module MiGA::Cli::Action::Download::Seqcode

# File lib/miga/cli/action/download/seqcode.rb, line 13
def cli_name_modifiers(opt)
  opt.on(
    '--no-version-name',
    'Do not add sequence version to the dataset name'
  ) { |v| cli[:add_version] = v }
end

# File lib/miga/cli/action/download/seqcode.rb, line 10
def cli_task_flags(_opt)
end

# File lib/miga/cli/action/download/seqcode.rb, line 24
def remote_list
  cli.say 'Downloading genome list'
  current_page = 1
  total_pages  = 1
  ds = {}

  while current_page <= total_pages
    json = MiGA::RemoteDataset.download(
      :seqcode, :'type-genomes', nil, :json, nil, page: current_page
    )
    doc = MiGA::Json.parse(json, contents: true)
    current_page = doc[:current_page] + 1
    total_pages  = doc[:total_pages]

    doc[:values].each do |name|
      next unless name[:type_material]
      acc = name[:type_material].values.first
      db  = name[:type_material].keys.first
      next unless %[assembly nuccore].include?(db) # No INSDC genome, ignore

      classif = name[:classification] || {}
      tax = MiGA::Taxonomy.new(Hash[classif.map { |i| [i[:rank], i[:name]] }])
      tax << { 'ns' => 'seqcode', name[:rank] => name[:name] }
      d = {
        ids: [acc], db: db, universe: :seqcode,
        md: {
          type: :genome, tax: tax, is_type: true,
          type_rel: 'SeqCode type genome',
          seqcode_url: "https://seqco.de/i:#{name[:id]}"
        }
      }
      d[:md][:get_ncbi_taxonomy] = true if cli[:get_ncbi_taxonomy]
      ds[remote_row_name(tax, db, acc)] = d
    end
  end
  ds
end

# File lib/miga/cli/action/download/seqcode.rb, line 62
def remote_row_name(tax, db, asm)
  acc = asm.to_s
  acc.gsub!(/\.\d+\Z/, '') unless cli[:add_version]
  db_short = { assembly: 'asm', nuccore: 'gb' }[db]
  "#{tax.lowest[1]}_#{db_short}_#{acc}".miga_name
end

# File lib/miga/cli/action/download/seqcode.rb, line 20
def sanitize_cli
  cli[:save_every] = 1 if cli[:dry]
end