Class: Receptacle
Overview
A receptacle is a container for aliquots, they are associated with Labware, which represents the physical object which moves round the lab. A Labware may have a single Receptacle, such as in the case of a Tube or multiple, in the case of a Plate. Work can be requested on a particular receptacle.
Defined Under Namespace
Classes: Qc
Constant Summary
collapse
- QC_STATE_ALIASES =
{
'passed' => 'pass',
'failed' => 'fail'
}.freeze
Transfer::State::ALL_STATES
Instance Method Summary
collapse
#qc_report
#on_downstream_aliquots, #process_aliquots, #remove_downstream_aliquots, #remove_matching_aliquots
#default_state, #state, #state_from, state_helper
#after_comment_addition
included, #unsaved_uuid!, #uuid
Methods inherited from Asset
#add_parent, #ancestor_of_purpose, #asset_type_for_request_types, #assign_relationships, #barcode_number, #compatible_purposes, #contained_samples, #external_identifier, #generate_barcode, #get_qc_result_value_for, #has_stock_asset?, #label, #label=, #original_stock_plates, #prefix, #printable?, #printable_target, #register_stock!, #request_types, #spiked_in_buffer, #summary_hash, #type
#has_many_events, #has_many_lab_events, #has_one_event_with_family
#event_date, #fluidigm_stamp_date, #gel_qc_date, #pico_date, #qc_started_date, #sequenom_stamp_date
convert_labware_to_receptacle_for, find_by_id_or_name, find_by_id_or_name!
Methods included from Squishify
extended
#broadcast, included, #queue_associated_for_broadcast, #queue_for_broadcast, #warren
Instance Method Details
#absolute_position_name ⇒ Object
Returns the name of the position (eg. A1) of the receptacle within the context of any tube-rack it may be contained within
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# File 'app/models/receptacle.rb', line 300
def absolute_position_name
racked_tube&.coordinate
end
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#any_barcode_matching?(other_barcode) ⇒ Boolean
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# File 'app/models/receptacle.rb', line 64
def any_barcode_matching?(other_barcode)
barcodes.any? { |barcode| barcode =~ other_barcode }
end
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#api_asset_type ⇒ Object
Compatibility for v1 API maintains legacy 'type' for assets
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# File 'app/models/receptacle.rb', line 285
def api_asset_type
legacy_asset_type.tableize
end
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#assign_tag2(tag) ⇒ Object
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# File 'app/models/receptacle.rb', line 211
def assign_tag2(tag)
aliquots.each do |aliquot|
aliquot.tag2 = tag
aliquot.save!
end
end
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#attach_tag(tag, tag2 = nil) ⇒ Object
Also known as:
attach_tags
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# File 'app/models/receptacle.rb', line 243
def attach_tag(tag, tag2 = nil)
tags = { tag: tag, tag2: tag2 }.compact
return if tags.empty?
raise StandardError, 'Cannot tag an empty asset' if aliquots.empty?
raise StandardError, 'Cannot tag multiple samples' if aliquots.size > 1
aliquots.first.update!(tags)
end
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#been_through_qc? ⇒ Boolean
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# File 'app/models/receptacle.rb', line 201
def been_through_qc?
qc_state.present?
end
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#compatible_qc_state ⇒ Object
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# File 'app/models/receptacle.rb', line 191
def compatible_qc_state
QC_STATE_ALIASES.fetch(qc_state, qc_state) || ''
end
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#created_with_request_options ⇒ Object
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# File 'app/models/receptacle.rb', line 218
def created_with_request_options
aliquots.first&.created_with_request_options || {}
end
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#details ⇒ Object
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# File 'app/models/receptacle.rb', line 280
def details
labware.try(:details).presence || 'Not on labware'
end
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#friendly_name ⇒ Object
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# File 'app/models/receptacle.rb', line 294
def friendly_name
labware&.friendly_name || id
end
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# File 'app/models/receptacle.rb', line 169
def
labware&.&.size || 0
end
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#latest_stock_metrics(_product, *_args) ⇒ Object
We only support wells for the time being
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# File 'app/models/receptacle.rb', line 257
def latest_stock_metrics(_product, *_args)
[]
end
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#legacy_asset_type ⇒ Object
Compatibility for v1 API maintains legacy 'type' for assets
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# File 'app/models/receptacle.rb', line 290
def legacy_asset_type
labware.sti_type
end
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# File 'app/models/receptacle.rb', line 209
def library_information; end
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#library_name ⇒ Object
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# File 'app/models/receptacle.rb', line 276
def library_name
labware.name
end
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#library_types ⇒ Object
Library types are still just a string on aliquot.
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# File 'app/models/receptacle.rb', line 223
def library_types
aliquots.pluck(:library_type).uniq
end
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#name ⇒ Object
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# File 'app/models/receptacle.rb', line 264
def name
labware_name = labware.present? ? labware.try(:name) : '(not on a labware)'
labware_name ||= labware.display_name labware_name
end
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#outer_request(submission_id) ⇒ Object
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# File 'app/models/receptacle.rb', line 234
def outer_request(submission_id)
transfer_requests_as_target.find_by(submission_id: submission_id).try(:outer_request)
end
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#primary_aliquot_if_unique ⇒ Object
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# File 'app/models/receptacle.rb', line 205
def primary_aliquot_if_unique
primary_aliquot if aliquots.count == 1
end
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All studies related to this asset
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# File 'app/models/receptacle.rb', line 239
def related_studies
(ordered_studies + studies).compact.uniq
end
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#role ⇒ Object
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# File 'app/models/receptacle.rb', line 304
def role
(requests_as_source.first || aliquot_requests.first).role
end
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#set_as_library(force: false) ⇒ Object
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# File 'app/models/receptacle.rb', line 227
def set_as_library(force: false)
aliquots.each do |aliquot|
aliquot.set_library(force: force)
aliquot.save!
end
end
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#set_qc_state(state) ⇒ Object
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# File 'app/models/receptacle.rb', line 195
def set_qc_state(state)
self.qc_state = QC_STATE_ALIASES.key(state) || state
save
set_external_release(qc_state)
end
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#tag_range ⇒ String?
Returns the map_id of the first and last tag in an asset eg 1-96. Caution: Used on barcode labels. Avoid using elsewhere as makes assumptions
about tag behaviour which may change shortly.
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# File 'app/models/receptacle.rb', line 182
def tag_range
map_ids = tags.order(:map_id).pluck(:map_id)
case map_ids.length
when 0; then nil
when 1; then map_ids.first
else "#{map_ids.first}-#{map_ids.last}"
end
end
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# File 'app/models/receptacle.rb', line 165
def
.size +
end
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#update_aliquot_quality(suboptimal_quality) ⇒ Object
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# File 'app/models/receptacle.rb', line 158
def update_aliquot_quality(suboptimal_quality)
aliquots.each { |a| a.update_quality(suboptimal_quality) }
true
end
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#update_from_qc(qc_result) ⇒ Object
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# File 'app/models/receptacle.rb', line 270
def update_from_qc(qc_result)
Tube::AttributeUpdater.update(self, qc_result)
end
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