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

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

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

begin
  Slop.parse!(strict: true, help: true) do
    banner <<BANNER
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

BANNER
    # - Add Web_dir ? or simply default to ~/.genevalidatorapp/runs/

    on 'c', 'config_file=',
       'Use the given configuration file',
       argument: true

    on 'b', 'bin=',
       'Load BLAST+ and/or MAFFT binaries from this directory',
       argument: true,
       as: Array

    on 'd', 'database_dir=',
       'Read BLAST database from this directory',
       argument: true

    on 'f', 'default_database_path=',
       'The path to the default BLAST database',
       argument: true

    on 'n', 'num_threads=',
       'Number of threads to use to run a BLAST search',
       argument: true

    on 'r', 'require=',
       'Load extension from this file',
       argument: true

    on 'H', 'host=',
       'Host to run GeneValidatorApp on',
       argument: true

    on 'p', 'port=',
       'Port to run GeneValidatorApp on',
       argument: true

    on 's', 'set',
       'Set configuration value in default or given config file'

    on 'l', 'list_databases',
       'List BLAST databases'

    on 'D', 'devel',
       'Start GeneValidatorApp in development mode'

    on '-v', '--version',
       'Print version number of GeneValidatorApp that will be loaded'

    on '-h', '--help',
       'Display this help message'

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

    run do
      if version?
        require 'genevalidatorapp/version'
        puts GeneValidatorApp::VERSION
        exit
      end

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

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

      require 'genevalidatorapp'

      begin
        GeneValidatorApp.init clean_opts[to_h]

      # The aim of following error recovery scenarios is to guide user to a
      # working GeneValidatorApp installation. We expect to land following
      # error scenarios either when creating a new GeneValidatorApp (first
      # time or later), or updating config values using -s CLI option.

      rescue GeneValidatorApp::CONFIG_FILE_ERROR,
             GeneValidatorApp::BLAST_DATABASE_ERROR => e

        puts e
        exit!

      rescue GeneValidatorApp::BIN_DIR_NOT_FOUND => e

        puts e

        unless bin?
          puts 'You can set the correct value by running:'
          puts
          puts '  genevalidatorapp -s -b <value>'
          puts
        end

        exit!

      rescue GeneValidatorApp::DATABASE_DIR_NOT_FOUND => e

        puts e

        unless database_dir?
          puts 'You can set the correct value by running:'
          puts
          puts '  genevalidatorapp -s -d <value>'
          puts
        end

        exit!

      rescue GeneValidatorApp::NUM_THREADS_INCORRECT => e

        puts e

        unless num_threads?
          puts 'You can set the correct value by running:'
          puts
          puts '  genevalidatorapp -s -n <value>'
          puts
        end

        exit!

      rescue GeneValidatorApp::EXTENSION_FILE_NOT_FOUND => e

        puts e

        unless require?
          puts 'You can set the correct value by running:'
          puts
          puts '  genevalidatorapp -s -r <value>'
          puts
        end

        exit!

      rescue GeneValidatorApp::BLAST_NOT_INSTALLED,
             GeneValidatorApp::BLAST_NOT_EXECUTABLE,
             GeneValidatorApp::BLAST_NOT_COMPATIBLE => e

        # Show original error message first.
        puts
        puts e

        # Set a flag so that if we recovered from error resulting config can be
        # saved. Config will be saved unless invoked with -b option.
        fetch_option(:set).value = !bin?

        # Ask user if she already has BLAST+ downloaded.
        puts
        puts <<MSG
GeneValidatorApp can use NCBI BLAST+ that you may have on your system already.
Please enter the path to NCBI BLAST+.

Press Ctrl+C to quit.
MSG
        puts
        response = Readline.readline('>> ').to_s.strip
        unless response.empty?
          unless File.basename(response) == 'bin'
            response = File.join(response, 'bin')
          end
          fetch_option(:bin).value = File.join(response)
          puts
          redo
        end

      rescue GeneValidatorApp::DATABASE_DIR_NOT_SET => e

        # Show original error message.
        puts
        puts e

        # Set a flag so that if we recovered from error resulting config can be
        # saved. Config will be saved unless invoked with -d option.
        fetch_option(:set).value = !database_dir?

        # Ask user for the directory containing sequences or BLAST+
        # databases.
        puts
        puts <<MSG
GeneValidatorApp needs to know where your BLAST+ databases are.
Please enter the path to the relevant directory.

Press Ctrl+C to quit.
MSG

        puts
        response = Readline.readline('>> ').to_s.strip
        fetch_option(:database_dir).value = response
        redo

      rescue GeneValidatorApp::NO_BLAST_DATABASE_FOUND => e
        unless list_databases?

          # Print error raised.
          puts
          puts e

        end

      rescue => e
        # This will catch any unhandled error and some very special errors.
        # Ideally we will never hit this block. If we do, there's a bug in
        # GeneValidatorApp or something really weird going on. If we hit this
        # error block we show the stacktrace to the user requesting them to
        # post the same to our Google Group.
        puts <<MSG
Something went wonky

Looks like you have encountered a bug in GeneValidatorApp. Please could you
report this incident here -
https://github.com/wurmlab/genevalidatorapp/issues

Error:
#{e.backtrace.unshift(e.message).join("\n")}
MSG
        exit
      end

      if list_databases?
        puts GeneValidatorApp::Database.all
        exit
      end

      if set?
        GeneValidatorApp.config.write_config_file
        exit
      end

      GeneValidatorApp.config.write_config_file if fetch_option(:set).value

      GeneValidatorApp.run
    end
  end
rescue Slop::Error => e
  puts e
  puts "Run '#{$PROGRAM_NAME} -h' for help with command line options."
  exit
end