Class: MiGA::Cli::Action::New

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

def parse_cli
  cli.parse do |opt|
    cli.opt_object(opt, [:project, :project_type_req])
    opt.on(
      '-n', '--name STRING',
      'Name of the project'
    ) { |v| cli[:name] = v }
    opt.on(
      '-d', '--description STRING',
      'Description of the project'
    ) { |v| cli[:description] = v }
    opt.on(
      '-c', '--comments STRING',
      'Comments on the project'
    ) { |v| cli[:comments] = v }
    opt.on(
      '--fast',
      'Use faster identity engines (Diamond-AAI and FastANI)',
      'Equivalent to: -m aai_p=diamond,ani_p=fastani'
    ) { |v| cli[:fast] = v }
    opt.on(
      '--sensitive',
      'Use more sensitive identity engines (BLAST+)',
      'Equivalent to: -m aai_p=blast+,ani_p=blast+'
    ) { |v| cli[:sensitive] = v }
    opt.on(
      '-m', '--metadata STRING',
      'Metadata as key-value pairs separated by = and delimited by comma',
      'Values are saved as strings except for booleans (true / false) or nil'
    ) { |v| cli[:metadata] = v }
    opt.on(
      '--ignore-init',
      'Ignore checks for MiGA initialization',
      'This can be used to create projects that are processed elsewhere'
    ) { |v| cli[:ignore_init] = v }
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/new.rb', line 45

def perform
  cli.ensure_type(MiGA::Project)
  cli.ensure_par(project: '-P')
  if !cli[:ignore_init] && !MiGA::MiGA.initialized?
    raise 'MiGA has not been initialized, please use "miga init" first'
  end
  cli.say "Creating project: #{cli[:project]}"
  raise 'Project already exists, aborting' if Project.exist?(cli[:project])

  p = Project.new(cli[:project], false)
  p = cli.add_metadata(p)

  if cli[:sensitive]
    p.set_option(:aai_p, 'blast+')
    p.set_option(:ani_p, 'blast+')
  elsif cli[:fast]
    p.set_option(:aai_p, 'diamond')
    p.set_option(:ani_p, 'fastani')
  end
end