Class: PhiXesController

Inherits:

ApplicationController

• Object
• ActionController::Base
• ApplicationController
• PhiXesController

Defined in:

app/controllers/phi_xes_controller.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 PhiX.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. PhiX::Stock and PhiX::SpikedBuffer act as factories

Constant Summary

Constants included from FlashTruncation

FlashTruncation::STRING_OVERHEAD

Instance Method Summary

• #show ⇒ Object

Methods inherited from ApplicationController

#block_api_access, #evil_parameter_hack!, #extract_header_info, #set_cache_disabled!

Methods included from AuthenticatedSystem

included

Methods included from FlashTruncation

#max_flash_size, #truncate_flash, #truncate_flash_array

Instance Method Details

#show ⇒ Object

# File 'app/controllers/phi_xes_controller.rb', line 18

has_metadata do
  # NOTE: The following attribute is not required for Microarray Genotyping.
  # I think this might be broken and suggests that there should be separate classes for project: one for
  # next-gen sequencing that includes this attribute in it's metadata, and one for microarray genotyping
  # that doesn't.
  include ProjectManager::Associations
  include BudgetDivision::Associations

  custom_attribute(:project_cost_code, required: true)
  custom_attribute(:funding_comments)
  custom_attribute(:collaborators)
  custom_attribute(:external_funding_source)
  custom_attribute(:sequencing_budget_cost_centre)
  custom_attribute(:project_funding_model, in: PROJECT_FUNDING_MODELS)
  custom_attribute(:gt_committee_tracking_id)

  before_validation do |record|
    record.project_cost_code = nil if record.project_cost_code.blank?
    record.project_funding_model = nil if record.project_funding_model.blank?
  end
end