From 23ecfc6fa5ae4913e5cd17b7d58432d1f88d780c Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 10 Aug 2015 09:48:57 +0200
Subject: transfer to new git project started

---
 lib/lazar.rb | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 lib/lazar.rb

(limited to 'lib/lazar.rb')

diff --git a/lib/lazar.rb b/lib/lazar.rb
new file mode 100644
index 0000000..8831ba2
--- /dev/null
+++ b/lib/lazar.rb
@@ -0,0 +1,46 @@
+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 }
+
-- 
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