require 'rubygems'
require "bundler/setup"
#require 'rdf'
#require 'rdf/raptor'
#require 'rdf/turtle'
require "rest-client"
require 'uri'
require 'yaml'
require 'json'
require 'logger'
require "securerandom"
require 'mongoid'

default_config = File.join(ENV["HOME"],".opentox","config","default.rb")
client_config = File.join(ENV["HOME"],".opentox","config","opentox-client.rb")

puts "Could not find configuration files #{default_config} or #{client_config}" unless File.exist? default_config or File.exist? client_config
require default_config if File.exist? default_config
require client_config if File.exist? client_config
# TODO switch to production
ENV["MONGOID_ENV"] = "development"
Mongoid.load!("#{ENV['HOME']}/.opentox/config/mongoid.yml")

# define constants and global variables
#RDF::OT =  RDF::Vocabulary.new 'http://www.opentox.org/api/1.2#'
#RDF::OT1 =  RDF::Vocabulary.new 'http://www.opentox.org/api/1.1#'
#RDF::OTA =  RDF::Vocabulary.new 'http://www.opentox.org/algorithmTypes.owl#'
#RDF::OLO =  RDF::Vocabulary.new 'http://purl.org/ontology/olo/core#'
#RDF::TB  = RDF::Vocabulary.new "http://onto.toxbank.net/api/"
#RDF::ISA = RDF::Vocabulary.new "http://onto.toxbank.net/isa/"
#RDF::OWL = RDF::Vocabulary.new "http://www.w3.org/2002/07/owl#"

#CLASSES = ["Compound", "Feature", "Dataset", "Validation", "Task", "Investigation"]
CLASSES = ["Feature", "Dataset", "Validation", "Task", "Investigation"]
#RDF_FORMATS = [:rdfxml,:ntriples,:turtle]

# Regular expressions for parsing classification data
TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i
FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-mutagenic)$/i

[
  "overwrite.rb",
  "rest-client-wrapper.rb", 
  "error.rb",
  "authorization.rb", 
  "policy.rb", 
  "otlogger.rb", 
  "opentox.rb",
  "task.rb",
  "compound.rb",
  "feature.rb",
  "dataset.rb",
  "algorithm.rb",
  "model.rb",
  "validation.rb"
].each{ |f| require_relative f }

#if defined?($aa) and $aa[:uri] 
#  OpenTox::Authorization.authenticate($aa[:user],$aa[:password])
#  unauthorized_error "Failed to authenticate user \"#{$aa[:user]}\"." unless OpenTox::Authorization.is_token_valid(OpenTox::RestClientWrapper.subjectid)
#end

# defaults to stderr, may be changed to file output (e.g in opentox-service)
$logger = OTLogger.new(STDERR) 
$logger.level = Logger::DEBUG
#Mongo::Logger.logger = $logger
Mongo::Logger.level = Logger::WARN 
#$mongo = Mongo::Client.new($mongodb[:uri])
Mongoid.logger.level = Logger::WARN
Mongoid.logger = $logger
#Moped.logger = $logger