model adapted to OWL-DL, dataset predictions added

4 files changed, 166 insertions, 145 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index a32a462..7fe08fa 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -14,6 +14,10 @@ module OpenTox
 					"Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri" }
 				}
 			end
+
+			def self.create_feature_dataset(params)
+				RestClient.post params[:feature_generation_uri], :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri] 
+			end
 		end
 
 		class Lazar #< OpenTox
@@ -35,5 +39,23 @@ module OpenTox
 			end
 		end
 
+		class Similarity
+
+			def self.weighted_tanimoto(fp_a,fp_b,p)
+				common_features = fp_a & fp_b
+				all_features = fp_a + fp_b
+				common_p_sum = 0.0
+				if common_features.size > 0
+					common_features.each{|f| common_p_sum += p[f]}
+					all_p_sum = 0.0
+					all_features.each{|f| all_p_sum += p[f]}
+					common_p_sum/all_p_sum
+				else
+					0.0
+				end
+			end
+
+		end
+
 	end
 end
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 225b900..30f9644 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -8,7 +8,6 @@ module OpenTox
 		end
 
 		# create/add to entry from uris or Redland::Resources
-		# TODO add tuple
 		def add(compound,feature,value)
 			compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
 			feature = self.find_or_create_feature feature unless feature.class == Redland::Resource
@@ -57,7 +56,6 @@ module OpenTox
 		def find_or_create_compound(uri)
 			compound = @model.subject(DC["identifier"], uri)
 			if compound.nil?
-				#puts uri
 				compound = @model.create_resource
 				@model.add compound, RDF['type'], OT["Compound"]
 				@model.add compound, DC["identifier"], uri
@@ -78,29 +76,6 @@ module OpenTox
 			feature
 		end
 
-		# find or create a new value and return the resource
-=begin
-		def find_or_create_value(v)
-			value = @model.subject OT["value"], v.to_s
-			if value.nil?
-				value = @model.create_resource
-				@model.add value, RDF['type'], OT["FeatureValue"]
-				@model.add value, OT["value"], v.to_s
-			end
-			value
-		end
-=end
-
-=begin
-		def add_data_entry(compound,feature,value)
-			data_entry = @model.create_resource
-			@model.add data_entry, RDF['type'], OT["DataEntry"]
-			@model.add data_entry, OT['compound'], compound
-			@model.add data_entry, OT['feature'], feature
-			@model.add data_entry, OT['values'], value
-		end
-=end
-
 		def self.create(data, content_type = 'application/rdf+xml')
 			uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => content_type
 			dataset = Dataset.new
@@ -127,30 +102,35 @@ module OpenTox
 			features
 		end
 
-		def data_entries
-			data_entries = {}
-			self.compounds.each do |compound|
-				compound_node = @model.subject(DC["identifier"],compound)
-				compound = compound.to_s.sub(/^\[(.*)\]$/,'\1')
-				data_entries[compound] = {} unless data_entries[compound]
-				@model.subjects(OT['compound'], compound_node).each do |data_entry|
-					feature_node = @model.object(data_entry, OT['feature'])
-					feature = @model.object(feature_node,DC['identifier']).to_s
-					values_node = @model.object(data_entry, OT['values'])
-					data_entries[compound][feature] = [] unless data_entries[compound][feature]
-					@model.find(values_node, OT['value'], nil) do |s,p,value| 
-						case value.to_s
-						when "true"
-							data_entries[compound][feature] << true
-						when "false"
-							data_entries[compound][feature] << false
-						else
-							data_entries[compound][feature] << value.to_s
+		def data
+			data = {}
+			@model.subjects(RDF['type'], OT['DataEntry']).each do |data_entry|
+				compound_node  = @model.object(data_entry, OT['compound'])
+				@model.find(compound_node, OT['identifier'],nil) {|s,p,o| puts o.to_s}
+				compound_uri = @model.object(compound_node, DC['identifier']).to_s
+				data[compound_uri] = [] unless data[compound_uri]
+				@model.find(data_entry, OT['values'], nil) do |s,p,values|
+					entry = {}
+					feature_node = @model.object values, OT['feature']
+					feature_uri = @model.object(feature_node, DC['identifier']).to_s
+					# TODO simple features
+					type = @model.object(values, RDF['type'])
+					if type == OT['FeatureValue']
+						#entry[feature_uri] = [] unless entry[feature_uri]
+						entry[feature_uri] = @model.object(values, OT['value']).to_s
+					elsif type == OT['Tuple']
+						entry[feature_uri] = {} unless entry[feature_uri]
+						@model.find(values, OT['complexValue'],nil) do |s,p,complex_value|
+							name_node = @model.object complex_value, OT['feature']
+							name = @model.object(name_node, DC['title']).to_s
+							value = @model.object(complex_value, OT['value']).to_s
+							entry[feature_uri][name] = value
 						end
 					end
+					data[compound_uri] << entry
 				end
 			end
-			data_entries
+			data
 		end
 
