Class: LabwareCreators::StampedPlateAddingRandomisedControls

Inherits:
StampedPlate
  • Object
show all
Defined in:
app/models/labware_creators/stamped_plate_adding_randomised_controls.rb

Overview

Stamps the majority of samples from the parent plate straight into the child plate (A1 to A1, B1 to B1 etc.). Also creates and adds a number of randomised control samples according to configuration from the plate purpose. NB. This was specifically made for adding 2 controls in Bioscan Lysate plates, with specific sample metdata, and is fairly specific for that purpose.

Constant Summary collapse

PARENT_PLATE_INCLUDES =

rubocop:todo Metrics/ClassLength

'wells.requests_as_source,wells.requests_as_source.request_type,' \
'wells.aliquots,wells.aliquots.sample,wells.aliquots.sample.sample_metadata'

Instance Method Summary collapse

Constructor Details

This class inherits a constructor from LabwareCreators::Base

Instance Method Details

#control_project_name ⇒ Object

fetch the project name to use for the control sample from the purpose configuration



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# File 'app/models/labware_creators/stamped_plate_adding_randomised_controls.rb', line 32

def control_project_name
  @control_project_name ||= purpose_config.fetch(:control_project_name)
end

#control_study_name ⇒ Object

fetch the study name to use for the control sample from the purpose configuration



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# File 'app/models/labware_creators/stamped_plate_adding_randomised_controls.rb', line 37

def control_study_name
  @control_study_name ||= purpose_config.fetch(:control_study_name)
end

#control_well_locations ⇒ Object 



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# File 'app/models/labware_creators/stamped_plate_adding_randomised_controls.rb', line 58

def control_well_locations
  @control_well_locations ||= generate_control_well_locations
end

#generate_control_well_locations ⇒ Object

generate randomised well locations for each control

Raises:

  • (StandardError) 


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# File 'app/models/labware_creators/stamped_plate_adding_randomised_controls.rb', line 42

def generate_control_well_locations
  max_retries = 5
  retries_count = 0

  until retries_count >= max_retries
    # use purpose config settings to create control locations
    control_locations = generate_control_locations_from_purpose_config

    # check control locations selected pass rules, otherwise we retry with new locations
    return control_locations if validate_control_rules(control_locations)
    retries_count += 1
  end

  raise StandardError, "Control well location randomisation failed to pass rules after #{max_retries} attempts"
end

#labware_wells ⇒ Object 



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# File 'app/models/labware_creators/stamped_plate_adding_randomised_controls.rb', line 62

def labware_wells
  parent.wells.filter_map { |well| well unless control_well_locations.include?(well.position['name']) }
end

#list_of_controls ⇒ Object

fetch list of controls to add from the child purpose configuration



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# File 'app/models/labware_creators/stamped_plate_adding_randomised_controls.rb', line 22

def list_of_controls
  purpose_config.fetch(:controls)
end

#list_of_rules ⇒ Object

fetch list of rules from the child purpose configuration



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# File 'app/models/labware_creators/stamped_plate_adding_randomised_controls.rb', line 27

def list_of_rules
  purpose_config.fetch(:control_location_rules)
end

#parent ⇒ Object 



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# File 'app/models/labware_creators/stamped_plate_adding_randomised_controls.rb', line 17

def parent
  @parent ||= Sequencescape::Api::V2.plate_with_custom_includes(PARENT_PLATE_INCLUDES, uuid: parent_uuid)
end

#validate_control_rules(control_locations) ⇒ Object

check the selected well locations meet rules specified in purpose configuration



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# File 'app/models/labware_creators/stamped_plate_adding_randomised_controls.rb', line 67

def validate_control_rules(control_locations)
  # first check for duplicates, in case the sampling chose the same well more than once
  return false if control_locations.uniq.length != control_locations.length

  # check the chosen locations against the purpose config rules (will add more options as required)
  check_control_rules_from_config(control_locations)
end