#!/usr/bin/env ruby

$LOAD_PATH.unshift(File.expand_path("../../lib", __FILE__))

require 'trollop'
require 'active_record'
require 'search_tools/blast'

# Quorum search tools and dependencies.
SEARCH_TOOLS = {
  "blastn"  => ["blastn"],
  "blastx"  => ["blastx"],
  "tblastn" => ["tblastn"],
  "blastp"  => ["blastp"]
}

module Quorum
  #
  # Parse Options for Quorum Search Tools
  #
  class Search

    def initialize
      opts = Trollop::options do
        text <<-HEAD

Quorum

A flexible bioinformatics search tool.

Options:

        HEAD

        # Search tool
        opt :search_tool, "Search tool to execute. Available tools: " << 
        "#{SEARCH_TOOLS.keys.join(', ')}", :type => :string, 
          :required => true, :short => "-s"

        # General settings
        opt :log_directory, "Path to log directory", :type => :string,
          :required => true, :short => "-l"
        opt :tmp_directory, "Path to tmp directory", :type => :string,
          :required => true, :short => "-m"

        # ActiveRecord database settings
        opt :id, "Database record ID", :type => :int, :required => true,
          :short => "-i"
        opt :database, "Database name", :type => :string, :required => true,
          :short => "-d"
        opt :database_adapter, "ActiveRecord database adapter", 
          :type => :string, :required => true, :short => "-a"
        opt :database_host, "Database host", :type => :string, 
          :required => true, :short => "-k"
        opt :database_user, "Database username", :type => :string, 
          :required => true, :short => "-u"
        opt :database_password, "Database password", :type => :string,
          :required => true, :short => "-p"
       
        # Global settings
        opt :search_database, "Path to search tool database", :type => :string,
          :short => "-b"
        opt :threads, "Number of threads to spawn for search tool", 
          :type => :int, :short => "-t"
      end

      @args = {} # Contains valid opts.

      ## Additional opt validation. ##

      unless SEARCH_TOOLS.keys.include?(opts[:search_tool].downcase)
        Trollop::die :search_tool, "search_tool not found\n" <<
        "Available search tools: " + SEARCH_TOOLS.keys.join(", ")
      end

      @args[:search_tool] = opts[:search_tool].downcase

      unless opts[:search_database] && Dir.exists?(opts[:search_database])
        Trollop::die :search_database, "search tool database not found\n" <<
        "Supplied directory: " + opts[:search_database]
      end

      @args[:search_database] = opts[:search_database]

      @args[:id]      = opts[:id]
      @args[:threads] = opts[:threads]

      unless Dir.exists?(opts[:log_directory])
        Trollop::die :log_directory, "log directory not found\n" <<
        "Supplied directory: " + opts[:log_directory]
      end

      @args[:log_directory] = opts[:log_directory]
      @args[:tmp_directory] = opts[:tmp_directory]

      ## Check System Dependancies ##

      check_dependencies

      ## Establish ActiveRecord Connection ##

      begin
        ActiveRecord::Base.establish_connection(
          :adapter  => opts[:database_adapter],
          :host     => opts[:database_host],
          :username => opts[:database_user],
          :password => opts[:database_password],
          :database => opts[:database]
        )
      rescue Exception => e
        Trollop::die puts e.message
      end

      ## Execute search tool ##

      if @args[:search_tool].include? "blast"
        blast = Quorum::SearchTools::Blast.new(@args)
        blast.execute_blast
      end
    end

    #
    # Check system dependencies.
    #
    def check_dependencies
      SEARCH_TOOLS[@args[:search_tool]].each do |b|
        system("which #{b} > /dev/null 2>&1")
        if $?.exitstatus > 0
          Trollop::die "Quorum dependency not found for tool " <<
          "#{@args[:search_tool].to_s}. Please add `#{b}` to your PATH."
        end
      end
    end

  end
end

if __FILE__ == $0
  Quorum::Search.new  
end