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, #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

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 7

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 }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/ls.rb', line 48

def perform
  ds = cli.load_and_filter_datasets(cli[:silent])
  exit(ds.empty? ? 1 : 0) if cli[:silent]
  if !cli[:datum].nil?
    cli[:tabular] = true
    format_table(ds, [nil, nil]) { |d| [d.name, d.metadata[cli[:datum]]] }
  elsif !cli[:fields].nil?
    format_table(ds, [:name] + cli[:fields]) do |d|
      [d.name] + cli[:fields].map { |f| d.metadata[f] }
    end
  elsif cli[:info]
    format_table(ds, Dataset.INFO_FIELDS) { |d| d.info }
  elsif cli[:processing]
    comp = %w[- done queued]
    format_table(ds, [:name] + MiGA::Dataset.PREPROCESSING_TASKS) do |d|
      [d.name] + d.profile_advance.map { |i| comp[i] }
    end
  elsif cli[:taskstatus]
    format_table(ds, [:name] + MiGA::Dataset.PREPROCESSING_TASKS) do |d|
      [d.name] + d.results_status.values
    end
  else
    cli[:tabular] = true
    format_table(ds, [nil]) { |d| [d.name] }
  end
end