class MiGA::Cli::Action::TaxSet

# File lib/miga/cli/action/tax_set.rb, line 7
def parse_cli
  cli.parse do |opt|
    cli.opt_object(opt, [:project, :dataset_opt])
    opt.on(
      '-s', '--tax-string STRING',
      'String corresponding to the taxonomy of the dataset',
      'A space-delimited set of \rank:name\ pairs'
    ) { |v| cli[:taxstring] = v }
    opt.on(
      '-t', '--tax-file PATH',
      '(Mandatory unless -D and -s are provided)',
      'Tab-delimited file containing datasets taxonomy',
      'Each row corresponds to a datasets and each column to a rank',
      'The first row must be a header with the rank names,',
      'and the first column must contain dataset names'
    ) { |v| cli[:taxfile] = v }
  end
end

# File lib/miga/cli/action/tax_set.rb, line 26
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