Merge pull request #1293 from sanger/bioscan-tube-label

DPL-749 Bioscan - traction compatible tube label class

app/helpers/search_helper.rb

@@ -9,6 +9,11 @@ def self.stock_plate_names
     Settings.purposes.values.select(&:input_plate).map(&:name)
   end
 
+  # Returns purpose names of stock plates using stock_plate flag instead of input_plate.
+  def self.stock_plate_names_with_flag
+    Settings.purposes.values.select(&:stock_plate).map(&:name)
+  end
+
   def self.purpose_config_for_purpose_name(purpose_name)
     Settings.purposes.values.find { |obj| obj[:name] == purpose_name }
   end

app/models/labels/plate_384_single_label.rb

@@ -0,0 +1,92 @@
+# frozen_string_literal: true
+
+# This label class provides attributes for Bioscan 384-well plate labels,
+# which have only a single sticker. The placement of barcode and text fields
+# is similar to 96-well plate labels. Note that other 384-well plate labels
+# have double stickers.
+#
+# The label contains a barcode image in the middle and text on the corners.
+# * The barcode image in the middle contains human barcode in code128, which
+#   is more compact and readable than code39. It needs empty space on both
+#   sides for readabilty.
+# * Top-left contains date of printing
+# * Bottom-left contains human barcode of the plate
+# * Top-right contains the barcode of the an ancestor stock plate. For Bioscan
+#   384-well plates, we show the first LILYS barcode, or the first LYSATE
+#   barcode; not last.
+#
+# We show an ancestor stock plate barcode; not the parent. The algorithm
+# below is generic to handle the cases when ancestor plates with the same
+# purpose can be stock plates or non stock plates because of alternative
+# pipeline paths and/or when ancestor plates from different paths are used
+# together to make a plate. We show the first of the configured alternative
+# or the first of closest stock plate ancestors.
+#
+# Only Squix printers are used for printing 384-well plate labels. We do not
+# send print requests to PMB service, instead we send them directly to SPrint
+# service, which talks to Squix printers.
+#
+class Labels::Plate384SingleLabel < Labels::PlateLabelBase
+  def attributes
+    {
+      top_left: date_today,
+      bottom_left: labware.barcode.human,
+      top_right: workline_identifier,
+      bottom_right: labware.purpose_name,
+      barcode: labware.barcode.human
+    }
+  end
+
+  def workline_identifier
+    workline_reference&.barcode&.human
+  end
+
+  # Returns stock plate with fallbacks
+  def workline_reference
+    # Find the plates with configured purpose (using alternative_workline_identifier setting) and return the first.
+    plate = first_of_configured_purpose
+    return plate if plate.present?
+
+    # Find the plates of the last purpose (using input_plate setting) and return the first.
+    plate = first_of_last_purpose(SearchHelper.stock_plate_names)
+    return plate if plate.present?
+
+    # Find the plates of last purpose (using stock_plate setting) and return the first.
+    first_of_last_purpose(SearchHelper.stock_plate_names_with_flag)
+  end
+
+  # Returns the first stock plate of the configured purpose
+  def first_of_configured_purpose
+    alternative_workline_identifier_purpose = SearchHelper.alternative_workline_reference_name(labware)
+    return if alternative_workline_identifier_purpose.blank?
+
+    labware.ancestors.where(purpose_name: alternative_workline_identifier_purpose).first
+  end
+
+  # Returns the first stock plate of the last purpose
+  def first_of_last_purpose(purpose_names)
+    return if purpose_names.blank?
+
+    last_purpose_name = labware.ancestors.where(purpose_name: purpose_names).order(id: :asc).last&.purpose&.name
+
+    return if last_purpose_name.blank?
+
+    labware.ancestors.where(purpose_name: [last_purpose_name]).order(id: :asc).first
+  end
+
+  # There are no defaults configured for this label in the label_templates config.
+  # It is configured using its section in there. The following methods are to make
+  # sure that inherited defaults are not captured accidentially.
+
+  def default_printer_type
+    default_printer_type_for(:plate_384_single)
+  end
+
+  def default_label_template
+    default_label_template_for(:plate_384_single)
+  end
+
+  def default_sprint_label_template
+    default_sprint_label_template_for(:plate_384_single)
+  end
+end

