YAML output for datasets added

2 files changed, 86 insertions, 46 deletions

diff --git a/lib/dataset.rb b/lib/dataset.rb
index fad6baa..895c9fc 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -3,8 +3,6 @@ module OpenTox
 	class Dataset 
 		include Owl
 
-		#attr_accessor :model
-
 		def initialize 
 			super
 		end
@@ -28,7 +26,7 @@ module OpenTox
 				@model.add feature, RDF['type'], OT["Feature"]
 				@model.add feature, DC["identifier"], File.join("feature",feature.to_s.gsub(/[()]/,'')) # relative uri as we don know the final uri
 				@model.add feature, DC["title"], f[:name].to_s
-				@model.add feature, OT['hasSource'], f[:source].to_s if f[:source]
+				@model.add feature, DC['source'], f[:source].to_s if f[:source]
 			end
 			feature
 		end
@@ -66,9 +64,12 @@ module OpenTox
 				feature = self.find_or_create_feature(:name => name)
 				value = self.find_or_create_value(value)
 				pair = @model.create_resource
-				@model.add tuple, OT['tuple'], pair
+				@model.add pair, RDF['type'], OT['FeatureValue']
+				@model.add tuple, OT['complexValue'], pair
 				@model.add pair, OT['feature'], feature
-				@model.add pair, OT['value'], value
+				@model.add pair, OT['value'], value #FIX
+				#@model.add tuple, OT['feature'], feature
+				#@model.add tuple, OT['values'], value
 			end
 			tuple
 		end
@@ -98,7 +99,7 @@ module OpenTox
 
 		def self.find(uri)
 			begin
-				RestClient.get uri # check if the resource is available
+				RestClient.get uri, :accept => 'application/rdf+xml' # check if the resource is available
 				dataset = Dataset.new
 				dataset.read uri.to_s
 				dataset
@@ -108,11 +109,42 @@ module OpenTox
 		end
 
 		def features
+			features = []
+			@model.subjects(RDF['type'], OT["Feature"]).each do |feature_node|
+				features << @model.object(feature_node,  DC["identifier"])#
+			end
+			features
 		end
 
-		def feature_values(uri)
+		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
+						end
+					end
+				end
+			end
+			data_entries
+		end
+
+		def feature_values(feature_uri)
 			features = {}
-			feature = @model.subject(DC["identifier"],uri)
+			feature = @model.subject(DC["identifier"],feature_uri)
 			@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]
@@ -176,7 +208,7 @@ module OpenTox
 		def compounds
 			compounds = []
 			@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
-				compounds << @model.object(compound_node,  DC["identifier"])#.to_s.sub(/^\[(.*)\]$/,'\1')
+				compounds << @model.object(compound_node,  DC["identifier"])#
 			end
 			compounds
 		end
@@ -190,6 +222,28 @@ module OpenTox
 			RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type =>  "application/rdf+xml").to_s
 		end
 
+		def to_yaml
+			#compounds.each do |c|
+			#end
+			{
+				:uri => self.uri,
+				:opentox_class => self.owl_class,
+				:title => self.title,
+				: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,
+=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)} }
+			}.to_yaml
+		end
+
 	end
 
 end
diff --git a/lib/owl.rb b/lib/owl.rb
index 81f2e57..d0d3ee0 100644
--- a/lib/owl.rb
+++ b/lib/owl.rb
@@ -2,7 +2,7 @@ module OpenTox
 
 	module Owl
 
-		attr_reader :uri, :model
+		attr_reader :uri#, :model
 
 		def initialize
 
@@ -10,36 +10,10 @@ module OpenTox
 			@parser = Redland::Parser.new
 			@serializer = Redland::Serializer.ntriples
 			
