Module: MiGA::Cli::OptHelper

Included in:
MiGA::Cli
Defined in:
lib/miga/cli/opt_helper.rb

Overview

Helper module including functions for CLI options

Instance Method Summary collapse

Instance Method Details

Send MiGA’s banner to OptionParser opt



8
9
10
11
12
13
14
15
 
# File 'lib/miga/cli/opt_helper.rb', line 8

def banner(opt)
  usage = "Usage: miga #{action.name}"
  usage += ' {operation}' if expect_operation
  usage += ' [options]'
  usage += ' {FILES...}' if expect_files
  opt.banner = "\n#{task_description}\n\n#{usage}\n"
  opt.separator ''
end

#opt_common(opt) ⇒ Object

Common options at the end of most actions, passed to OptionParser opt No action is performed if #opt_common = false is passed Executes only once, unless #opt_common = true is passed between calls



21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
 
# File 'lib/miga/cli/opt_helper.rb', line 21

def opt_common(opt)
  return unless @opt_common

  if interactive
    opt.on(
      '--auto',
      'Accept all defaults as answers'
    ) { |v| self[:auto] = v }
  end
  opt.on(
    '--rand-seed INT', Integer,
    'Set this seed to initialize pseudo-randomness'
  ) { |v| srand(v) }
  opt.on(
    '-v', '--verbose',
    'Print additional information to STDERR'
  ) { |v| self[:verbose] = v }
  opt.on(
    '-d', '--debug INT', Integer,
    'Print debugging information to STDERR (1: debug, 2: trace)'
  ) { |v| v > 1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON }
  opt.on(
    '-h', '--help',
    'Display this screen'
  ) do
    puts opt
    exit
  end
  opt.separator ''
  self.opt_common = false
end

#opt_filter_datasets(opt, what = %i[ref multi active taxonomy]) ⇒ Object

Options to filter a list of datasets passed to OptionParser opt, as determined by what an Array with any combination of:

  • :ref To filter by reference (–ref) or query (–no-ref)

  • :multi To filter by multiple (–multi) or single (–no-multi) species

  • :active To filter by active (–active) or inactive (–no-active)

  • :taxonomy To filter by taxonomy (–taxonomy)

The “k-th” filter (–dataset-k) is always included



126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
 
# File 'lib/miga/cli/opt_helper.rb', line 126

def opt_filter_datasets(opt, what = %i[ref multi active taxonomy])
  what.each do |w|
    case w
    when :ref
      opt.on(
        '--[no-]ref',
        'Use only reference (or only non-reference) datasets'
      ) { |v| self[:ref] = v }
    when :multi
      opt.on(
        '--[no-]multi',
        'Use only multi-species (or only single-species) datasets'
      ) { |v| self[:multi] = v }
    when :active
      opt.on(
        '--[no-]active',
        'Use only active (or inactive) datasets'
      ) { |v| self[:active] = v }
    when :taxonomy
      opt.on(
        '-t', '--taxonomy RANK:TAXON',
        'Filter by taxonomy'
      ) { |v| self[:taxonomy] = MiGA::Taxonomy.new(v) }
    else
      raise "Internal error: Unrecognized option: #{w}"
    end
  end
  opt.on(
    '--ds-list FILE',
    'File containing a list of dataset names, one per line'
  ) { |v| self[:ds_list] = v }
  opt.on(
    '--dataset-k INTEGER', Integer,
    'Use only the k-th dataset in the list'
  ) { |v| self[:dataset_k] = v }
end

#opt_flag(opt, flag, description, sym = nil) ⇒ Object

Add a flag (true/false) to the OptionParser opt defined by flag (without –) and description, and save it in the CLI as sym. If sym is nil, flag is used as Symbol



167
168
169
170
 
# File 'lib/miga/cli/opt_helper.rb', line 167

def opt_flag(opt, flag, description, sym = nil)
  sym = flag.to_sym if sym.nil?
  opt.on("--#{flag.to_s.tr('_', '-')}", description) { |v| self[sym] = v }
end

#opt_object(opt, what = %i[project dataset]) ⇒ Object

Options to load an object passed to OptionParser opt, as determined by what an Array with any combination of:

  • :project To require a project

  • :dataset To require a dataset

  • :dataset_opt To allow (optionally) a dataset

  • :dataset_type To allow (optionally) a type of dataset

  • :dataset_type_req To require a type of dataset

  • :project_type To allow (optionally) a type of project

  • :project_type_req To require a type of project

  • :result To require a type of project or dataset result

  • :result_opt To allow (optionally) a type of result

  • :result_dataset To require a type of dataset result

  • :result_project To require a type of project result

The options :result, :result_opt, :result_dataset, and :result_project are mutually exclusive



69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
 
# File 'lib/miga/cli/opt_helper.rb', line 69

def opt_object(opt, what = %i[project dataset])
  what.each do |w|
    case w
    when :project
      opt.on(
        '-P', '--project PATH',
        '(Mandatory) Path to the project'
      ) { |v| self[:project] = v }
    when :dataset, :dataset_opt
      opt.on(
        '-D', '--dataset STRING',
        (w == :dataset ? '(Mandatory) ' : '') + 'Name of the dataset'
      ) { |v| self[:dataset] = v }
    when :dataset_type, :dataset_type_req, :project_type, :project_type_req
      obj = w.to_s.gsub(/_.*/, '')
      klass = Object.const_get("MiGA::#{obj.capitalize}")
      req = w.to_s =~ /_req$/ ? '(Mandatory) ' : ''
      opt.on(
        '-t', '--type STRING',
        "#{req}Type of #{obj}. Recognized types include:",
        *klass.KNOWN_TYPES.map { |k, v| "~ #{k}: #{v[:description]}" }
      ) { |v| self[:type] = v.downcase.to_sym }
    when :result, :result_opt
      opt.on(
        '-r', '--result STRING',
        "#{'(Mandatory) ' if w == :result}Name of the result",
        'Recognized names for dataset-specific results include:',
        *MiGA::Dataset.RESULT_DIRS.keys.map { |n| " ~ #{n}" },
        'Recognized names for project-wide results include:',
        *MiGA::Project.RESULT_DIRS.keys.map { |n| " ~ #{n}" }
      ) { |v| self[:result] = v.downcase.to_sym }
    when :result_dataset
      opt.on(
        '-r', '--result STRING',
        '(Mandatory) Name of the result, one of:',
        *MiGA::Dataset.RESULT_DIRS.keys.map { |n| " ~ #{n}" }
      ) { |v| self[:result] = v.downcase.to_sym }
    when :result_project
      opt.on(
        '-r', '--result STRING',
        '(Mandatory) Name of the result, one of:',
        *MiGA::Project.RESULT_DIRS.keys.map { |n| " ~ #{n}" }
      ) { |v| self[:result] = v.downcase.to_sym }
    else
      raise "Internal error: Unrecognized option: #{w}"
    end
  end
end