Class: MiGA::Cli::Action::AddResult

Inherits:
MiGA::Cli::Action show all
Defined in:
lib/miga/cli/action/add_result.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 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/add_result.rb', line 7

def parse_cli
  cli.defaults = { force: false, stdin_versions: false }
  cli.parse do |opt|
    cli.opt_object(opt, [:project, :dataset_opt, :result])
    opt.on(
      '-f', '--force',
      'Force re-indexing of the result even if it\'s already registered'
    ) { |v| cli[:force] = v }
    opt.on(
      '--stdin-versions',
      'Read Software versions from STDIN'
    ) { |v| cli[:stdin_versions] = v }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/add_result.rb', line 22

def perform
  cli.ensure_par(result: '-r')
  obj = cli.load_project_or_dataset
  cli.say "Registering result: #{cli[:result]}"
  r = obj.add_result(cli[:result], true, force: cli[:force])
  raise 'Cannot add result, incomplete expected files' if r.nil?

  # Add Software version data
  if cli[:stdin_versions]
    versions = {}
    sw = nil
    $stdin.each do |ln|
      ln = ln.chomp.strip
      if ln =~ /^=> (.*)/
        sw = $1
        versions[sw] = ''
      else
        versions[sw] += ln
      end
    end
    r.add_versions(versions)
    r.save
  end
end