Y26-085 submission template for ultima ug200 sequencing

app/helpers/submissions_helper.rb

@@ -139,7 +139,8 @@ def submission_link(submission, options)
   def field_selection_tag(request_options, field_info, name_format, enforce_required)
     select_tag(
       name_format % field_info.key,
-      options_for_select(field_info.selection.map(&:to_s), request_options[field_info.key]),
+      options_for_select(field_info.selection.map(&:to_s),
+                         request_options[field_info.key].presence || field_info.default_value),
       class: 'custom-select',
       required: enforce_required && field_info.required,
       read_only: field_info.selection.size == 1

app/models/bulk_submission.rb

@@ -253,7 +253,8 @@ def process # rubocop:todo Metrics/CyclomaticComplexity
     'scrna core cells per chip well',
     '% phix requested',
     'low diversity',
-    'ot recipe'
+    'ot recipe',
+    'wafer size'
   ].freeze
 
   ALIAS_FIELDS = { 'plate barcode' => 'barcode', 'tube barcode' => 'barcode' }.freeze
@@ -360,7 +361,8 @@ def extract_request_options(details)
         ['scrna core cells per chip well', 'cells_per_chip_well'],
         ['% phix requested', 'percent_phix_requested'],
         ['low diversity', 'low_diversity'],
-        ['ot recipe', 'ot_recipe']
+        ['ot recipe', 'ot_recipe'],
+        ['wafer size', 'wafer_size']
       ].each do |source_key, target_key|
         assign_value_if_source_present(details, source_key, request_options, target_key)
       end

app/models/ultima_sequencing_pipeline.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-# Specialized sequencing pipeline for Ultima
+# Specialized sequencing pipeline for Ultima UG100
 class UltimaSequencingPipeline < SequencingPipeline
   def ot_recipe_consistent_for_batch?(batch)
     ot_recipe_list = batch.requests.filter_map { |request| request.request_metadata.ot_recipe }

app/models/ultima_ug200_sequencing_pipeline.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+# Specialized sequencing pipeline for Ultima UG200
+class UltimaUG200SequencingPipeline < UltimaSequencingPipeline
+  def wafer_size_consistent_for_batch?(batch)
+    wafer_size_list = batch.requests.filter_map { |request| request.request_metadata.wafer_size }
+
+    # There are some requests that don't have the wafer_size attribute
+    return false if wafer_size_list.size != batch.requests.size
+
+    (wafer_size_list.uniq.size == 1)
+  end
+end

app/models/ultima_ug200_sequencing_request.rb

@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+# Request class specific to the Ultima UG200 sequencing platform.
+# Includes wafer size and OT recipe.
+class UltimaUG200SequencingRequest < SequencingRequest
+  include Api::Messages::UseqWaferIo::LaneExtensions
+
+  FREE = 'Free'
+  FLEX = 'Flex'
+  OT_RECIPE_OPTIONS = [FREE, FLEX].freeze
+
+  has_metadata as: Request do
+    # Defining the sequencing request metadata here again, as 'has_metadata'
+    # does not automatically append these custom attributes to the request.
+    #
+    # The has_metadata call dynamically defines an inner Metadata class and
+    # takes the attributes from the block and adds them to the Metadata class.
+    # There is an assumption that the inner Metadata class is available in a
+    # sequencing request class defintion. Calling has_metadata again does not
+    # inherit the attributes given in the block supplied in the superclass.
+    # They need to be supplied again for this class for a proper inner Metadata
+    # class definition. In a future refactoring these attributes can be moved a
+    # class attribute and subclasses can merge its own attibutes to that. A
+    # common method can set up the inner Metadata class in the subclasses.
+    custom_attribute(:fragment_size_required_from, integer: true, minimum: 1)
+    custom_attribute(:fragment_size_required_to, integer: true, minimum: 1)
+
+    custom_attribute(:ot_recipe, default: FREE, in: OT_RECIPE_OPTIONS, required: true)
+    enum :ot_recipe, { Free: 0, Flex: 1 }
+    custom_attribute(:wafer_size, default: '10TB', validator: true, required: true, selection: true)
+  end
+
+  # Delegate to request_metadata so the attributes are visible to the validator in the RSpec tests.
+  # This delegation has no real effect outside of the tests.
+  delegate :wafer_size, :ot_recipe, to: :request_metadata
+
+  # Generates unique wafer ID, concatenation of batch_for_opentrons,
+  # id_pool_lims, and request_order.
+  # @return [String] unique wafer ID for LIMS
+  def id_wafer_lims
+    "#{batch.id}_#{source_labware.human_barcode}_#{position}"
+  end
+end

