Class: Genomer::Runtime

Inherits:
Object
  • Object
show all
Defined in:
lib/genomer/runtime.rb

Constant Summary collapse

MESSAGES = 
{
  :error  => {
    :init_again =>
      "This directory contains a 'Gemfile' and already appears to be a genomer project."
},
  :output => {
    :version => "Genomer version #{Genomer::VERSION}",
    :not_project =>
      "Use `genomer init NAME` to create a new genomer project called NAME",
    :simple_help =>
      "genomer COMMAND [options]\nrun `genomer help` for a list of available commands",
    :man =>
      "genomer man COMMAND\nrun `genomer help` for a list of available commands"
  }
}

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(settings) ⇒ Runtime

Returns a new instance of Runtime.



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# File 'lib/genomer/runtime.rb', line 36

def initialize(settings)
  @command   = settings.rest.shift
  @arguments = settings.rest
  @flags     = settings
end

Instance Attribute Details

#arguments ⇒ Object (readonly)

Returns the value of attribute arguments.



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# File 'lib/genomer/runtime.rb', line 10

def arguments
  @arguments
end

#command ⇒ Object (readonly)

Returns the value of attribute command.



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# File 'lib/genomer/runtime.rb', line 9

def command
  @command
end

#flags ⇒ Object (readonly)

Returns the value of attribute flags.



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# File 'lib/genomer/runtime.rb', line 11

def flags
  @flags
end

Instance Method Details

#execute! ⇒ Object 



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# File 'lib/genomer/runtime.rb', line 42

def execute!
  return message :output, :version if flags[:version]

  if genomer_project?
    case command
    when nil    then message :output, :simple_help
    when "help" then help
    when "init" then message :error, :init_again
    when "man"  then man
    else             run_plugin
    end
  else
    case command
    when "init" then init
    else             message :output, :not_project
    end
  end
end

#genomer_project? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/genomer/runtime.rb', line 146

def genomer_project?
  File.exists?('Gemfile')
end

#groffed_man_file(original_man_file) ⇒ Object 



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# File 'lib/genomer/runtime.rb', line 110

def groffed_man_file(original_man_file)
  converted_man = Tempfile.new("genome-manpage-")
  File.open(converted_man.path,'w') do |out|
    out.puts render_man(File.read(original_man_file))
  end
  converted_man
end

#help ⇒ Object 



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# File 'lib/genomer/runtime.rb', line 61

def help
  msg =<<-EOF
    genomer COMMAND [options]

    Available commands:
      init        Create a new genomer project
      man         View man page for the specified plugin
  EOF
  msg.unindent!

  if File.exists?('Gemfile')
    msg << Genomer::Plugin.plugins.inject(String.new) do |str,p|
      str << '  '
      str << p.name.gsub("genomer-plugin-","").ljust(12)
      str << p.summary
      str << "\n"
    end
  end
  msg.strip
end

#init ⇒ Object 



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# File 'lib/genomer/runtime.rb', line 118

def init
  project_name = arguments.first
  if File.exists?(project_name)
    raise Genomer::Error, "Directory '#{project_name}' already exists."
  end

  require 'genomer/files'

  Dir.mkdir project_name
  Dir.mkdir File.join(project_name,'assembly')

  File.open(File.join(project_name,'Gemfile'),'w') do |file|
    file.print Genomer::Files.gemfile
  end

  ['scaffold.yml','sequence.fna','annotations.gff'].each do |name|
    File.open(File.join(project_name,'assembly',name),'w') do |file|
      file.print Genomer::Files.send(name.gsub('.','_').to_sym)
    end
  end

  "Genomer project '#{project_name}' created.\n"
end

#man ⇒ Object 



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# File 'lib/genomer/runtime.rb', line 82

def man
  if not arguments.empty?
    location = if arguments.first == 'init'
                 File.expand_path File.dirname(__FILE__) + '/../../man/genomer-init.1.ronn'
               else
                 man_file(arguments.clone)
               end

    unless File.exists?(location)
      raise Genomer::Error, "No manual entry for command '#{arguments.join(' ')}'"
    end

    Kernel.exec "man #{groffed_man_file(location).path}"
  else
    message :output, :man
  end
end

#man_file(arguments) ⇒ Object 



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# File 'lib/genomer/runtime.rb', line 100

def man_file(arguments)
  plugin = arguments.first
  page = arguments.unshift("genomer").join('-') << ".ronn"
  File.join(Genomer::Plugin.fetch(plugin).full_gem_path, 'man', page)
end

#message(type, msg) ⇒ Object 



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# File 'lib/genomer/runtime.rb', line 30

def message(type,msg)
  content = MESSAGES[type][msg]
  type == :error ? raise(Genomer::Error, content) : content
end

#render_man(input) ⇒ Object 



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# File 'lib/genomer/runtime.rb', line 106

def render_man(input)
  Md2Man::ENGINE.render input
end

#run_plugin ⇒ Object 



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# File 'lib/genomer/runtime.rb', line 142

def run_plugin
  Genomer::Plugin[command].new(arguments,flags).run
end