diff options
Diffstat (limited to 'lib/opentox-client.rb')
| -rw-r--r-- | lib/opentox-client.rb | 18 |
1 files changed, 15 insertions, 3 deletions
diff --git a/lib/opentox-client.rb b/lib/opentox-client.rb index 9f3373d..6358705 100644 --- a/lib/opentox-client.rb +++ b/lib/opentox-client.rb @@ -9,8 +9,7 @@ require 'yaml' require 'json' require 'logger' require "securerandom" -require 'mongo' -require 'bson' +require 'mongoid' default_config = File.join(ENV["HOME"],".opentox","config","default.rb") client_config = File.join(ENV["HOME"],".opentox","config","opentox-client.rb") @@ -18,6 +17,9 @@ client_config = File.join(ENV["HOME"],".opentox","config","opentox-client.rb") puts "Could not find configuration files #{default_config} or #{client_config}" unless File.exist? default_config or File.exist? client_config require default_config if File.exist? default_config require client_config if File.exist? client_config +# TODO switch to production +ENV["MONGOID_ENV"] = "development" +Mongoid.load!("#{ENV['HOME']}/.opentox/config/mongoid.yml") # define constants and global variables #RDF::OT = RDF::Vocabulary.new 'http://www.opentox.org/api/1.2#' @@ -28,7 +30,8 @@ require client_config if File.exist? client_config #RDF::ISA = RDF::Vocabulary.new "http://onto.toxbank.net/isa/" #RDF::OWL = RDF::Vocabulary.new "http://www.w3.org/2002/07/owl#" -CLASSES = ["Compound", "Feature", "Dataset", "Validation", "Task", "Investigation"] +#CLASSES = ["Compound", "Feature", "Dataset", "Validation", "Task", "Investigation"] +CLASSES = ["Feature", "Dataset", "Validation", "Task", "Investigation"] #RDF_FORMATS = [:rdfxml,:ntriples,:turtle] # Regular expressions for parsing classification data @@ -57,3 +60,12 @@ FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-m # unauthorized_error "Failed to authenticate user \"#{$aa[:user]}\"." unless OpenTox::Authorization.is_token_valid(OpenTox::RestClientWrapper.subjectid) #end +# defaults to stderr, may be changed to file output (e.g in opentox-service) +$logger = OTLogger.new(STDERR) +$logger.level = Logger::DEBUG +#Mongo::Logger.logger = $logger +Mongo::Logger.level = Logger::WARN +#$mongo = Mongo::Client.new($mongodb[:uri]) +Mongoid.logger.level = Logger::WARN +Mongoid.logger = $logger +#Moped.logger = $logger |