[release] Merge Develop into Master for 14.89.0

.nvmrc

@@ -1 +1 @@
-24.13.0
+24.14.0

.release-version

@@ -1 +1 @@
-14.88.0
+14.89.0

Gemfile.lock

@@ -133,8 +133,8 @@ GEM
     backports (3.25.2)
     base64 (0.3.0)
     benchmark (0.5.0)
-    bigdecimal (3.3.1)
-    bootsnap (1.22.0)
+    bigdecimal (4.0.1)
+    bootsnap (1.23.0)
       msgpack (~> 1.2)
     builder (3.3.0)
     bullet (8.1.0)
@@ -167,7 +167,7 @@ GEM
       marcel (~> 1.0)
       nokogiri (~> 1.10, >= 1.10.4)
       rubyzip (>= 2.4, < 4)
-    cgi (0.5.0)
+    cgi (0.5.1)
     childprocess (5.1.0)
       logger (~> 1.5)
     choice (0.2.0)
@@ -247,14 +247,14 @@ GEM
     ffi (1.17.3-arm64-darwin)
     ffi (1.17.3-x86_64-darwin)
     ffi (1.17.3-x86_64-linux-gnu)
-    flipper (1.3.6)
+    flipper (1.4.0)
       concurrent-ruby (< 2)
-    flipper-active_record (1.3.6)
+    flipper-active_record (1.4.0)
       activerecord (>= 4.2, < 9)
-      flipper (~> 1.3.6)
-    flipper-ui (1.3.6)
+      flipper (~> 1.4.0)
+    flipper-ui (1.4.0)
       erubi (>= 1.0.0, < 2.0.0)
-      flipper (~> 1.3.6)
+      flipper (~> 1.4.0)
       rack (>= 1.4, < 4)
       rack-protection (>= 1.5.3, < 5.0.0)
       rack-session (>= 1.0.2, < 3.0.0)
@@ -272,14 +272,15 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.1.0)
       domain_name (~> 0.5)
-    i18n (1.14.7)
+    i18n (1.14.8)
       concurrent-ruby (~> 1.0)
     image_processing (1.14.0)
       mini_magick (>= 4.9.5, < 6)
       ruby-vips (>= 2.0.17, < 3)
-    io-console (0.8.1)
-    irb (1.15.3)
+    io-console (0.8.2)
+    irb (1.17.0)
       pp (>= 0.6.0)
+      prism (>= 1.3.0)
       rdoc (>= 4.0.0)
       reline (>= 0.4.2)
     json (2.18.1)
@@ -302,7 +303,7 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     logger (1.7.0)
-    loofah (2.24.1)
+    loofah (2.25.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     mail (2.9.0)
@@ -327,7 +328,7 @@ GEM
     minitest-profiler (0.0.2)
       activesupport (>= 4.1.0)
       minitest (>= 5.3.3)
-    mocha (3.0.1)
+    mocha (3.0.2)
       ruby2_keywords (>= 0.0.5)
     msgpack (1.8.0)
     multi_json (1.17.0)
@@ -430,8 +431,8 @@ GEM
       activesupport (>= 4.2)
       choice (~> 0.2.0)
       ruby-graphviz (~> 1.2)
-    rails-html-sanitizer (1.6.2)
-      loofah (~> 2.21)
+    rails-html-sanitizer (1.7.0)
+      loofah (~> 2.25)
       nokogiri (>= 1.15.7, != 1.16.7, != 1.16.6, != 1.16.5, != 1.16.4, != 1.16.3, != 1.16.2, != 1.16.1, != 1.16.0.rc1, != 1.16.0)
     rails-perftest (0.0.7)
     railties (7.2.3)
@@ -454,7 +455,7 @@ GEM
     rbtree (0.4.6)
     rdoc (6.3.4.1)
     regexp_parser (2.11.3)
-    reline (0.6.2)
+    reline (0.6.3)
       io-console (~> 0.5)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
@@ -474,9 +475,9 @@ GEM
       rspec-mocks (~> 3.13.0)
     rspec-collection_matchers (1.2.1)
       rspec-expectations (>= 2.99.0.beta1)
-    rspec-core (3.13.3)
+    rspec-core (3.13.6)
       rspec-support (~> 3.13.0)
-    rspec-expectations (3.13.3)
+    rspec-expectations (3.13.5)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
     rspec-github (3.0.0)
@@ -487,18 +488,18 @@ GEM
     rspec-json_expectations (2.2.0)
     rspec-longrun (3.1.0)
       rspec-core (>= 3.5.0, < 4)
-    rspec-mocks (3.13.2)
+    rspec-mocks (3.13.7)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-rails (8.0.2)
+    rspec-rails (8.0.3)
       actionpack (>= 7.2)
       activesupport (>= 7.2)
       railties (>= 7.2)
       rspec-core (~> 3.13)
       rspec-expectations (~> 3.13)
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
-    rspec-support (3.13.2)
+    rspec-support (3.13.7)
     rubocop (1.84.1)
       json (~> 2.3)
       language_server-protocol (~> 3.17.0.2)
@@ -542,8 +543,9 @@ GEM
       rubocop-rspec (~> 3.5)
     ruby-graphviz (1.2.5)
       rexml
-    ruby-prof (1.7.2)
+    ruby-prof (2.0.2)
       base64
+      ostruct
     ruby-progressbar (1.13.0)
     ruby-units (4.1.0)
     ruby-vips (2.2.3)
@@ -560,7 +562,7 @@ GEM
       crass (~> 1.0.2)
       nokogiri (>= 1.16.8)
     securerandom (0.4.1)
-    selenium-webdriver (4.40.0)
+    selenium-webdriver (4.41.0)
       base64 (~> 0.2)
       logger (~> 1.4)
       rexml (~> 3.2, >= 3.2.5)
@@ -604,7 +606,7 @@ GEM
       logger
     temple (0.10.4)
     test-prof (1.5.2)
-    thor (1.4.0)
+    thor (1.5.0)
     tilt (2.6.1)
     timecop (0.9.10)
     timeout (0.4.4)
@@ -633,7 +635,7 @@ GEM
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    webrick (1.9.1)
+    webrick (1.9.2)
     websocket (1.2.11)
     websocket-driver (0.8.0)
       base64
@@ -655,7 +657,7 @@ GEM
       ostruct
       rainbow
       yard
-    zeitwerk (2.7.3)
+    zeitwerk (2.7.5)
 
