class MiGA::Cli::Action::Get

def create_dataset(sub_cli, p, rd)
  sub_cli.say 'Creating dataset'
  if Dataset.exist?(p, sub_cli[:dataset])
    raise "Dataset already exists: #{sub_cli[:dataset]}"
  end
  dummy_d = Dataset.new(p, sub_cli[:dataset])
  md = sub_cli.add_metadata(dummy_d).metadata.data
  md[:metadata_only] = true if cli[:only_md]
  dummy_d.remove!
  rd.save_to(p, sub_cli[:dataset], !sub_cli[:query], md)
  p.add_dataset(sub_cli[:dataset])
end

def create_remote_dataset(sub_cli, p)
  sub_cli.ensure_par(dataset: '-D', ids: '-I')
  unless sub_cli[:api_key].nil?
    if sub_cli[:universe] == :web && sub_cli[:db] == :assembly_gz
      ENV['NCBI_API_KEY'] = sub_cli[:api_key]
    end
    var_space = sub_cli[:universe].to_s.upcase
    ENV["#{var_space}_API_KEY"] = sub_cli[:api_key]
  end
  sub_cli.say "Dataset: #{sub_cli[:dataset]}"
  if sub_cli[:ignore_dup] && !sub_cli[:get_md]
    return if Dataset.exist?(p, sub_cli[:dataset])
  end
  sub_cli.say 'Locating remote dataset'
  RemoteDataset.new(sub_cli[:ids], sub_cli[:db], sub_cli[:universe])
end

def get_sub_cli
  return [cli] if cli[:file].nil?
  glob = []
  File.open(cli[:file], 'r') do |fh|
    h = nil
    fh.each do |ln|
      r = ln.chomp.split(/\t/)
      if h.nil?
        h = r
      else
        argv_i = [self.name]
        h.each_with_index do |field, k|
          case field.downcase
          when *%w[query ignore-dup get-metadata only-metadata]
            argv_i << "--#{field.downcase}" if r[k].downcase == 'true'
          when *%w[project file verbose help debug]
            raise "Unsupported header: #{field}"
          else
            argv_i += ["--#{field.downcase}", r[k]]
          end
        end
        sub_cli = MiGA::Cli.new(argv_i)
        sub_cli.defaults = cli.data
        sub_cli.action.parse_cli
        glob << sub_cli
      end
    end
  end
  glob
end

def parse_cli
  cli.defaults = {
    query: false, universe: :ncbi, db: :nuccore, get_md: false, only_md: false
  }
  cli.parse do |opt|
    cli.opt_object(opt, [:project, :dataset, :dataset_type])
    opt.on(
      '-I', '--ids ID1,ID2,...', Array,
      '(Mandatory unless -F) IDs in the remote database separated by commas'
    ) { |v| cli[:ids] = v }
    opt.on(
      '-U', '--universe STRING',
      "Universe of the remote database. By default: #{cli[:universe]}",
      "Supported: #{MiGA::RemoteDataset.UNIVERSE.keys.join(', ')}"
    ) { |v| cli[:universe] = v.to_sym }
    opt.on(
      '--db STRING',
      "Name of the remote database. By default: #{cli[:db]}"
    ) { |v| cli[:db] = v.to_sym }
    opt.on(
      '-F', '--file PATH',
      'Tab-delimited file (with header) listing the datasets to download',
      'The long form of most options are supported as header (without --)',
      'including: dataset, ids, universe, db, metadata',
      'For flags without value (like query) use true/false',
      'Unsupported values are: project, file, verbose, help, and debug'
    ) { |v| cli[:file] = v }
    opt.on(
      '-q', '--query',
      'Register the dataset as a query, not a reference dataset'
    ) { |v| cli[:query] = v }
    opt.on(
      '--ignore-dup',
      'Ignore datasets that already exist'
    ) { |v| cli[:ignore_dup] = v }
    opt.on(
      '-d', '--description STRING',
      'Description of the dataset'
    ) { |v| cli[:description] = v }
    opt.on(
      '-c', '--comments STRING',
      'Comments on the dataset'
    ) { |v| cli[:comments] = v }
    opt.on(
      '-m', '--metadata STRING',
      'Metadata as key-value pairs separated by = and delimited by comma',
      'Values are saved as strings except for booleans (true / false) or nil'
    ) { |v| cli[:metadata] = v }
    opt.on(
      '--get-metadata',
      'Only download and update metadata for existing datasets'
    ) { |v| cli[:get_md] = v }
    opt.on(
      '--only-metadata',
      'Create datasets without input data but retrieve all metadata'
    ) { |v| cli[:only_md] = v }
    opt.on(
      '--api-key STRING',
      'API key for the given universe'
    ) { |v| cli[:api_key] = v }
  end
end

def perform
  glob = get_sub_cli
  p = cli.load_project
  glob.each do |sub_cli|
    rd = create_remote_dataset(sub_cli, p)
    next if rd.nil?
    if sub_cli[:get_md]
      update_metadata(sub_cli, p, rd)
    else
      create_dataset(sub_cli, p, rd)
    end
  end
end

def update_metadata(sub_cli, p, rd)
  sub_cli.say 'Updating dataset'
  d = p.dataset(sub_cli[:dataset])
  return if d.nil?
  md = sub_cli.add_metadata(d).metadata.data
  rd.update_metadata(d, md)
end