Class: MiGA::Cli::Action::Stats

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

def parse_cli
  cli.defaults = { try_load: false }
  cli.parse do |opt|
    cli.opt_object(opt, [:project, :dataset_opt, :result])
    opt.on(
      '--key STRING',
      'Return only the value of the requested key'
    ) { |v| cli[:key] = v }
    opt.on(
      '--compute-and-save',
      'Compute and save the statistics'
    ) { |v| cli[:compute] = v }
    opt.on(
      '--try-load',
      'Check if stat exists instead of computing on --compute-and-save'
    ) { |v| cli[:try_load] = v }
    opt.on(
      '--ignore-empty',
      'If the result does not exist, exit without throwing exceptions'
    ) { |v| cli[:ignore_result_empty] = v }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/stats.rb', line 30

def perform
  r = cli.load_result or return

  cli[:compute] = false if cli[:try_load] && !r[:stats]&.empty?

  if cli[:compute]
    cli.say 'Computing statistics'
    r.compute_stats
  end

  if cli[:key].nil?
    r[:stats].each do |k, v|
      k_n = k.to_s.unmiga_name.sub(/^./, &:upcase)
      cli.puts "#{k_n}: #{v.is_a?(Array) ? v.join(' ') : v}"
    end
  else
    v = r[:stats][cli[:key].downcase.miga_name.to_sym]
    puts v.is_a?(Array) ? v.first : v
  end
end