#!/usr/bin/env ruby

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

options = SOPT.get("--log* Log level from 0 (debug) 6 (errors):-cd--command_dir* Directory from where to load commands:--profile Profile execution:--no_color Disable colored output:--locate_file Locate file been executed")

ENV["RBBT_NOCOLOR"] = "true" if options[:no_color]
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

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

SOPT.synopsys = "rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value'"
SOPT.summary = "Ruby bioinformatics toolkit"
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

def commands(prev)
    rbbt_command_dir = $rbbt_command_dir

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

    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 
    commands(prev).each do |command|
      puts "  " << command
    end
  end
  puts
end

def print_error(error, backtrace = nil)
  puts Term::ANSIColor.red("Error:")
  puts
  puts error
  if backtrace
    puts
    puts Term::ANSIColor.red("Backtrace:")
    puts
    puts backtrace * "\n"
  end
  puts
end
    
dir = $rbbt_command_dir
prev = []

begin
  while ARGV.any?
    command = ARGV.shift
    case
    when File.directory?(dir[command].find)
      prev << 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(prev)
      print_error(error)
      exit -1
    end
  end

  rbbt_usage(prev)
  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