Module: Submission::ScrnaCoreCdnaPrepPoolingPlanGenerator

Defined in:
app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb

Overview

This module provides a basic pooling plan generator for scRNA core cDNA prep submissions. It generates a CSV string which outlines the pooling strategy for the submitted samples based on the number of pools and cells per chip well specified in the submission and grouped by study and project. The logic for determining the pool layout is aimed to be a mirror of the pooling logic used in Limber, specifically in the DonorPoolingCalculator's allocate_wells_to_pools method.

This module also assumes the submission has already been validated with the scrna_core_cdna_prep validators to ensure donor clashes and pooling parameters are already checked.

Class Method Summary collapse

Class Method Details

.calculate_pools_layout(number_of_samples, number_of_pools) ⇒ Object

This method calculates the layout of pools based on the total number of samples and the number of pools requested. It divides the samples as evenly as possible across the pools, and evenly distributes any remainder samples



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# File 'app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb', line 35

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

.generate_pooling_plan(submission) ⇒ Object

This logic attemps to mirror Limber's pooling logic See Limber LabwareCreators::DonorPoolingCalculator (allocate_wells_to_pools)



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# File 'app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb', line 14

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

.grouped_requests(submission) ⇒ Object

Groups the requests associated with a submission by study and project.



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# File 'app/models/submission/scrna_core_cdna_prep_pooling_plan_generator.rb', line 45

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