Class: Labware

Inherits:
Asset show all
Includes:
AssetLink::Associations, Commentable, SharedBehaviour::Named, Uuid::Uuidable
Defined in:
app/models/labware.rb

Overview

Labware represents a physical object which moves around the lab. It has one or more receptacles. rubocop:disable Metrics/ClassLength

Direct Known Subclasses

Fragment, Lane::Labware, Plate, Tube, TubeRack

Defined Under Namespace

Classes: CommentsController

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from SharedBehaviour::Named

included

Methods included from AssetLink::Associations

included

Methods included from Uuid::Uuidable

included, #unsaved_uuid!, #uuid

Methods included from Commentable

#after_comment_addition

Methods inherited from Asset

#asset_type_for_request_types, #barcode_number, #compatible_purposes, #contained_samples, #details, #generate_barcode, #get_qc_result_value_for, #has_stock_asset?, #label, #label=, #original_stock_plates, #prefix, #printable?, #printable_target, #register_stock!, #request_types, #type, #update_from_qc

Methods included from EventfulRecord

#has_many_events, #has_many_lab_events, #has_one_event_with_family

Methods included from Event::PlateEvents

#event_date, #fluidigm_stamp_date, #gel_qc_date, #pico_date, #qc_started_date, #sequenom_stamp_date

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

Methods included from Warren::Callback::ExceptExternallyManaged

#broadcast_except_externally_managed, included

Instance Attribute Details

#storage_location_service ⇒ Object (readonly)

Returns the value of attribute storage_location_service.



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# File 'app/models/labware.rb', line 12

def storage_location_service
  @storage_location_service
end

Class Method Details

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



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# File 'app/models/labware.rb', line 343

def find_by_barcode(source_barcode)
  with_barcode(source_barcode).first
end

.find_from_any_barcode(source_barcode) ⇒ Object 



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# File 'app/models/labware.rb', line 332

def find_from_any_barcode(source_barcode)
  if source_barcode.blank?
    nil
  elsif /\A[0-9]{1,7}\z/.match?(source_barcode)
    # Just a number
    joins(:barcodes).order(:id).find_by('barcodes.barcode LIKE "__?_"', source_barcode)
  else
    find_by_barcode(source_barcode)
  end
end

.labwhere_locations(labware_barcodes) ⇒ Object

Bulk retrieves locations for multiple labwares at once Returns hash { labware barcode => location string, .. } e.g. { 'DN1234' => 'Sanger - Room 1 - Shelf 2' } Hash has blank values where location was not found for a particular barcode Or raises LabWhereClient::LabwhereException if Labwhere response is unexpected



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# File 'app/models/labware.rb', line 313

def labwhere_locations(labware_barcodes) # rubocop:todo Metrics/MethodLength
  info_from_labwhere = LabWhereClient::LabwareSearch.find_locations_by_barcodes(labware_barcodes)

  if info_from_labwhere.blank?
    raise LabWhereClient::LabwhereException, 'Labwhere service did not return information'
  end

  barcodes_to_parentage =
    info_from_labwhere.labwares.each_with_object({}) { |info, obj| obj[info.barcode] = info.location.location_info }

  unless labware_barcodes.count == barcodes_to_parentage.count
    labware_barcodes.each do |barcode|
      # add missing barcodes to the hash, with an empty string for location, for ones that Labwhere didn't return
      barcodes_to_parentage[barcode] ||= ''
    end
  end
  barcodes_to_parentage
end

.map_retention_instructions(values) ⇒ Object

Used for location report



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# File 'app/models/labware.rb', line 166

def self.map_retention_instructions(values)
  return if values.blank?

  values.filter_map { |v| Labware.retention_instructions[v] }
end

.search_for_count_of_labware(params) ⇒ Object 



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# File 'app/models/labware.rb', line 184

def self.search_for_count_of_labware(params)
  with_faculty_sponsor_ids(params[:faculty_sponsor_ids] || nil)
    .with_study_id(params[:study_id] || nil)
    .with_plate_purpose_ids(params[:plate_purpose_ids] || nil)
    .created_between(params[:start_date], params[:end_date])
    .filter_by_barcode(params[:barcodes] || nil)
    .distinct
    .count
end

