Module: SampleManifest::CoreBehaviour::StockAssets

Included in:
PlateBehaviour::Core, SampleTubeBehaviour::Core, TubeRackBehaviour::Core
Defined in:
app/models/sample_manifest/core_behaviour.rb

Overview

The samples get registered in the stock resource table at the end of manifest upload and processing (It used to happen here)

Instance Method Summary collapse

Instance Method Details

#generate_sample_and_aliquot(sanger_sample_id, receptacle) ⇒ Object

Used in manifest upload code to insert the sample and aliquot into the database.  The receptacle and sanger_sample_id already exist as they are inserted upfront when the manifest is generated. tag_depth is set on the aliquot to avoid tag clash if a) pools are present, and b) if the samples are not tagged. The assumption is made that samples passed to the below method are never tagged, because we're in the 'StockAssets' module rather than the 'LibraryAssets' module.



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# File 'app/models/sample_manifest/core_behaviour.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

#stocks? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'app/models/sample_manifest/core_behaviour.rb', line 53

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

#tag_depth_for_sample(pools, receptacle, sanger_sample_id) ⇒ Object

Assigns a tag_depth to a sample in a pool.  Tag_depth just needs to be a unique integer for each sample in the pool, So we just use the index in the list of sample manifest assets in this receptacle.



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# File 'app/models/sample_manifest/core_behaviour.rb', line 60

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