#!/usr/bin/env ruby

require 'rbbt'
require 'rbbt/util/simpleopt'

options = SOPT.setup <<EOF
Ruby bioinformatics toolkit

$ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value'"


--log*                  #{Log.color :yellow, "Log level from 0 (debug) 6 (errors)"}
-cd--command_dir*       #{Log.color :yellow, "Directory from where to load command scripts"}
--profile               #{Log.color :yellow, "Profile execution"}
--nocolor               #{Log.color :yellow, "Disable colored output"}
--locate_file           #{Log.color :yellow, "Report the location of the script instead of executing it"}
EOF

Log.nocolor = true if options[:nocolor]
locate = options.delete :locate_file

if options[:log]
  Log.severity = options[:log].to_i
end

if options[:command_dir]
  $rbbt_command_dir = Path.setup(options[:command_dir].dup)
else
  $rbbt_command_dir = Rbbt.share.rbbt_commands
end

SOPT.description =<<EOF
This command controls many aspects of the Rbbt framework, from configuration tasks to running applications. 

Commands are implemented in separate files under the Rbbt path '#{$rbbt_command_dir}'. 
Known locations are: #{([$rbbt_command_dir] + $rbbt_command_dir.find_all) * ", " }. 
You can place your own commads at #{$rbbt_command_dir.find(:user)}.
EOF

if options[:profile]
  require 'ruby-prof'
  RubyProf.start
end


def prev_dir(prev)
    rbbt_command_dir = $rbbt_command_dir

    prev.each do |previous_command|
        rbbt_command_dir = rbbt_command_dir[previous_command]
    end

    rbbt_command_dir
end

def commands(prev)
    rbbt_command_dir = prev_dir(prev)

    command_file_dirs = rbbt_command_dir.find_all
    command_files = command_file_dirs.collect{|d| d.glob('*') }.flatten
    command_files.collect{|p| File.basename(p) }.uniq.reject{|p| p =~ /\.desc$/}.sort
end

def rbbt_usage(prev = nil)
  puts
  puts SOPT.doc

  if prev
    puts
    puts Log.color :magenta, "## COMMANDS"
    puts
    puts Log.color :magenta, "Command:"
    puts 
    puts "  #{File.basename($0)} #{prev * " "}"
    puts 
    puts Log.color :magenta, "Subcommands:"
    puts 
    prev_dir = prev_dir(prev)
    commands(prev).each do |command|
      directory = File.directory? prev_dir[command].find
      if directory
        puts "  " << Log.color(:blue, command)
      else
        puts "  " << command
      end
    end
  end
  puts
  true
end

def print_error(error, backtrace = nil)
  puts Log.color :red, "Error:"
  puts
  puts error
  if backtrace
    puts
    puts Log.color :red, "Backtrace:"
    puts
    puts backtrace * "\n"
  end
  puts
end

def aliases
  @aliases ||= Rbbt.etc.cmd_alias.exists? ? Rbbt.etc.cmd_alias.yaml : {}
end

def cmd_alias
  while aliases.include? ARGV[0]
    ARGV.replace Misc.parse_cmd_params(aliases[ARGV[0]]) + ARGV[1..-1]
  end
end
    
dir = $rbbt_command_dir
$previous_commands = []

cmd_alias

begin
  while ARGV.any?
    $command = ARGV.shift
    case
    when File.directory?(dir[$command].find)
      $previous_commands << $command
      dir = dir[$command]
    when dir[$command].exists?
      if locate
        puts dir[$command].find
        exit 0
      else
        load dir[$command].find
        exit 0
      end
    else
      error = "Command '#{$command }' not understood"
      rbbt_usage($previous_commands)
      print_error(error)
      exit -1
    end
  end

  rbbt_usage($previous_commands)
  exit 0

rescue ParameterException
  puts
  rbbt_usage
  print_error($!.message, $!.backtrace)
  puts
  exit -1
ensure
  if options[:profile]
    result = RubyProf.stop
    printer = RubyProf::FlatPrinter.new(result)
    printer.print(STDOUT, :min_percent => 10)
  end
end