class MiGA::Cli::Action::TaxSet

def perform
  p = cli.load_project
  if !cli[:taxfile].nil?
    cli.say 'Reading tax-file and registering taxonomy'
    tfh = File.open(cli[:taxfile], 'r')
    header = nil
    tfh.each_line do |ln|
      next if ln =~ /^\s*?$/
      r = ln.chomp.split(/\t/, -1)
      dn = r.shift
      if header.nil?
        header = r
        next
      end
      d = p.dataset(dn)
      if d.nil?
        warn "Impossible to find dataset at line #{$.}: #{dn}. Ignoring..."
        next
      end
      d.metadata[:tax] = Taxonomy.new(r, header)
      d.save
      cli.say "o #{d.name} registered"
    end
    tfh.close
  else
    cli.ensure_par({ dataset: '-D', taxstring: '-s' },
                   '%<flag>s is mandatory unless -t is provided')
    cli.say 'Registering taxonomy'
    d = cli.load_dataset
    d.metadata[:tax] = Taxonomy.new(cli[:taxstring])
    d.save
  end
end