.search_for_labware(params) ⇒ Object 



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

def self.search_for_labware(params)
  with_faculty_sponsor_ids(params[:faculty_sponsor_ids] || nil)
    .with_study_id(params[:study_id] || nil)
    .with_plate_purpose_ids(params[:plate_purpose_ids] || nil)
    .created_between(params[:start_date], params[:end_date])
    .filter_by_barcode(params[:barcodes] || nil)
    .with_retention_instructions(
      map_retention_instructions(params[:retention_instructions])
    )
    .distinct
end

Instance Method Details

#ancestor_of_purpose(ancestor_purpose_id) ⇒ Object 



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# File 'app/models/labware.rb', line 235

def ancestor_of_purpose(ancestor_purpose_id)
  return self if plate_purpose_id == ancestor_purpose_id

  ancestors.order(id: :desc).find_by(plate_purpose_id: ancestor_purpose_id)
end

#ancestors_of_purpose(ancestor_purpose_id) ⇒ Object 



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# File 'app/models/labware.rb', line 241

def ancestors_of_purpose(ancestor_purpose_id)
  return [self] if plate_purpose_id == ancestor_purpose_id

  ancestors.order(id: :desc).where(plate_purpose_id: ancestor_purpose_id)
end

#child ⇒ Object 



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# File 'app/models/labware.rb', line 353

def child
  children.last
end

#display_name ⇒ Object 



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# File 'app/models/labware.rb', line 274

def display_name
  name.presence || "#{sti_type} #{id}"
end

#external_identifier ⇒ Object 



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# File 'app/models/labware.rb', line 231

def external_identifier
  "#{sti_type}#{id}"
end

#generate_name(new_name) ⇒ Object

Note:

Overridden on subclasses to append the asset id to the name via on_create callbacks

Assigns name



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# File 'app/models/labware.rb', line 270

def generate_name(new_name)
  self.name = new_name
end

#labware ⇒ Object

Labware reflects the physical piece of plastic corresponding to an asset



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# File 'app/models/labware.rb', line 283

def labware
  self
end

#labwhere_location ⇒ Object 



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# File 'app/models/labware.rb', line 278

def labwhere_location
  @labwhere_location ||= lookup_labwhere_location
end

#parent ⇒ Object 



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# File 'app/models/labware.rb', line 349

def parent
  parents.first
end

#poly_metadata ⇒ ActiveRecord::Relation

Returns a collection of PolyMetadatum records.

Returns:

  • (ActiveRecord::Relation) —

    a collection of PolyMetadatum records



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# File 'app/models/labware.rb', line 161

def poly_metadata
  PolyMetadatum.where(metadatable_id: id, metadatable_type: self.class.name)
end

#received_date ⇒ Object 



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# File 'app/models/labware.rb', line 295

def received_date
  asset_audits # rubocop:disable Style/SafeNavigationChainLength
    &.where('`key` = ? AND message LIKE ?', 'slf_receive_plates', '%Reception fridge%')
    &.order(:created_at)
    &.last
    &.created_at
end

#retention_instructions ⇒ Object 



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

def retention_instructions
  @retention_instructions ||= obtain_retention_instructions
end

#role ⇒ Object 



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

def role
  (requests_as_source.first || in_progress_requests.first)&.role
end

#scanned_in_date ⇒ Object 



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# File 'app/models/labware.rb', line 291

def scanned_in_date
  scanned_into_lab_event.try(:content) || ''
end

#source_plate ⇒ Object 



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

def source_plate
  @source_plate ||= purpose&.source_plate(self)
end

#source_plates ⇒ Object 



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# File 'app/models/labware.rb', line 263

def source_plates
  @source_plates ||= purpose&.source_plates(self)
end

#spiked_in_buffer ⇒ Object

Gets the relevant SpikedBuffer tube, if one exists, by using the two associations. A direct parent SpikedBuffer tube is used if it exists, otherwise the most recent ancestor. This was necessary to avoid affecting historical data, for which the direct parent should be used, even though there is another ancestor that was created more recently.



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# File 'app/models/labware.rb', line 251

def spiked_in_buffer
  direct_spiked_in_buffer || most_recent_spiked_in_buffer
end

#state ⇒ Object

Provided for API compatibility



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# File 'app/models/labware.rb', line 227

def state
  nil
end

#storage_location ⇒ Object 



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# File 'app/models/labware.rb', line 287

def storage_location
  @storage_location ||= obtain_storage_location
end