[release] Merge Develop into Master for 3.67.0

.nvmrc

@@ -1 +1 @@
-v22.13.0
+v22.13.1

.ruby-version

@@ -1 +1 @@
-3.2.5
+3.2.6

Dockerfile

@@ -1,4 +1,7 @@
-FROM ruby:3.2.5-slim
+FROM ruby:3.2.6-slim
+
+# Major version of Node.js to install
+ARG nodeVersion=22
 
 ARG bundlerWithout="development test lint"
 ARG yarnFlags="--production"
@@ -13,7 +16,7 @@ RUN apt-get install -y curl
 RUN apt-get install -y git
 
 RUN set -uex \
-    && NODE_MAJOR=20 \
+    && NODE_MAJOR=${nodeVersion} \
     && apt-get update \
     && apt-get install -y ca-certificates curl gnupg \
     && mkdir -p /etc/apt/keyrings \

Gemfile.lock

@@ -145,7 +145,7 @@ GEM
     exception_notification (4.5.0)
       actionmailer (>= 5.2, < 8)
       activesupport (>= 5.2, < 8)
-    factory_bot (6.4.6)
+    factory_bot (6.5.0)
       activesupport (>= 5.0.0)
     faraday (1.10.3)
       faraday-em_http (~> 1.0)
@@ -194,7 +194,7 @@ GEM
       temple (>= 0.8.2)
       thor
       tilt
-    hashdiff (1.1.0)
+    hashdiff (1.1.2)
     hashie (5.0.0)
     i18n (1.14.6)
       concurrent-ruby (~> 1.0)
@@ -210,7 +210,7 @@ GEM
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    logger (1.6.4)
+    logger (1.6.5)
     loofah (2.24.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
@@ -265,7 +265,7 @@ GEM
     psych (5.2.2)
       date
       stringio
-    public_suffix (6.0.0)
+    public_suffix (6.0.1)
     puma (6.4.3)
       nio4r (~> 2.0)
     racc (1.8.1)
@@ -326,7 +326,7 @@ GEM
     regexp_parser (2.9.2)
     reline (0.6.0)
       io-console (~> 0.5)
-    rexml (3.3.9)
+    rexml (3.4.0)
     rspec (3.13.0)
       rspec-core (~> 3.13.0)
       rspec-expectations (~> 3.13.0)
@@ -428,7 +428,7 @@ GEM
       activemodel (>= 6.0.0)
       bindex (>= 0.4.0)
       railties (>= 6.0.0)
-    webmock (3.23.1)
+    webmock (3.24.0)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)

README.md

@@ -317,3 +317,9 @@ In addition you can also run `lefthook run fix` to run the auto-fixers on staged
 Note that after doing this you will still need to stage the fixes before committing. I'd love to be
 able to automate this, but haven't discovered a solution that maintains the ability to partially
 stage a file, and doesn't involve running the linters directly on files in the .git folder.
+
+## Miscellaneous
+
+### Sprint Templates for Barcode Label Printing
+
+In order to create new label templates or update the existing ones, use the deployment project. The templates must be defined in the sprint role, in the directory `sprint/files/label_templates` . The local directory `config/sprint/label_templates` is **not** supposed to be used for this purpose.

app/frontend/javascript/custom-tagged-plate/components/TagOffset.vue

@@ -18,6 +18,9 @@
       :state="offsetTagsByState"
       @input="offsetTagChanged"
     />
+    <b-form-text>
+      <strong> Tags will start from {{ offsetTagsByAsNumber + 1 }} </strong>
+    </b-form-text>
   </b-form-group>
 </template>
 

app/models/labware_creators/pooled_tubes_by_submission.rb

@@ -28,7 +28,7 @@ def all_wells_in_pool_passed?(pool_info)
     end
 
     def pick?(location)
-      well_locations.fetch(location).passed?
+      !(well_locations.fetch(location).failed? || well_locations.fetch(location).empty?)
     end
   end
 end

app/models/print_job.rb

@@ -103,32 +103,9 @@ def print_to_sprint
 
     merge_fields_list = label_array * number_of_copies
 
-    # assumes all labels use the same label template
-    SPrintClient.send_print_request(printer_name, label_template, merge_fields_list)
-
-    # TODO: DPL-865 [Limber] Handle sprint client response
-    #
-    # This print_to_sprint call fails silently if there is an error. Instead
-    # of returning success, the result of the send_print_request call should
-    # be used to check the response status and response body. Examples:
-    #
-    # The following response body is returned in a 200 response.
-    # {"errors":[{"message":"Variable 'printRequest' has an invalid value: Expected
-    #   type 'Int' but was
-    #   'Double'.","locations":[{"line":1,"column":16}],"extensions":{"classification":"
-    #   ValidationError"}}]}
-    #
-    # The following response body is returned in a 500 response.
-    # {"timestamp": "2023-08-02T14:46:30.160+00:00","status": 500,"error": "Internal
-    #   Server Error","path": "/graphql"}
-    #
-    # When sprint cannot log in to printer, the details are available in response body.
-    #
-    # A successful response has a job id in response body.
-    #
-    # Use errors.add to show proper feedback in the view.
-
-    true
+    response = SPrintClient.send_print_request(printer_name, label_template, merge_fields_list)
+
+    handle_sprint_response(response)
   end
 