app/validators/ultima_ug200_validator.rb

@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+class UltimaUG200Validator < UltimaValidator
+  WAFER_SIZE_CONSISTENT_MSG = 'Wafer size must be the same for both requests.'
+
+  # Used in _pipeline_limit.html to display custom validation warnings
+  def self.validation_info
+    'Wafer Size and OT Recipe must be the same for both requests.'
+  end
+
+  # Validates that a batch contains the two requests.
+  def validate(record)
+    validate_exactly_two_requests(record)
+    requests_have_same_ot_recipe(record)
+    requests_have_same_wafer_size(record)
+  end
+
+  private
+
+  def requests_have_same_wafer_size(record)
+    return if record.pipeline.wafer_size_consistent_for_batch?(record)
+
+    record.errors.add(:base, WAFER_SIZE_CONSISTENT_MSG)
+  end
+end

app/views/bulk_submissions/_guidance.html.erb

@@ -47,4 +47,5 @@ used to split a submission up into orders, and as a result must have the same re
   <dt>% PhiX requested</dt><dd>Required percentage of PhiX needed.</dd>
   <dt>Low Diversity</dt><dd>Low Diversity value being "Yes" or "No"</dd>
   <dt>OT Recipe</dt><dd>OT (OpenTron liquid handler) Recipe value being "Free" or "Flex"</dd>
+  <dt>Wafer Size</dt><dd>Wafer size value being "5TB", "10TB" or "20TB"</dd>
 </dl>

config/bulk_submission_excel/columns.yml

@@ -367,3 +367,22 @@ ot_recipe:
     range_name: :ot_recipe
   conditional_formattings:
     empty_cell:
+wafer_size:
+  heading: "Wafer Size"
+  unlocked: true
+  attribute: :wafer_size
+  validation:
+    options:
+      type: :list
+      formula1: "$A$1:$A$2"
+      allowBlank: false
+      showInputMessage: true
+      showErrorMessage: true
+      errorStyle: :stop
+      errorTitle: "Wafer Size"
+      error: "You must enter a value from the list provided."
+      promptTitle: "Wafer Size"
+      prompt: "Select a value type from the approved list"
+    range_name: :wafer_size
+  conditional_formattings:
+    empty_cell:

config/bulk_submission_excel/ranges.yml

@@ -27,3 +27,8 @@ ot_recipe:
   options:
     - "Free"
     - "Flex"
+wafer_size:
+  options:
+    - "5TB"
+    - "10TB"
+    - "20TB"

