Fix tests

app/controllers/isa_assays_controller.rb

@@ -9,17 +9,19 @@ class IsaAssaysController < ApplicationController
   after_action :rearrange_assay_positions_create_isa_assay, only: :create
 
   def new
+    study = Study.find(params[:study_id])
     new_position =
-      if params[:is_assay_stream] || params[:source_assay_id].nil? || (params[:source_assay_id] == params[:assay_stream_id])
+      if params[:is_assay_stream] || params[:source_assay_id].nil? # If first assay is of class assay stream
+        study.assay_streams.any? ? study.assay_streams.map(&:position).max + 1 : 0
+      elsif params[:source_assay_id] == params[:assay_stream_id] # If first assay in the stream
         0
       else
         Assay.find(params[:source_assay_id]).position + 1
       end
 
-    study = Study.find(params[:study_id])
     source_assay = Assay.find(params[:source_assay_id]) if params[:source_assay_id]
     input_sample_type_id =
-      if params[:is_assay_stream] || source_assay.is_assay_stream?
+      if params[:is_assay_stream] || source_assay&.is_assay_stream?
         study.sample_types.second.id
       else
         source_assay&.sample_type&.id
@@ -29,7 +31,7 @@ def new
       if params[:is_assay_stream]
         IsaAssay.new({ assay: { assay_class_id: AssayClass.assay_stream.id,
                                 study_id: study.id,
-                                position: 0 },
+                                position: new_position },
                        input_sample_type_id: })
       else
         IsaAssay.new({ assay: { assay_class_id: AssayClass.experimental.id,
@@ -67,7 +69,7 @@ def update
     @isa_assay.assay.attributes = isa_assay_params[:assay]
 
     # update the sample_type
-    unless @isa_assay.assay.is_assay_stream?
+    unless @isa_assay&.assay&.is_assay_stream?
       if requested_item_authorized?(@isa_assay.sample_type)
         @isa_assay.sample_type.update(isa_assay_params[:sample_type])
         @isa_assay.sample_type.resolve_inconsistencies
@@ -202,13 +204,19 @@ def find_requested_item
     @isa_assay = IsaAssay.new
     @isa_assay.populate(params[:id])
 
-    @isa_assay.errors.add(:assay, "The #{t('isa_assay')} was not found.") if @isa_assay.assay.nil?
-    @isa_assay.errors.add(:assay, "You are not authorized to edit this #{t('isa_assay')}.") unless requested_item_authorized?(@isa_assay.assay)
+    if @isa_assay.assay.nil?
+      @isa_assay.errors.add(:assay, "The #{t('isa_assay')} was not found.")
+    else
+      @isa_assay.errors.add(:assay, "You are not authorized to edit this #{t('isa_assay')}.") unless requested_item_authorized?(@isa_assay.assay)
+    end
 
     # Should not deal with sample type if assay has assay_class assay stream
     unless @isa_assay.assay&.is_assay_stream?
-      @isa_assay.errors.add(:sample_type, 'Sample type not found.') if @isa_assay.sample_type.nil?
-      @isa_assay.errors.add(:sample_type, "You are not authorized to edit this assay's #{t('sample_type')}.") unless requested_item_authorized?(@isa_assay.sample_type)
+      if @isa_assay.sample_type.nil?
+        @isa_assay.errors.add(:sample_type, 'Sample type not found.')
+      else
+        @isa_assay.errors.add(:sample_type, "You are not authorized to edit this assay's #{t('sample_type')}.") unless requested_item_authorized?(@isa_assay.sample_type)
+      end
     end
 
     if @isa_assay.errors.any?

app/views/isa_assays/_form.html.erb

@@ -15,7 +15,7 @@
     <%= assay_fields.text_area :description, rows: 5, class: "form-control rich-text-edit" -%>
   </div>
 
-  # Show extended metadata is assay is of class assay_stream
+  <%# Show extended metadata is assay is of class assay_stream %>
   <% if is_assay_stream %>
     <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals:{f:assay_fields, resource:@isa_assay.assay} %>
     <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals:{f:assay_fields,resource:@isa_assay.assay, parent_resource: "isa_assay"} %>

test/functional/isa_assays_controller_test.rb

@@ -76,8 +76,7 @@ def setup
     end
     isa_assay = assigns(:isa_assay)
     assert_redirected_to controller: 'single_pages', action: 'show', id: isa_assay.assay.projects.first.id,
-                         params: { notice: 'The ISA assay was created successfully!',
-                                   item_type: 'assay', item_id: Assay.last.id }
+                         params: { item_type: 'assay', item_id: Assay.last.id }
 
     sample_types = SampleType.last(2)
     title = sample_types[0].sample_attributes.detect(&:is_title).title
@@ -139,7 +138,7 @@ def setup
     assay = FactoryBot.create(:assay, study:, contributor: person)
     put :update, params: { id: assay, isa_assay: { assay: { title: 'assay title' } } }
     assert_redirected_to single_page_path(id: project, item_type: 'assay', item_id: assay.id)
-    assert flash[:error].include?('Resource not found.')
+    assert flash[:error].include?('Sample type not found.')
 
     assay = FactoryBot.create(:assay, study:, sample_type: assay_type, contributor: person)
 
@@ -359,7 +358,7 @@ def setup
     end
 
     isa_assay = assigns(:isa_assay)
-    assert_redirected_to single_page_path(id: project, item_type: 'assay', item_id: isa_assay.assay.id, notice: 'The ISA assay was created successfully!')
+    assert_redirected_to single_page_path(id: project, item_type: 'assay', item_id: isa_assay.assay.id)
 
     assert_equal isa_assay.assay.sample_type.previous_linked_sample_type, study.sample_types.second
     assert_equal isa_assay.assay.next_linked_child_assay, end_assay
@@ -455,7 +454,7 @@ def setup
     end
 
     isa_assay = assigns(:isa_assay)
-    assert_redirected_to single_page_path(id: project, item_type: 'assay', item_id: isa_assay.assay.id, notice: 'The ISA assay was created successfully!')
+    assert_redirected_to single_page_path(id: project, item_type: 'assay', item_id: isa_assay.assay.id)
 
     assert_equal begin_assay.previous_linked_sample_type, study.sample_types.second
     assert_equal isa_assay.assay.sample_type.previous_linked_sample_type, begin_assay.sample_type
@@ -619,7 +618,7 @@ def setup
     # New assay stream should have position 1 and is of type 'number'
     assert_select 'input[type=number][value=1]#isa_assay_assay_position', count: 1
 
-    assay_stream2 = FactoryBot.create(:assay_stream, study: , contributor: person, position: 5)
+    FactoryBot.create(:assay_stream, study: , contributor: person, position: 5)
     get :new, params: { study_id: study.id, is_assay_stream: true }
     assert_response :success
     # New assay stream should have position 6 and is of type 'number'