opentox-ruby-api-wrapper 1.4.0 → 1.5.0

data/lib/model.rb

@@ -1,10 +1,93 @@
 module OpenTox
 	module Model
-   
-		class Lazar
 
-			attr_accessor :dependent_variable, :activity_dataset_uri, :feature_dataset_uri, :effects, :activities, :p_values, :fingerprints, :features, :algorithm
-			
+		class Generic
+
+      MODEL_ATTRIBS = [:uri, :title, :creator, :date, :format, :predictedVariables, :independentVariables, :dependentVariables, :trainingDataset, :algorithm]
+      MODEL_ATTRIBS.each{ |a| attr_accessor(a) }
+
+			def self.find(uri)
+				owl = OpenTox::Owl.from_uri(uri, "Model")
+        return self.new(owl)
+      end
+      
+      def self.to_rdf(model)
+        owl = OpenTox::Owl.create 'Model', model.uri
+        (MODEL_ATTRIBS - [:uri]).each do |a|
+          owl.set(a.to_s,model.send(a.to_s))
+        end
+        owl.rdf
+      end
+      
+      protected
+      def initialize(owl)
+        [:date, :creator, :title, :format, :algorithm, :dependentVariables, 
+         :independentVariables, :predictedVariables, :trainingDataset].each do |a|
+            self.send("#{a.to_s}=".to_sym, owl.get(a.to_s))
+        end
+        @uri = owl.uri 
+        if ENV['RACK_ENV'] =~ /test|debug/
+          begin
+            raise "uri invalid" unless Utils.is_uri?(@uri)
+            raise "no algorithm" unless @algorithm and @algorithm.size>0
+            raise "no dependent variables" unless @dependentVariables and @dependentVariables.size>0 
+            raise "no indenpendent variables" unless @independentVariables
+            raise "no predicted variables" unless @predictedVariables and @predictedVariables.size>0
+          rescue => ex
+            RestClientWrapper.raise_uri_error "invalid model: '"+ex.message+"'\n"+self.to_yaml+"\n",@uri.to_s    
+          end
+        end
+			end
+	 end
+  
+   class PredictionModel < Generic
+     
+     def self.build( algorithm_uri, algorithm_params )
+        
+       if algorithm_uri =~ /ambit2/
+         LOGGER.warn "Ambit hack, replacing 'prediction_feature' with 'target'"
+         algorithm_params[:target] = algorithm_params[:prediction_feature]
+         algorithm_params.delete(:prediction_feature)
+       end
+       
+       LOGGER.debug "Build model, algorithm_uri:"+algorithm_uri.to_s+", algorithm_parms: "+algorithm_params.inspect.to_s
+       uri = OpenTox::RestClientWrapper.post(algorithm_uri,algorithm_params).to_s
+       LOGGER.debug "Build model done: "+uri.to_s
+       RestClientWrapper.raise_uri_error("Invalid build model result: '"+uri.to_s+"'", algorithm_uri, algorithm_params ) unless Utils.model_uri?(uri)
+       return PredictionModel.find(uri)
+     end
+    
+     def predict_dataset( dataset_uri )
+
+       LOGGER.debug "Predict dataset: "+dataset_uri.to_s+" with model "+@uri.to_s
+       uri = RestClientWrapper.post(@uri, {:dataset_uri=>dataset_uri})
+       RestClientWrapper.raise_uri_error("Prediciton result no dataset uri: "+uri.to_s, @uri, {:dataset_uri=>dataset_uri} ) unless Utils.dataset_uri?(uri)
+       uri
+     end
+    
+     def classification?
+       #HACK replace with request to ontology server
+       if @title =~ /lazar classification/
+         return true
+       elsif @uri =~/ntua/ and @title =~ /mlr/
+         return false
+       elsif @uri =~/tu-muenchen/ and @title =~ /regression|M5P|GaussP/
+         return false
+       elsif @uri =~/ambit2/ and @title =~ /pKa/
+         return false
+       elsif @uri =~/majority/
+         return (@uri =~ /class/) != nil
+       else
+         raise "unknown model, uri:'"+@uri.to_s+"' title:'"+@title.to_s+"'"
+       end
+     end
+   end
+  
+   
+		class Lazar < Generic
+      
+      attr_accessor :feature_dataset_uri, :effects, :activities, :p_values, :fingerprints, :features
+      
 			def initialize
 				@source = "http://github.com/helma/opentox-model"
 				@algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
@@ -22,107 +105,9 @@ module OpenTox
 			  resource.post(self.to_yaml, :content_type => "application/x-yaml").chomp.to_s
 			end
 
