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

Instance Attribute Details

#storage_location_service ⇒ Object (readonly)

Returns the value of attribute storage_location_service.



12
13
14
 
# 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 



321
322
323
 
# File 'app/models/labware.rb', line 321

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

.find_from_any_barcode(source_barcode) ⇒ Object 



310
311
312
313
314
315
316
317
318
319
 
# File 'app/models/labware.rb', line 310

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



291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
 
# File 'app/models/labware.rb', line 291

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

.search_for_count_of_labware(params) ⇒ Object 



166
167
168
169
170
171
172
173
174
 
# File 'app/models/labware.rb', line 166

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

Used for location report



157
158
159
160
161
162
163
164
 
# File 'app/models/labware.rb', line 157

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)
    .distinct
end

Instance Method Details

#ancestor_of_purpose(ancestor_purpose_id) ⇒ Object 



213
214
215
216
217
 
# File 'app/models/labware.rb', line 213

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 



219
220
221
222
223
 
# File 'app/models/labware.rb', line 219

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 



331
332
333
 
# File 'app/models/labware.rb', line 331

def child
  children.last
end

#display_name ⇒ Object 



252
253
254
 
# File 'app/models/labware.rb', line 252

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

#external_identifier ⇒ Object 



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

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



248
249
250
 
# File 'app/models/labware.rb', line 248

def generate_name(new_name)
  self.name = new_name
end

#labware ⇒ Object

Labware reflects the physical piece of plastic corresponding to an asset



261
262
263
 
# File 'app/models/labware.rb', line 261

def labware
  self
end

#labwhere_location ⇒ Object 



256
257
258
 
# File 'app/models/labware.rb', line 256

def labwhere_location
  @labwhere_location ||= lookup_labwhere_location
end

#parent ⇒ Object 



327
328
329
 
# File 'app/models/labware.rb', line 327

def parent
  parents.first
end

#received_date ⇒ Object 



273
274
275
276
277
278
279
 
# File 'app/models/labware.rb', line 273

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 



281
282
283
 
# File 'app/models/labware.rb', line 281

def retention_instructions
  @retention_instructions ||= obtain_retention_instructions
end

#role ⇒ Object 



233
234
235
 
# File 'app/models/labware.rb', line 233

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

#scanned_in_date ⇒ Object 



269
270
271
 
# File 'app/models/labware.rb', line 269

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

#source_plate ⇒ Object 



237
238
239
 
# File 'app/models/labware.rb', line 237

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

#source_plates ⇒ Object 



241
242
243
 
# File 'app/models/labware.rb', line 241

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.



229
230
231
 
# File 'app/models/labware.rb', line 229

def spiked_in_buffer
  direct_spiked_in_buffer || most_recent_spiked_in_buffer
end

#state ⇒ Object

Provided for API compatibility



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

def state
  nil
end

#storage_location ⇒ Object 



265
266
267
 
# File 'app/models/labware.rb', line 265

def storage_location
  @storage_location ||= obtain_storage_location
end