 PLATFORMS
   arm64-darwin

app/controllers/sample_manifest_upload_with_tag_sequences_controller.rb

@@ -10,7 +10,7 @@ def create
     return error('No file attached') if params[:upload].blank?
 
     if upload_manifest
-      success('Sample manifest successfully uploaded.')
+      set_upload_flash_message
     else
       error('Your sample manifest couldn\'t be uploaded.')
     end
@@ -27,6 +27,29 @@ def upload_manifest
     @uploader.run!
   end
 
+  def set_upload_flash_message
+    warning_rows = rows_with_warnings
+    return success('Sample manifest successfully uploaded.') if warning_rows.empty?
+
+    apply_warning_flash(warning_rows)
+  end
+
+  def rows_with_warnings
+    @uploader.upload.rows.select do |row|
+      row.respond_to?(:warnings) && row.warnings.any?
+    end
+  end
+
+  def apply_warning_flash(rows)
+    flash[:warning] = {
+      'Sample manifest uploaded with warnings!':
+        rows.flat_map { |row| row.warnings.full_messages }.uniq
+    }
+
+    redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)
+    redirect_to redirect_target
+  end
+
   def success(message)
     flash[:notice] = message
     redirect_target = (@uploader.study.present? ? sample_manifests_study_path(@uploader.study) : sample_manifests_path)

app/controllers/submissions_controller.rb

@@ -115,6 +115,29 @@ def study
     @submissions = @study.submissions
   end
 
+  def download_scrna_core_pooling_plan # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
+    begin
+      submission = Submission.find(params[:id])
+    rescue ActiveRecord::RecordNotFound
+      flash[:error] = "Submission not found with id #{params[:id]}"
+      redirect_to submissions_path
+      return
+    end
+
+    unless submission.scrna_core_cdna_prep_gem_x_5p_submission?
+      flash[:error] =
+        'This submission does not have the correct template for downloading a scRNA Core pooling plan'
+      redirect_to submission
+      return
+    end
+
+    # Generate the pooling plan CSV string using the ScrnaCoreCdnaPrepPoolingPlanGenerator module
+    csv_string = Submission::ScrnaCoreCdnaPrepPoolingPlanGenerator.generate_pooling_plan(submission)
+
+    send_data csv_string, type: 'text/plain', filename: "#{params[:id]}_scrna_core_pooling_plan.csv",
+                          disposition: 'attachment'
+  end
+
   ###################################################               AJAX ROUTES
   # TODO[sd9]: These AJAX routes could be re-factored
 

app/frontend/stylesheets/all/sequencescape.scss

@@ -149,7 +149,10 @@ h3.card-header-custom {
   }
 }
 
-.alert-error ul {
+.alert-error ul,
+.alert-warning ul,
+.alert-notice ul,
+.alert-success ul {
   margin: 0;
 }
 
