diff options
Diffstat (limited to 'lib/lazar.rb')
-rw-r--r-- | lib/lazar.rb | 17 |
1 files changed, 11 insertions, 6 deletions
diff --git a/lib/lazar.rb b/lib/lazar.rb index 32f0317..e77de9d 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -17,19 +17,22 @@ raise "Incorrect lazar environment variable LAZAR_ENV '#{ENV["LAZAR_ENV"]}', ple 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 +# 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 => (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://#{(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 @@ -68,13 +71,15 @@ 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","LazarPrediction","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules +CLASSES = ["Feature","Substance","Dataset","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation"]# 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", @@ -94,6 +99,6 @@ CLASSES = ["Feature","Substance","Dataset","LazarPrediction","CrossValidation"," "train-test-validation.rb", "leave-one-out-validation.rb", "crossvalidation.rb", - #"experiment.rb", + "download.rb", "import.rb", ].each{ |f| require_relative f } |