Class: PhiX::Stock

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

Overview

== PhiX PhiX is a well characterized bacteriophage with a small, known, genome. It is used to provide short DNA sequences which can get added to sequencing lanes for control and calibration purposes.

== Process PhiX samples arrive on site and have tags applied as required. These may be single indexed (i7 only) or dual indexed (i5 & i7) as required. The single and dual indexed tag sets are fixed and are selected from the ‘Control Tag Group 888’ TagGroup.

Library information is filled in on the PhiXesController#show page and one or more library tubes are generated via PhiX::StocksController#create and the Stock factory. These tubes are considered stocks, and get transferred to the sequencing teams.

Subsequently the sequencing team will split the contents of each LibraryTube into a number of SpikedBuffer tubes, adjusting the volume and concentration as required. This is achieved via a separate form on the PhiXesController#show page, followed by PhiX::SpikedBuffersController#create and the SpikedBuffer factory.

Finally, during the processing of a SequencingPipeline the SpikedBuffer barcode is scanned in during the AddSpikedInControlTask. This adds the SpikedBuffer in as a parent of each Lane in the Batch, which in turn ensures the control can be found by batch.xml generation and Api::Messages::FlowcellIO.

== Configuration Configuration and values are stored in config/phi_x.yml tag_group_name: The name of the tag group to use tag_map_id: The default map_id for tags tag_options: Hash of available tag options, indexed by option name. Values are hashes of i5 and i7 oligos. null indicates no tag. default_tag_option: The option which will be initially selected

PhiX::Stock acts as a factory to generate the required library tubes

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/stock.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/stock.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/stock.rb', line 22

def number
  @number
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/stock.rb', line 25

def study_id
  @study_id
end

#tags ⇒ String

Returns The name for the set of tags to apply. eg. ‘Single’, ‘Dual’ Valid options are taken from PhiX.tag_option_names.

Returns:

  • (String) —

    The name for the set of tags to apply. eg. ‘Single’, ‘Dual’ Valid options are taken from PhiX.tag_option_names



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

def tags
  @tags
end

Instance Method Details

#created_stocks ⇒ Array

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

Returns:

  • (Array) —

    Array of the stocks created by the factory.



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# File 'app/models/phi_x/stock.rb', line 49

def created_stocks
  @created_stocks || []
end

#save ⇒ Boolean

Generates stocks 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/stock.rb', line 37

def save
  return false unless valid?

  @created_stocks = generate_stocks
  true
end