@@ -171,6 +174,7 @@ h3.card-header-custom {
 .alert-cancelled {
   @extend .alert-warning;
 }
+
 .text-notice,
 .text-passed {
   @extend .text-success;

app/helpers/application_helper.rb

@@ -76,17 +76,37 @@ def render_flashes
     nil
   end
 
-  # A helper method for render_flashes - If multiple messages, render them as a list, else render as a single div
-  # @param messages [Array<String>, String] The flash message or messages to be rendered
-  def render_message(messages)
-    messages = Array(messages)
-    if messages.size > 1
-      tag.ul { messages.each { |m| concat tag.li(m) } }
+  # A helper method for render_flashes.
+  # If messages is a Hash, renders them as a described list, with the keys as the description and
+  # the values as the items.
+  # If messages is an Array with multiple messages, renders them as a list.
+  # If a single message, renders as a single div.
+  #
+  # @param messages [Hash, Array<String>, String] The flash message or messages to be rendered
+  # @return [ActiveSupport::SafeBuffer] HTML-safe string for rendering the messages
+  def render_message(messages) # rubocop:disable Metrics/MethodLength
+    case messages
+    when Hash
+      safe_join(
+        messages.map do |description, items|
+          tag.div(description) + render_in_list(Array(items))
+        end
+      )
+    when Array
+      if messages.size > 1
+        render_in_list(messages)
+      else # messages has only one element, render it as a single div
+        tag.div(messages.first)
+      end
     else
-      tag.div(messages.first)
+      tag.div(messages)
     end
   end
 
+  def render_in_list(messages)
+    tag.ul { messages.each { |message| concat tag.li(message) } }
+  end
+
   def api_data
     { api_version: RELEASE.api_version }
   end

app/models/ability/base_user.rb

@@ -32,7 +32,7 @@ def grant_privileges # rubocop:todo Metrics/AbcSize, Metrics/MethodLength
     can %i[read create], Study
     can :print_asset_group_labels, Study, owners: { id: user.id }
     can :print_asset_group_labels, Study, managers: { id: user.id }
-    can %i[read create update edit], Submission
+    can %i[read create update edit download_scrna_core_pooling_plan], Submission
     can :read, [TagGroup, TagLayoutTemplate, TagSet]
     can %i[read update print_swipecard], User, { id: user.id }
     can %i[projects study_reports], User

app/models/multiplexed_library_tube.rb

@@ -18,7 +18,7 @@ def asset_type_for_request_types
   end
 
   def team
-    creation_requests.first&.product_line
+    creation_requests&.first&.product_line
   end
 
   def role
@@ -41,6 +41,8 @@ def creation_requests
     direct = requests_as_target.where_is_a(Request::LibraryCreation)
     return direct unless direct.empty?
 
-    parents.includes(:requests_as_target).first.requests_as_target
+    # Parents should exist but in the case they don't (e.g. asset_links are yet to be created)
+    # we want to avoid an error and just return an empty array.
+    parents.includes(:requests_as_target).first&.requests_as_target || []
   end
 end

app/models/submission.rb

@@ -22,6 +22,7 @@ class Submission < ApplicationRecord # rubocop:todo Metrics/ClassLength
   include Submission::Priorities
 
   PER_ORDER_REQUEST_OPTIONS = %w[pre_capture_plex_level gigabases_expected].freeze
+  SCRNA_CORE_CDNA_PREP_GEM_X_5P = 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p'
 
   self.per_page = 500
 
@@ -125,6 +126,10 @@ def multiplexed?
     orders.any?(&:multiplexed?)
   end
 
+  def scrna_core_cdna_prep_gem_x_5p_submission?
+    orders.first.template_name == SCRNA_CORE_CDNA_PREP_GEM_X_5P
+  end
+
   # Attempts to find the multiplexed asset (usually a multiplexed library tube) associated
   # with the submission. Useful when trying to pool requests into a pre-existing tube at the
   # end of the process.