Merge pull request #1449 from sanger/develop

Merging develop to master - v7.13.1

.release-version

@@ -1 +1 @@
-7.13.0
+7.13.1

Gemfile.lock

@@ -130,7 +130,7 @@ GEM
     globalid (1.2.1)
       activesupport (>= 6.1)
     hashdiff (1.1.0)
-    i18n (1.14.5)
+    i18n (1.14.6)
       concurrent-ruby (~> 1.0)
     io-console (0.7.2)
     irb (1.14.0)
@@ -187,7 +187,7 @@ GEM
     psych (5.1.2)
       stringio
     public_suffix (6.0.0)
-    puma (6.4.2)
+    puma (6.4.3)
       nio4r (~> 2.0)
     racc (1.8.1)
     rack (2.2.9)
@@ -279,12 +279,12 @@ GEM
       parser (>= 3.3.1.0)
     rubocop-factory_bot (2.26.1)
       rubocop (~> 1.61)
-    rubocop-rails (2.26.1)
+    rubocop-rails (2.26.2)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.52.0, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rspec (3.0.4)
+    rubocop-rspec (3.0.5)
       rubocop (~> 1.61)
     ruby-graphviz (1.2.5)
       rexml
@@ -315,13 +315,13 @@ GEM
     timeout (0.4.1)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.5.0)
+    unicode-display_width (2.6.0)
     useragent (0.16.10)
     webmock (3.23.1)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    webrick (1.8.1)
+    webrick (1.8.2)
     websocket-driver (0.7.6)
       websocket-extensions (>= 0.1.0)
     websocket-extensions (0.1.5)

app/exchanges/volume_tracking/message_builder.rb

@@ -1,18 +1,26 @@
 # frozen_string_literal: true
 
 module VolumeTracking
-  # Message::Message
   # Creates a message in the correct structure for the warehouse
+  # @example
+  #   {
+  #     "limsId"=>"Traction",
+  #     "messageCreateDateUtc"=>Mon, 15 Jul 2024 15:16:54.877858000 UTC +00:00,
+  #     "messageUuid"=>"0a62ee15-bbf6-46f0-ba95-01d42622d076",
+  #     "recordedAt"=>Mon, 15 Jul 2024 15:16:54.867713000 UTC +00:00,
+  #     "volume"=>1.5,
+  #     "concentration"=>10.0,
+  #     "insertSize"=>100,
+  #     "aliquotType"=>"primary",
+  #     "aliquotUuid"=>"",
+  #     "sourceType"=>"library",
+  #     "sourceBarcode"=>"TRAC-2-35805",
+  #     "sampleName"=>"Sample1",
+  #     "usedByBarcode"=>"TRAC-2-35806",
+  #     "usedByType"=>"pool"
+  #   }
+  #
   class MessageBuilder < Message::Message
-    # Produces the message in the correct format
-    # Example:
-    #   {"limsId"=>"Traction",
-    #    "messageCreateDateUtc"=>Mon, 15 Jul 2024 15:16:54.877858000 UTC +00:00,
-    #    "messageUuid"=>"0a62ee15-bbf6-46f0-ba95-01d42622d076",
-    #    "recordedAt"=>Mon, 15 Jul 2024 15:16:54.867713000 UTC +00:00,
-    #    "volume"=>1.5, "concentration"=>10.0, "insertSize"=>100, "aliquotType"=>"primary",
-    #    "aliquotUuid"=>"", "sourceType"=>"library", "sourceBarcode"=>"TRAC-2-35805",
-    #    "sampleName"=>"Sample1", "usedByBarcode"=>"TRAC-2-35806", "usedByType"=>"pool"}}
     def publish_data
       @publish_data ||= generate_publish_data
     end

app/messages/emq/publishing_job.rb

@@ -18,10 +18,11 @@ def initialize
       @bunny_config = PublishingJob.deep_open_struct(Rails.configuration.bunny)
     end
 
