OWL-DL export added

3 files changed, 137 insertions, 107 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 11c619d..8083db2 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -4,18 +4,6 @@ module OpenTox
   module Algorithm 
 
     class Fminer 
-      include Owl
-
-      def initialize
-        super
-        self.uri = File.join(@@config[:services]["opentox-algorithm"],'fminer')
-        self.title = "fminer"
-        self.source = "http://github.com/amaunz/libfminer"
-        self.parameters = {
-          "Dataset URI" => { :scope => "mandatory", :value => "dataset_uri" },
-          "Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri" }
-        }
-      end
 
       def self.create_feature_dataset(params)
 				LOGGER.debug File.basename(__FILE__) + ": creating feature dataset"
@@ -29,22 +17,6 @@ module OpenTox
     end
 
     class Lazar 
-      include Owl
-
-			def initialize
-				super
-				self.uri = File.join(@@config[:services]["opentox-algorithm"],'lazar')
-				self.title = "lazar"
-				self.source = "http://github.com/helma/opentox-algorithm"
-				self.parameters = {
-					"Dataset URI" =>
-						{ :scope => "mandatory", :value => "dataset_uri" },
-					"Feature URI for dependent variable" =>
-						{ :scope => "mandatory", :value => "feature_uri" },
-					"Feature generation URI" =>
-						{ :scope => "mandatory", :value => "feature_generation_uri" }
-				}
-			end
 			
 			def self.create_model(params)
 				LOGGER.debug params
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 468af04..ab363a9 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -3,7 +3,6 @@ LOGGER.progname = File.expand_path(__FILE__)
 module OpenTox
 
 	class Dataset 
-		#include Owl
 
 		attr_accessor :uri, :title, :source, :identifier, :data, :features, :compounds
 
@@ -14,7 +13,6 @@ module OpenTox
 		end
 
 		def self.find(uri)
-			#LOGGER.debug "Getting data from #{uri}"
 			YAML.load RestClient.get(uri, :accept => 'application/x-yaml').to_s 
 		end
 
@@ -23,19 +21,7 @@ module OpenTox
 			LOGGER.debug "Saving dataset"
 			@features.uniq!
 			@compounds.uniq!
-      #task_uri = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]).post(self.to_yaml, :content_type =>  "application/x-yaml").chomp.to_s		
-      uri = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]).post(self.to_yaml, :content_type =>  "application/x-yaml").chomp.to_s		
-			#task = OpenTox::Task.find(task_uri)
-			#LOGGER.debug "Waiting for task #{task_uri}"
-			#task.wait_for_completion
-			#LOGGER.debug "Dataset task #{task_uri} completed"
-			#if task.failed?
-				#LOGGER.error "Saving dataset failed"
-				#task.failed
-				#exit
-			#end
-			#task.resource
-			uri
+      RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]).post(self.to_yaml, :content_type =>  "application/x-yaml").chomp.to_s		
 		end
 
 =begin
diff --git a/lib/owl.rb b/lib/owl.rb
index 146bce7..05152a3 100644
--- a/lib/owl.rb
+++ b/lib/owl.rb
@@ -1,31 +1,132 @@
 module OpenTox
 
-	module Owl
+	class Owl
 
-		attr_reader :uri
+		attr_reader :uri, :ot_class
 
-		def initialize
-
-			@model = Redland::Model.new Redland::MemoryStore.new
-			@parser = Redland::Parser.new
-			#@serializer = Redland::Serializer.ntriples
+		def initialize(ot_class,uri)
 			
 			# 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")),'/')
-			# 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
-			@model.add tmp, RDF['type'], OT[self.owl_class]
+
+			@model = Redland::Model.new Redland::MemoryStore.new
+			@parser = Redland::Parser.new
+			@ot_class = ot_class
+			@uri = Redland::Uri.new(uri.chomp)
+			@model.add @uri, RDF['type'], OT[@ot_class]
+			
+		end
+
+		def method_missing(name, *args)
+			methods = ['title', 'source', 'identifier', 'algorithm', 'independentVariables', 'dependentVariable']
+			if methods.include? name.to_s.sub(/=/,'')
+				if /=/ =~ name.to_s # setter
+					name = name.to_s.sub(/=/,'')
+					begin # delete existing entry
+						t = @model.object(@uri, DC[name])
+						@model.delete @uri, DC[name], t
+					rescue
+					end
+					@model.add @uri, DC[name], args.first
+				else # getter
+					@model.object(@uri, DC['title']).to_s
+				end
+			else
+				raise "Method '#{name.to_s}' not found."
+			end
+		end
+
+		def parameters=(params)
+			params.each do |name, settings|
+				parameter = @model.create_resource
+				@model.add parameter, RDF['type'], OT['Parameter']
+				@model.add parameter, DC['title'], name
+				@model.add parameter, OT['paramScope'], settings[:scope]
+				@model.add parameter, OT['paramValue'],  settings[:value]
+			end
+		end
+
+		def add_data_entries(compound_uri,features)
+			# add compound
+			compound = @model.subject(DC["identifier"], compound_uri)
+			if compound.nil?
+				compound = @model.create_resource(compound_uri)
+				@model.add compound, RDF['type'], OT["Compound"]
+				@model.add compound, DC["identifier"], compound_uri
+			end
+			features.each do |f|
+				f.each do |feature_uri,value|
+					# add feature
+					feature = find_or_create_feature feature_uri
+					if value.class.to_s == 'Hash'
+						# create tuple
+						tuple = @model.create_resource
+						@model.add tuple, RDF['type'], OT["Tuple"]
+						@model.add tuple, OT['feature'], feature
+						value.each do |uri,v|
+							f = find_or_create_feature uri
+							complex_value = @model.create_resource
+							@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'], v.to_s
+						end
+						# add data entry
+						data_entry = @model.subject OT['compound'], compound
+						if data_entry.nil?
+							data_entry = @model.create_resource
+							@model.add @uri, OT['dataEntry'], data_entry
+							@model.add data_entry, RDF['type'], OT["DataEntry"]
+							@model.add data_entry, OT['compound'], compound
+						end
+						@model.add data_entry, OT['values'], tuple
+					else
+						data_entry = @model.subject OT['compound'], compound
+						if data_entry.nil?
+							data_entry = @model.create_resource
+							@model.add @uri, OT['dataEntry'], data_entry
+							@model.add data_entry, RDF['type'], OT["DataEntry"]
+							@model.add data_entry, OT['compound'], compound
+						end
+						values = @model.create_resource
+						@model.add data_entry, OT['values'], values
+						@model.add values, RDF['type'], OT['FeatureValue']
+						@model.add values, OT['feature'], feature
+						@model.add values, OT['value'], value.to_s
+					end
+				end
+			end
+		end
+
+		def find_or_create_feature(feature_uri)
+			feature = @model.subject(DC["identifier"], feature_uri)
+			if feature.nil?
+				feature = @model.create_resource(feature_uri)
+				@model.add feature, RDF['type'], OT["Feature"]
+				@model.add feature, DC["identifier"], feature_uri
+				@model.add feature, DC["title"], File.basename(feature_uri).split(/#/)[1]
+				@model.add feature, DC['source'], feature_uri
+			end
+			feature
+		end
+
+		def rdf
+			@model.to_string
+		end
+
+=begin
+
+		def to_ntriples
+			@serializer.model_to_string(Redland::Uri.new(@uri), @model)
 		end
 
