Class: SampleManifestExcel::Upload::Processor::OneDTube

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

Overview

TODO: had to explicitly specify the namespace for Base here otherwise it picks up Upload::Base Processor to handle 1dtube uploads

Constant Summary

Constants inherited from Base

Base::MANDATORY_FIELDS

Instance Attribute Summary

Attributes inherited from Base

#upload

Instance Method Summary collapse

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_retention_instruction ⇒ Object

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



12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
 
# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/one_d_tube.rb', line 12

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) ⇒ Object

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



36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
 
# File 'app/sample_manifest_excel/sample_manifest_excel/upload/processor/one_d_tube.rb', line 36

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