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

Inherits:
MiGA::Cli::Action show all
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

Instance Method Summary collapse

Methods inherited from MiGA::Cli::Action

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

Methods inherited from MiGA

CITATION, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, initialized?, #result_files_exist?

Methods included from MiGA::Common::Path

#root_path, #script_path

Methods included from MiGA::Common::Format

#clean_fasta_file, #seqs_length, #tabulate

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 9

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]}"
      ){ |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

#perform ⇒ Object 



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# File 'lib/miga/cli/action/get.rb', line 69

def perform
  glob = [cli]
  unless 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
  end

  p = cli.load_project
  glob.each do |sub_cli|
    sub_cli.ensure_par(dataset: '-D', ids: '-I')
    unless sub_cli[:api_key].nil?
      ENV["#{sub_cli[:universe].to_s.upcase}_API_KEY"] = sub_cli[:api_key]
    end

    sub_cli.say "Dataset: #{sub_cli[:dataset]}"
    if sub_cli[:ignore_dup] && !sub_cli[:get_md]
      next if Dataset.exist?(p, sub_cli[:dataset])
    end

    sub_cli.say 'Locating remote dataset'
    rd = RemoteDataset.new(sub_cli[:ids], sub_cli[:db], sub_cli[:universe])

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