config/default_records/descriptors/005_ultima_ug200_descriptors.wip.yml

@@ -0,0 +1,86 @@
+---
+# Section names must be unique inside the record loader folder.
+"OTR carrier Lot # UG200":
+  name: "OTR carrier Lot #"
+  task: Opentrons
+  workflow: Ultima UG200
+  kind: Text
+  required: false
+  sorter: 0
+OTR carrier expiry UG200:
+  name: OTR carrier expiry
+  task: Opentrons
+  workflow: Ultima UG200
+  kind: Date
+  required: false
+  sorter: 1
+"Reaction Mix 7 Lot # UG200":
+  name: "Reaction Mix 7 Lot #"
+  task: Opentrons
+  workflow: Ultima UG200
+  kind: Text
+  required: false
+  sorter: 2
+Reaction Mix 7 expiry UG200:
+  name: Reaction Mix 7 expiry
+  task: Opentrons
+  workflow: Ultima UG200
+  kind: Date
+  required: false
+  sorter: 3
+"NFW Lot # UG200":
+  name: "NFW Lot #"
+  task: Opentrons
+  workflow: Ultima UG200
+  kind: Text
+  required: false
+  sorter: 4
+NFW expiry UG200:
+  name: NFW expiry
+  task: Opentrons
+  workflow: Ultima UG200
+  kind: Date
+  required: false
+  sorter: 5
+"Oil Lot # UG200":
+  name: "Oil Lot #"
+  task: Opentrons
+  workflow: Ultima UG200
+  kind: Text
+  required: false
+  sorter: 6
+Oil expiry UG200:
+  name: Oil expiry
+  task: Opentrons
+  workflow: Ultima UG200
+  kind: Date
+  required: false
+  sorter: 7
+Pipette carousel UG200:
+  name: Pipette carousel
+  task: Opentrons
+  workflow: Ultima UG200
+  kind: Text
+  required: false
+  sorter: 8
+Opentrons Inst. Name UG200:
+  name: Opentrons Inst. Name
+  task: Opentrons
+  workflow: Ultima UG200
+  kind: Text
+  required: true
+  sorter: 9
+Assign Control Bead Tube UG200:
+  name: Assign Control Bead Tube
+  task: Amp
+  workflow: Ultima UG200
+  kind: Text
+  required: false
+  sorter: 0
+UG AMP Inst. Name UG200:
+  name: UG AMP Inst. Name
+  task: Amp
+  workflow: Ultima UG200
+  kind: Text
+  required: true
+  sorter: 1

config/default_records/pipeline_request_information_types/004_ultima_ug200_pipeline_request_information_types.wip.yml

@@ -0,0 +1,16 @@
+---
+FragmentSizeRequiredFromInformationTypeForUltimaUG200:
+  pipeline_name: Ultima UG200
+  request_information_type_key: fragment_size_required_from
+
+FragmentSizeRequiredToInformationTypeForUltimaUG200:
+  pipeline_name: Ultima UG200
+  request_information_type_key: fragment_size_required_to
+
+WaferSizeInformationTypeForUltimaUG200:
+  pipeline_name: Ultima UG200
+  request_information_type_key: wafer_size
+
+OTRecipeInformationTypeForUltimaUG200:
+  pipeline_name: Ultima UG200
+  request_information_type_key: ot_recipe

config/default_records/pipelines/004_ultima_ug200_pipelines.wip.yml

@@ -0,0 +1,17 @@
+---
+Ultima UG200:
+  name: Ultima UG200 Sequencing
+  sti_type: UltimaUG200SequencingPipeline
+  validator_class_name: UltimaUG200Validator
+  sorter: 10
+  max_size: 2
+  summary: 1
+  externally_managed: 0
+  group_name: Sequencing
+  control_request_type_id: 0
+  min_size: 1
+  request_type_keys:
+    - ultima_ug200_sequencing
+  workflow:
+    name: Ultima UG200
+    item_limit: 2

config/default_records/plate_purposes/017_ultima_ug200_purposes.wip.yml

@@ -0,0 +1,9 @@
+---
+# 96 well input plates
+UPF2 Cherrypicked:
+  type: PlatePurpose::Input
+  stock_plate: true
+  default_state: passed
+  cherrypickable_target: true
+  target_type: Plate
+  size: 96

config/default_records/request_information_types/004_ultima_ug200_request_information_types.wip.yml

@@ -0,0 +1,7 @@
+---
+wafer_size:
+  name: Wafer size
+  key: wafer_size
+  label: Wafer size
+  width: 5
+  hide_in_inbox: 0

config/default_records/request_type_validators/003_ultima_ug200_request_type_validators.wip.yml