 		def feature_values(feature_uri)
@@ -159,18 +139,17 @@ module OpenTox
 			@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
 				compound = @model.object(compound_node,  DC["identifier"]).to_s.sub(/^\[(.*)\]$/,'\1')
 				features[compound] = [] unless features[compound]
-				@model.subjects(OT['compound'], compound_node).each do |data_entry|
-					if feature == @model.object(data_entry, OT['feature'])
-						values_node = @model.object(data_entry, OT['values'])
-						@model.find(values_node, OT['value'], nil) do |s,p,value| 
-							case value.to_s
-							when "true"
-								features[compound] << true
-							when "false"
-								features[compound] << false
-							else
-								features[compound] << value.to_s
-							end
+				data_entry = @model.subject(OT['compound'], compound_node)
+				@model.find( data_entry, OT['values'], nil ) do |s,p,values|
+					if feature == @model.object(values, OT['feature'])
+						value = @model.object(values, OT['value'])
+						case value.to_s
+						when "true"
+							features[compound] << true
+						when "false"
+							features[compound] << false
+						else
+							features[compound] << value.to_s
 						end
 					end
 				end
@@ -178,6 +157,7 @@ module OpenTox
 			features
 		end
 
+=begin
 		def tuples
 			tuples = []
 			@model.subjects(RDF['type'], OT["Tuple"]).each do |t|
@@ -215,11 +195,12 @@ module OpenTox
 				#puts values_node
 			end
 		end
+=end
 
 		def compounds
 			compounds = []
 			@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
-				compounds << @model.object(compound_node,  DC["identifier"])#
+				compounds << @model.object(compound_node,  DC["identifier"]).to_s
 			end
 			compounds
 		end
@@ -234,8 +215,6 @@ module OpenTox
 		end
 
 		def to_yaml
-			#compounds.each do |c|
-			#end
 			{
 				:uri => self.uri,
 				:opentox_class => self.owl_class,
@@ -244,42 +223,10 @@ module OpenTox
 				:identifier => self.identifier,
 				:compounds => self.compounds.collect{|c| c.to_s.to_s.sub(/^\[(.*)\]$/,'\1')},
 				:features => self.features.collect{|f| f.to_s },
-				#:data_entries => self.data_entries,
-=begin
-				:tuples =>  self.compounds.collect{|c|
-					compound_uri = c.to_s.to_s.sub(/^\[(.*)\]$/,'\1')
-					{compound_uri => self.tuple(compound_uri)}
-				},
-=end
-				#:feature_values => self.features.collect{|f| { f.to_s => self.feature_values(f.to_s)} }
+				:data_entries => self.data_entries,
 			}.to_yaml
 		end
 
 	end
 
 end
-=begin
-		def tuple?(t)
-			statements = []
-			has_tuple = true
-			t.each do |name,v|
-				feature = self.find_or_create_feature(:name => name)
-				value = self.find_or_create_value(v)
-				tuple = @model.subject(feature,value)
-				has_tuple = false if tuple.nil?
-				statements << [tuple,feature,value]
-			end
-			tuples_found = statements.collect{|s| s[0]}.uniq
-			has_tuple = false unless tuples_found.size == 1
-			has_tuple
-		end
-
-		def find_or_create_tuple(t)
-			if self.tuple?(t)
-				t 
-			else
-				self.create_tuple(t)
-			end
-		end
-=end
-
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
diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec
index 827296f..41335e9 100644
--- a/opentox-ruby-api-wrapper.gemspec
+++ b/opentox-ruby-api-wrapper.gemspec
@@ -5,15 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = %q{opentox-ruby-api-wrapper}
-  s.version = "1.2.1"
+  s.version = "1.2.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Christoph Helma"]
-  s.date = %q{2009-12-16}
-  s.default_executable = %q{opentox-install-debian.sh}
+  s.date = %q{2009-12-20}
   s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
   s.email = %q{helma@in-silico.ch}
-  s.executables = ["opentox-install-debian.sh"]
+  s.executables = ["opentox-install-debian.sh", "yaml2owl.rb"]
   s.extra_rdoc_files = [
     "LICENSE",
      "README.rdoc"
@@ -24,6 +23,7 @@ Gem::Specification.new do |s|
      "Rakefile",
      "VERSION",
      "bin/opentox-install-debian.sh",
+     "bin/yaml2owl.rb",
      "lib/algorithm.rb",
      "lib/compound.rb",
      "lib/dataset.rb",
@@ -32,6 +32,7 @@ Gem::Specification.new do |s|
      "lib/helper.rb",
      "lib/model.rb",
      "lib/opentox-ruby-api-wrapper.rb",
+     "lib/opentox.owl",
      "lib/owl.rb",
      "lib/spork.rb",
      "lib/task.rb",