Class: MiGA::Cli::Action::Get

Inherits:
MiGA::Cli::Action show all
Includes:
Download::Base
Defined in:
lib/miga/cli/action/get.rb

Constant Summary

Constants included from MiGA

MiGA::CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary

Attributes inherited from MiGA::Cli::Action

#cli

Attributes included from MiGA::Common::Net

#remote_connection_uri

Instance Method Summary collapse

Methods included from Download::Base

#cli_base_flags, #cli_filters, #cli_save_actions, #discard_excluded, #download_entries, #exclude_newer, #finalize_tasks, #generic_perform, #impose_limit, #load_ncbi_taxonomy_dump, #load_tasks, #save_entry, #unlink_entries

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, rc_path, #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, #http_request, #known_hosts, #main_server, #net_method, #normalize_encoding, #remote_connection

Methods included from MiGA::Common::SystemCall

#run_cmd, #run_cmd_opts

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/get.rb', line 11

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.map(&:strip) }
    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(
      '--bypass-metadata',
      'Do not gather optional metadata such as the dataset taxonomy'
    ) { |v| cli[:bypass_md] = v }
    opt.on(
      '--api-key STRING',
      'API key for the given universe'
    ) { |v| cli[:api_key] = v }
    opt.on(
      '--ncbi-taxonomy-dump [path]',
      'Path to an NCBI Taxonomy dump directory to query instead of API calls',
      'If the path is not passed, the dump is automatically downloaded'
    ) { |v| cli[:ncbi_taxonomy_dump] = v || true }
    opt.on(
      '--ignore-file', '::HIDE::' # Only for internal use
    ) { |v| cli[:ignore_file] = v }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/get.rb', line 86

def perform
  glob = get_sub_cli
  p = cli.load_project
  load_ncbi_taxonomy_dump
  glob.each do |sub_cli|
    rd = create_remote_dataset(sub_cli, p)
    next if rd.nil?

    rd.metadata[:bypass_metadata] = true if sub_cli[:bypass_md]
    if sub_cli[:get_md]
      update_metadata(sub_cli, p, rd)
    else
      create_dataset(sub_cli, p, rd)
    end
  end
end