Class: SampleManifestExcel::Upload::Processor::Plate

Inherits:
Base
  • Object
show all
Includes:
RetentionInstructionHelper
Defined in:
app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb

Overview

TODO: had to explicitly specify the namespace for Base here otherwise it picks up Upload::Base

Processor to handle plate manifest uploads.

Constant Summary

Constants inherited from Base

Base::MANDATORY_FIELDS

Instance Attribute Summary

Attributes inherited from Base

#upload

Instance Method Summary collapse

Methods included from RetentionInstructionHelper

#find_retention_instruction_from_key, #find_retention_instruction_key_for_value, #find_retention_instruction_to_display, #retention_instruction_option_for_select

Methods inherited from Base

#aliquots_updated?, #create_samples_if_not_present, #downstream_aliquots_updated?, #initialize, #processed?, #run, #sample_manifest_updated?, #samples_updated?, #samples_valid?, #substitutions, #type, #update_sample_manifest, #update_samples_and_aliquots

Constructor Details

This class inherits a constructor from SampleManifestExcel::Upload::Processor::Base

Instance Method Details

#check_for_barcodes_unique ⇒ Object

For plate manifests the barcodes (sanger plate id column) should be the same for each well from the same plate, and different for each plate. Uniqueness of foreign barcodes in the database is checked in the specialised field sanger_plate_id.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb', line 17

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

#check_for_retention_instruction_by_plate ⇒ Object

A subset of the plate manifests (stock plates not library plates) are required to have a retention instruction column to describe how they should be disposed of. The column should have the same value for all manifest rows for the same plate.



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb', line 70

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

#check_row_retention_value(row, plate_barcode, retention_instructions) ⇒ Object

rubocop:enable Metrics/PerceivedComplexity, Metrics/CyclomaticComplexity, Metrics/AbcSize, Metrics/MethodLength



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb', line 104

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

#duplicate_barcodes ⇒ Object

Return the row of the first encountered barcode mismatch rubocop:todo Metrics/PerceivedComplexity, Metrics/MethodLength, Metrics/AbcSize



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb', line 26

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

#find_plate_id_for_sample_id(sample_id) ⇒ Object

rubocop:enable Metrics/AbcSize, Metrics/MethodLength, Metrics/PerceivedComplexity



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb', line 62

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

#non_matching_retention_instructions_for_plates ⇒ Object

rubocop:disable Metrics/PerceivedComplexity, Metrics/CyclomaticComplexity, Metrics/AbcSize, Metrics/MethodLength



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# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/plate.rb', line 78

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