   def number_of_copies=(number)
@@ -155,4 +132,71 @@ def get_label_template_by_service(print_service)
     templates_by_service = JSON.parse(label_templates_by_service)
     templates_by_service[print_service]
   end
+
+  # Handles the response from the SPrintClient and checks for success.
+  # If the response is successful and contains a job ID, it returns true.
+  # Otherwise, it adds an error message to the errors object and returns false.
+  #
+  # The print_to_sprint call fails silently if there is an error. Instead
+  # of returning success, the result of the send_print_request call should
+  # be used to check the response status and response body. Examples:
+  #
+  # The following response body is returned in a 200 response.
+  # {"errors":[{"message":"Variable 'printRequest' has an invalid value: Expected
+  #   type 'Int' but was
+  #   'Double'.","locations":[{"line":1,"column":16}],"extensions":{"classification":"
+  #   ValidationError"}}]}
+  #
+  # The following response body is returned in a 500 response.
+  # {"timestamp": "2023-08-02T14:46:30.160+00:00","status": 500,"error": "Internal
+  #   Server Error","path": "/graphql"}
+  #
+  # When sprint cannot log in to printer, the details are available in response body.
+  #
+  # A successful response has a job id in response body.
+  #
+  # Use errors.add to show proper feedback in the view.
+  #
+  # @param response [Net::HTTPResponse] The response object from the SPrintClient.
+  # @return [Boolean] True if the response is successful and contains a job ID, false otherwise.
+  def handle_sprint_response(response)
+    # Non-200 errors are treated as failures
+    # Ref: https://ruby-doc.org/stdlib-2.7.0/libdoc/net/http/rdoc/Net/HTTP.html#class-Net::HTTP-label-GET+with+Dynamic+Parameters
+    unless response.is_a?(Net::HTTPSuccess)
+      case response
+      when Net::HTTPUnprocessableEntity
+        errors.add(:sprint, 'Sprint could not understand the request. Please check the label data.')
+      when Net::HTTPInternalServerError
+        errors.add(:sprint, 'Internal server error at SPrint. Please try again later.')
+      else
+        errors.add(:sprint, 'Trouble connecting to SPrint. Please try again later.')
+      end
+      return false
+    end
+    if response.body.present? && response.body['jobId'].present?
+      true
+    else
+      errors.add(:sprint, extract_error_message(response))
+      false
+    end
+  end
+
+  def extract_error_message(response)
+    if response.body.present?
+      begin
+        response_body = JSON.parse(response.body)
+        if response_body['errors'].present?
+          messages =
+            response_body['errors'].map do |error|
+              extension = error['extensions'] ? " (#{error['extensions']['classification']})" : ''
+              "#{error['message']}#{extension}"
+            end
+          return messages.join(' - ')
+        end
+      rescue JSON::ParserError
+        return 'Failed to parse JSON response from SprintClient'
+      end
+    end
+    'Unknown error'
+  end
 end

app/models/validators/in_progress_validator.rb

@@ -4,12 +4,14 @@ module Validators
   # Displays a warning if the requests on the plate have already been completed
   class InProgressValidator < ActiveModel::Validator
     def validate(presenter)
-      return true unless presenter.labware.any_complete_requests?
+      return true unless presenter.labware.any_non_create_asset_requests_completed?
 
+      first_request = presenter.labware.active_non_create_asset_requests.first
+
+      return true if first_request.nil?
       presenter.errors.add(
         :submission,
-        '(active) is not present for this labware. ' \
-          'Any further work conducted from this plate may run into issues at the end of the pipeline.'
+        "Requests of type #{first_request.request_type.name} have already been down the pipeline and were completed."
       )
     end
   end

app/sequencescape/sequencescape/api/v2/shared/has_requests.rb

@@ -36,6 +36,16 @@ def any_complete_requests?
       active_requests.any?(&:passed?)
     end
 
