Class: Inferno::Terminology::Tasks::ProcessUMLSTranslations

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

Instance Method Summary collapse

Methods included from DownloadUMLSNotice

#download_umls_notice

Instance Method Details

#run ⇒ Object

rubocop:disable Metrics/CyclomaticComplexity



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# File 'lib/inferno/terminology/tasks/process_umls_translations.rb', line 11

def run # rubocop:disable Metrics/CyclomaticComplexity
  Inferno.logger.info 'Looking for `./tmp/terminology/MRCONSO.RRF`...'
  input_file = Find.find(File.join(TEMP_DIR, 'terminology')).find { |f| /MRCONSO.RRF$/ =~f }
  if input_file
    start = Time.now
    output_filename = File.join(TEMP_DIR, 'translations_umls.txt')
    output = File.open(output_filename, 'w:UTF-8')
    line = 0
    excluded_systems = Hash.new(0)
    begin
      entire_file = File.read(input_file)
      Inferno.logger.info "Writing to #{output_filename}..."
      current_umls_concept = nil
      translation = Array.new(10)
      entire_file.split("\n").each do |l|
        row = l.split('|')
        line += 1
        concept = row[0]
        if concept != current_umls_concept && !current_umls_concept.nil?
          output.write("#{translation.join('|')}\n") unless translation[1..-2].compact.length < 2
          translation = Array.new(10)
          current_umls_concept = concept
          translation[0] = current_umls_concept
        elsif current_umls_concept.nil?
          current_umls_concept = concept
          translation[0] = current_umls_concept
        end
        code_system = row[11]
        code = row[13]
        translation[9] = row[14]
        case code_system
        when 'SNOMEDCT_US'
          translation[1] = code if row[4] == 'PF' && ['FN', 'OAF'].include?(row[12])
        when 'LNC'
          translation[2] = code
        when 'ICD10CM', 'ICD10PCS'
          translation[3] = code if row[12] == 'PT'
        when 'ICD9CM'
          translation[4] = code if row[12] == 'PT'
        when 'MTHICD9'
          translation[4] = code
        when 'RXNORM'
          translation[5] = code
        when 'CVX'
          translation[6] = code if ['PT', 'OP'].include?(row[12])
        when 'CPT'
          translation[7] = code if row[12] == 'PT'
        when 'HCPCS'
          translation[8] = code if row[12] == 'PT'
        when 'SRC'
          # 'SRC' rows define the data sources in the file
        else
          excluded_systems[code_system] += 1
        end
      end
    rescue StandardError => e
      Inferno.logger.info "Error at line #{line}"
      Inferno.logger.info e.message
    end
    output.close
    Inferno.logger.info "Processed #{line} lines."
    Inferno.logger.info "Excluded code systems: #{excluded_systems}" unless excluded_systems.empty?
    finish = Time.now
    minutes = ((finish - start) / 60)
    seconds = (minutes - minutes.floor) * 60
    Inferno.logger.info "Completed in #{minutes.floor} minute(s) #{seconds.floor} second(s)."
    Inferno.logger.info 'Done.'
  else
    download_umls_notice
  end
end