Class: MiGA::Cli

Inherits:
MiGA
  • Object
show all
Includes:
Base, ObjectsHelper, OptHelper
Defined in:
lib/miga/cli.rb,
lib/miga/cli/base.rb

Overview

MiGA Command Line Interface API.

Defined Under Namespace

Modules: Base, ObjectsHelper, OptHelper Classes: Action

Constant Summary

Constants included from MiGA

CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from ObjectsHelper

#add_metadata, #load_and_filter_datasets, #load_dataset, #load_project, #load_project_or_dataset, #load_result

Methods included from OptHelper

#banner, #opt_common, #opt_filter_datasets, #opt_flag, #opt_object

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, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, rc_path, #result_files_exist?

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

#initialize(argv) ⇒ Cli

Returns a new instance of Cli.



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# File 'lib/miga/cli.rb', line 61

def initialize(argv)
  @data = {}
  @defaults = { verbose: false, tabular: false }
  @opt_common = true
  @objects = {}
  if argv[0].nil? or argv[0].to_s[0] == '-'
    @task = :generic
  else
    @task = argv.shift.to_sym
    @task = @@TASK_ALIAS[task] unless @@TASK_ALIAS[task].nil?
  end
  @argv = argv
  reset_action
end

Instance Attribute Details

#action ⇒ Object

Action to launch, an object inheriting from MiGA::Cli::Action



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# File 'lib/miga/cli.rb', line 27

def action
  @action
end

#argv ⇒ Object

The CLI parameters (except the task), and Array of String



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# File 'lib/miga/cli.rb', line 23

def argv
  @argv
end

#data ⇒ Object (readonly)

Parsed values as a Hash



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# File 'lib/miga/cli.rb', line 59

def data
  @data
end

#defaults ⇒ Object

Default values as a Hash



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# File 'lib/miga/cli.rb', line 55

def defaults
  @defaults
end

#expect_files ⇒ Object

If files are expected after the parameters, a boolean



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# File 'lib/miga/cli.rb', line 31

def expect_files
  @expect_files
end

#expect_operation ⇒ Object

If an operation verb preceding all other arguments is to be expected



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# File 'lib/miga/cli.rb', line 39

def expect_operation
  @expect_operation
end

#files ⇒ Object

Files passed after all other options, if #expect_files = true



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# File 'lib/miga/cli.rb', line 35

def files
  @files
end

#interactive ⇒ Object

Interactivity with the user is expected



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# File 'lib/miga/cli.rb', line 43

def interactive
  @interactive
end

#operation ⇒ Object

Operation preceding all other options, if #expect_operation = true



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# File 'lib/miga/cli.rb', line 47

def operation
  @operation
end

#opt_common=(value) ⇒ Object (writeonly)

Include common options, a boolean (true by default)



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# File 'lib/miga/cli.rb', line 51

def opt_common=(value)
  @opt_common = value
end

#task ⇒ Object

Task to execute, a symbol



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# File 'lib/miga/cli.rb', line 19

def task
  @task
end

Class Method Details

.EXECS ⇒ Object 



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# File 'lib/miga/cli/base.rb', line 111

def EXECS
  @@EXECS
end

.FILE_REGEXP(paired = false) ⇒ Object 



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# File 'lib/miga/cli/base.rb', line 115

def FILE_REGEXP(paired = false)
  paired ? @@PAIRED_FILE_REGEXP : @@FILE_REGEXP
end

.TASK_ALIAS ⇒ Object 



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# File 'lib/miga/cli/base.rb', line 107

def TASK_ALIAS
  @@TASK_ALIAS
end

.TASK_DESC ⇒ Object 



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# File 'lib/miga/cli/base.rb', line 103

def TASK_DESC
  @@TASK_DESC
end

Instance Method Details

#[](k) ⇒ Object

Access parsed data



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# File 'lib/miga/cli.rb', line 148

def [](k)
  k = k.to_sym
  @data[k].nil? ? @defaults[k] : @data[k]
end

#[]=(k, v) ⇒ Object

Set parsed data



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# File 'lib/miga/cli.rb', line 155

def []=(k, v)
  @data[k.to_sym] = v
end

#advance(*par) ⇒ Object

Same as MiGA::MiGA#advance, but checks if the CLI is verbose



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# File 'lib/miga/cli.rb', line 114

def advance(*par)
  super(*par) if self[:verbose]
end

#ask_user(question, default = nil, answers = nil, force = false) ⇒ Object

Ask a question question to the user (requires #interactive = true) The default is used if the answer is empty The answers are supported values, unless nil If –auto, all questions are anwered with default unless force