app/models/labels/tube_label_traction_compatible.rb

@@ -0,0 +1,58 @@
+# frozen_string_literal: true
+
+# This label class provides attributes for Bioscan tube labels. The labels have
+# two stickers, side and cap.
+#
+# The side contain a 2D barcode image and four text lines.
+# * The barcode image contains human barcode.
+# * The first line contains parent barcode and well range for PCR2 Pool tube
+#   and only the parent parcode for others.
+# * The second line contains current tube barcode without prefix and number of
+#   pooled samples, the third line contains the labware purpose.
+# * The third line contains current tube labware purpose
+# # The last line contains date of printing.
+#
+# The cap contains two text lines.
+# * The first contains barcode prefix.
+# * The last contains current tube barcode without prefix.
+#
+# Initially, this arrangement was only intended for Traction compatibility of
+# Lib PCR XP (final) tube. However, difficulty of printing 1D barcodes for PCR2
+# and Lib PCR tubes made us using 2D barcodes for all three Bioscan tubes.
+#
+# Only Squix printers are used for printing labels for Bioscan labware from
+# Limber. We do not send the print requests to PMB service, instead we send them
+# directly to SPrint service, which talks to Squix printers.
+#
+class Labels::TubeLabelTractionCompatible < Labels::TubeLabel
+  def attributes
+    {
+      first_line: first_line,
+      second_line: second_line,
+      third_line: labware.purpose_name,
+      fourth_line: date_today,
+      round_label_top_line: labware.barcode.prefix,
+      round_label_bottom_line: barcode_human_without_prefix,
+      barcode: labware.barcode.human
+    }
+  end
+
+  def first_line
+    # Parent barcode for PCR 2 Pool tube.
+    # This is the asset name (plate barcode and well range)
+    barcode_and_wells_format = /^.+?\s[A-Z]\d{1,2}:[A-Z]\d{1,2}$/
+    return labware.name if labware.name&.match?(barcode_and_wells_format)
+
+    # Parent barcode for Lib PCR Pool and Lib PCR XP tubes
+    labware.parents[0].barcode.human
+  end
+
+  def second_line
+    pools_size = @options[:pool_size] || labware.aliquots.count
+    "#{barcode_human_without_prefix}, P#{pools_size}"
+  end
+
+  def barcode_human_without_prefix
+    labware.barcode.human.sub(/\A#{Regexp.escape(labware.barcode.prefix)}/, '')
+  end
+end

app/models/presenters.rb

@@ -3,14 +3,11 @@
 module Presenters # rubocop:todo Style/Documentation
   def self.lookup_for(labware)
     presentation_classes = Settings.purposes[labware.purpose&.uuid || :unknown]
+    return presentation_classes[:presenter_class].constantize if presentation_classes
 
-    if presentation_classes
-      presentation_classes[:presenter_class].constantize
-    else
-      return Presenters::UnknownPlatePresenter if labware.plate?
-      return Presenters::UnknownTubePresenter if labware.tube?
+    return Presenters::UnknownPlatePresenter if labware.plate?
+    return Presenters::UnknownTubePresenter if labware.tube?
 
-      raise UnknownLabwareType
-    end
+    raise UnknownLabwareType
   end
 end

app/models/presenters/tag_plate_384_presenter.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+module Presenters
+  # This presenter enables printing labels for 'Tag Plate - 384' plates.
+  class TagPlate384Presenter < UnknownPlatePresenter
+    def label
+      label_class = purpose_config.fetch(:label_class) || 'Labels::Plate384SingleLabel'
+      label_class.constantize.new(labware)
+    end
+
+    def add_unknown_plate_warnings
+      errors.add(
+        :plate,
+        "type '#{labware.purpose_name}' is not a limber plate. " \
+          'You can still use this page to print labels.'
+      )
+    end
+  end
+end

app/models/presenters/tube_presenter.rb

@@ -24,7 +24,9 @@ class TubePresenter # rubocop:todo Style/Documentation
     delegate :purpose, :state, :human_barcode, to: :labware
 
     def label
-      Labels::TubeLabel.new(labware)
+      # fetch label class from purpose if present
+      label_class = purpose_config.fetch(:label_class) || 'Labels::TubeLabel'
+      label_class.constantize.new(labware)
     end
 
     def sample_count

app/models/presenters/tubes_with_sources.rb

@@ -20,7 +20,13 @@ def tube_labels
       # Optimization: To avoid needing to load in the tube aliquots, we use the transfers into the
       # tube to work out the pool size. This information is already available. Two values are different
       # for ISC though. TODO: MUST RE-JIG
-      @array.map { |tube| Labels::TubeLabel.new(tube, pool_size: tube.pool_size) }
+
+      # Tubes might have different labels in purpose config. Load the right labels to avoid different behaviour.
+      @array.map do |tube|
+        config = Settings.purposes.fetch(tube.purpose&.uuid, {})
+        label_class = config.fetch(:label_class, 'Labels::TubeLabel')
+        label_class.constantize.new(tube, pool_size: tube.pool_size)
+      end
     end
 
     delegate_missing_to :array

app/sequencescape/sequencescape/api/v2/tube.rb

@@ -61,4 +61,8 @@ def stock_plate(purpose_names: SearchHelper.stock_plate_names)
     # max_by naturally sorts in ascending order
     @stock_plate ||= ancestors.where(purpose_name: purpose_names).max_by(&:id)
   end
+
+  def workline_identifier
+    stock_plate&.barcode&.human
+  end
 end

