diff options
author | Christoph Helma <helma@in-silico.ch> | 2019-08-24 14:44:52 +0200 |
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committer | Christoph Helma <helma@in-silico.ch> | 2019-08-24 14:44:52 +0200 |
commit | 1f789133d961c29d3babfaf69cdde3d675288537 (patch) | |
tree | 25fcae7c3aa4c86a8f69708393d720afd78ce711 /lib/lazar.rb | |
parent | faccda14c0f98333bf7623d4caef00eea7bb1933 (diff) |
initial refactored version for mutagenicity paper
Diffstat (limited to 'lib/lazar.rb')
-rw-r--r-- | lib/lazar.rb | 96 |
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 } |