-			# explicit typing
-			# this should come from http://opentox.org/data/documents/development/RDF%20files/OpenToxOntology/at_download/file (does not pass OWL-DL validation)
-			@parser.parse_into_model(@model,"http://opentox.org/data/documents/development/RDF%20files/OpenToxOntology/at_download/file")
-=begin
-			@model.add @uri, RDF['type'], OWL['Ontology']
-			# annotation properties
-			@model.add DC['source'], RDF['type'], OWL["AnnotationProperty"]
-			@model.add DC['identifier'], RDF['type'], OWL["AnnotationProperty"]
-			@model.add DC['title'], RDF['type'], OWL["AnnotationProperty"]
-			# object properties
-			@model.add OT['feature'], RDF['type'], OWL["ObjectProperty"]
-			@model.add OT['compound'], RDF['type'], OWL["ObjectProperty"]
-			@model.add OT['values'], RDF['type'], OWL["ObjectProperty"]
-			@model.add OT['tuple'], RDF['type'], OWL["ObjectProperty"] # added by ch
-			@model.add OT['parameters'], RDF['type'], OWL["ObjectProperty"]
-			# datatype properties
-			@model.add OT['value'], RDF['type'], OWL["DatatypeProperty"]
-			@model.add OT['paramValue'], RDF['type'], OWL["DatatypeProperty"]
-			@model.add OT['paramScope'], RDF['type'], OWL["DatatypeProperty"]
-			@model.add OT['hasSource'], RDF['type'], OWL["DatatypeProperty"]
-			# classes
-			@model.add OT['Dataset'], RDF['type'], OWL["Class"]
-			@model.add OT['FeatureValue'], RDF['type'], OWL["Class"]
-			@model.add OT['Tuple'], RDF['type'], OWL["Class"] # added by ch
-			@model.add OT['Feature'], RDF['type'], OWL["Class"]
-			@model.add OT['Compound'], RDF['type'], OWL["Class"]
-			@model.add OT['DataEntry'], RDF['type'], OWL["Class"]
-			@model.add OT['Parameter'], RDF['type'], OWL["Class"]
-			@model.add OT['Algorithm'], RDF['type'], OWL["Class"]
-=end
+			# 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")),'/')
+			#@model.add OT['ComplexValue'], RDF['type'], OWL["Class"] # added by ch
 		end
 
 		def owl_class
@@ -62,7 +36,11 @@ module OpenTox
 		end
 
 		def uri=(uri)
-			identifier = uri
+			@uri = uri
+			me = @model.subject(RDF['type'],OT[self.owl_class])
+			identifier = @model.object(me, DC['identifier'])
+			@model.delete me, DC['identifier'], identifier
+			@model.add me, DC['identifier'], uri
 		end
 
 		def to_ntriples
@@ -70,8 +48,18 @@ module OpenTox
 		end
 
 		def title
-			#puts OT[self.owl_class]
-			@model.object(OT[self.owl_class], DC['title']).to_s
+			me = @model.subject(RDF['type'],OT[self.owl_class])
+			@model.object(me, DC['title']).to_s unless me.nil?
+		end
+
+		def source
+			me = @model.subject(RDF['type'],OT[self.owl_class])
+			@model.object(me, DC['source']).to_s unless me.nil?
+		end
+
+		def identifier
+			me = @model.subject(RDF['type'],OT[self.owl_class])
+			@model.object(me, DC['identifier']).to_s unless me.nil?
 		end
 
 		def parameters=(params)
@@ -87,12 +75,10 @@ module OpenTox
 		def create_owl_statement(name,value)
 			r = @model.create_resource
 			dc_class = DC[name.gsub(/^[a-z]/) { |a| a.upcase }] # capitalize only the first letter
+			#puts "DC:" + name.gsub(/^[a-z]/) { |a| a.upcase }
 			@model.add dc_class, RDF['type'], OWL["Class"]
 			@model.add r, RDF['type'], dc_class
 			@model.add r, DC[name], value
-			#puts r
-			#puts DC[name.gsub(/^[a-z]/) { |a| a.upcase }] # capitalize only the first letter
-			#puts DC[name] # capitalize only the first letter
 		end
 
 		def method_missing(name, *args)