+    def any_non_create_asset_requests_completed?
+      # Filter out CreateAssetRequests which will be associated for an input plate and completed by the time we get here
+      # and not relevant to this check
+      active_non_create_asset_requests.filter_map(&:passed?).any?
+    end
+
+    def active_non_create_asset_requests
+      active_requests.reject { |r| r.request_type_key == 'create_asset' }
+    end
+
     def pcr_cycles
       active_requests.map(&:pcr_cycles).uniq
     end

config/pipelines/high_throughput_lcmb.yml

@@ -15,4 +15,4 @@ LCMB: # Top of the pipeline (Library Prep)
     LCMB End Prep: LCMB Lib PCR
     LCMB Lib PCR: LCMB Lib PCR-XP
     LCMB Lib PCR-XP: LCMB Custom Pool
-    LCMB Custom Pool: LCMB Custom Pool Norm
+    LCMB Custom Pool: LCMB Custom Norm

config/pipelines/multiplexing.yml

@@ -0,0 +1,8 @@
+Multiplexing:
+  pipeline_group: Multiplexing
+  filters:
+    request_type_key:
+      - limber_multiplexing
+  relationships:
+    Library Stock Plate: LB Lib Pool #These are supplied as ready-made libraries and enter the pipeline at this point.
+    LB Lib Pool: LB Lib Pool Norm

config/purposes/lcmb.yml

@@ -42,7 +42,7 @@ LCMB Custom Pool:
   :creator_class: LabwareCreators::CustomPooledTubes
   :presenter_class: Presenters::SimpleTubePresenter
   :default_printer_type: :tube
-LCMB Custom Pool Norm:
+LCMB Custom Norm:
   :asset_type: tube
   :target: MultiplexedLibraryTube
   :type: IlluminaHtp::InitialStockTubePurpose

config/purposes/library_stock_plate.yml

@@ -0,0 +1,8 @@
+# A plate provided as ready-made libraries.
+# These used to be imported as Stock Plates and then 'fake cherrypicked' onto 'LB Lib PCR XP', which were allowed down the multiplexing pipelines.
+# Now, they can be imported and submitted as this more accurate plate purpose.
+Library Stock Plate:
+  :asset_type: plate
+  :stock_plate: true
+  :input_plate: true
+  :presenter_class: Presenters::StockPlatePresenter

config/sprint/label_templates/plate_384.yml.erb

@@ -2,8 +2,8 @@
   {
     "barcodeFields": [
       {
-        "x": 21,
-        "y": 0,
+        "x": 17,
+        "y": 1,
         "cellWidth": 0.2,
         "barcodeType": "code39",
         "value": "<%= merge_fields[:barcode] %>",
@@ -19,7 +19,7 @@
         "fontSize": 1.7
       },
       {
-        "x": 50,
+        "x": 55,
         "y": 4,
         "value": "<%= merge_fields[:right_text] %>",
         "font": 'proportional',
@@ -37,12 +37,12 @@
         "fontSize": 1.7
       },
       {
-        "x": 20,
+        "x": 17,
         "y": 3,
         "value": "<%= merge_fields[:extra_right_text] %>",
         "font": 'proportional',
         "fontSize": 1.7
       }
     ]
   }
-]
+]

config/sprint/label_templates/plate_96.yml.erb

@@ -2,7 +2,7 @@
   {
     "barcodeFields": [
       {
-        "x": 16,
+        "x": 17,
         "y": 1,
         "cellWidth": 0.2,
         "barcodeType": "code39",
@@ -12,33 +12,33 @@
     ],
     "textFields": [
       {
-        "x": 3,
+        "x": 2,
         "y": 3,
         "value": "<%= merge_fields[:top_left] %>",
         "font": 'proportional',
-        "fontSize": 1.7
+        "fontSize": 2
       },
       {
-        "x": 3,
+        "x": 2,
         "y": 6,
         "value": "<%= merge_fields[:bottom_left] %>",
         "font": 'proportional',
-        "fontSize": 1.7
+        "fontSize": 2
       },
       {
-        "x": 57,
+        "x": 58,
         "y": 3,
         "value": "<%= merge_fields[:top_right] %>",
         "font": 'proportional',
-        "fontSize": 1.7
+        "fontSize": 2
       },
       {
-        "x": 57,
+        "x": 58,
         "y": 6,
         "value": "<%= merge_fields[:bottom_right] %>",
         "font": 'proportional',
-        "fontSize": 1.7
+        "fontSize": 2
       }
     ]
   }
-]
+]

package.json

@@ -24,19 +24,19 @@
     "eslint": "^8.0.0",
     "eslint-config-prettier": "^8.10.0",
     "eslint-plugin-vitest": "^0.5.4",
-    "eslint-plugin-vue": "^9.30.0",
+    "eslint-plugin-vue": "^9.32.0",
     "jsdom": "^24.1.2",
     "postcss": "^8.4.49",
     "postcss-flexbugs-fixes": "^5.0.2",
     "postcss-import": "16.1.0",
     "postcss-nested": "^6.0.1",
     "postcss-preset-env": "^9.6.0",
-    "prettier": "^3.0.0",
+    "prettier": "^3.4.2",
     "sass": "^1.77.8",
     "typescript": "^4.6.3",
-    "vite": "^5.4.11",
+    "vite": "^5.4.14",
     "vite-plugin-ruby": "^5.1.1",
-    "vitest": "^2.1.4",
+    "vitest": "^2.1.8",
     "vue-template-compiler": "^2.7.0"
   },
   "_comment": "Required to address https://github.com/npm/cli/issues/4828",