require 'rubygems'
require "bundler/setup"
require "rest-client"
require 'yaml'
require 'json'
require 'logger'
require 'mongoid'
require 'rserve'

# Mongo setup
# TODO retrieve correct environment from Rack/Sinatra
ENV["MONGOID_ENV"] ||= "development"
# TODO remove config files, change default via ENV or directly in Mongoid class
Mongoid.load!("#{ENV['HOME']}/.opentox/config/mongoid.yml")
# TODO get Mongo::Client from Mongoid
$mongo = Mongo::Client.new('mongodb://127.0.0.1:27017/opentox')
# TODO same for GridFS
$gridfs = $mongo.database.fs

# R setup
R = Rserve::Connection.new

# Logger setup
$logger = Logger.new STDOUT # STDERR did not work on my development machine (CH)
$logger.level = Logger::DEBUG
Mongo::Logger.logger = $logger
Mongo::Logger.level = Logger::WARN 
#Mongoid.logger = $logger

# OpenTox classes and includes
CLASSES = ["Feature","Compound",  "Dataset", "Validation", "CrossValidation"]# Algorithm and Models are modules

[ # be aware of the require sequence as it affects class/method overwrites
  "overwrite.rb",
  "rest-client-wrapper.rb", 
  "error.rb",
  "opentox.rb",
  "feature.rb",
  "compound.rb",
  "dataset.rb",
  "descriptor.rb",
  #"algorithm.rb",
  #"model.rb",
  #"validation.rb"
].each{ |f| require_relative f }