Class: Insdc::ImportCountries

Inherits:
Object
  • Object
show all
Defined in:
lib/insdc/import_countries.rb

Overview

Handles the download and import of permitted country fields from the ENA

Constant Summary collapse

FILE_ROOT = 
Rails.root.join('data/ena_sample_checklists')
FIELD_NAME = 
'geographic location (country and/or sea)'
XPATH = 
"//FIELD//NAME[text() = '#{FIELD_NAME}']/following-sibling::FIELD_TYPE//TEXT_VALUE//VALUE".freeze

Instance Method Summary collapse

Constructor Details

#initialize(ena_root:, sample_checklist:, priorities: {}) ⇒ ImportCountries

Returns a new instance of ImportCountries.



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# File 'lib/insdc/import_countries.rb', line 11

def initialize(ena_root:, sample_checklist:, priorities: {})
  @ena_root = ena_root
  @sample_checklist = sample_checklist
  @priorities = priorities
end

Instance Method Details

#download(force: false) ⇒ Object 



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# File 'lib/insdc/import_countries.rb', line 17

def download(force: false)
  return unless force || file_missing?

  payload = RestClient.get(url).body
  File.write(file_name, payload)
end

#import ⇒ Object 



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# File 'lib/insdc/import_countries.rb', line 24

def import
  no_file_error if file_missing?

  pending_countries = countries_to_import

  # Mark countries as invalid if they aren't on the list
  Insdc::Country.find_each { |country| country.invalid! unless pending_countries.delete(country.name) }

  generate_countries(pending_countries)
end