module NeuroHmmerApp

# File lib/neurohmmerapp.rb, line 80
def call(env)
  env['rack.logger'] = logger
  Routes.call(env)
end

# File lib/neurohmmerapp.rb, line 17
def environment
  ENV['RACK_ENV']
end

# File lib/neurohmmerapp.rb, line 34
def init(config = {})
  @config = Config.new(config)

  init_binaries
  init_dirs
  check_num_threads
  check_max_characters
  self
end

# File lib/neurohmmerapp.rb, line 29
def logger
  @logger ||= Logger.new(STDERR, verbose?)
end

# File lib/neurohmmerapp.rb, line 62
def on_start
  puts '** NeuroHmmer is ready.'
  puts "   Go to #{server_url} in your browser and start analysing genes!"
  puts '   Press CTRL+C to quit.'
  open_in_browser(server_url)
end

# File lib/neurohmmerapp.rb, line 69
def on_stop
  puts
  puts '** Thank you for using NeuroHmmerApp :).'
  puts '   Please cite: '
  puts '        Moghul M.I., Elphick M & Wurm Y (in prep).'
  puts '        NeuroHmmer: identify Neuropeptide Precursors.'
end

# File lib/neurohmmerapp.rb, line 25
def root
  File.dirname(File.dirname(__FILE__))
end

# File lib/neurohmmerapp.rb, line 47
def run
  check_host
  Server.run(self)
rescue Errno::EADDRINUSE
  puts "** Could not bind to port #{config[:port]}."
  puts "   Is NeuroHmmer already accessible at #{server_url}?"
  puts '   No? Try running NeuroHmmer on another port, like so:'
  puts
  puts '       neurohmmerapp -p 4570.'
rescue Errno::EACCES
  puts "** Need root privilege to bind to port #{config[:port]}."
  puts '   It is not advisable to run NeuroHmmer as root.'
  puts '   Please use Apache/Nginx to bind to a privileged port.'
end

# File lib/neurohmmerapp.rb, line 21
def verbose?
  @verbose ||= (environment == 'development')
end

# File lib/neurohmmerapp.rb, line 149
def assert_blast_installed_and_compatible
  fail HMMER_NOT_INSTALLED unless command? 'hmmscan'
  # version = `hmmscan -version`.split[1]
  # fail HMMER_NOT_COMPATIBLE, version unless version >= MINIMUM_HMMER_VERSION
end

# File lib/neurohmmerapp.rb, line 155
def assert_mafft_installed
  fail MAFFT_NOT_INSTALLED unless command? 'mafft'
end

# File lib/neurohmmerapp.rb, line 160
def check_host
  return unless config[:host] == '0.0.0.0'
  logger.warn 'Will listen on all interfaces (0.0.0.0).' \
              ' Consider using 127.0.0.1 (--host option).'
end

# File lib/neurohmmerapp.rb, line 122
def check_max_characters
  if config[:max_characters] != 'undefined'
    config[:max_characters] = Integer(config[:max_characters])
  end
rescue
  raise MAX_CHARACTERS_INCORRECT
end

# File lib/neurohmmerapp.rb, line 110
def check_num_threads
  num_threads = Integer(config[:num_threads])
  fail NUM_THREADS_INCORRECT unless num_threads > 0

  logger.debug "Will use #{num_threads} threads to run BLAST."
  if num_threads > 256
    logger.warn "Number of threads set at #{num_threads} is unusually high."
  end
rescue
  raise NUM_THREADS_INCORRECT
end

# File lib/neurohmmerapp.rb, line 190
def command?(command)
  system("which #{command} > /dev/null 2>&1")
end

# File lib/neurohmmerapp.rb, line 143
def export_bin_dir(bin_dir)
  return unless bin_dir
  return if ENV['PATH'].split(':').include?(bin_dir)
  ENV['PATH'] = "#{bin_dir}:#{ENV['PATH']}"
end

# File lib/neurohmmerapp.rb, line 104
def init_binaries
  config[:bin] = init_bins if config[:bin]
  assert_blast_installed_and_compatible
  assert_mafft_installed
end

# File lib/neurohmmerapp.rb, line 130
def init_bins
  bins = []
  config[:bin].each do |bin|
    bins << File.expand_path(bin)
    unless File.exist?(bin) && File.directory?(bin)
      fail BIN_DIR_NOT_FOUND, config[:bin]
    end
    export_bin_dir(bin)
  end
  bins
end

# File lib/neurohmmerapp.rb, line 87
def init_dirs
  config[:public_dir] = File.expand_path(config[:public_dir])
  unique_start_id     = 'NH_' + "#{Time.now.strftime('%Y%m%d-%H-%M-%S')}"
  @public_dir         = File.join(config[:public_dir], unique_start_id)
  init_public_dir
end

# File lib/neurohmmerapp.rb, line 96
def init_public_dir
  FileUtils.mkdir_p(File.join(@public_dir, 'NeuroHmmer'))
  root_web_files = File.join(NeuroHmmerApp.root, 'public/web_files')
  root_gv        = File.join(NeuroHmmerApp.root, 'public/NeuroHmmer')
  FileUtils.cp_r(root_web_files, @public_dir)
  FileUtils.cp_r(root_gv, @public_dir)
end

# File lib/neurohmmerapp.rb, line 172
def open_in_browser(server_url)
  return if using_ssh? || verbose?
  if RUBY_PLATFORM =~ /linux/ && xdg?
    system "xdg-open #{server_url}"
  elsif RUBY_PLATFORM =~ /darwin/
    system "open #{server_url}"
  end
end

# File lib/neurohmmerapp.rb, line 166
def server_url
  host = config[:host]
  host = 'localhost' if host == '127.0.0.1' || host == '0.0.0.0'
  "http://#{host}:#{config[:port]}"
end

# File lib/neurohmmerapp.rb, line 181
def using_ssh?
  true if ENV['SSH_CLIENT'] || ENV['SSH_TTY'] || ENV['SSH_CONNECTION']
end

# File lib/neurohmmerapp.rb, line 185
def xdg?
  true if ENV['DISPLAY'] && command?('xdg-open')
end