#!/usr/bin/env ruby
require 'slop'

ENV['RACK_ENV'] ||= 'production'

# display name for tools like `ps`
$PROGRAM_NAME = 'genevalidatorapp'

opts = Slop.parse do |o|
  o.banner = <<BNR

SUMMARY:
  GeneValidator - Identify problems with predicted genes

USAGE:
  $ genevalidatorapp [options]

Examples:
  # Launch GeneValidatorApp with the given config file
  $ genevalidatorapp --config ~/.genevalidatorapp.conf

  # Launch GeneValidatorApp with 8 threads at port 8888
  $ genevalidatorapp --num_threads 8 --port 8888

  # Create a config file with the other arguments
  $ genevalidatorapp -s -d ~/database_dir
BNR

  o.separator 'Compulsory Argument, unless set in a config file'

  o.string '-d', '--database_dir',
           'Read BLAST database from this directory'

  o.separator ''
  o.separator 'Optional Arguments'

  o.string '-f', '--default_db',
           'The Path to the the default database'

  o.string '-n', '--num_threads',
           'Number of threads to use to run a BLAST search'

  o.string '-c', '--config_file',
           'Use the given configuration file'

  o.string '-r', '--require',
           'Load extension from this file'

  o.string '--host',
           'Host to run GeneValidatorApp on'

  o.string '-p', '--port',
           'Port to run GeneValidatorApp on'

  o.string '-s', '--set',
           'Set configuration value in the config file'

  o.string '-l', '--list_dbs',
           'List BLAST databases'

  o.string '-b', '--blast_bin',
           'Load BLAST+ binaries from this directory'

  o.string '-m', '--mafft_bin',
           'Load Mafft binaries from this directory'

  o.string '-w', '--web_dir',
           'Path to the web directory (contains ' \
           'supporting files utilised by the app).'

  o.bool   '-D', '--devel',
           'Start GeneValidatorApp in development mode'

  o.bool   '-v', '--version',
           'Print version number of GeneValidatorApp that will be loaded'

  o.on     '-h', '--help',
           'Display this help message'
end

if opts.help?
  puts opts
  exit
end

if opts.version?
  require 'GeneValidatorApp/version'
  puts GeneValidatorApp::VERSION
  exit
end

ENV['RACK_ENV'] = 'development' if opts.devel?

# Exit gracefully on SIGINT.
stty = `stty -g`.chomp
trap('INT') do
  puts ''
  puts 'Aborted.'
  system('stty', stty)
  exit
end

clean_opts = lambda do |hash|
  hash.delete_if { |k, v| k == :set || k == :version || v.nil? }
  hash
end

require 'GeneValidatorApp'
begin
  GeneValidatorApp.init clean_opts[opts.to_hash]
rescue SystemExit => e
  puts '*** Error: GeneValidator failed to initialise properly.'
  puts '    Please check all paramaters and try again.'
  puts '    See https://github.com/IsmailM/GeneValidatorApp for more help'
  exit e.status
end

puts GeneValidatorApp::Database.all? if opts.list_databases?

GeneValidatorApp.send(:write_config_file) if opts.set?

GeneValidatorApp.run