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.

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, #summary_hash, #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

convert_labware_to_receptacle_for, find_by_id_or_name, find_by_id_or_name!

Methods included from Squishify

extended

Instance Attribute Details

#storage_location_serviceObject (readonly)

Returns the value of attribute storage_location_service.


11
12
13
# File 'app/models/labware.rb', line 11

def storage_location_service
  @storage_location_service
end

Class Method Details

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


266
267
268
# File 'app/models/labware.rb', line 266

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

.find_from_any_barcode(source_barcode) ⇒ Object


255
256
257
258
259
260
261
262
263
264
# File 'app/models/labware.rb', line 255

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


236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
# File 'app/models/labware.rb', line 236

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

Instance Method Details

#ancestor_of_purpose(ancestor_purpose_id) ⇒ Object


166
167
168
169
170
# File 'app/models/labware.rb', line 166

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


172
173
174
175
176
# File 'app/models/labware.rb', line 172

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

#childObject


276
277
278
# File 'app/models/labware.rb', line 276

def child
  children.last
end

#display_nameObject


209
210
211
# File 'app/models/labware.rb', line 209

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

#external_identifierObject


162
163
164
# File 'app/models/labware.rb', line 162

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


205
206
207
# File 'app/models/labware.rb', line 205

def generate_name(new_name)
  self.name = new_name
end

#human_barcodeObject


186
187
188
# File 'app/models/labware.rb', line 186

def human_barcode
  'UNKNOWN'
end

#labwareObject

Labware reflects the physical piece of plastic corresponding to an asset


218
219
220
# File 'app/models/labware.rb', line 218

def labware
  self
end

#labwhere_locationObject


213
214
215
# File 'app/models/labware.rb', line 213

def labwhere_location
  @labwhere_location ||= lookup_labwhere_location
end

#parentObject


272
273
274
# File 'app/models/labware.rb', line 272

def parent
  parents.first
end

#roleObject


190
191
192
# File 'app/models/labware.rb', line 190

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

#scanned_in_dateObject


226
227
228
# File 'app/models/labware.rb', line 226

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

#source_plateObject


194
195
196
# File 'app/models/labware.rb', line 194

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

#source_platesObject


198
199
200
# File 'app/models/labware.rb', line 198

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

#spiked_in_bufferObject

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.


182
183
184
# File 'app/models/labware.rb', line 182

def spiked_in_buffer
  direct_spiked_in_buffer || most_recent_spiked_in_buffer
end

#storage_locationObject


222
223
224
# File 'app/models/labware.rb', line 222

def storage_location
  @storage_location ||= obtain_storage_location
end