model adapted to OWL-DL, dataset predictions added

1 files changed, 99 insertions, 48 deletions

diff --git a/lib/model.rb b/lib/model.rb
index 50d6bea..2f4525a 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -1,16 +1,18 @@
 module OpenTox
 	module Model
+
 		class Lazar
 			include Owl
+
+			attr_accessor :dataset, :predictions
 			
 			# Create a new prediction model from a dataset
-			def initialize
-				super
-			end
-
-			def read_yaml(id,yaml)
-				@lazar = YAML.load yaml
-				self.identifier = File.join(@@config[:services]["opentox-model"],'lazar',id)
+			def initialize(yaml)
+				super()
+				id = File.basename(yaml,'.yaml')
+				# TODO Untyped Individual: http://localhost:4003/lazar/{id} ????
+				@lazar = YAML.load_file yaml
+				self.uri = File.join(@@config[:services]["opentox-model"],'lazar',id)
 				self.title = "lazar model for #{@lazar[:endpoint]}"
 				self.source = "http://github.com/helma/opentox-model"
 				self.parameters = {
@@ -18,19 +20,24 @@ module OpenTox
 					"Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri=#{@lazar[:endpoint]}" },
 					"Feature generation URI" => { :scope => "mandatory", :value => "feature_generation_uri=" } #TODO write to yaml
 				}
-				self.algorithm = File.join(@@config[:services]["opentox-model"],"lazar")
+				self.algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
 				self.trainingDataset = @lazar[:activity_dataset]
 				self.dependentVariables = @lazar[:endpoint]
-				self.predictedVariables = @lazar[:endpoint] + " lazar prediction"
+				self.independentVariables = "http://localhost:4002/fminer#BBRC_representative" # TODO read this from dataset
+				self.predictedVariables = @lazar[:endpoint] #+ " lazar prediction"
+				@dataset = OpenTox::Dataset.new
+				@predictions = {}
 			end
 
 			def self.find(uri)
+=begin
 				begin
 					YAML.load(RestClient.get uri)
 					Lazar.new uri
 				rescue
 					halt 404, "Model #{uri} not found."
 				end
+=end
 			end
 
 			def self.find_all
@@ -42,6 +49,65 @@ module OpenTox
 				RestClient.post(@uri, :compound_uri => compound.uri)
 			end
 
+			def database_activity?(compound_uri)
+				# find database activities
+				db_activities = @lazar[:activities][compound_uri]
+				if db_activities
+					c = @dataset.find_or_create_compound(compound_uri)
+					f = @dataset.find_or_create_feature(@lazar[:endpoint])
+					v = db_activities.join(',')
+					@dataset.add c,f,v
+					@predictions[compound_uri] = { @lazar[:endpoint] => {:measured_activities => db_activities}}
+					true
+				else
+					false
+				end
+			end
+
+			def classify(compound_uri)
+
+				compound = OpenTox::Compound.new(:uri => compound_uri)
+				compound_matches = compound.match @lazar[:features]
+
+				conf = 0.0
+				neighbors = []
+				classification = nil
+
+				@lazar[:fingerprints].each do |uri,matches|
+
+					sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(compound_matches,matches,@lazar[:p_values])
+					if sim > 0.3
+						neighbors << uri
+						@lazar[:activities][uri].each do |act|
+							case act.to_s
+							when 'true'
+								conf += OpenTox::Utils.gauss(sim)
+							when 'false'
+								conf -= OpenTox::Utils.gauss(sim)
+							end
+						end
+					end
+				end
+
+				conf = conf/neighbors.size
+				if conf > 0.0
+					classification = true
+				elsif conf < 0.0
+					classification = false
+				end
+			
+				compound = @dataset.find_or_create_compound(compound_uri)
+				feature = @dataset.find_or_create_feature(@lazar[:endpoint])
+				tuple = @dataset.create_tuple(feature,{ 'lazar#classification' => classification, 'lazar#confidence' => conf})
+				@dataset.add_tuple compound,tuple
+				@predictions[compound_uri] = { @lazar[:endpoint] => { :lazar_prediction => {
+						:classification => classification,
+						:confidence => conf,
+						:neighbors => neighbors,
+						:features => compound_matches
+					} } }
+			end
+
 			def self.base_uri
 				@@config[:services]["opentox-model"]
 			end
@@ -54,50 +120,35 @@ module OpenTox
 				YAML.load(RestClient.get uri)[:endpoint]
 			end
 
-		end
-	end
-
-
-=begin
-	module Model 
-
-		class LazarClassification < OpenTox
-
-
-		end
-
-	end
-
-	module Prediction
-
-		module Classification
-
-			class Lazar < OpenTox
-
-				def initialize(params)
-					super(params[:uri])
-				end
-
-				def classification
-					YAML.load(RestClient.get(@uri))[:classification]
-				end
-
-				def confidence
-					YAML.load(RestClient.get(@uri))[:confidence]
-				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 neighbors
-					RestClient.get @uri + '/neighbors' 
-				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 features
-					RestClient.get @uri + '/features' 
-				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']
+			end
 		end
-
 	end
-=end
 end