+    ##
     # Publish a message to the EMQ
     # @param [Object] objects the object or objects to publish
-    # @param [Object] the pipeline configuration to construct
-    #                 the message to publish from the given object(s)
+    # @param [Object] message_config the pipeline configuration to construct the message
+    # to publish from the given object(s)
     # @param [String] schema_key the key of the schema to validate the message against
     # Note:-
     # The schema_key must exist within the subjects hash of the bunny configuration and

app/models/aliquot.rb

@@ -50,7 +50,10 @@ def sample_sheet_behaviour
   #
   # @return [Boolean] Returns true if the aliquot is tagged, false otherwise.
   def tagged?
-    tag.present?
+    # This feels like a bit of a hack but I wasn't exactly sure where the best place to
+    # it. I tried to follow the sample sheet behaviour but got lost.
+    # it looks like the only place this is used is in the sample sheet generation
+    tag.present? && tag_set&.sample_sheet_behaviour != 'hidden'
   end
 
   # Generic method used by pacbio sample sheet generation to

app/models/concerns/dual_sourced_pool.rb

@@ -33,7 +33,7 @@ def source_identifier
     end.join(',')
     formatted_tubes = source_tubes.pluck(:barcode).join(',')
     # Combines the two outputs checking neither are empty
-    [formatted_wells, formatted_tubes].filter(&:present?).join(',')
+    [formatted_wells, formatted_tubes].compact_blank.join(',')
   end
 
   private

app/models/concerns/multi_sourced_pool.rb

@@ -34,7 +34,7 @@ def source_identifier
     formatted_tubes = source_tubes.pluck(:barcode).join(',')
     formatted_libraries = libraries.collect(&:tube).pluck(:barcode).join(',')
     # Combines the two outputs checking neither are empty
-    [formatted_wells, formatted_tubes, formatted_libraries].filter(&:present?).join(',')
+    [formatted_wells, formatted_tubes, formatted_libraries].compact_blank.join(',')
   end
 
   private

app/models/concerns/nested_validation.rb

@@ -62,7 +62,7 @@ def add_errors(nested, record, attribute, index)
   #
   # Records of this class will call valid? on any associations provided
   # as attr_names. Errors on these records will be propagated out
-  # @param *attr_names [Symbol] One or more associations to validate
+  # @param attr_names [Symbol] One or more associations to validate
   #
   # @return [NestedValidator]
   def validates_nested(*attr_names)

app/models/pacbio/run.rb

@@ -12,8 +12,6 @@ class Run < ApplicationRecord
     # Sequel II and Sequel I are now deprecated
     enum :system_name, { 'Sequel II' => 0, 'Sequel I' => 1, 'Sequel IIe' => 2, 'Revio' => 3 }
 
-    # before_create :generate_comment, unless: -> { wells.nil? }
-
     # We want to generate comments before the run was created
     # but tube barcodes aren't generated until the run is created.
 
@@ -33,6 +31,7 @@ class Run < ApplicationRecord
 
     validates :system_name, presence: true
 
+    # Uses the configuration provided in `config/pacbio_instrument_types.yml`
     validates_with InstrumentTypeValidator,
                    instrument_types: Rails.configuration.pacbio_instrument_types,
                    if: lambda {
@@ -49,8 +48,11 @@ class Run < ApplicationRecord
     # If plate/well data is required via the run, use ?include=plates.wells
     attr_reader :plates_attributes
 
-    # if comments are nil this blows up so add try.
-
+    # combines the library concentration or on plate loading concentration
+    # with the tube barcode to generate a comment
+    # for each well in the run
+    # @example
+    #   TRAC-2-10850 304pM  TRAC-2-10851 273pM  TRAC-2-10852 301pM  TRAC-2-10853 315pM
     def generate_comment
       comment = wells.collect do |well|
         concentration = well.library_concentration || well.on_plate_loading_concentration

app/models/pacbio/well.rb

@@ -25,6 +25,7 @@ class Well < ApplicationRecord
     # See https://api.rubyonrails.org/classes/ActiveRecord/Store.html
     # We now get the accessors from configuration
     store :smrt_link_options
+
     # using store_accessor allows you to lazy load the accessors
     store_accessor :smrt_link_options, Rails.configuration.pacbio_smrt_link_versions.options.keys
 

app/models/qc_results_upload_factory.rb

@@ -24,7 +24,6 @@ class QcResultsUploadFactory
 
   delegate :csv_data, :used_by, to: :qc_results_upload
 
-  # @param [csv] csv rows
   # creates data from the initial csv
   def rows
     return unless qc_results_upload
@@ -39,7 +38,7 @@ def create_entities!
     true
   end
 
-  # @param [Object] CSV row e.g. { col_header_1: row_1_col_1 }
+  # @param row_object [Object] csv row e.g. { col_header_1: row_1_col_1 }
   def create_data(row_object)
     # 1. Create QC Decisions
     qc_decisions = create_qc_decisions(row_object)
@@ -66,8 +65,8 @@ def create_qc_decisions(row_object)
     { lr_qc_decision:, tol_qc_decision: }
   end
 
-  # @returns [List] of created QcResults
-  # @param [Object] CSV row e.g. { col_header_1: row_1_col_1 }
+  # @return [List] of created QcResults
+  # @param row_object [Object] csv row e.g. { col_header_1: row_1_col_1 }
   def create_qc_results(row_object)
     # Get relevant QcAssayTypes, for used_by
     qc_assay_types = QcAssayType.where(used_by:)
@@ -128,7 +127,7 @@ def create_qc_decision_result!(qc_result, qc_decision)
     QcDecisionResult.create!(qc_result:, qc_decision:)
   end
 
-  # @returns [List] of all QcResultMessages - a different one is needed for each decision point
+  # @return [List] of all QcResultMessages - a different one is needed for each decision point
   def messages
     @messages ||= []
   end

app/resources/v1/ont/plate_resource.rb

@@ -8,7 +8,7 @@ module Ont
     #
     # @note Access this resource via the `/v1/ont/plates/` endpoint.
     #
-    # Provides a JSON:API representation of {Ont::Plate}.
+    # Provides a JSON:API representation of {Plate}.
     #
     # For more information about JSON:API see the [JSON:API Specifications](https://jsonapi.org/format/)
     # or look at the [JSONAPI::Resources](http://jsonapi-resources.com/) package

app/resources/v1/ont/tag_resource.rb

@@ -8,7 +8,7 @@ module Ont
     #
     # @note Access this resource via the `/v1/ont/tags/` endpoint.
     #
-    # Provides a JSON:API representation of {Ont::Tag}. This is a resource to return all of the ONT
+    # Provides a JSON:API representation of {Tag}. This is a resource to return all of the ONT
     #  tags.
     #
     # For more information about JSON:API see the [JSON:API Specifications](https://jsonapi.org/format/)

app/resources/v1/pacbio/smrt_link_version_resource.rb

@@ -8,7 +8,7 @@ module Pacbio
     #
     # @note Access this resource via the `/v1/pacbio/smrt_link_versions/` endpoint.
     #
-    # Provides a JSON:API representation of {Pacbio::Pacbio::SmrtLinkVersion}. Returns the SMRT Link
+    # Provides a JSON:API representation of {Pacbio::SmrtLinkVersion}. Returns the SMRT Link
     #  Versions.
     #
     # For more information about JSON:API see the [JSON:API Specifications](https://jsonapi.org/format/)

app/resources/v1/printer_resource.rb

@@ -7,7 +7,7 @@ module V1
   #
   # @note Access this resource via the `/v1/printer_types` endpoint.
   #
-  # Provides a JSON:API representation of {PrinterType} and exposes valid library type options
+  # Provides a JSON:API representation of {Printer} and exposes valid library type options
   # for use by the UI.
   #
   # For more information about JSON:API see the [JSON:API Specifications](https://jsonapi.org/format/)

app/validators/has_filters.rb

@@ -14,7 +14,7 @@ def exclude_marked_for_destruction
 
   private
 
-  # @param [ActiveRecord::Base] record
+  # @param records [ActiveRecord::Base]
   # @return [Array]
   # filter out records which are marked for destruction
   def filtered(records)

app/validators/instrument_type_validator.rb

@@ -1,11 +1,13 @@
 # frozen_string_literal: true
 
-# Validator for InstrumentType
-# Validates the InstrumentType and its associated Plates and Wells
-# Validates the presence of required attributes
-# Validates the number of Plates and Wells
-# Validates the positions of Wells
-# Validates the combinations of Wells
+##
+# Validator for Pacbio InstrumentType:
+#
+# - Validates the InstrumentType and its associated Plates and Wells
+# - Validates the presence of required attributes
+# - Validates the number of Plates and Wells
+# - Validates the positions of Wells
+# - Validates the combinations of Wells
 class InstrumentTypeValidator < ActiveModel::Validator
   attr_reader :instrument_types, :instrument_type
 

app/validators/smrt_link_options_validator.rb

@@ -1,23 +1,25 @@
 # frozen_string_literal: true
 
-# validate SmrtLinkOptions by version
-# This allows more flexible modification of fields by version
-# each version will have a set of validations
-# on validate it will loop through each of those validations
-# build a validator and validate the record for each specified attribute
-# the validations are standard ActiveRecord ones with specified options
+##
+# validate SmrtLinkOptions by version:
+#
+# - This allows more flexible modification of fields by version
+# - each version will have a set of validations
+# - on validate it will loop through each of those validations
+# - build a validator and validate the record for each specified attribute
+# - the validations are standard ActiveRecord ones with specified options
 # @example
 #   smrt_link_option = { key: attribute_1, validations: { required: {},
 #                        numericality: { greater_than_equal_to: 0,
 #                        less_than_or_equal_to: 1}} }
-# This will then run each validator against the specified key
+# - This will then run each validator against the specified key
 # @example
 #   ActiveModel::Validations::NumericalityValidator.new(attributes: attribute_1,
 #   greater_than_equal_to: 0, less_than_or_equal_to: 1).validate(record)
-# Any errors will be added to the record
-# The validator must be a recognised validator as per
+# - Any errors will be added to the record
+# - The validator must be a recognised validator as per
 # https://github.com/rails/rails/tree/main/activemodel/lib/active_model/validations
-# Or you need to create your own validator as per
+# - Or you need to create your own validator as per
 # https://api.rubyonrails.org/classes/ActiveModel/Validator.html
 class SmrtLinkOptionsValidator < ActiveModel::Validator
   def validate(record)

config/pipelines/reception.yml

@@ -43,7 +43,7 @@ default: &default
           last_updated: *timestamp
           id_sample_lims:
             type: :model
-            value: id
+            value: name
           uuid_sample_lims:
             type: :model
             value: external_id

db/migrate/20240927074405_drop_pacbio_request_libraries_table.rb

@@ -0,0 +1,5 @@
+class DropPacbioRequestLibrariesTable < ActiveRecord::Migration[7.2]
+  def change
+    drop_table :pacbio_request_libraries
+  end
+end

db/migrate/20240927074531_remove_sequencing_kit_box_barcode_column_from_pacbio_runs.rb

@@ -0,0 +1,5 @@
+class RemoveSequencingKitBoxBarcodeColumnFromPacbioRuns < ActiveRecord::Migration[7.2]
+  def change
+    remove_column :pacbio_runs, :sequencing_kit_box_barcode
+  end
+end

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.2].define(version: 2024_09_09_163449) do
+ActiveRecord::Schema[7.2].define(version: 2024_09_27_074531) do
   create_table "aliquots", charset: "utf8mb3", force: :cascade do |t|
     t.float "volume"
     t.float "concentration"
@@ -216,17 +216,6 @@
     t.index ["tube_id"], name: "index_pacbio_pools_on_tube_id"
   end
 
-  create_table "pacbio_request_libraries", charset: "utf8mb3", force: :cascade do |t|
-    t.bigint "pacbio_request_id"
-    t.bigint "pacbio_library_id"
-    t.bigint "tag_id"
-    t.index ["pacbio_library_id"], name: "index_pacbio_request_libraries_on_pacbio_library_id"
-    t.index ["pacbio_request_id", "pacbio_library_id"], name: "index_rl_request_library", unique: true
-    t.index ["pacbio_request_id"], name: "index_pacbio_request_libraries_on_pacbio_request_id"
-    t.index ["tag_id", "pacbio_library_id"], name: "index_rl_tag_library", unique: true
-    t.index ["tag_id"], name: "index_pacbio_request_libraries_on_tag_id"
-  end
-
   create_table "pacbio_requests", charset: "utf8mb3", force: :cascade do |t|
     t.string "library_type"
     t.string "estimate_of_gb_required"
@@ -240,7 +229,6 @@
 
   create_table "pacbio_runs", charset: "utf8mb3", force: :cascade do |t|
     t.string "name"
-    t.string "sequencing_kit_box_barcode"
     t.string "dna_control_complex_box_barcode"
     t.text "comments"
     t.string "uuid"