module SequenceServer

# File lib/sequenceserver.rb, line 94
def call(env)
  env['rack.logger'] = logger
  Routes.call(env)
end

# File lib/sequenceserver.rb, line 20
def environment
  ENV['RACK_ENV']
end

# File lib/sequenceserver.rb, line 36
def init(config = {})
  @config = Config.new(config)

  init_binaries
  init_database
  load_extension
  check_num_threads
  self

  # We don't validate port and host settings. If SequenceServer is run
  # self-hosted, bind will fail on incorrect values. If SequenceServer
  # is run via Apache+Passenger, we don't need to worry.
end

# File lib/sequenceserver.rb, line 100
def irb
  ARGV.clear
  require 'irb'
  IRB.setup nil
  IRB.conf[:MAIN_CONTEXT] = IRB::Irb.new.context
  require 'irb/ext/multi-irb'
  IRB.irb nil, self
end

# File lib/sequenceserver.rb, line 32
def logger
  @logger ||= Logger.new(STDERR, verbose?)
end

# File lib/sequenceserver.rb, line 69
def on_start
  puts '** SequenceServer is ready.'
  puts "   Go to #{server_url} in your browser and start BLASTing!"
  puts '   Press CTRL+C to quit.'
  open_in_browser(server_url)
end

# File lib/sequenceserver.rb, line 76
def on_stop
  puts
  puts '** Thank you for using SequenceServer :).'
  puts '   Please cite: '
  puts '       Priyam A, Woodcroft BJ, Rai V, Moghul I, Munagala A, Ter F,'
  puts '       Chowdhary H, Pieniak I, Maynard LJ, Gibbins MA, Moon H,'
  puts '       Davis-Richardson A, Uludag M, Watson-Haigh N, Challis R,'
  puts '       Nakamura H, Favreau E, Gómez EA, Pluskal T, Leonard G,'
  puts '       Rumpf W & Wurm Y.'
  puts '       Sequenceserver: A modern graphical user interface for'
  puts '       custom BLAST databases.'
  puts '       Molecular Biology and Evolution (2019)'
end

# File lib/sequenceserver.rb, line 28
def root
  File.dirname(File.dirname(__FILE__))
end

# File lib/sequenceserver.rb, line 53
def run
  check_host
  Server.run(self)
rescue Errno::EADDRINUSE
  puts "** Could not bind to port #{config[:port]}."
  puts "   Is SequenceServer already accessible at #{server_url}?"
  puts '   No? Try running SequenceServer on another port, like so:'
  puts
  puts '       sequenceserver -p 4570.'
rescue Errno::EACCES
  puts "** Need root privilege to bind to port #{config[:port]}."
  puts '   It is not advisable to run SequenceServer as root.'
  puts '   Please use Apache/Nginx to bind to a privileged port.'
  puts '   Instructions available on http://sequenceserver.com.'
end

# File lib/sequenceserver.rb, line 24
def verbose?
  @verbose ||= (environment == 'development')
end

# File lib/sequenceserver.rb, line 185
def assert_blast_installed_and_compatible
  fail BLAST_NOT_INSTALLED unless command? 'blastdbcmd'
  version = `blastdbcmd -version`.split[1]
  fail BLAST_NOT_EXECUTABLE if !$CHILD_STATUS.success? || version.empty?
  if (parse_version(version) <=> parse_version(MINIMUM_BLAST_VERSION)) < 0
    fail BLAST_NOT_COMPATIBLE, version
  end
end

# File lib/sequenceserver.rb, line 156
def check_host
  # rubocop:disable Style/GuardClause
  if 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
  # rubocop:enable Style/GuardClause
end

# File lib/sequenceserver.rb, line 143
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/sequenceserver.rb, line 218
def command?(command)
  system("which #{command} > /dev/null 2>&1")
end

# File lib/sequenceserver.rb, line 178
def export_bin_dir
  bin_dir = config[:bin]
  return unless bin_dir
  return if ENV['PATH'].split(':').include? bin_dir
  ENV['PATH'] = "#{bin_dir}:#{ENV['PATH']}"
end

# File lib/sequenceserver.rb, line 111
def init_binaries
  if config[:bin]
    config[:bin] = File.expand_path config[:bin]
    unless File.exist?(config[:bin]) && File.directory?(config[:bin])
      fail BIN_DIR_NOT_FOUND, config[:bin]
    end
    logger.debug("Will use NCBI BLAST+ at: #{config[:bin]}")
    export_bin_dir
  else
    logger.debug('Will use NCBI BLAST+ at: $PATH')
  end

  assert_blast_installed_and_compatible
end

# File lib/sequenceserver.rb, line 126
def init_database
  fail DATABASE_DIR_NOT_SET unless config[:database_dir]

  config[:database_dir] = File.expand_path(config[:database_dir])
  unless File.exist?(config[:database_dir]) &&
         File.directory?(config[:database_dir])
    fail DATABASE_DIR_NOT_FOUND, config[:database_dir]
  end

  logger.debug("Will use BLAST+ databases at: #{config[:database_dir]}")
  Database.scan_databases_dir
  Database.each do |database|
    logger.debug("Found #{database.type} database '#{database.title}'" \
                 " at '#{database.name}'")
  end
end

# File lib/sequenceserver.rb, line 165
def load_extension
  return unless config[:require]

  config[:require] = File.expand_path config[:require]
  unless File.exist?(config[:require]) && File.file?(config[:require])
    fail EXTENSION_FILE_NOT_FOUND, config[:require]
  end

  logger.debug("Loading extension: #{config[:require]}")
  require config[:require]
end

# File lib/sequenceserver.rb, line 200
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/sequenceserver.rb, line 222
def parse_version(version_string)
  version_string.split('.').map(&:to_i)
end

# File lib/sequenceserver.rb, line 194
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/sequenceserver.rb, line 209
def using_ssh?
  true if ENV['SSH_CLIENT'] || ENV['SSH_TTY'] || ENV['SSH_CONNECTION']
end

# File lib/sequenceserver.rb, line 213
def xdg?
  true if ENV['DISPLAY'] && command?('xdg-open')
end