Module: Lab::Loaders::SpecimensLoader

Extended by:
LoaderMixin
Defined in:
lib/tasks/loaders/specimens_loader.rb

Overview

Load specimens and their tests into the database

Constant Summary

Constants included from LoaderMixin

LoaderMixin::CONCEPT_CLASS_TEST, LoaderMixin::CONCEPT_DATATYPE_CODED

Class Method Summary collapse

Methods included from LoaderMixin

add_concept_to_set, data_path, find_or_create_concept, included

Class Method Details

.create_specimen_type(name, test_type) ⇒ Object 



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# File 'lib/tasks/loaders/specimens_loader.rb', line 52

def create_specimen_type(name, test_type)
  concept_id = find_or_create_concept(name).concept_id

  [
    add_concept_to_set(set_concept_id: specimen_type_concept_id, concept_id: concept_id),
    add_concept_to_set(set_concept_id: test_type.concept_id, concept_id: concept_id)
  ]
rescue StandardError => e
  raise "Failed to create specimen type `#{name}`: #{e}"
end

.create_test_type(name) ⇒ Object 



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# File 'lib/tasks/loaders/specimens_loader.rb', line 44

def create_test_type(name)
  concept_id = find_or_create_concept(name, is_set: true).concept_id

  add_concept_to_set(set_concept_id: test_type_concept_id, concept_id: concept_id)
rescue StandardError => e
  raise "Failed to create test type `#{name}`: #{e}"
end

.load ⇒ Object 



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# File 'lib/tasks/loaders/specimens_loader.rb', line 14

def load
  puts "------- Loading tests and specimens ---------"
  CSV.open(data_path('tests.csv'), headers: :first_row) do |csv|
    csv.each_with_object({}) do |row, test_types|
      specimen_name = row['specimen_name']
      test_name = row['test_name']

      ActiveRecord::Base.transaction do
        test_type = test_types[test_name] || create_test_type(test_name)
        create_specimen_type(specimen_name, test_type)

        test_types[test_name] ||= test_type
      end

      puts "Created test #{test_name} <--< #{specimen_name}"
    rescue StandardError => e
      puts "Error: #{test_name}: #{e}"
    end
  end
end

.specimen_type_concept_id ⇒ Object 



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# File 'lib/tasks/loaders/specimens_loader.rb', line 39

def specimen_type_concept_id
  find_or_create_concept(Lab::Metadata::SPECIMEN_TYPE_CONCEPT_NAME).concept_id
end

.test_type_concept_id ⇒ Object 



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# File 'lib/tasks/loaders/specimens_loader.rb', line 35

def test_type_concept_id
  find_or_create_concept(Lab::Metadata::TEST_TYPE_CONCEPT_NAME).concept_id
end