Merge remote-tracking branch 'origin/develop' into 1958-y24-335-creat…

…e-a-new-barcode-for-normalised-xp-plates-for-the-hic-process-in-limber

.pryrc

@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+if defined?(PryByebug)
+ Pry.commands.alias_command 's', 'step'
+ Pry.commands.alias_command 'n', 'next'
+ Pry.commands.alias_command 'f', 'finish'
+ Pry.commands.alias_command 'c', 'continue'
+end

.release-version

@@ -1 +1 @@
-3.61.0
+3.61.1

Gemfile.lock

@@ -136,7 +136,7 @@ GEM
  diff-lcs (1.5.1)
  docile (1.4.0)
  drb (2.2.1)
- dry-cli (1.1.0)
+ dry-cli (1.2.0)
  erubi (1.13.0)
  exception_notification (4.5.0)
  actionmailer (>= 5.2, < 8)
@@ -192,10 +192,10 @@ GEM
  tilt
  hashdiff (1.1.0)
  hashie (5.0.0)
- i18n (1.14.5)
+ i18n (1.14.6)
  concurrent-ruby (~> 1.0)
  io-console (0.7.2)
- irb (1.14.0)
+ irb (1.14.1)
  rdoc (>= 4.0.0)
  reline (>= 0.4.2)
  json (2.7.2)
@@ -264,7 +264,7 @@ GEM
  puma (6.4.3)
  nio4r (~> 2.0)
  racc (1.8.1)
- rack (3.1.7)
+ rack (3.1.8)
  rack-mini-profiler (3.3.1)
  rack (>= 1.2.0)
  rack-proxy (0.7.7)
@@ -319,7 +319,7 @@ GEM
  rdoc (6.7.0)
  psych (>= 4.0.0)
  regexp_parser (2.9.2)
- reline (0.5.9)
+ reline (0.5.10)
  io-console (~> 0.5)
  rexml (3.3.6)
  strscan
@@ -404,7 +404,7 @@ GEM
  rbs
  syntax_tree (>= 2.0.1)
  temple (0.10.3)
- thor (1.3.1)
+ thor (1.3.2)
  tilt (2.4.0)
  timeout (0.4.1)
  tzinfo (2.0.6)
@@ -413,8 +413,9 @@ GEM
  vite_rails (3.0.17)
  railties (>= 5.1, < 8)
  vite_ruby (~> 3.0, >= 3.2.2)
- vite_ruby (3.6.0)
+ vite_ruby (3.9.0)
  dry-cli (>= 0.7, < 2)
+ logger (~> 1.6)
  rack-proxy (~> 0.6, >= 0.6.1)
  zeitwerk (~> 2.2)
  web-console (4.2.1)
@@ -434,7 +435,7 @@ GEM
  xpath (3.2.0)
  nokogiri (~> 1.8)
  yard (0.9.36)
- zeitwerk (2.6.17)
+ zeitwerk (2.6.18)
 
 PLATFORMS
  ruby

app/frontend/javascript/custom-tagged-plate/components/CustomTaggedPlate.spec.js

@@ -833,8 +833,8 @@ describe('CustomTaggedPlate', () => {
  purpose_uuid: 'purpose-uuid',
  parent_uuid: 'parent-plate-uuid',
  tag_layout: {
- tag_group: 'tag-1-group-uuid',
- tag2_group: 'tag-2-group-uuid',
+ tag_group_uuid: 'tag-1-group-uuid',
+ tag2_group_uuid: 'tag-2-group-uuid',
  direction: 'column',
  walking_by: 'manual by plate',
  initial_tag: 1,

