Develop to master

.gitignore

@@ -53,3 +53,6 @@ release.tar.gz
 
 # Bye-bug history
 .byebug_history
+
+# RubyMine
+.idea

.release-version

@@ -1 +1 @@
-3.58.0
+3.59.0

app/models/labware_creators/plate_split_to_tube_racks.rb

@@ -53,7 +53,7 @@
     validates_nested :well_filter
 
     # Don't create the tubes until at least the contingency file has been uploaded
-    validates :contingency_file, presence: true
+    validate :validate_file_presence
 
     # N.B. contingency file is required, sequencing file is optional
     validates_nested :sequencing_csv_file, if: :sequencing_file
@@ -72,6 +72,14 @@
     PARENT_PLATE_INCLUDES =
       'wells.aliquots,wells.aliquots.sample,wells.downstream_tubes,wells.downstream_tubes.custom_metadatum_collection'
 
+    def validate_file_presence
+      if sequencing_file.blank?
+        errors.add(:base, "Sequencing file can't be blank")
+      elsif contingency_file.present? && sequencing_file.blank?
+        errors.add(:base, 'If contingency_file is present, sequencing_file must also be present.')
+      end
+    end
+
     def save
       # NB. need the && true!!
       super && upload_tube_rack_files && true
@@ -111,15 +119,15 @@
     #
     # @return [Array<Tube>] The child sequencing tubes.
     def create_child_sequencing_tubes
-      return [] if require_contingency_tubes_only?
-
       create_tubes(sequencing_tube_purpose_uuid, parent_wells_for_sequencing.length, sequencing_tube_attributes)
     end
 
     # Creates a child contingency tube for each parent well not already assigned to a sequencing tube.
     #
     # @return [Array<Tube>] The child contingency tubes.
     def create_child_contingency_tubes
+      return [] if require_sequencing_tubes_only?
+
       create_tubes(contingency_tube_purpose_uuid, parent_wells_for_contingency.length, contingency_tube_attributes)
     end
 
@@ -201,7 +209,7 @@
     #
     # Sets errors if the tube rack barcodes are the same
     def check_tube_barcodes_differ_between_files
-      return unless contingency_file_valid? && sequencing_file_valid?
+      return unless sequencing_file_valid? && contingency_file_valid?
 
       seq_barcodes = extract_barcodes(sequencing_csv_file)
       cont_barcodes = extract_barcodes(contingency_csv_file)
@@ -227,22 +235,19 @@
     # Sets errors if there are insufficient or too many tubes.
     def must_have_correct_number_of_tubes_in_rack_files
       return unless files_valid?
-
-      if require_contingency_tubes_only?
-        add_error_if_wrong_number_of_tubes(:contingency_csv_file, num_contingency_tubes, num_parent_wells)
-      else
+      unless require_sequencing_tubes_only?
         add_error_if_wrong_number_of_tubes(
           :contingency_csv_file,
           num_contingency_tubes,
           num_parent_wells - num_parent_unique_samples
         )
-        add_error_if_wrong_number_of_tubes(:sequencing_csv_file, num_sequencing_tubes, num_parent_unique_samples)
       end
+      add_error_if_wrong_number_of_tubes(:sequencing_csv_file, num_sequencing_tubes, num_parent_unique_samples)
     end
 
     # Checks the files passed their validations
     def files_valid?
-      return contingency_file_valid? if require_contingency_tubes_only?
+      return sequencing_file_valid? if require_sequencing_tubes_only?
 
       contingency_file_valid? && sequencing_file_valid?
     end
@@ -347,17 +352,17 @@
     #
     # @return [void]
     def upload_tube_rack_files
-      unless require_contingency_tubes_only?
-        parent_v1.qc_files.create_from_file!(sequencing_file, 'scrna_core_sequencing_tube_rack_scan.csv')
+      unless require_sequencing_tubes_only?
+        parent_v1.qc_files.create_from_file!(contingency_file, 'scrna_core_contingency_tube_rack_scan.csv')
       end
-      parent_v1.qc_files.create_from_file!(contingency_file, 'scrna_core_contingency_tube_rack_scan.csv')
+      parent_v1.qc_files.create_from_file!(sequencing_file, 'scrna_core_sequencing_tube_rack_scan.csv')
     end
 
     # Returns true if only contingency tubes are required for the parent plate, false otherwise.
     #
     # @return [Boolean]
-    def require_contingency_tubes_only?
-      sequencing_file.blank?
+    def require_sequencing_tubes_only?
+      contingency_file.blank?
     end
 
