find method fixed

5 files changed, 39 insertions, 23 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 7fe08fa..9918110 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -1,7 +1,7 @@
 module OpenTox
 	module Algorithm 
 
-		class Fminer #< OpenTox
+		class Fminer 
 			include Owl
 
 			def initialize
@@ -20,7 +20,7 @@ module OpenTox
 			end
 		end
 
-		class Lazar #< OpenTox
+		class Lazar 
 			include Owl
 
 			def initialize
@@ -37,6 +37,11 @@ module OpenTox
 						{ :scope => "mandatory", :value => "feature_generation_uri" }
 				}
 			end
+			
+			def self.create_model(params)
+				@uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "lazar"), :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
+			end
+
 		end
 
 		class Similarity
diff --git a/lib/compound.rb b/lib/compound.rb
index 9e1cee7..4385a7d 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -34,6 +34,14 @@ module OpenTox
 			obconversion(@inchi,'inchi','sdf')
 		end
 
+		def image
+			RestClient.get("#{@@cactus_uri}#{@inchi}/image")
+		end
+
+		def image_uri
+			"#{@@cactus_uri}#{@inchi}/image"
+		end
+
 		# Matchs a smarts string
 		def match?(smarts)
 			obconversion = OpenBabel::OBConversion.new
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 4d05e73..ad69038 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -47,8 +47,9 @@ module OpenTox
 				@model.add tuple, OT['complexValue'], complex_value
 				@model.add complex_value, RDF['type'], OT["FeatureValue"]
 				@model.add complex_value, OT['feature'], f
-				@model.add complex_value, OT['value'], value.to_s 
-			end
+				@model.add complex_value, OT['value'], value.to_s
+      end
+  	
 			tuple
 		end
 
@@ -77,7 +78,7 @@ module OpenTox
 		end
 
 		def self.create(data, content_type = 'application/rdf+xml')
-			uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => content_type
+      uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => content_type
 			dataset = Dataset.new
 			dataset.read uri.to_s
 			dataset
@@ -85,9 +86,9 @@ module OpenTox
 
 		def self.find(uri)
 			begin
-				dataset = Dataset.new
-				data = RestClient.get uri, :accept => 'application/rdf+xml' # check if the resource is available
-				dataset.rdf = data
+        dataset = Dataset.new
+        data = RestClient.get uri, :accept => 'application/rdf+xml' # check if the resource is available
+        dataset.rdf = data
 				dataset
 			rescue
 				nil
@@ -222,8 +223,7 @@ module OpenTox
 				:source => self.source,
 				: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,
+				:features => self.features.collect{|f| f.to_s }
 			}.to_yaml
 		end
 
diff --git a/lib/model.rb b/lib/model.rb
index 2f4525a..cd35f09 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -1,6 +1,6 @@
 module OpenTox
 	module Model
-
+   
 		class Lazar
 			include Owl
 
@@ -87,25 +87,28 @@ module OpenTox
 							end
 						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
-					} } }
+
+        if (classification != nil)
+  				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
 			end
 
 			def self.base_uri
diff --git a/lib/owl.rb b/lib/owl.rb
index d9da563..9cb73f2 100644
--- a/lib/owl.rb
+++ b/lib/owl.rb
@@ -12,7 +12,7 @@ module OpenTox
 			
 			# read OT Ontology
 			#@parser.parse_into_model(@model,"http://opentox.org/data/documents/development/RDF%20files/OpenToxOntology/at_download/file")
-			@parser.parse_string_into_model(@model,File.read(File.join(File.dirname(__FILE__),"opentox.owl")),'/')
+			#@parser.parse_string_into_model(@model,File.read(File.join(File.dirname(__FILE__),"opentox.owl")),'/')
 			# reate an anonymous resource for metadata
 			# this has to be rewritten with an URI as soon as the resource has been saved at an definitive location
 			tmp = @model.create_resource