require 'rubygems' require "bundler/setup" require "rest-client" require 'addressable' require 'yaml' require 'json' require 'logger' require 'mongoid' require 'rserve' require "nokogiri" require "base64" require 'openbabel' # Environment setup ENV["LAZAR_ENV"] ||= "production" raise "Incorrect lazar environment variable LAZAR_ENV '#{ENV["LAZAR_ENV"]}', please set it to 'production' or 'development'." unless ENV["LAZAR_ENV"].match(/production|development/) ENV["MONGOID_ENV"] = ENV["LAZAR_ENV"] ENV["RACK_ENV"] = ENV["LAZAR_ENV"] # should set sinatra environment # search for a central mongo database in use # http://opentox.github.io/installation/2017/03/07/use-central-mongodb-in-docker-environment CENTRAL_MONGO_IP = `grep -oP '^\\d{1,3}\\.\\d{1,3}\\.\\d{1,3}\\.\\d{1,3}(?=.*mongodb)' /etc/hosts`.chomp Mongoid.load_configuration({ :clients => { :default => { :database => ENV["LAZAR_ENV"], :hosts => (CENTRAL_MONGO_IP.blank? ? ["localhost:27017"] : ["#{CENTRAL_MONGO_IP}:27017"]), } } }) Mongoid.raise_not_found_error = false # return nil if no document is found $mongo = Mongo::Client.new("mongodb://#{(CENTRAL_MONGO_IP.blank? ? "127.0.0.1" : CENTRAL_MONGO_IP)}:27017/#{ENV['LAZAR_ENV']}") $gridfs = $mongo.database.fs # Logger setup STDOUT.sync = true # for redirection, etc see http://stackoverflow.com/questions/8549443/why-doesnt-logger-output-to-stdout-get-redirected-to-files $logger = Logger.new STDOUT # STDERR did not work on my development machine (CH) case ENV["LAZAR_ENV"] when "production" $logger.level = Logger::WARN Mongo::Logger.level = Logger::WARN when "development" $logger.level = Logger::DEBUG Mongo::Logger.level = Logger::WARN end # R setup rlib = File.expand_path(File.join(File.dirname(__FILE__),"..","R")) # should work on POSIX including os x # http://stackoverflow.com/questions/19619582/number-of-processors-cores-in-command-line NR_CORES = `getconf _NPROCESSORS_ONLN`.to_i R = Rserve::Connection.new R.eval ".libPaths('#{rlib}')" R.eval " suppressPackageStartupMessages({ library(labeling,lib=\"#{rlib}\") library(iterators,lib=\"#{rlib}\") library(foreach,lib=\"#{rlib}\") library(ggplot2,lib=\"#{rlib}\") library(grid,lib=\"#{rlib}\") library(gridExtra,lib=\"#{rlib}\") library(pls,lib=\"#{rlib}\") library(caret,lib=\"#{rlib}\") library(doMC,lib=\"#{rlib}\") library(randomForest,lib=\"#{rlib}\") library(plyr,lib=\"#{rlib}\") registerDoMC(#{NR_CORES}) }) " # OpenTox classes and includes CLASSES = ["Feature","Substance","Dataset","LazarPrediction","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# 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", "physchem.rb", "substance.rb", "compound.rb", "nanoparticle.rb", "dataset.rb", "algorithm.rb", "similarity.rb", "feature_selection.rb", "model.rb", "classification.rb", "regression.rb", "caret.rb", "validation-statistics.rb", "validation.rb", "train-test-validation.rb", "leave-one-out-validation.rb", "crossvalidation.rb", #"experiment.rb", "import.rb", ].each{ |f| require_relative f }