Class: PhiX::SpikedBuffer

Inherits:
Object
  • Object
show all
Includes:
ActiveModel::Model
Defined in:
app/models/phi_x/spiked_buffer.rb

Overview

PhiX is a short DNA fragment of known sequence which gets added into lanes of sequencing to provide a control. PhiX arrives on site in bulk where it is tagged with a fixed i7 tag, or fixed i5 and i7 tags. - When this occurs one or more library tubes are created in Sequencescape each containing an aliquot of the PhiX Sample (See #sample) with the appropriate tags applied. - At a later date, the LibraryTube Barcode is scanned in to Sequencescape and is used to create one or more tubes of SpikedBuffer. - Finally these tubes get used in the AddSpikedInControlTask during the SequencingPipeline

This controller handles the rendering of the two forms for creating the LibraryTube and the SpikedBuffer. Actual creation is handled by the respective controllers. Stock and SpikedBuffer act as factories

PhiX::SpikedBuffer acts as a factory to generate the required spiked buffer

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#concentration ⇒ Float

Returns The concentration of the created library in nM.

Returns:

  • (Float) —

    The concentration of the created library in nM



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# File 'app/models/phi_x/spiked_buffer.rb', line 19

def concentration
  @concentration
end

#name ⇒ String

Returns the base name for the created library tubes Will be appended with #n to distinguish multiple tubes. eg. (‘Tube name #1’, ‘Tube name #2’).

Returns:

  • (String) —

    the base name for the created library tubes Will be appended with #n to distinguish multiple tubes. eg. (‘Tube name #1’, ‘Tube name #2’)



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# File 'app/models/phi_x/spiked_buffer.rb', line 12

def name
  @name
end

#number ⇒ Integer

Returns The number of library tubes to create.

Returns:



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# File 'app/models/phi_x/spiked_buffer.rb', line 25

def number
  @number
end

#parent ⇒ Tube

Returns the provided parent, or the matching tube found via the parent_barcode

Returns:

  • (Tube) —

    The parent tube



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# File 'app/models/phi_x/spiked_buffer.rb', line 64

def parent
  @parent ||= Tube.includes(aliquots: %i[sample tag tag2]).find_by_barcode(parent_barcode)
end

#parent_barcode ⇒ String

has been created

Returns:

  • (String) —

    The barcode of the LibraryTube from which the SpikedBuffer



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# File 'app/models/phi_x/spiked_buffer.rb', line 16

def parent_barcode
  @parent_barcode
end

#study_id ⇒ Integer

Returns The id of the Study to associate with the Aliquot.

Returns:

  • (Integer) —

    The id of the Study to associate with the Aliquot



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# File 'app/models/phi_x/spiked_buffer.rb', line 31

def study_id
  @study_id
end

#volume ⇒ Float

Returns The volume of the created library in ul.

Returns:

  • (Float) —

    The volume of the created library in ul



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# File 'app/models/phi_x/spiked_buffer.rb', line 22

def volume
  @volume
end

Instance Method Details

#created_spiked_buffers ⇒ Array

Returns the spiked_buffers that were create as part of #save Will be an empty array if called before the #save method

Returns:

  • (Array) —

    Array of the spiked_buffers created by the factory.



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# File 'app/models/phi_x/spiked_buffer.rb', line 56

def created_spiked_buffers
  @created_spiked_buffers || []
end

#parent_contains_phi_x ⇒ Object

Validates the contents of the parent The parent MUST contain one aliquot, and it MUST be a PhiX sample This MAY be a stock, or a previously created spiked buffer



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# File 'app/models/phi_x/spiked_buffer.rb', line 71

def parent_contains_phi_x
  return true if parent.aliquots.one? && parent.aliquots.all? { |aliquot| aliquot.sample == PhiX.sample }

  errors.add(:parent_barcode, 'does not contain PhiX')
end

#save ⇒ Boolean

Generates spiked buffers if the factory is valid, otherwise returns false and does nothing

Returns:

  • (Boolean) —

    true if the operation completed successfully, false otherwise



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# File 'app/models/phi_x/spiked_buffer.rb', line 44

def save
  return false unless valid?

  @created_spiked_buffers = generate_spiked_buffers
  true
end

#tags ⇒ Object 



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# File 'app/models/phi_x/spiked_buffer.rb', line 77

def tags
  i7_oligo, i5_oligo = parent.aliquots.first.tags_combination
  PhiX.tag_option_for(i7_oligo:, i5_oligo:)
end