Merge pull request #4480 from sanger/develop

[automated] Merge Develop into Master

.github/workflows/check_release_version.yml

@@ -5,12 +5,21 @@ on:
   pull_request:
     branches:
       - master
+    types:
+      # defaults
+      - opened
+      - synchronize
+      - reopened
+      # custom
+      - ready_for_review # required for Github-created PRs
 
 jobs:
   check:
     runs-on: ubuntu-latest
+    # only run when PR is not draft
+    if: ${{ !github.event.pull_request.draft }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Get specific changed files
         id: changed-files-specific

.github/workflows/create_release_pr.yml

@@ -0,0 +1,10 @@
+# Create or update merge-to-master pull requests for production releases
+# Note that by design, creating or editing a PR will not trigger a downstream `pull_request` event as this could lead to recursion
+name: Release
+on:
+  push:
+    branches:
+      - develop
+jobs:
+  pull_request:
+    uses: sanger/.github/.github/workflows/create-release-pr.yml@master

.release-version

@@ -1 +1 @@
-14.47.0
+14.48.0

app/controllers/api/v2/bait_library_layouts_controller.rb

@@ -33,7 +33,7 @@ def preview
           respond_with_errors('Validation failed', e.record.errors.full_messages, :unprocessable_entity) and return
         end
 
-        json = { data: { type: 'bait_library_layouts', attributes: { layout: preview.layout } } }
+        json = { data: { type: 'bait_library_layouts', attributes: { well_layout: preview.well_layout } } }
         render json: json, status: :ok
       end
 

app/models/delegate_validation.rb

@@ -101,7 +101,11 @@ def valid?
       return true if @validators.map(&:valid?).all?(true)
 
       @validators.each do |validator|
-        validator.errors.each { |attrib, message| errors.add(attrib, message) unless errors.include?(attrib) }
+        validator.errors.each do |error|
+          attrib = error.attribute
+          message = error.message
+          errors.add(attrib, message) unless errors.include?(attrib)
+        end
       end
 
       false

app/views/receptacles/new_request.html.erb

@@ -9,7 +9,9 @@
     <% instance_variable_or_id_param(:request_type) do |field_name, value| %>
       <div class="form-group  col-xs-12">
         <%= label_tag(field_name, 'Request type', class: 'col-md-4') %>
-        <%= select_field_sorted_by_name(field_name, @request_types, value, can_edit) %>
+        <%= select_field_sorted_by_name(field_name, @request_types, value, can_edit, prompt: 'Select a request type', required: true,
+                                        data: { novaseq_ids: RequestType.where(key: %w[illumina_htp_novaseq_6000_paired_end_sequencing illumina_htp_novaseqx_paired_end_sequencing]).pluck(:id).join(',') }
+            ) %>
       </div>
     <% end %>
     <% if @asset.studies.uniq.count > 1 -%>
@@ -104,13 +106,25 @@
       var disable_inputs = function(context) { $('input,select,textarea', context).attr('disabled', true);  }
       var enable_inputs  = function(context) { $('input,select,textarea', context).attr('disabled', false); }
 
+
+      <!-- Sets the 'required' attribute for the flowcell type input field based on the selected request type.-->
+      setFlowcellTypeRequiredForNovaseq = function() {
+        var selected_request_type_id = $('option:selected', request_type_element).attr('value');
+        var flowcell_type_element = $('[name="request[request_metadata_attributes][requested_flowcell_type]"]:not(:disabled)');
+        if(flowcell_type_element && flowcell_type_element.length > 0) {
+          var novaseq_ids = $(request_type_element).data('novaseq-ids').split(',');
+          flowcell_type_element.attr('required', novaseq_ids.includes(selected_request_type_id));
+        }
+      }
+
       handler = function() {
         var selected_request_type_id = $('option:selected', request_type_element).attr('value');
 
         // Not only hide but disable inputs; not only show, but enable inputs.  If this isn't done
         // the parameters passed to the server are incorrect.
         disable_inputs(request_options.hide());
         enable_inputs($('#request_type_options_for_' + selected_request_type_id).show());
+        setFlowcellTypeRequiredForNovaseq()
       }
 
       request_type_element.change(handler);

app/views/shared/metadata/edit/_request.html.erb

@@ -5,7 +5,7 @@
     <%- request.request_metadata.field_infos.each do |field_info| %>
       <!-- todo unify with how submission use field info-->
       <%- if field_info.selection %>
-        <%= metadata_fields.select(field_info.key, field_info.selection) %>
+        <%= metadata_fields.select(field_info.key, field_info.selection, { prompt: "Select a #{field_info.key.to_s.gsub( '_', ' ')}"  }) %>
       <%- elsif field_info.kind == FieldInfo::BOOLEAN %>
         <%= metadata_fields.check_box(field_info.key) %>
       <%- elsif field_info.kind == FieldInfo::NUMERIC %>

config/default_records/plate_purposes/005_limber_purposes.yml

@@ -72,3 +72,8 @@ LTN AL Lib:
 LTN Lib PCR XP:
   type: PlatePurpose
   stock_plate: false
+
+# RVI BCL plate for reISC
+RVI Lib PCR XP:
+  type: PlatePurpose
+  stock_plate: false

config/default_records/request_types/004_limber_high_throughput.yml

@@ -37,13 +37,15 @@ limber_reisc:
   acceptable_purposes:
     - LB Lib PCR-XP
     - LTN Lib PCR XP # for Targeted NanoSeq ReISC
+    - RVI Lib PCR XP # for RVI Bait Capture Library
   library_types:
     - Agilent Pulldown
     - Twist Pulldown
     - Duplex-Seq
     - Targeted NanoSeq Pulldown Twist
     - Targeted NanoSeq Pulldown Agilent
     - BGE
+    - RVI-BCL
 limber_pcr_free:
   <<: *limber_htp_library
   name: Limber PCR Free

