resolved conflicts

1 files changed, 37 insertions, 34 deletions

diff --git a/lib/model.rb b/lib/model.rb
index b4ef86c..8877b84 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -1,44 +1,47 @@
 module OpenTox
 	module Model
+
+		class Generic
+
+			attr_accessor :predicted_variables, :independent_variables, :dependent_variables, :activity_dataset_uri, :feature_dataset_uri, :effects, :activities, :p_values, :fingerprints, :features, :algorithm
+
+			def self.find(uri)
+				owl = OpenTox::Owl.from_uri(uri)
+				@title = owl.title
+				@source = owl.source
+				@identifier = owl.identifier.sub(/^\[/,'').sub(/\]$/,'')
+				@uri = @identifier
+				@algorithm = owl.algorithm
+				@dependent_variables = owl.dependentVariables
+				@independent_variables = owl.independentVariables
+				@predicted_variables = owl.predictedVariables
+			end
+			
+		end
    
-		class Lazar
-    	include Owl
-      
-      PREDICTION_FEATURE_MODIFIER = "_lazar_prediction"
+		class Lazar < Generic
 
-			# 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
+				@source = "http://github.com/helma/opentox-model"
+				@algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
+				#@independent_variables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative")
+				@features = []
+				@effects = {}
+				@activities = {}
+				@p_values = {}
+				@fingerprints = {}
 			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] + PREDICTION_FEATURE_MODIFIER
-				lazar
+			def save
+				@features.uniq!
+			  resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			  resource.post(self.to_yaml, :content_type => "application/x-yaml").chomp.to_s
 			end
 
 			def self.find_all
-				RestClient.get(@@config[:services]["opentox-model"]).split("\n")
+				RestClient.get(@@config[:services]["opentox-model"]).chomp.split("\n")
 			end
-
-			def self.find(uri)
-				yaml = RestClient.get(uri, :accept => "application/x-yaml")
-				OpenTox::Model::Lazar.from_yaml(yaml)
-  		end
-    
+=begin
 			
 			# Predict a compound
 			def predict(compound)
@@ -48,12 +51,12 @@ module OpenTox
 			end
 
 			def self.base_uri
-				@@config[:services]["opentox-model"]
+				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").to_s
+			  resource.post(data, :content_type => "application/x-yaml").chomp.to_s
 			end
 
 			def delete
@@ -103,8 +106,8 @@ module OpenTox
 				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']
-		  end
-    
+			end
+=end
 		end
 	end
 end