config/label_templates.yml

@@ -46,3 +46,19 @@ plate_ltn_al_lib:
 plate_cellaca_qc:
   :label_class: Labels::PlateLabelCellacaQc
   :pmb_template: sqsc_96plate_label_template_code39
+
+# Only Squix printers are used through SPrint for tube_traction_compatible
+# pmb_template setting is for completeness; it is not used.
+tube_traction_compatible:
+  :label_class: Labels::TubeLabelTractionCompatible
+  :printer_type: 1D Tube
+  :pmb_template: tube_label_template_1d
+  :sprint_template: tube_label_traction_compatible.yml.erb
+
+# Only Squix printers are used through SPrint for plate_384_single
+# pmb_template setting is for completeness; it is not used.
+plate_384_single:
+  :label_class: Labels::Plate384SingleLabel
+  :printer_type: 384 Well Plate Double
+  :pmb_template: sqsc_384plate_label_template_code39
+  :sprint_template: plate_384_single.yml.erb

config/purposes/bioscan.yml

@@ -15,8 +15,10 @@ LILYS-96 Stock:
 # and we use the AutomaticPlateStateChanger for this.
 LBSN-96 Lysate:
   :asset_type: plate
+  # LYSATE plate can be starting plate as well. The following must be true.
   :stock_plate: true
   :cherrypickable_target: false
+  # LYSATE plate can be created from LILYS as well. The following must be false.
   :input_plate: false
   :type: PlatePurpose::AdditionalInput
   :presenter_class: Presenters::StockPlatePresenter
@@ -45,14 +47,18 @@ LBSN-384 PCR 1:
   :creator_class: LabwareCreators::QuadrantStamp
   :merger_plate: true
   :presenter_class: Presenters::MinimalPcrPlatePresenter
-  :label_template: plate_6mm_double
+  :label_template: plate_384_single
   :size: 384
+  # LILYS plate barcode is shown on barcode label top-right if possible; LYSATE otherwise.
+  :alternative_workline_identifier: LILYS-96 Stock
 LBSN-384 PCR 2:
   :asset_type: plate
   :creator_class: LabwareCreators::TaggedPlate
   :presenter_class: Presenters::MinimalPcrPlatePresenter
-  :label_template: plate_6mm_double
+  :label_template: plate_384_single
   :size: 384
+  # LILYS plate barcode is shown on barcode label top-right if possible; LYSATE otherwise.
+  :alternative_workline_identifier: LILYS-96 Stock
   # NB. will need to update this list to include new versions of the templates
   # as we generate new sets after changes from the scripts in Sequencescape
   :tag_layout_templates:
@@ -106,6 +112,7 @@ LBSN-384 PCR 2:
     - Bioscan_384_template_24_v1
 LBSN-384 PCR 2 Pool:
   :asset_type: tube
+  :label_template: tube_traction_compatible
   :target: StockMultiplexedLibraryTube
   :type: IlluminaHtp::StockTubePurpose
   :creator_class: LabwareCreators::PooledTubesFromWholePlates
@@ -114,13 +121,15 @@ LBSN-384 PCR 2 Pool:
   :number_of_parent_labwares: 1
 LBSN-9216 Lib PCR Pool:
   :asset_type: tube
+  :label_template: tube_traction_compatible
   :target: StockMultiplexedLibraryTube
   :type: IlluminaHtp::StockTubePurpose
   :creator_class: LabwareCreators::PooledTubesFromWholeTubes
   :number_of_parent_labwares: 24
   :presenter_class: Presenters::SimpleTubePresenter
 LBSN-9216 Lib PCR Pool XP:
   :asset_type: tube
+  :label_template: tube_traction_compatible
   :target: MultiplexedLibraryTube
   :type: IlluminaHtp::MxTubePurpose
   :creator_class: LabwareCreators::TubeFromTube

config/purposes/tag_plate_384.yml

@@ -0,0 +1,7 @@
+---
+# Tag Plate - 384 is not a Limber plate. This config is used for printing.
+Tag Plate - 384:
+  :asset_type: plate
+  :presenter_class: Presenters::TagPlate384Presenter
+  :size: 384
+  :label_template: plate_384_single

config/sprint/label_templates/plate_384_single.yml.erb

@@ -0,0 +1,44 @@
+[
+  {
+    "barcodeFields": [
+      {
+        "x": 17,
+        "y": 1,
+        "cellWidth": 0.2,
+        "barcodeType": "code128",
+        "value": "<%= merge_fields[:barcode] %>",
+        "height": 5
+      }
+    ],
+    "textFields": [
+      {
+        "x": 1,
+        "y": 2,
+        "value": "<%= merge_fields[:top_left] %>",
+        "fontSize": 1.5,
+        "font": "proportional"
+      },
+      {
+        "x": 1,
+        "y": 5,
+        "value": "<%= merge_fields[:bottom_left] %>",
+        "fontSize": "1.5",
+        "font": "proportional"
+      },
+      {
+        "x": 55,
+        "y": 2,
+        "value":  "<%= merge_fields[:top_right] %>",
+        "fontSize": 1.5,
+        "font": "proportional"
+      },
+      { 
+        "x": 55,
+        "y": 5,
+        "value": "<%= merge_fields[:bottom_right] %>",
+        "fontSize": 1.5,
+        "font": "proportional"
+      }
+    ]
+  }
+]