stream_2 = FactoryBot.create(:assay, position: 1, sample_type: assay_1_stream_2_sample_type, study: accessible_study, contributor: current_user.person, assay_stream_id: stream_2.id)
+      assay_2_stream_2_sample_type = FactoryBot.create(:isa_assay_data_file_sample_type, contributor: current_user.person, linked_sample_type: assay_1_stream_2_sample_type, template_id: FactoryBot.create(:isa_assay_data_file_template).id)
+      assay_2_stream_2 = FactoryBot.create(:assay, position: 2, sample_type: assay_2_stream_2_sample_type, study: accessible_study, contributor: current_user.person, assay_stream_id: stream_2.id)
 
       # create samples in second assay stream with viewing permission
 
@@ -1096,8 +1102,13 @@ def test_title
       assert json_investigation['studies'].map { |s| s['title'] }.include? accessible_study.title
       study_json = json_investigation['studies'].first
 
+      # Total assays
+      assert_equal accessible_study.assays.count, 6
+      # Assay_streams
+      assert_equal accessible_study.assay_streams.count, 2
+      # Child assays
+      assert_equal accessible_study.assay_streams.map(&:child_assays).compact.flatten.count, 4
       # Only one assay should end up in 1 assay stream in the ISA JSON
-      assert_equal accessible_study.assays.count, 4
       assert_equal study_json['assays'].count, 1
 
       sample_ids = study_json['materials']['samples'].map { |sample| sample['@id'] }