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

@@ -619,8 +619,8 @@ export default {
  purpose_uuid: this.purposeUuid,
  parent_uuid: this.parentUuid,
  tag_layout: {
- tag_group: this.tag1GroupUuid,
- tag2_group: this.tag2GroupUuid,
+ tag_group_uuid: this.tag1GroupUuid,
+ tag2_group_uuid: this.tag2GroupUuid,
  direction: this.direction,
  walking_by: this.walkingBy,
  initial_tag: initialTag,

app/frontend/javascript/pipeline-graph/index.js

@@ -226,6 +226,8 @@ const applyMouseEvents = function () {
  // when an edge is clicked, filter the graph to show only that pipeline
  core.on('click', 'edge', (event) => {
  const pipeline = event.target.data('pipeline')
- applyFilter(pipeline)
+ const group = event.target.data('group')
+ const pipelineOrGroup = pipeline || group
+ applyFilter(pipelineOrGroup)
  })
 }

app/models/labware_creators/baited_plate.rb

@@ -25,12 +25,13 @@ def plate
  end
 
  def bait_library_layout_preview
- @bait_library_layout_preview ||= api.bait_library_layout.preview!(plate: parent_uuid, user: user_uuid).layout
+ @bait_library_layout_preview ||=
+ Sequencescape::Api::V2::BaitLibraryLayout.preview(plate_uuid: parent_uuid, user_uuid: user_uuid).first.layout
  end
 
  def create_labware!
  create_plate_with_standard_transfer! do |child|
- api.bait_library_layout.create!(plate: child.uuid, user: user_uuid)
+ Sequencescape::Api::V2::BaitLibraryLayout.create!(plate_uuid: child.uuid, user_uuid: user_uuid)
  end
  end
 

app/models/labware_creators/custom_tagged_plate.rb

@@ -18,10 +18,10 @@ class CustomTaggedPlate < Base
  {
  tag_plate: %i[asset_uuid template_uuid state],
  tag_layout: [
- :user,
- :plate,
- :tag_group,
- :tag2_group,
+ :user_uuid,
+ :plate_uuid,
+ :tag_group_uuid,
+ :tag2_group_uuid,
  :direction,
  :walking_by,
  :initial_tag,
@@ -47,14 +47,11 @@ def initialize(*args, &)
 
  def create_plate! # rubocop:todo Metrics/AbcSize
  @child =
- api
- .pooled_plate_creation
- .create!(
- child_purpose: purpose_uuid,
- user: user_uuid,
- parents: [parent_uuid, tag_plate.asset_uuid].compact_blank
- )
- .child
+ Sequencescape::Api::V2::PooledPlateCreation.create!(
+ child_purpose_uuid: purpose_uuid,
+ parent_uuids: [parent_uuid, tag_plate.asset_uuid].compact_blank,
+ user_uuid: user_uuid
+ ).child
 
  transfer_material_from_parent!(@child.uuid)
 
@@ -107,7 +104,7 @@ def tag_layout_attributes
 
  def create_labware!
  create_plate! do |plate_uuid|
- api.tag_layout.create!(tag_layout_attributes.merge(plate: plate_uuid, user: user_uuid))
+ Sequencescape::Api::V2::TagLayout.create!(tag_layout_attributes.merge(plate_uuid:, user_uuid:))
  end
  end
  end

app/models/labware_creators/merged_plate.rb

@@ -51,10 +51,10 @@ def barcodes=(barcodes)
  private
 
  def create_plate_from_parent!
- api.pooled_plate_creation.create!(
- child_purpose: purpose_uuid,
- user: user_uuid,
- parents: source_plates.map(&:uuid)
+ Sequencescape::Api::V2::PooledPlateCreation.create!(
+ child_purpose_uuid: purpose_uuid,
+ parent_uuids: source_plates.map(&:uuid),
+ user_uuid: user_uuid
  )
  end
 

app/models/labware_creators/multi_plate_pool.rb

@@ -17,10 +17,12 @@ class MultiPlatePool < Base
  private
 
  def create_labware!
- plate_creation =
- api.pooled_plate_creation.create!(parents: transfers.keys, child_purpose: purpose_uuid, user: user_uuid)
-
- @child = plate_creation.child
+ @child =
+ Sequencescape::Api::V2::PooledPlateCreation.create!(
+ child_purpose_uuid: purpose_uuid,
+ parent_uuids: transfers.keys,
+ user_uuid: user_uuid
+ ).child
 
