Class: MiGA::Cli::Action::Ls

Inherits:
MiGA::Cli::Action show all
Defined in:
lib/miga/cli/action/ls.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/ls.rb', line 6

def parse_cli
  cli.defaults = { info: false, processing: false, silent: false }
  cli.parse do |opt|
    cli.opt_object(opt, [:project, :dataset_opt])
    cli.opt_filter_datasets(opt)
    opt.on(
      '-i', '--info',
      'Print additional information on each dataset'
    ) { |v| cli[:info] = v }
    opt.on(
      '-p', '--processing',
      'Print information on processing advance'
    ) { |v| cli[:processing] = v }
    opt.on(
      '-t', '--task-status',
      'Print the status of each processing step'
    ) { |v| cli[:taskstatus] = v }
    opt.on(
      '-m', '--metadata STRING',
      'Print name and metadata field only',
      'If set, ignores --info and forces --tab (without header)'
    ) { |v| cli[:datum] = v }
    opt.on(
      '-f', '--fields STR1,STR2,STR3', Array,
      'Comma-delimited metadata fields to print'
    ) { |v| cli[:fields] = v }
    opt.on(
      '--tab',
      'Return a tab-delimited table'
    ) { |v| cli[:tabular] = v }
    opt.on(
      '-o', '--output PATH',
      'Create output file instead of returning to STDOUT'
    ) { |v| cli[:output] = v }
    opt.on(
      '-s', '--silent',
      'No output and exit with non-zero status if the dataset list is empty'
    ) { |v| cli[:silent] = v }
    opt.on(
      '--exec CMD',
      'Command to execute per dataset, with the following token variables:',
      '~ {{dataset}}: Name of the dataset',
      '~ {{project}}: Path to the project'
    ) { |v| cli[:exec] = v }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/ls.rb', line 53

def perform
  ds = cli.load_and_filter_datasets(cli[:silent])
  p  = cli.load_project
  exit(ds.empty? ? 1 : 0) if cli[:silent]

  head = nil
  fun  = nil
  if cli[:datum]
    cli[:tabular] = true
    head = [nil, nil]
    fun  = proc { |d| [d.name, d.metadata[cli[:datum]]] }
  elsif cli[:fields]
    head = [:name] + cli[:fields]
    fun  = proc { |d| [d.name] + cli[:fields].map { |f| d.metadata[f] } }
  elsif cli[:info]
    head = Dataset.INFO_FIELDS
    fun  = proc(&:info)
  elsif cli[:processing]
    head = [:name] + MiGA::Dataset.PREPROCESSING_TASKS
    fun  = proc do |d|
      [d.name] + d.profile_advance.map { |i| %w[- done queued][i] }
    end
  elsif cli[:taskstatus]
    head = [:name] + MiGA::Dataset.PREPROCESSING_TASKS
    fun  = proc { |d| [d.name] + d.results_status.values }
  else
    cli[:tabular] = true
    head = [nil]
    fun  = proc { |d| [d.name] }
  end

  format_table(ds, head) do |d|
    if cli[:exec]
      MiGA::MiGA.run_cmd(
        cli[:exec].miga_variables(dataset: d.name, project: p.path)
      )
    end
    fun[d]
  end
end