Class: IlluminaHtp::StockTubePurpose

Inherits:
Tube::Purpose
  • Object
show all
Defined in:
app/models/illumina_htp/stock_tube_purpose.rb

Overview

Represents a prepared library or multiplexed library which is still undergoing normalization, or is at a higher concentration than is required for SequencingPipeline. A stock may be stored to return to later is more material is required. (Although in practice the Lims doesn't always make) this as easy as it should. Used by external applications.

Direct Known Subclasses

InitialStockTubePurpose

Instance Method Summary collapse

Instance Method Details

#create_with_request_options(_tube) ⇒ Object 



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# File 'app/models/illumina_htp/stock_tube_purpose.rb', line 11

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

#stock_plate(tube) ⇒ Plate?

Deprecated.

Do not use this for new behaviour.

Attempts to find the 'stock_plate' for a given tube. However this is a fairly nebulous concept. Often it means the plate that first entered a pipeline, but in other cases it can be the XP plate part way through the process. Further complication comes from tubes which pool across multiple plates, where identifying a single stock plate is meaningless. In other scenarios, you split plates out again and the asset link graph is insufficient.

JG: 2021-02-11: Previously this code attempted to walk the request graph, but this is slow, and failed with a no method error if it reached the end of the graph without finding a stock plate. This change does change the behaviour of this method for some tubes, most notably those in the PF and GBS pipelines. However an audit determined that we're not really using that code in those contexts. I've decided to unify the behaviour with that in plate, and deprecate it. See https://github.com/sanger/sequencescape/issues/3040 for more information

Parameters:

  • tube (Tube) —

    The tube for which to find the stock_plate

Returns:

  • (Plate, nil) —

    The stock plate if found



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# File 'app/models/illumina_htp/stock_tube_purpose.rb', line 37

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

#stock_wells(tube) ⇒ Object 



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# File 'app/models/illumina_htp/stock_tube_purpose.rb', line 43

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