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# File 'lib/miga/cli.rb', line 123

def ask_user(question, default = nil, answers = nil, force = false)
  ans = " (#{answers.join(' / ')})" unless answers.nil?
  dft = " [#{default}]" unless default.nil?
  print "#{question}#{ans}#{dft} > "
  if self[:auto] && !force
    puts ''
  else
    y = gets.chomp
  end
  y = default.to_s if y.nil? or y.empty?
  unless answers.nil? or answers.map(&:to_s).include?(y)
    warn "Answer not recognized: '#{y}'"
    return ask_user(question, default, answers, force)
  end
  y
end

#ensure_par(req, msg = '%<name>s is mandatory: please provide %<flag>s') ⇒ Object

Ensure that these parameters have been passed to the CLI, as defined by par, a Hash with object names as keys and parameter flag as values. If missing, raise an error with message msg



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# File 'lib/miga/cli.rb', line 207

def ensure_par(req, msg = '%<name>s is mandatory: please provide %<flag>s')
  req.each do |k, v|
    raise (msg % { name: k, flag: v }) if self[k].nil?
  end
end

#ensure_type(klass) ⇒ Object

Ensure that “type” is passed and valid for the given klass



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# File 'lib/miga/cli.rb', line 215

def ensure_type(klass)
  ensure_par(type: '-t')
  if klass.KNOWN_TYPES[self[:type]].nil?
    raise "Unrecognized type: #{self[:type]}"
  end
end

#launch(abort_on_error = false) ⇒ Object

Perform the task requested (see #task); if abort_on_error, abort on error



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# File 'lib/miga/cli.rb', line 173

def launch(abort_on_error = false)
  begin
    raise "See `miga -h`" if action.nil?

    action.launch
  rescue => err
    $stderr.puts "Exception: #{err}"
    $stderr.puts ''
    err.backtrace.each { |l| $stderr.puts "DEBUG: #{l}" }
    abort if abort_on_error
    err
  end
end

#parse(&fun) ⇒ Object

Parse the #argv parameters



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# File 'lib/miga/cli.rb', line 189

def parse(&fun)
  if expect_operation
    @operation = @argv.shift unless argv.first =~ /^-/
  end
  OptionParser.new do |opt|
    banner(opt)
    fun[opt]
    opt_common(opt)
  end.parse!(@argv)
  if expect_files
    @files = argv
  end
end

#print(*par) ⇒ Object

Print par. If the first parameter is IO, the output is sent there, otherwise it’s sent to $stdout



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# File 'lib/miga/cli.rb', line 89

def print(*par)
  io = par.first.is_a?(IO) ? par.shift : $stdout
  io.print(*par)
end

#puts(*par) ⇒ Object

Print par, ensuring new line at the end. If the first parameter is IO, the output is sent there, otherwise it’s sent to $stdout



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# File 'lib/miga/cli.rb', line 80

def puts(*par)
  io = par.first.is_a?(IO) ? par.shift : $stdout
  io.puts(*par)
end

#reset_action ⇒ Object

Redefine #action based on #task



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# File 'lib/miga/cli.rb', line 161

def reset_action
  @action = nil
  if @@EXECS.include? task
    @action = Action.load(task, self)
  else
    warn "No action set for #{task}"
  end
end

#say(*par) ⇒ Object

Print par ensuring new line at the end, iff –verbose. Date/time each line. If the first parameter is IO, the output is sent there, otherwise it’s sent to $stderr



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# File 'lib/miga/cli.rb', line 106

def say(*par)
  return unless self[:verbose]

  super(*par)
end

#table(header, values, io = $stdout) ⇒ Object

Display a table with headers header and contents values, both Array. The output is printed to io



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# File 'lib/miga/cli.rb', line 97

def table(header, values, io = $stdout)
  self.puts(io, MiGA.tabulate(header, values, self[:tabular]))
end

#task_description ⇒ Object

Task description



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# File 'lib/miga/cli.rb', line 224

def task_description
  @@TASK_DESC[task]
end