  api.bulk_transfer.create!(user: user_uuid, well_transfers: well_transfers)
 

app/models/labware_creators/multi_stamp.rb

@@ -30,10 +30,12 @@ class MultiStamp < Base # rubocop:todo Style/Documentation
  private
 
  def create_labware!
- plate_creation =
- api.pooled_plate_creation.create!(parents: parent_uuids, child_purpose: purpose_uuid, user: user_uuid)
-
- @child = plate_creation.child
+ @child =
+ Sequencescape::Api::V2::PooledPlateCreation.create!(
+ child_purpose_uuid: purpose_uuid,
+ parent_uuids: parent_uuids,
+ user_uuid: user_uuid
+ ).child
 
  transfer_material_from_parent!(@child.uuid)
 

app/models/labware_creators/multi_stamp_tubes.rb

@@ -41,13 +41,14 @@ def create_labware!
  create_and_build_submission
  return if errors.size.positive?
 
- plate_creation =
- api.pooled_plate_creation.create!(parents: parent_uuids, child_purpose: purpose_uuid, user: user_uuid)
+ @child =
+ Sequencescape::Api::V2::PooledPlateCreation.create!(
+ child_purpose_uuid: purpose_uuid,
+ parent_uuids: parent_uuids,
+ user_uuid: user_uuid
+ ).child
 
- @child = plate_creation.child
- child_v2 = Sequencescape::Api::V2.plate_with_wells(@child.uuid)
-
- transfer_material_from_parent!(child_v2)
+ transfer_material_from_parent!
 
  yield(@child) if block_given?
  true
@@ -87,15 +88,12 @@ def parent_tubes
  Sequencescape::Api::V2::Tube.find_all(uuid: parent_uuids, includes: 'receptacle,aliquots,aliquots.study')
  end
 
- def transfer_material_from_parent!(child_plate)
- api.transfer_request_collection.create!(
- user: user_uuid,
- transfer_requests: transfer_request_attributes(child_plate)
- )
+ def transfer_material_from_parent!
+ api.transfer_request_collection.create!(user: user_uuid, transfer_requests: transfer_request_attributes)
  end
 
- def transfer_request_attributes(child_plate)
- transfers.map { |transfer| request_hash(transfer, child_plate) }
+ def transfer_request_attributes
+ transfers.map { |transfer| request_hash(transfer) }
  end
 
  def source_tube_outer_request_uuid(tube)
@@ -108,13 +106,13 @@ def source_tube_outer_request_uuid(tube)
  pending_reqs.first.uuid || nil
  end
 
- def request_hash(transfer, child_plate)
+ def request_hash(transfer)
  tube = Sequencescape::Api::V2::Tube.find_by(uuid: transfer[:source_tube])
 
  {
  'source_asset' => transfer[:source_asset],
  'target_asset' =>
- child_plate.wells.detect { |child_well| child_well.location == transfer.dig(:new_target, :location) }&.uuid,
+ @child.wells.detect { |child_well| child_well.location == transfer.dig(:new_target, :location) }&.uuid,
  'outer_request' => source_tube_outer_request_uuid(tube)
  }
  end

app/models/labware_creators/multi_stamp_tubes_using_tube_rack_scan.rb

@@ -65,13 +65,14 @@ def save
  #
  # @return [Boolean] true if the child plate was created successfully.
  def create_labware!
- plate_creation =
- api.pooled_plate_creation.create!(parents: parent_tube_uuids, child_purpose: purpose_uuid, user: user_uuid)
+ @child =
+ Sequencescape::Api::V2::PooledPlateCreation.create!(
+ child_purpose_uuid: purpose_uuid,
+ parent_uuids: parent_tube_uuids,
+ user_uuid: user_uuid
+ ).child
 