-
 			def self.find_all
-				RestClient.get(@@config[:services]["opentox-model"]).chomp.split("\n")
-			end
-=begin
-			include Owl
-
-			# Create a new prediction model from a dataset
-			def initialize
-				super
-				self.source = "http://github.com/helma/opentox-model"
-				self.algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
-				self.independentVariables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative") # TODO read this from dataset
-			end
-
-			def self.from_yaml(yaml)
-				yaml = YAML.load yaml
-				lazar = Lazar.new
-				lazar.title = "lazar model for #{yaml[:endpoint]}"
-				lazar.parameters = {
-					"Dataset URI" => { :scope => "mandatory", :value => "dataset_uri=#{yaml[:activity_dataset]}" },
-					"Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri=#{yaml[:endpoint]}" },
-					"Feature generation URI" => { :scope => "mandatory", :value => "feature_generation_uri=#{File.join(@@config[:services]["opentox-algorithm"],"fminer")}"} #TODO write to yaml
-				}
-				lazar.algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
-				lazar.trainingDataset = yaml[:activity_dataset]
-				lazar.dependentVariables = yaml[:endpoint]
-				lazar.predictedVariables = yaml[:endpoint] + "_lazar_prediction"
-				lazar
-			end
-
-			def self.find(uri)
-				yaml = RestClient.get(uri, :accept => "application/x-yaml")
-				OpenTox::Model::Lazar.from_yaml(yaml)
-			end
-			
-			# Predict a compound
-			def predict(compound)
-				# nicht absichern??
-				resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-				resource.post(:compound_uri => compound.uri)
-			end
-
-			def self.base_uri
-				File.join @@config[:services]["opentox-model"],'lazar'
-			end
-
-			def self.create(data)
-			  resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-			  resource.post(data, :content_type => "application/x-yaml").chomp.to_s
-			end
-
-			def delete
-			  resource = RestClient::Resource.new(self.uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-				resource.delete
-				#RestClient.delete @uri if @uri
-				#RestClient.delete model.task_uri if model.task_uri
-			end
-
-#			def self.create(task)
-#				@uri = RestClient.post(@@config[:services]["opentox-model"], :task_uri => task.uri)
-#			end
-
-#			def yaml=(data)
-#				RestClient.put(@@uri, data, :content_type => "application/x-yaml").to_s
-#			end
-
-			def endpoint
-				YAML.load(RestClient.get(uri))[:endpoint]
-			end
-
-			def algorithm=(algorithm)
-				me = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add me, OT['algorithm'], Redland::Uri.new(algorithm) # untyped individual comes from this line, why??
-				@model.add Redland::Uri.new(algorithm), RDF['type'], OT['Algorithm']
-			end
-
-			def trainingDataset=(trainingDataset)
-				me = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add me, OT['trainingDataset'], Redland::Uri.new(trainingDataset) # untyped individual comes from this line, why??
-				@model.add Redland::Uri.new(trainingDataset), RDF['type'], OT['Dataset']
-			end
-
-			def dependentVariables=(dependentVariables)
-				me = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add me, OT['dependentVariables'], Redland::Uri.new(dependentVariables) # untyped individual comes from this line, why??
-				@model.add Redland::Uri.new(dependentVariables), RDF['type'], OT['Feature']
-			end
-
-			def independentVariables=(independentVariables)
-				me = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add me, OT['independentVariables'], Redland::Uri.new(independentVariables) # untyped individual comes from this line, why??
-				@model.add Redland::Uri.new(independentVariables), RDF['type'], OT['Feature']
-			end
-
-			def predictedVariables=(predictedVariables)
-				me = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add me, OT['predictedVariables'], Redland::Uri.new(predictedVariables) # untyped individual comes from this line, why??
-				@model.add Redland::Uri.new(predictedVariables), RDF['type'], OT['Feature']
+				RestClientWrapper.get(@@config[:services]["opentox-model"]).chomp.split("\n")
 			end
-=end
 		end
 	end
 end

data/lib/opentox-ruby-api-wrapper.rb

@@ -8,6 +8,6 @@ rescue LoadError
 	puts "Please install Openbabel with 'rake openbabel:install' in the compound component"
 end
 
-['owl', 'compound','dataset','algorithm','model','task','validation','utils','authorization'].each do |lib|
+['owl', 'compound','dataset','algorithm','model','task','validation','utils','authorization','features', 'rest_client_wrapper'].each do |lib|
 	require lib
 end