     # Returns an array of parent wells that should be transferred to sequencing tubes based on the current well filter.
@@ -372,8 +377,6 @@
     #
     # @return [Array<Well>] An array of parent wells.
     def find_parent_wells_for_sequencing
-      return [] if require_contingency_tubes_only?
-
       unique_sample_uuids = []
       parent_wells_for_seq = []
 
@@ -607,8 +610,8 @@
     # @param well [Well] The well to find the child tube for.
     # @return [Tube, nil] The child tube corresponding to the given well, or nil if no child tube was found.
     def find_child_tube(well)
-      if require_contingency_tubes_only?
-        @child_contingency_tubes[@contingency_wells_to_tube_names[well]]
+      if require_sequencing_tubes_only?
+        @child_sequencing_tubes[@sequencing_wells_to_tube_names[well]]
       else
         @child_sequencing_tubes[@sequencing_wells_to_tube_names[well]] ||
           @child_contingency_tubes[@contingency_wells_to_tube_names[well]]
@@ -619,9 +622,9 @@
     #
     # @return [void]
     def add_child_tube_metadata
-      add_sequencing_tube_metadata unless require_contingency_tubes_only?
+      add_sequencing_tube_metadata
 
-      add_contingency_tube_metadata
+      add_contingency_tube_metadata unless require_sequencing_tubes_only?
     end
 
     # Adds tube rack barcode and position metadata to child sequencing tubes.

app/views/tube_creation/plate_split_to_tube_racks.html.erb

@@ -26,16 +26,16 @@
   <% end %>
   <%= sidebar do %>
     <%= card title: 'Upload tube rack scan files' do %>
-      <p>For this parent plate with <b><%= @labware_creator.num_parent_unique_samples %></b> distinct samples and a total of <b><%= @labware_creator.num_parent_wells %></b> transferable wells, you will need <b><%= @labware_creator.num_parent_unique_samples %></b> sequencing and <b><%= @labware_creator.num_parent_wells - @labware_creator.num_parent_unique_samples %></b> contingency tubes (or if just doing contingency <b><%= @labware_creator.num_parent_wells %></b> contingency tubes).</p>
+      <p>For this parent plate with <b><%= @labware_creator.num_parent_unique_samples %></b> distinct samples and a total of <b><%= @labware_creator.num_parent_wells %></b> transferable wells, you will need <b><%= @labware_creator.num_parent_unique_samples %></b> sequencing and <b><%= @labware_creator.num_parent_wells - @labware_creator.num_parent_unique_samples %></b> contingency tubes.</p>
       <%= form_for(@labware_creator, as: :tube, url: limber_plate_tubes_path(@labware_creator.parent)) do |f| %>
         <%= f.hidden_field :purpose_uuid %>
-        <h4>Sequencing tube rack scan file (optional)</h4>
+        <h4>Sequencing tube rack scan file (required)</h4>
         <div class="form-group">
-          <%= f.file_field :sequencing_file, accept: '.csv', required: false %>
+          <%= f.file_field :sequencing_file, accept: '.csv', required: true %>
         </div>
-        <h4>Contingency tube rack scan file (required)</h4>
+        <h4>Contingency tube rack scan file (sequencing file is required to be uploaded)</h4>
         <div class="form-group">
-          <%= f.file_field :contingency_file, accept: '.csv', required: true %>
+          <%= f.file_field :contingency_file, accept: '.csv', required: false %>
         </div>
         <%= f.submit class: 'btn btn-success' %>
       <% end %>

config/pipelines/bespoke_pcr.yml

@@ -32,6 +32,7 @@ Bespoke PCR:
       - Standard
       - TraDIS
       - TruSeq mRNA (RNA Seq)
+      - SGE Library v0.2
   library_pass: LBB Lib PCR-XP
   relationships:
     LBB Cherrypick: LBB Ligation

config/robots.rb

@@ -3649,10 +3649,10 @@
           states: ['passed'],
           label: 'Bed 15'
         },
-        bed(14).barcode => {
+        bed(13).barcode => {
           purpose: 'LRC PBMC Pools',
           states: ['pending'],
-          label: 'Bed 14',
+          label: 'Bed 13',
           parent: bed(15).barcode,
           target_state: 'passed'
         }

package.json

@@ -38,6 +38,12 @@
     "vitest": "^2.0.5",
     "vue-template-compiler": "^2.7.0"
   },
+  "_comment": "Required to address https://github.com/npm/cli/issues/4828",
+  "optionalDependencies": {
+    "@rollup/rollup-darwin-arm64": "*",
+    "@rollup/rollup-linux-x64-gnu": "*",
+    "@rollup/rollup-win32-x64-msvc": "*"
+  },
   "name": "limber",
   "scripts": {
     "dev": "vite dev",