 		def uri=(uri)
 			@uri = uri.chomp
-			uri = Redland::Uri.new(uri)
 			# rewrite uri
-			@model.subjects(RDF['type'],OT[self.owl_class]).each do |me|
-				@model.delete(me,RDF['type'],OT[self.owl_class])
-				@model.add(uri,RDF['type'],OT[self.owl_class])
+			@model.subjects(RDF['type'],OT[@ot_class]).each do |me|
+				@model.delete(me,RDF['type'],OT[@ot_class])
+				@model.add(uri,RDF['type'],OT[@ot_class])
 				id = @model.object(me, DC['identifier'])
 				@model.delete me, DC['identifier'], id
 				# find/replace metadata
@@ -37,17 +138,18 @@ module OpenTox
 			end
 		end
 
-		def title
-			# I have no idea, why 2 subjects are returned
-			# iterating over all subjects leads to memory allocation problems
-			# SPARQL queries also do not work 
-			#me = @model.subjects(RDF['type'],OT[self.owl_class])[1]
-			me = @model.subject(RDF['type'],OT[self.owl_class])
-			@model.object(me, DC['title']).to_s
+		def read(uri)
+			@parser.parse_into_model(@model,uri)
+			@uri = uri
+		end
+
+		def identifier
+			me = @model.subject(RDF['type'],OT[@ot_class])
+			@model.object(me, DC['identifier']).to_s unless me.nil?
 		end
 
 		def title=(title)
-			me = @model.subject(RDF['type'],OT[self.owl_class])
+			me = @model.subject(RDF['type'],OT[@ot_class])
 			begin
 				t = @model.object(me, DC['title'])
 				@model.delete me, DC['title'], t
@@ -56,13 +158,8 @@ module OpenTox
 			@model.add me, DC['title'], title
 		end
 
-		def source
-			me = @model.subject(RDF['type'],OT[self.owl_class])
-			@model.object(me, DC['source']).to_s unless me.nil?
-		end
-
 		def source=(source)
-			me = @model.subject(RDF['type'],OT[self.owl_class])
+			me = @model.subject(RDF['type'],OT[@ot_class])
 			begin
 				t = @model.object(me, DC['source'])
 				@model.delete me, DC['source'], t
@@ -71,44 +168,19 @@ module OpenTox
 			@model.add me, DC['source'], source
 		end
 
-		def identifier
-			me = @model.subject(RDF['type'],OT[self.owl_class])
-			@model.object(me, DC['identifier']).to_s unless me.nil?
-		end
-
-		def owl_class
-			self.class.to_s.sub(/^OpenTox::/,'').sub(/::.*$/,'')
-		end
-
-		def read(uri)
-			@parser.parse_into_model(@model,uri)
-			@uri = uri
-		end
-
-		def rdf=(rdf)
-			@uri = '/' unless @uri
-			@parser.parse_string_into_model(@model,rdf,@uri)
-		end
-
-		def rdf
-			@model.to_string
-		end
-
-		def to_ntriples
-			@serializer.model_to_string(Redland::Uri.new(@uri), @model)
+		def title
+			# I have no idea, why 2 subjects are returned
+			# iterating over all subjects leads to memory allocation problems
+			# SPARQL queries also do not work 
+			#me = @model.subjects(RDF['type'],OT[@ot_class])[1]
+			me = @model.subject(RDF['type'],OT[@ot_class])
+			@model.object(me, DC['title']).to_s
 		end
 
-		def parameters=(params)
-			params.each do |name, settings|
-				parameter = @model.create_resource
-				@model.add parameter, RDF['type'], OT['Parameter']
-				@model.add parameter, DC['title'], name
-				@model.add parameter, OT['paramScope'], settings[:scope]
-				@model.add parameter, OT['paramValue'],  settings[:value]
-			end
+		def source
+			me = @model.subject(RDF['type'],OT[@ot_class])
+			@model.object(me, DC['source']).to_s unless me.nil?
 		end
-
-=begin
 		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