spec/features/assets/asset_submission_spec.rb

@@ -7,12 +7,126 @@
   let(:study) { create(:study) }
   let(:request_factory) { :sequencing_request }
   let(:asset) { create(:library_tube) }
+  let(:flowcell_types) { create_list(:flowcell_type, 2) }
   let(:request_types) { create_list(:sequencing_request_type, 2) }
   let(:original_request_type) { request_types.first }
   let(:selected_request_type) { original_request_type }
   let(:selected_read_length) { '76' }
+  let(:request_flowcell_type_validator) do
+    RequestType::Validator.create(
+      request_type: selected_request_type,
+      request_option: 'requested_flowcell_type',
+      valid_options: flowcell_types.map(&:name)
+    )
+  end
   let!(:original_request) do
-    create(request_factory, study: study, project: project, asset: asset, request_type: original_request_type)
+    create(request_factory, study: study, project: project, asset: asset, request_type: selected_request_type)
+  end
+
+  describe 'The request form does not set default values' do
+    let(:user) { create(:admin) }
+
+    before do
+      login_user user
+      visit labware_path(asset)
+      click_link 'Request additional sequencing'
+    end
+
+    describe 'when the form is loaded' do
+      it 'does not set request type' do
+        expect(page).to have_select('Request type', selected: 'Select a request type')
+      end
+    end
+
+    describe 'when the user selects a request type' do
+      before { select 'Request Type 1', from: 'Request type' }
+
+      it 'does not set flowcell type to default value' do
+        expect(page).to have_select('Flowcell type', selected: 'Select a requested flowcell type')
+      end
+
+      it 'does not set read length to default value' do
+        expect(page).to have_select('Read length', selected: 'Select a read length')
+      end
+    end
+  end
+
+  describe 'Validation of Flowcell Type field for request types that require a Flowcell Type' do
+    let(:user) { create(:admin) }
+
+    # Mock the validator for the selected request type to return the predefined flowcell type validator
+    # the predefined flowcell type validator require a specific flowcell type to be selected
+    before do
+      allow(selected_request_type).to receive(:validator_for).with('requested_flowcell_type').and_return(
+        request_flowcell_type_validator
+      )
+      login_user user
+      visit labware_path(asset)
+      click_link 'Request additional sequencing'
+    end
+
+    it 'displays an error if Flowcell Type is not set' do
+      select(selected_request_type.name, from: 'Request type')
+      select(study.name, from: 'Study')
+      select(project.name, from: 'Project')
+      fill_in 'Fragment size required (from)', with: '100'
+      fill_in 'Fragment size required (to)', with: '200'
+      select(selected_read_length, from: 'Read length')
+      click_button 'Create'
+
+      # The JS native validation error 'Please select an item in the list' is being displayed but cannot be inspected.
+      expect(page).to have_no_text 'Created request'
+
+      redirect_path =
+        new_request_receptacle_path(
+          asset.receptacle,
+          study_id: study.id,
+          project_id: project.id,
+          request_type_id: selected_request_type.id
+        )
+      expect(page).to have_current_path(redirect_path)
+    end
+
+    it 'creates a new request successfully when Flowcell Type is correctly set' do
+      select(selected_request_type.name, from: 'Request type')
+      select(study.name, from: 'Study')
+      select(project.name, from: 'Project')
+      fill_in 'Fragment size required (from)', with: '100'
+      fill_in 'Fragment size required (to)', with: '200'
+      select(selected_read_length, from: 'Read length')
+      select('Flowcell 1', from: 'Flowcell type')
+      fill_in 'Fragment size required (from)', with: '100'
+      fill_in 'Fragment size required (to)', with: '200'
+      select(selected_read_length, from: 'Read length')
+      click_button 'Create'
+
+      expect(page).to have_text 'Created request'
+    end
+  end
+
+  describe 'Validation of Flowcell Type field for request types that do not require a Flowcell Type' do
+    let(:user) { create(:admin) }
+
+    before do
+      login_user user
+      visit labware_path(asset)
+      click_link 'Request additional sequencing'
+    end
+
+    it 'creates a new request successfully even when Flowcell Type is not specified' do
+      select(selected_request_type.name, from: 'Request type')
+      select(study.name, from: 'Study')
+      select(project.name, from: 'Project')
+      fill_in 'Fragment size required (from)', with: '100'
+      fill_in 'Fragment size required (to)', with: '200'
+      select(selected_read_length, from: 'Read length')
+      fill_in 'Fragment size required (from)', with: '100'
+      fill_in 'Fragment size required (to)', with: '200'
+      select(selected_read_length, from: 'Read length')
+      click_button 'Create'
+
+      expect(page).to have_text 'Created request'
+    end
   end
 
   shared_examples 'it allows additional sequencing' do

spec/requests/api/v2/bait_library_layouts_spec.rb

@@ -308,8 +308,8 @@ def perform_post
           expect(json.dig('data', 'type')).to eq(resource_type)
         end
 
-        it 'returns a layout as an attribute' do
-          expect(json.dig('data', 'attributes', 'layout')).not_to be_nil
+        it 'returns a well_layout as an attribute' do
+          expect(json.dig('data', 'attributes', 'well_layout')).not_to be_nil
         end
       end