Class: MiGA::Cli::Action::NcbiGet

Inherits:
MiGA::Cli::Action show all
Includes:
Downloads
Defined in:
lib/miga/cli/action/ncbi_get.rb

Defined Under Namespace

Modules: Downloads

Constant Summary

Constants included from MiGA

MiGA::CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary

Attributes inherited from MiGA::Cli::Action

#cli

Instance Method Summary collapse

Methods included from Downloads

#cli_filters, #cli_name_modifiers, #cli_save_actions, #cli_task_flags, #discard_blacklisted, #download_entries, #impose_limit, #remote_list, #remote_list_url, #remote_row_name, #remote_row_replicons, #sanitize_cli, #save_entry

Methods inherited from MiGA::Cli::Action

#complete, #empty_action, #initialize, #launch, load, #name

Methods inherited from MiGA

CITATION, CITATION_ARRAY, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, #advance, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, #result_files_exist?, #say

Methods included from MiGA::Common::Path

#root_path, #script_path

Methods included from MiGA::Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from MiGA::Common::Net

#download_file_ftp, #known_hosts, #remote_connection

Constructor Details

This class inherits a constructor from MiGA::Cli::Action

Instance Method Details

#parse_cli ⇒ Object 



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# File 'lib/miga/cli/action/ncbi_get.rb', line 9

def parse_cli
  cli.defaults = {
    query: false, unlink: false,
    reference: false, legacy_name: false,
    complete: false, chromosome: false,
    scaffold: false, contig: false, add_version: true, dry: false,
    get_md: false, only_md: false, save_every: 1
  }
  cli.parse do |opt|
    cli.opt_object(opt, [:project])
    opt.on(
      '-T', '--taxon STRING',
      '(Mandatory) Taxon name (e.g., a species binomial)'
    ) { |v| cli[:taxon] = v }
    opt.on(
      '--max INT', Integer,
      'Maximum number of datasets to download (by default: unlimited)'
    ) { |v| cli[:max_datasets] = 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 }
    cli_task_flags(opt)
    cli_name_modifiers(opt)
    cli_filters(opt)
    cli_save_actions(opt)
    opt.on(
      '--api-key STRING',
      'NCBI API key'
    ) { |v| ENV['NCBI_API_KEY'] = v }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/ncbi_get.rb', line 43

def perform
  sanitize_cli
  p = cli.load_project
  ds = remote_list
  ds = discard_blacklisted(ds)
  ds = impose_limit(ds)
  d, downloaded = download_entries(ds, p)

  # Finalize
  cli.say "Datasets listed: #{d.size}"
  act = cli[:dry] ? 'to download' : 'downloaded'
  cli.say "Datasets #{act}: #{downloaded}"
  unless cli[:remote_list].nil?
    File.open(cli[:remote_list], 'w') do |fh|
      d.each { |i| fh.puts i }
    end
  end
  return unless cli[:unlink]

  unlink = p.dataset_names - d
  unlink.each { |i| p.unlink_dataset(i).remove! }
  cli.say "Datasets unlinked: #{unlink.size}"
end