diff options
Diffstat (limited to 'lib/opentox-client.rb')
| -rw-r--r-- | lib/opentox-client.rb | 44 |
1 files changed, 12 insertions, 32 deletions
diff --git a/lib/opentox-client.rb b/lib/opentox-client.rb index 40f87cf..6bffc39 100644 --- a/lib/opentox-client.rb +++ b/lib/opentox-client.rb @@ -1,38 +1,17 @@ require 'rubygems' require "bundler/setup" -#require 'rdf' -#require 'rdf/raptor' -#require 'rdf/turtle' require "rest-client" -#require 'uri' require 'yaml' require 'json' require 'logger' -#require "securerandom" require 'mongoid' -default_config = File.join(ENV["HOME"],".opentox","config","default.rb") -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 +# TODO store development/test, validation, production in separate databases 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#' -#RDF::OT1 = RDF::Vocabulary.new 'http://www.opentox.org/api/1.1#' -#RDF::OTA = RDF::Vocabulary.new 'http://www.opentox.org/algorithmTypes.owl#' -#RDF::OLO = RDF::Vocabulary.new 'http://purl.org/ontology/olo/core#' -#RDF::TB = RDF::Vocabulary.new "http://onto.toxbank.net/api/" -#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 = ["Feature", "Dataset", "Validation", "Task", "Investigation"] -#RDF_FORMATS = [:rdfxml,:ntriples,:turtle] +CLASSES = ["Compound", "Feature", "DataEntry","Dataset"]#, "Validation", "Task", "Investigation"] +#CLASSES = ["Feature", "Dataset", "Validation", "Task", "Investigation"] # Regular expressions for parsing classification data TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i @@ -41,14 +20,15 @@ FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-m [ "overwrite.rb", "rest-client-wrapper.rb", - "error.rb", - "authorization.rb", - "policy.rb", - "otlogger.rb", + #"error.rb", + #"authorization.rb", + #"policy.rb", + #"otlogger.rb", "opentox.rb", - "task.rb", + #"task.rb", "compound.rb", "feature.rb", + "data_entry.rb", "dataset.rb", #"algorithm.rb", #"model.rb", @@ -61,11 +41,11 @@ FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-m #end # defaults to stderr, may be changed to file output (e.g in opentox-service) -$logger = OTLogger.new(STDOUT) # STDERR did not work on my development machine (CH) +$logger = Logger.new STDOUT #OTLogger.new(STDOUT) # STDERR did not work on my development machine (CH) $logger.level = Logger::DEBUG #Mongo::Logger.logger = $logger Mongo::Logger.level = Logger::WARN -#$mongo = Mongo::Client.new($mongodb[:uri]) +$mongo = Mongo::Client.new('mongodb://127.0.0.1:27017/opentox') +$gridfs = $mongo.database.fs Mongoid.logger.level = Logger::WARN Mongoid.logger = $logger -#Moped.logger = $logger |