initial refactored version for mutagenicity paper

1 files changed, 24 insertions, 72 deletions

diff --git a/lib/lazar.rb b/lib/lazar.rb
index e77de9d..2cc1321 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -1,52 +1,5 @@
-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
-# CH: this interferes with /etc/hosts on my machine
-# 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"]),
-      :hosts => ["localhost:27017"]
-    }
-  }
-})
-Mongoid.raise_not_found_error = false # return nil if no document is found
-#$mongo = Mongo::Client.new("mongodb://#{(CENTRAL_MONGO_IP.blank? ? "127.0.0.1" : CENTRAL_MONGO_IP)}:27017/#{ENV['LAZAR_ENV']}")
-$mongo = Mongo::Client.new("mongodb://127.0.0.1:27017/#{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
-
+require 'fileutils'
+=begin
 # R setup
 rlib = File.expand_path(File.join(File.dirname(__FILE__),"..","R"))
 # should work on POSIX including os x
@@ -72,33 +25,32 @@ suppressPackageStartupMessages({
 "
 
 PUBCHEM_URI = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/"
-CHEMBL_URI = "https://www.ebi.ac.uk/chembl/api/data/molecule/"
-
-# OpenTox classes and includes
-CLASSES = ["Feature","Substance","Dataset","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation"]# Algorithm and Models are modules
+=end
 
 [ # be aware of the require sequence as it affects class/method overwrites
-  "overwrite.rb",
-  "rest-client-wrapper.rb", 
-  "opentox.rb",
-  "feature.rb",
-  "physchem.rb",
-  "substance.rb",
+  "array.rb",
+#  "overwrite.rb",
+#  "rest-client-wrapper.rb", 
+#  "opentox.rb",
+#  "feature.rb",
+#  "physchem.rb",
+#  "substance.rb",
   "compound.rb",
-  "nanoparticle.rb",
+#  "nanoparticle.rb",
   "dataset.rb",
-  "algorithm.rb",
+#  "algorithm.rb",
   "similarity.rb",
-  "feature_selection.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",
-  "download.rb",
-  "import.rb",
+  "statistics.rb",
+#  "classification.rb",
+#  "regression.rb",
+#  "caret.rb",
+#  "validation-statistics.rb",
+#  "validation.rb",
+#  "train-test-validation.rb",
+#  "leave-one-out-validation.rb",
+#  "crossvalidation.rb",
+#  "download.rb",
+#  "import.rb",
 ].each{ |f| require_relative f }