Class: TubeRack

Inherits:
Labware show all
Includes:
Asset::Ownership::Unowned, Barcode::Barcodeable
Defined in:
app/models/tube_rack.rb

Overview

A rack that holds tubes Tubes are linked via the RackedTubes association

Defined Under Namespace

Classes: Purpose

Constant Summary collapse

LAYOUTS = 
{ 48 => { rows: 6, columns: 8 }, 96 => { rows: 8, columns: 12 } }.freeze
TUBE_RACK_STATES = 
%w[started qc_complete pending passed failed cancelled mixed empty].freeze
STATES_TO_FILTER_OUT = 
%w[cancelled failed].freeze
STATE_EMPTY = 
'empty'
STATE_MIXED = 
'mixed'

Instance Attribute Summary

Attributes inherited from Labware

#storage_location_service

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Asset::Ownership::Unowned

#change_owner_to

Methods included from Barcode::Barcodeable

#any_barcode_matching?, #barcode_format, #barcode_number, #cgap_barcode, #cgap_barcode=, #external_barcode, #external_barcode=, #external_identifier, #fluidigm_barcode, #fluidigm_barcode=, #foreign_barcode=, #generate_barcode, included, #infinium_barcode, #infinium_barcode=, #prefix, #primary_barcode, #printable_target, #sanger_barcode

Methods inherited from Labware

#ancestor_of_purpose, #ancestors_of_purpose, #child, #display_name, #external_identifier, find_by_barcode, find_from_any_barcode, #generate_name, #labware, #labwhere_location, labwhere_locations, #parent, #received_date, #retention_instructions, #role, #scanned_in_date, search_for_labware, #source_plate, #source_plates, #spiked_in_buffer, #storage_location

Methods included from SharedBehaviour::Named

included

Methods included from AssetLink::Associations

included

Methods included from Uuid::Uuidable

included, #unsaved_uuid!, #uuid

Methods inherited from Asset

#ancestor_of_purpose, #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

Class Method Details

.generate_valid_row_values(num_rows) ⇒ Object 



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# File 'app/models/tube_rack.rb', line 59

def self.generate_valid_row_values(num_rows)
  ('A'..).first(num_rows)
end

.invalid_coordinates(rack_size, list_coordinates) ⇒ Object 



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# File 'app/models/tube_rack.rb', line 46

def self.invalid_coordinates(rack_size, list_coordinates)
  num_rows = LAYOUTS.fetch(rack_size)[:rows]
  num_columns = LAYOUTS.fetch(rack_size)[:columns]
  valid_row_values = generate_valid_row_values(num_rows)
  valid_column_values = (1..num_columns)

  list_coordinates.reject do |coordinate|
    row = coordinate[/[A-Za-z]+/].capitalize
    column = coordinate[/[0-9]+/]
    valid_row_values.include?(row) && valid_column_values.cover?(column.to_i)
  end
end

Instance Method Details

#after_comment_addition(comment) ⇒ Object

Handles the addition of a comment to the tube rack and its associated submissions and tubes. Adds the comment to the submissions to avoid duplicate comments and also adds the comment to the tubes.

Parameters:

  • comment (String) —

    The comment to be added.



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# File 'app/models/tube_rack.rb', line 97

def after_comment_addition(comment)
  # We don't let the tubes handle addition to submissions, as if they
  # all belong to the same submission, we'll get duplicate comments
  comments.add_comment_to_submissions(comment)

  # But we still want to add to the tube anyway, as we may have some
  # tubes that don't have submissions. Or even a mixed rack.
  comments.add_comment_to_tubes(comment)
end

#comments ⇒ Object

Comments are proxied as they need to collect comments from various different associations, not just the tubes



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# File 'app/models/tube_rack.rb', line 65

def comments
  @comments ||= CommentsProxy::TubeRack.new(self)
end

#number_of_columns ⇒ Integer Also known as: width

Returns the number of columns in the tube rack based on its size.

Returns:

  • (Integer) —

    The number of columns in the tube rack.



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# File 'app/models/tube_rack.rb', line 88

def number_of_columns
  LAYOUTS.fetch(size)[:columns]
end

#number_of_rows ⇒ Integer Also known as: height

Returns the number of rows in the tube rack based on its size.

Returns:

  • (Integer) —

    The number of rows in the tube rack.



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# File 'app/models/tube_rack.rb', line 80

def number_of_rows
  LAYOUTS.fetch(size)[:rows]
end

#receptacles_with_position ⇒ ActiveRecord::Relation

Used to unify interface with TubeRacks. Returns a list of all receptacles with position information included for aid performance.

Returns:

  • (ActiveRecord::Relation) —

    A relation of tube receptacles with position information.



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# File 'app/models/tube_rack.rb', line 73

def receptacles_with_position
  tube_receptacles.includes(:racked_tube)
end

#state ⇒ Object

The state of a tube rack is based on the transfer requests in the tubes. If they are all in the same state then it takes that state.



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# File 'app/models/tube_rack.rb', line 109

def state
  # fetch states from ther transfer requests in all racked tubes in the rack.
  unique_states = transfer_requests_as_target.map(&:state).uniq

  return STATE_EMPTY if unique_states.empty?
  return unique_states.first if unique_states.size == 1

  STATES_TO_FILTER_OUT.each do |filter|
    unique_states.delete(filter)
    return unique_states.first if unique_states.one?
  end

  # we still have tubes with a mixed state
  STATE_MIXED
end