Class: Inferno::Terminology::Tasks::DownloadUMLS

Inherits:
Object
  • Object
show all
Includes:
TempDir
Defined in:
lib/inferno/terminology/tasks/download_umls.rb

Constant Summary collapse

UMLS_FILE_URLS = 
{
  '2019' => 'https://download.nlm.nih.gov/umls/kss/2019AB/umls-2019AB-full.zip',
  '2020' => 'https://download.nlm.nih.gov/umls/kss/2020AB/umls-2020AB-full.zip',
  '2021' => 'https://download.nlm.nih.gov/umls/kss/2021AA/umls-2021AA-full.zip',
  '2022' => 'https://download.nlm.nih.gov/umls/kss/2022AA/umls-2022AA-full.zip',
  '2023' => 'https://download.nlm.nih.gov/umls/kss/2023AA/umls-2023AA-full.zip',
  '2024' => 'https://download.nlm.nih.gov/umls/kss/2024AA/umls-2024AA-full.zip'
}.freeze
TICKET_GRANTING_TICKET_URL = 
'https://utslogin.nlm.nih.gov/cas/v1/api-key'.freeze

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from TempDir

#pipe_files, #umls_dir, #umls_subset_dir, #umls_zip_path, #versioned_temp_dir

Constructor Details

#initialize(version:, apikey:) ⇒ DownloadUMLS

Returns a new instance of DownloadUMLS.



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# File 'lib/inferno/terminology/tasks/download_umls.rb', line 23

def initialize(version:, apikey:)
  @version = version
  @api_key = apikey
end

Instance Attribute Details

#api_key ⇒ Object (readonly)

Returns the value of attribute api_key.



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# File 'lib/inferno/terminology/tasks/download_umls.rb', line 21

def api_key
  @api_key
end

#version ⇒ Object (readonly)

Returns the value of attribute version.



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# File 'lib/inferno/terminology/tasks/download_umls.rb', line 21

def version
  @version
end

Instance Method Details

#follow_redirect(location, file_location, ticket, cookie = nil) ⇒ Object 



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# File 'lib/inferno/terminology/tasks/download_umls.rb', line 76

def follow_redirect(location, file_location, ticket, cookie = nil)
  return unless location

  size = 0
  percent = 0
  current_percent = 0
  File.open(file_location, 'w') do |f|
    f.binmode
    block = proc do |response|
      Inferno.logger.info response.header['content-type']
      if response.header['content-type'] == 'application/zip'
        total = response.header['content-length'].to_i
        response.read_body do |chunk|
          f.write chunk
          size += chunk.size
          percent = ((size * 100) / total).round unless total.zero?
          if current_percent != percent
            current_percent = percent
            Inferno.logger.info "#{percent}% complete"
          end
        end
      else
        follow_redirect(response.header['location'], file_location, ticket, response.header['set-cookie'])
      end
    end
    RestClient::Request.execute(
      method: :get,
      url: "#{location}?ticket=#{ticket}",
      headers: { cookie: },
      block_response: block
    )
  end
end

#run ⇒ Object 



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# File 'lib/inferno/terminology/tasks/download_umls.rb', line 28

def run
  # Adapted from https://documentation.uts.nlm.nih.gov/automating-downloads.html

  FileUtils.mkdir_p(versioned_temp_dir)

  target_file = UMLS_FILE_URLS[version]

  Inferno.logger.info 'Getting Ticket Granting Ticket'
  ticket_granting_ticket_html = RestClient::Request.execute(
    method: :post,
    url: TICKET_GRANTING_TICKET_URL,
    payload: {
      apikey: api_key
    }
  )
  ticket_granting_ticket =
    Nokogiri::HTML(ticket_granting_ticket_html.body).at_css('form').attributes['action'].value

  Inferno.logger.info 'Getting ticket'
  ticket = RestClient::Request.execute(
    method: :post,
    url: ticket_granting_ticket,
    payload: {
      service: target_file
    }
  ).body

  begin
    Inferno.logger.info 'Downloading'
    RestClient::Request.execute(
      method: :get,
      url: "#{target_file}?ticket=#{ticket}",
      max_redirects: 0
    )
  rescue RestClient::ExceptionWithResponse => e
    ticket = RestClient::Request.execute(
      method: :post,
      url: ticket_granting_ticket,
      payload: {
        service: e.response.headers[:location]
      }
    ).body
    target_location = umls_zip_path
    follow_redirect(e.response.headers[:location], target_location, ticket, e.response.headers[:set_cookie])
  end
  Inferno.logger.info 'Finished Downloading!'
end