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-rw-r--r--lib/lazar.rb17
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 }