@@ -0,0 +1,8 @@
+---
+WaferSizeRequestedUltimaUG200Sequencing:
+  request_type_key: ultima_ug200_sequencing
+  request_option: wafer_size
+  valid_options:
+    - 5TB
+    - 10TB
+    - 20TB

config/default_records/request_types/026_ultima_ug200_request_types.wip.yml

@@ -0,0 +1,31 @@
+# Request types for Ultima UG200 sequencing platform.
+---
+limber_ultima_ug200_htp_pcr_free:
+  name: Limber Ultima UG200 HTP PCR Free
+  order: 1
+  request_class_name: IlluminaHtp::Requests::StdLibraryRequest
+  asset_type: Well
+  for_multiplexing: false
+  billable: true
+  product_line_name: Ultima # same as UG100
+  acceptable_purposes:
+    - UPF2 Cherrypicked
+  library_types:
+    - Ultima High Throughput PCR Free 96 # same as UG100
+limber_multiplexing_ultima_ug200:
+  name: Limber Multiplexing Ultima UG200
+  asset_type: Well
+  order: 2
+  request_class_name: Request::Multiplexing
+  for_multiplexing: true
+  product_line_name: Ultima # same as UG100
+  target_purpose_name: UPF2 EqVol Norm
+ultima_ug200_sequencing:
+  name: Ultima UG200 sequencing
+  asset_type: LibraryTube
+  order: 2
+  initial_state: pending
+  billable: true
+  product_line_name: Ultima # same as UG100
+  request_class_name: UltimaUG200SequencingRequest
+  request_purpose: standard

config/default_records/submission_templates/021_ultima_ug200_submission_templates.wip.yml

@@ -0,0 +1,18 @@
+# This submission template is associated with the Ultima PCR Free Library preparation pipeline
+# and the Ultima UG200 sequencing platform.
+---
+Limber-Htp - Ultima UG200 PCR Free - Ultima UG200 sequencing:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys:
+      ["limber_ultima_ug200_htp_pcr_free", "limber_multiplexing_ultima_ug200", "ultima_ug200_sequencing"]
+    order_role: PCR Free
+    product_line_name: Ultima # same as UG100
+    product_catalogue_name: GenericNoPCR
+Limber-Htp - Ultima UG200 PCR Free - Ultima UG200 sequencing Automated:
+  submission_class_name: "LinearSubmission"
+  related_records:
+    request_type_keys: ["ultima_ug200_sequencing"]
+    order_role: PCR Free
+    product_line_name: Ultima # same as UG100
+    product_catalogue_name: GenericNoPCR

config/default_records/tasks/005_ultima_ug200_tasks.wip.yml

@@ -0,0 +1,14 @@
+---
+# Section names must be unique inside the record loader folder.
+Opentrons UG200:
+  name: Opentrons
+  workflow: Ultima UG200
+  sorted: 0
+  lab_activity: true
+  sti_type: SetDescriptorsTask
+Amp UG200:
+  name: Amp
+  workflow: Ultima UG200
+  sorted: 1
+  lab_activity: true
+  sti_type: SetDescriptorsTask

config/default_records/tube_purposes/011_ultima_ug200_tube_purposes.wip.yml

@@ -0,0 +1,6 @@
+---
+UPF2 EqVol Norm:
+  # Even though this is Ultima, not Illumina, the MX tube has the same behaviour
+  type: IlluminaHtp::MxTubePurpose
+  target_type: MultiplexedLibraryTube
+  stock_plate: false

config/initializers/inflections.rb

@@ -16,6 +16,7 @@
   inflect.acronym 'ENA' # European Nucleotide Archive
   inflect.acronym 'HTTP' # HyperText Transfer Protocol
   inflect.acronym 'EBI'  # European Bioinformatics Institute
+  inflect.acronym 'UG200' # Ultima UG200
 end
 
 # These inflection rules are supported but not enabled by default: