Class: Batch

Inherits:
ApplicationRecord show all
Extended by:
EventfulRecord
Includes:
AASM, Api::BatchIo::Extensions, Api::Messages::FlowcellIo::Extensions, PipelineBehaviour, PolyMetadataBehaviour, StateMachineBehaviour, Commentable, HasPolyMetadata, SequencingQcBatch, StandardNamedScopes, UnderRepWellCommentsToBroadcast, Uuid::Uuidable
Defined in:
app/models/batch.rb

Overview

A Batch groups 1 or more requests together to enable processing in a Pipeline. All requests in a batch get usually processed together, although it is possible for requests to get removed from a batch in a handful of cases.

Defined Under Namespace

Modules: PipelineBehaviour, PolyMetadataBehaviour, RequestBehaviour, StateMachineBehaviour Classes: RequestFailAndRemover

Constant Summary collapse

DEFAULT_VOLUME =

The three states of Batch Also @see SequencingQcBatch

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Constants included from UnderRepWellCommentsToBroadcast

UnderRepWellCommentsToBroadcast::UNDER_REPRESENTED_KEY

Constants included from StandardNamedScopes

StandardNamedScopes::SORT_FIELDS, StandardNamedScopes::SORT_ORDERS

Constants included from SequencingQcBatch

SequencingQcBatch::VALID_QC_STATES

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from EventfulRecord

has_many_events, has_many_lab_events, has_one_event_with_family

Methods included from PolyMetadataBehaviour

#automatic_buffer_addition?, #buffer_volume_for_empty_wells, #plate_template_for_buffer_addition

Methods included from HasPolyMetadata

#get_poly_metadata, #set_poly_metadata

Methods included from UnderRepWellCommentsToBroadcast

#comments, #request_with_under_represented_wells, #under_represented_well_comments

Methods included from StateMachineBehaviour

#complete_with_user!, #editable?, #finished?, included, #release_with_user!, #start_with_user!

Methods included from PipelineBehaviour

#has_item_limit?, included, #last_completed_task

Methods included from StandardNamedScopes

included

Methods included from Uuid::Uuidable

included, #unsaved_uuid!, #uuid

Methods included from Commentable

#after_comment_addition

Methods included from SequencingQcBatch

adjacent_state_helper, included, #processing_in_manual_qc?, #qc_manual_in_progress, #qc_previous_state!, #qc_states, state_transition_helper

Methods included from Api::BatchIo::Extensions

included

Methods inherited from ApplicationRecord

alias_association, convert_labware_to_receptacle_for, find_by_id_or_name, find_by_id_or_name!

Methods included from Squishify

extended

Instance Attribute Details

#production_state ⇒ Object

Also referenced in StateMachineBehaviour. Either nil, or fail. This is updated in Batch#fail_requests and Batch#fail. The former is used via BatchesController#fail_items, the latter seems to be unused. Is intended to take precedence over both other states to track failures in-spite of QC results.



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# File 'app/models/batch.rb', line 34

DEFAULT_VOLUME = 13

#qc_state ⇒ Object

Primarily for sequencing batches. See SequencingQcBatch. Holds the sequencing QC state



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# File 'app/models/batch.rb', line 34

DEFAULT_VOLUME = 13

#state ⇒ Object

The main state machine, used to track the batch through the pipeline. Handled by StateMachineBehaviour



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# File 'app/models/batch.rb', line 34

DEFAULT_VOLUME = 13

Class Method Details

.barcode_without_pick_number(code) ⇒ Object 



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# File 'app/models/batch.rb', line 546

def self.barcode_without_pick_number(code)
  code.split('-').first
end

.extract_pick_number(code) ⇒ Object 



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# File 'app/models/batch.rb', line 550

def self.extract_pick_number(code)
  # expecting format 550000555760-1 with pick number at end
  split_code = code.split('-')
  return Integer(split_code.last) if split_code.size > 1

  # default to 1 if the pick number is not present
  1
end

.find_by_barcode(code) ⇒ Object Also known as: find_from_barcode 



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# File 'app/models/batch.rb', line 560

def find_by_barcode(code)
  split_code = barcode_without_pick_number(code)
  human_batch_barcode = Barcode.number_to_human(split_code)
  batch = Batch.find_by(barcode: human_batch_barcode)
  batch ||= Batch.find_by(id: human_batch_barcode)

  batch
end

.prefix ⇒ Object 



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# File 'app/models/batch.rb', line 529

def self.prefix
  'BA'
end

.valid_barcode?(code) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/batch.rb', line 533

def self.valid_barcode?(code)
  begin
    split_code = barcode_without_pick_number(code)
    Barcode.barcode_to_human!(split_code, prefix)
  rescue StandardError
    return false
  end

  return false if find_from_barcode(code).nil?

  true
end

Instance Method Details

#all_requests_are_ready? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/batch.rb', line 120

def all_requests_are_ready?
  # Checks that SequencingRequests have at least one LibraryCreationRequest in passed status before being processed
  # (as referred by #75102998)
  errors.add :base, 'All requests must be ready to be added to a batch' unless requests.all?(&:ready?)
end

#assign_positions_to_requests!(request_ids_in_position_order) ⇒ Object

Sets the position of the requests in the batch to their index in the supplied array.

Raises:

  • (StandardError) 


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# File 'app/models/batch.rb', line 217

def assign_positions_to_requests!(request_ids_in_position_order)
  request_ids_in_batch = batch_requests.map(&:request_id)
  # checking for both missing and extra requests
  missing_requests = request_ids_in_batch.any? { |id| request_ids_in_position_order.exclude?(id) }
  extra_requests = request_ids_in_position_order.any? { |id| request_ids_in_batch.exclude?(id) }
  raise StandardError, 'Can only sort all the requests in the batch at once' if missing_requests || extra_requests

  BatchRequest.transaction do
    batch_requests.each do |batch_request|
      batch_request.move_to_position!(request_ids_in_position_order.index(batch_request.request_id) + 1)
    end
  end
end

#assigned_user ⇒ Object 



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# File 'app/models/batch.rb', line 233

def assigned_user
  assignee.try(:login) || ''
end

#batch_id_matches(scanned_batch_id) ⇒ Object 



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# File 'app/models/batch.rb', line 377

def batch_id_matches(scanned_batch_id)
  scanned_batch_id == id.to_s
end

#control ⇒ Object 



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# File 'app/models/batch.rb', line 201

def control
  requests.detect { |request| request.try(:asset).try(:resource?) }
end

#detach_request(request, current_user = nil) ⇒ Object

Remove a request from the batch and reset it to a point where it can be put back into the pending queue.



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# File 'app/models/batch.rb', line 402

def detach_request(request, current_user = nil)
  ActiveRecord::Base.transaction do
    unless current_user.nil?
      request.add_comment("Used to belong to Batch #{id} removed at #{Time.zone.now}", current_user)
    end
    pipeline.detach_request_from_batch(self, request)
  end
end

#displayed_status ⇒ Object

Summarise the state encapsulated by state and production_state Essentially a 'fail' production_state over-rides the 'state' We don't use production_state directly as it it 'fail' rather than ' failed' qc_state it kept separate as its a fairly distinct concept and is summarised elsewhere in the interface.



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# File 'app/models/batch.rb', line 602

def displayed_status
  failed? ? 'failed' : state
end

#downstream_requests_needing_asset(request) {|next_requests_needing_asset| ... } ⇒ Object

Yields:

  • (next_requests_needing_asset) 


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# File 'app/models/batch.rb', line 583

def downstream_requests_needing_asset(request)
  next_requests_needing_asset = request.next_requests.select { |r| r.asset_id.blank? }
  yield(next_requests_needing_asset) if next_requests_needing_asset.present?
end

#event_with_description(name) ⇒ Object 



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# File 'app/models/batch.rb', line 189

def event_with_description(name)
  lab_events.order(id: :desc).find_by(description: name)
end

#eventful_studies ⇒ Object 



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# File 'app/models/batch.rb', line 130

def eventful_studies
  requests.reduce([]) { |studies, request| studies.concat(request.eventful_studies) }.uniq
end

#fail(reason, comment, ignore_requests = false) ⇒ Object

Fail was removed from State Machine (as a state) to allow the addition of qc_state column and features

Raises:

  • (StandardError) 


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# File 'app/models/batch.rb', line 139

def fail(reason, comment, ignore_requests = false)
  # We've deprecated the ability to fail a batch but not its requests.
  # Keep this check here until we're sure we haven't missed anything.
  raise StandardError, 'Can not fail batch without failing requests' if ignore_requests

  # create failures
  failures.create(reason: reason, comment: comment, notify_remote: false)

  requests.each do |request|
    request.failures.create(reason: reason, comment: comment, notify_remote: true)
    EventSender.send_fail_event(request, reason, comment, id) unless request.asset && request.asset.resource?
  end

  self.production_state = 'fail'
  save!
end

#fail_requests(requests_to_fail, reason, comment, fail_but_charge = false) ⇒ Object

Fail specific requests on this batch



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# File 'app/models/batch.rb', line 157

def fail_requests(requests_to_fail, reason, comment, fail_but_charge = false) # rubocop:todo Metrics/MethodLength
  ActiveRecord::Base.transaction do
    requests
      .find(requests_to_fail)
      .each do |request|
        logger.debug "SENDING FAIL FOR REQUEST #{request.id}, BATCH #{id}, WITH REASON #{reason}"

        request.customer_accepts_responsibility! if fail_but_charge
        request.failures.create(reason: reason, comment: comment, notify_remote: true)
        EventSender.send_fail_event(request, reason, comment, id)
      end
    update_batch_state(reason, comment)
  end
end

#failed? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/batch.rb', line 180

def failed?
  production_state == 'fail'
end

#first_output_plate ⇒ Object 



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# File 'app/models/batch.rb', line 276

def first_output_plate
  Plate.output_by_batch(self).with_wells_and_requests.first
end

#flowcell ⇒ Object 



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# File 'app/models/batch.rb', line 134

def flowcell
  self if sequencing?
end

#has_control? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/batch.rb', line 205

def has_control?
  control.present?
end

#has_event(event_name) ⇒ Object

Tests whether this Batch has any associated LabEvents



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# File 'app/models/batch.rb', line 185

def has_event(event_name)
  lab_events.any? { |event| event_name.downcase == event.description.try(:downcase) }
end

#id_dup ⇒ Object 



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# File 'app/models/batch.rb', line 298

def id_dup
  id
end

#input_labware_report ⇒ Labware::ActiveRecord_Relation

Returns a list of input labware including their barcodes, purposes, and a count of the number of requests associated with the batch. Output depends on Pipeline. Some pipelines return an empty relationship

Returns:

  • (Labware::ActiveRecord_Relation) —

    The associated labware



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# File 'app/models/batch.rb', line 246

def input_labware_report
  pipeline.input_labware requests
end

#input_plate_group ⇒ Object 



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# File 'app/models/batch.rb', line 259

def input_plate_group
  source_assets.group_by(&:plate)
end

#npg_set_state ⇒ Object 



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# File 'app/models/batch.rb', line 575

def npg_set_state
  if all_requests_qced?
    self.state = 'released'
    qc_complete
    save!
  end
end

#output_labware_report ⇒ Labware::ActiveRecord_Relation

Returns a list of output labware including their barcodes, purposes, and a count of the number of requests associated with the batch. Output depends on Pipeline. Some pipelines return an empty relationship

Returns:

  • (Labware::ActiveRecord_Relation) —

    The associated labware



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# File 'app/models/batch.rb', line 255

def output_labware_report
  pipeline.output_labware requests.with_target
end

#output_plate_group ⇒ Object

This looks odd. Why would a request have the same asset as target asset? Why are we filtering them out here?



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# File 'app/models/batch.rb', line 264

def output_plate_group
  requests.select { |r| r.target_asset != r.asset }.map(&:target_asset).select(&:present?).group_by(&:plate)
end

#output_plate_purpose ⇒ Object 



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# File 'app/models/batch.rb', line 280

def output_plate_purpose
  output_plates[0].plate_purpose unless output_plates[0].nil?
end

#output_plate_role ⇒ Object 



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# File 'app/models/batch.rb', line 284

def output_plate_role
  requests.first.try(:role)
end

#output_plates ⇒ Object 



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# File 'app/models/batch.rb', line 268

def output_plates
  # We use re-order here as batch_requests applies a default sort order to
  # the relationship, which takes preference, even though we're has_many throughing
  return output_labware.sort_by(&:id) if output_labware.loaded?

  output_labware.reorder(id: :asc)
end

#pick_information? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/batch.rb', line 592

def pick_information?
  pipeline.pick_information?(self)
end

#plate_barcode(barcode) ⇒ Object 



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# File 'app/models/batch.rb', line 294

def plate_barcode(barcode)
  barcode.presence || requests.first.target_asset.plate.human_barcode
end

#plate_group_barcodes ⇒ Object 



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# File 'app/models/batch.rb', line 288

def plate_group_barcodes
  return nil unless pipeline.group_by_parent || requests.first.target_asset.is_a?(Well)

  output_plate_group.presence || input_plate_group
end

#plate_ids_in_study(study) ⇒ Object

rubocop:enable Metrics/AbcSize, Metrics/MethodLength, Metrics/PerceivedComplexity



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# File 'app/models/batch.rb', line 506

def plate_ids_in_study(study)
  Plate.plate_ids_from_requests(requests.for_studies(study))
end

#rebroadcast ⇒ Object 



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# File 'app/models/batch.rb', line 588

def rebroadcast
  messengers.each(&:resend)
end

#release_pending_requests ⇒ Object 



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# File 'app/models/batch.rb', line 381

def release_pending_requests
  # We set the unused requests to pending.
  # this is to allow unused well to be cherry-picked again
  requests.each { |request| detach_request(request) if request.started? }
end

#remove_request_ids(request_ids, reason = nil, comment = nil) ⇒ Object

Remove the request from the batch and remove asset information



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# File 'app/models/batch.rb', line 388

def remove_request_ids(request_ids, reason = nil, comment = nil)
  ActiveRecord::Base.transaction do
    Request
      .find(request_ids)
      .each do |request|
        request.failures.create(reason: reason, comment: comment, notify_remote: true)
        detach_request(request)
      end
    update_batch_state(reason, comment)
  end
end

#request_count ⇒ Object 



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# File 'app/models/batch.rb', line 571

def request_count
  requests.count
end

#reset!(current_user) ⇒ Object

rubocop:todo Metrics/MethodLength



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# File 'app/models/batch.rb', line 424

def reset!(current_user) # rubocop:todo Metrics/AbcSize
  ActiveRecord::Base.transaction do
    discard!

    requests.each do |request|
      request.batch = nil
      return_request_to_inbox(request, current_user)
    end

    if requests.last.submission_id.present?
      Request
        .where(submission_id: requests.last.submission_id, state: 'pending')
        .where.not(request_type_id: pipeline.request_type_ids)
        .find_each do |request|
          request.asset_id = nil
          request.save!
        end
    end
  end
end

#return_request_to_inbox(request, current_user = nil) ⇒ Object 



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# File 'app/models/batch.rb', line 411

def return_request_to_inbox(request, current_user = nil)
  ActiveRecord::Base.transaction do
    unless current_user.nil?
      request.add_comment(
        "Used to belong to Batch #{id} returned to inbox unstarted at #{Time.zone.now}",
        current_user
      )
    end
    request.return_pending_to_inbox!
  end
end

#robot_id ⇒ Object 



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# File 'app/models/batch.rb', line 193

def robot_id
  event_with_description('Cherrypick Layout Set')&.descriptor_value('robot_id')
end

#robot_verified!(user_id) ⇒ Object 



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# File 'app/models/batch.rb', line 518

def robot_verified!(user_id)
  return if has_event('robot verified')

  pipeline.robot_verified!(self)
  lab_events.create(
    description: 'Robot verified',
    message: 'Robot verification completed and source volumes updated.',
    user_id: user_id
  )
end

#set_position_based_on_asset_barcode ⇒ Object

Sets the position of the requests in the batch based on their asset barcodes. This was done at Lab request to make it easier to order the tubes in the batch.



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# File 'app/models/batch.rb', line 211

def set_position_based_on_asset_barcode
  request_ids_in_position_order = requests.sort_by { |r| r.asset.human_barcode }.map(&:id)
  assign_positions_to_requests!(request_ids_in_position_order)
end

#source_labware ⇒ Object

Source Labware returns the physical pieces of labware (ie. a plate for wells, but tubes for tubes)



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# File 'app/models/batch.rb', line 303

def source_labware
  input_labware
end

#start_requests ⇒ Object 



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# File 'app/models/batch.rb', line 237

def start_requests
  requests.with_assets_for_starting_requests.not_failed.map(&:start!)
end

#subject_type ⇒ Object 



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# File 'app/models/batch.rb', line 126

def subject_type
  sequencing? ? 'flowcell' : 'batch'
end

#swap(current_user, batch_info = {}) ⇒ Object

rubocop:todo Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/AbcSize



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# File 'app/models/batch.rb', line 448

def swap(current_user, batch_info = {}) # rubocop:todo Metrics/CyclomaticComplexity
  return false if batch_info.empty?

  # Find the two lanes that are to be swapped
  batch_request_left =
    BatchRequest.find_by(batch_id: batch_info['batch_1']['id'], position: batch_info['batch_1']['lane']) or
    errors.add('Swap: ', 'The first lane cannot be found')
  batch_request_right =
    BatchRequest.find_by(batch_id: batch_info['batch_2']['id'], position: batch_info['batch_2']['lane']) or
    errors.add('Swap: ', 'The second lane cannot be found')
  return unless batch_request_left.present? && batch_request_right.present?

  ActiveRecord::Base.transaction do
    # Update the lab events for the request so that they reference the batch that the request is moving to
    batch_request_left.request.lab_events.each do |event|
      event.update!(batch_id: batch_request_right.batch_id) if event.batch_id == batch_request_left.batch_id
    end
    batch_request_right.request.lab_events.each do |event|
      event.update!(batch_id: batch_request_left.batch_id) if event.batch_id == batch_request_right.batch_id
    end

    # Swap the two batch requests so that they are correct.  This involves swapping both the batch and the lane but
    # ensuring that the two requests don't clash on position by removing one of them.
    original_left_batch_id, original_left_position, original_right_request_id =
      batch_request_left.batch_id,
      batch_request_left.position,
      batch_request_right.request_id
    batch_request_right.destroy
    batch_request_left.update!(batch_id: batch_request_right.batch_id, position: batch_request_right.position)
    batch_request_right =
      BatchRequest.create!(
        batch_id: original_left_batch_id,
        position: original_left_position,
        request_id: original_right_request_id
      )

    # Finally record the fact that the batch was swapped
    batch_request_left.batch.lab_events.create!(
      description: 'Lane swap',
      message:
        "Lane #{batch_request_right.position} moved to #{batch_request_left.batch_id} " \
        "lane #{batch_request_left.position}",
      user_id: current_user.id
    )
    batch_request_right.batch.lab_events.create!(
      description: 'Lane swap',
      message:
        "Lane #{batch_request_left.position} moved to #{batch_request_right.batch_id} " \
        "lane #{batch_request_right.position}",
      user_id: current_user.id
    )
  end

  true
end

#total_volume_to_cherrypick ⇒ Object 



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# File 'app/models/batch.rb', line 510

def total_volume_to_cherrypick
  request = requests.first
  return DEFAULT_VOLUME unless request.asset.is_a?(Well)
  return DEFAULT_VOLUME unless request.target_asset.is_a?(Well)

  request.target_asset.get_requested_volume
end

#tube_barcode_matches(request, scanned_barcode) ⇒ Object 



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# File 'app/models/batch.rb', line 373

def tube_barcode_matches(request, scanned_barcode)
  scanned_barcode == request.asset.machine_barcode || scanned_barcode == request.asset.human_barcode
end

#underrun ⇒ Object 



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# File 'app/models/batch.rb', line 197

def underrun
  has_limit? ? (item_limit - batch_requests.size) : 0
end

#update_batch_state(reason, comment) ⇒ Object 



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# File 'app/models/batch.rb', line 172

def update_batch_state(reason, comment)
  if requests.all?(&:terminated?)
    failures.create(reason: reason, comment: comment, notify_remote: false)
    self.production_state = 'fail'
    save!
  end
end

#verify_amp_plate_layout(barcodes, user = nil) ⇒ Bool

Used in the Ultima sequencing pipelines to check AMP plates are in the correct position.

Verifies that provided barcodes are in the correct locations according to the request 'position' within the batch. Logs an event if the layout is correct.

Parameters:

  • barcodes (Array<Integer>) —

    An array of AMP plate barcodes, assumed ordered by position

  • user (User) (defaults to: nil) —

    The user validating the barcode layout

Returns:

  • (Bool) —

    true if the layout is correct, false otherwise



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# File 'app/models/batch.rb', line 351

def verify_amp_plate_layout(barcodes, user = nil)
  requests.each { |request| verify_amp_plate_position(request, barcodes) }

  if errors.empty?
    lab_events.create(description: 'AMP plate layout verified', user: user)
    true
  else
    false
  end
end

#verify_amp_plate_position(request, barcodes) ⇒ Object 



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# File 'app/models/batch.rb', line 362

def verify_amp_plate_position(request, barcodes)
  divider = '-'
  scanned_barcode = barcodes[request.position - 1]
  scanned_batch_id, tube_barcode = scanned_barcode.split(divider)

  unless batch_id_matches(scanned_batch_id) && tube_barcode_matches(request, tube_barcode)
    expected_barcode = "#{id}#{divider}#{request.asset.human_barcode}"
    errors.add(:base, "The barcode at position #{request.position} is incorrect: expected #{expected_barcode}.")
  end
end

#verify_tube_layout(barcodes, user = nil) ⇒ Bool

Used in Sequencing pipelines to check tubes are in the correct position on the flowcell.

Verifies that provided barcodes are in the correct locations according to the request 'position' within the batch. Logs an event if the layout is correct.

Parameters:

  • barcodes (Array<Integer>) —

    An array of 1-7 digit long barcodes, assumed ordered by position

  • user (User) (defaults to: nil) —

    The user validating the barcode layout

Returns:

  • (Bool) —

    true if the layout is correct, false otherwise



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# File 'app/models/batch.rb', line 319

def verify_tube_layout(barcodes, user = nil)
  requests.each { |request| verify_tube_position(request, barcodes) }

  if errors.empty?
    lab_events.create(description: 'Tube layout verified', user: user)
    true
  else
    false
  end
end

#verify_tube_position(request, barcodes) ⇒ Object 



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# File 'app/models/batch.rb', line 330

def verify_tube_position(request, barcodes)
  scanned_barcode = barcodes[request.position - 1]

  unless tube_barcode_matches(request, scanned_barcode)
    expected_barcode = request.asset.human_barcode
    errors.add(:base, "The tube at position #{request.position} is incorrect: expected #{expected_barcode}.")
  end
end