Class: MiGA::Cli::Action::Cmd

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

def parse_cli
  cli.expect_files = true
  cli.files_label  = 'CMD'
  cli.defaults = {
    raise: false, return: :status, source: :miga_env,
    stdout: nil, stderr: nil, dry: false, show_cmd: false,
    err2out: false
  }
  cli.parse do |opt|
    opt.separator 'To separate command flags from MiGA flags, use --:'
    opt.separator 'miga cmd --verbose -- rbm.rb --version'
    opt.separator ''
    opt.separator 'To run the command as is (no escaping), use single-quotes:'
    opt.separator 'miga cmd \'echo $MIGA\''
    opt.separator ''
    opt.on(
      '-o', '--stdout FILE',
      'Save STDOUT to this file instead of displaying it'
    ) { |v| cli[:stdout] = v }
    opt.on(
      '-e', '--stderr FILE',
      'Save STDERR to this file instead of displaying it'
    ) { |v| cli[:stderr] = v }
    opt.on(
      '--err2out',
      'Combine STDERR and STDOUT into one single channel (STDOUT)'
    ) { |v| cli[:err2out] = v }
    opt.on(
      '--show-cmd',
      'Show exact command being launched before running it'
    ) { |v| cli[:show_cmd] = v }
    opt.on(
      '--dry',
      'Prepare the command but stop short of executing it',
      'Useful in combination with --show-cmd; it always exits with code 1'
    ) { |v| cli[:dry] = v }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/cmd.rb', line 46

def perform
  cli.files
  cli.say 'Running command:'
  cmd = cli.files.size == 1 ? cli.files[0] : cli.files
  cli.say cmd
  status = MiGA::MiGA.run_cmd(cmd, cli.to_h)
  cli.say 'Exit status: %s' % status
  unless status&.success?
    exit(status.nil? ? 1 : status.exitstatus)
  end
end