- @child = plate_creation.child
- child_v2 = Sequencescape::Api::V2.plate_with_wells(@child.uuid)
-
- transfer_material_from_parent!(child_v2)
+ transfer_material_from_parent!
 
  yield(@child) if block_given?
  true
@@ -232,23 +233,18 @@ def tube_has_expected_active_request?(tube_in_db)
  end
 
  # Transfers material from the parent tubes to the given child plate.
- # @param child_plate [Sequencescape::Api::V2::Plate] The plate to transfer material to.
- def transfer_material_from_parent!(child_plate)
- api.transfer_request_collection.create!(
- user: user_uuid,
- transfer_requests: transfer_request_attributes(child_plate)
- )
+ def transfer_material_from_parent!
+ api.transfer_request_collection.create!(user: user_uuid, transfer_requests: transfer_request_attributes)
  end
 
  # Returns an array of hashes representing the transfer requests for the given child plate.
  # Each hash includes the UUIDs of the parent tube and child well, and the UUID of the outer request.
- # @param child_plate [Sequencescape::Api::V2::Plate] The plate to get the transfer requests for.
  # @return [Array<Hash>] An array of hashes representing the transfer requests.
- def transfer_request_attributes(child_plate)
+ def transfer_request_attributes
  parent_tubes.each_with_object([]) do |(foreign_barcode, parent_tube), tube_transfers|
  tube_transfers << request_hash(
  parent_tube.uuid,
- child_plate
+ @child
  .wells
  .detect { |child_well| child_well.location == csv_file.location_by_barcode_details[foreign_barcode] }
  &.uuid,

app/models/labware_creators/plate_split_to_tube_racks.rb

@@ -408,13 +408,12 @@ def parent_wells_for_contingency
  # @param tube_attributes [Hash] A hash of attributes to use for the created tubes.
  # @return [Hash<String, Tube>] A hash of the created tubes indexed by name.
  def create_tubes(tube_purpose_uuid, number_of_tubes, tube_attributes)
- api
- .specific_tube_creation
+ Sequencescape::Api::V2::SpecificTubeCreation
  .create!(
- user: user_uuid,
- parent: parent_uuid,
- child_purposes: [tube_purpose_uuid] * number_of_tubes,
- tube_attributes: tube_attributes
+ child_purpose_uuids: [tube_purpose_uuid] * number_of_tubes,
+ parent_uuids: [parent_uuid],
+ tube_attributes: tube_attributes,
+ user_uuid: user_uuid
  )
  .children
  .index_by(&:name)

app/models/labware_creators/pooled_tubes_base.rb

@@ -20,13 +20,12 @@ def create_labware!
  end
 
  def create_child_stock_tubes
- api
- .specific_tube_creation
+ Sequencescape::Api::V2::SpecificTubeCreation
  .create!(
- user: user_uuid,
- parent: parent_uuid,
- child_purposes: [purpose_uuid] * pool_uuids.length,
- tube_attributes: tube_attributes
+ child_purpose_uuids: [purpose_uuid] * pool_uuids.length,
+ parent_uuids: [parent_uuid],
+ tube_attributes: tube_attributes,
+ user_uuid: user_uuid
  )
  .children
  .index_by(&:name)

app/models/labware_creators/pooled_tubes_by_sample.rb

@@ -47,13 +47,12 @@ def parent_v1
  # Have we made this class so cardinal-specific (e.g. lookup of ancestor vac tubes) that it cannot be re-used?
 
  def create_child_stock_tubes
- api
- .specific_tube_creation
+ Sequencescape::Api::V2::SpecificTubeCreation
  .create!(
- user: user_uuid,
- parent: parent_uuid,
- child_purposes: [purpose_uuid] * pool_uuids.length,
- tube_attributes: tube_attributes
+ child_purpose_uuids: [purpose_uuid] * pool_uuids.length,
+ parent_uuids: [parent_uuid],
+ tube_attributes: tube_attributes,
+ user_uuid: user_uuid
  )
  .children
  .index_by(&:name)