resolved conflicts

10 files changed, 280 insertions, 229 deletions

diff --git a/Rakefile b/Rakefile
index 102160f..2dfb2c6 100644
--- a/Rakefile
+++ b/Rakefile
@@ -10,14 +10,14 @@ begin
     gem.email = "helma@in-silico.ch"
     gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper"
     gem.authors = ["Christoph Helma"]
-		["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets"].each do |dep|
+		["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets"].each do |dep|
 			gem.add_dependency dep
 		end
-		['cucmber','jeweler'].each do |dep|
+		['cucumber','jeweler', "thin"].each do |dep|
 			gem.add_development_dependency dep
 		end
 		gem.files =  FileList["[A-Z]*", "{bin,generators,lib,test}/**/*", 'lib/jeweler/templates/.gitignore']
-		gem.files.include %w(lib/tasks/owl.rb, lib/environment.rb, lib/algorithm.rb, lib/compound.rb, lib/dataset.rb, lib/model.rb, lib/utils.rb, lib/templates/*)
+		gem.files.include %w(lib/tasks/owl.rb, lib/environment.rb, lib/algorithm.rb, lib/compound.rb, lib/dataset.rb, lib/model.rb, lib/utils.rb, lib/validation.rb, lib/templates/*)
     # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
   end
 	Jeweler::GemcutterTasks.new
diff --git a/VERSION b/VERSION
index c04c650..88c5fb8 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.2.7
+1.4.0
diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 2a781d8..8083db2 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -1,51 +1,32 @@
+LOGGER.progname = File.expand_path(__FILE__)
+
 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"
         resource = RestClient::Resource.new(params[:feature_generation_uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
         resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri]
       end
+
+			def self.uri
+				File.join(@@config[:services]["opentox-algorithm"], "fminer")
+			end
     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
 				LOGGER.debug File.basename(__FILE__) + ": creating model"
-				#@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")
-        resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-        @uri = resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
+        resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0], :content_type => "application/x-yaml")
+        @uri = resource.post(:dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).chomp
+			end
+
+			def self.uri
+				File.join(@@config[:services]["opentox-algorithm"], "lazar")
 			end
 
     end
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 2d49829..f416921 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -1,12 +1,47 @@
+LOGGER.progname = File.expand_path(__FILE__)
+
 module OpenTox
 
 	class Dataset 
-		include Owl
+
+		attr_accessor :uri, :title, :source, :identifier, :data, :features, :compounds
 
 		def initialize 
-			super
+			@data = {}
+			@features = []
+			@compounds = []
+		end
+
+		def self.find(uri)
+			if uri.match(/webservices.in-silico.ch|localhost/) # try to get YAML first
+				YAML.load RestClient.get(uri, :accept => 'application/x-yaml').to_s 
+			else # get default rdf+xml
+				owl = OpenTox::Owl.from_uri(uri)
+				@title = owl.title
+				@source = owl.source
+				@identifier = owl.identifier.sub(/^\[/,'').sub(/\]$/,'')
+				@uri = @identifier
+				@data = owl.data
+				halt 404, "Dataset #{uri} empty!" if @data.empty?
+				@data.each do |compound,features|
+					@compounds << compound
+					features.each do |f,v|
+						@features << f
+					end
+				end
+				@compounds.uniq!
+				@features.uniq!
+			end
 		end
 
+
+		def save
+			@features.uniq!
+			@compounds.uniq!
+      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
 		# create/add to entry from uris or Redland::Resources
 		def add(compound,feature,value)
 			compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
@@ -85,6 +120,7 @@ module OpenTox
       resource = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])		  
 		  uri = resource.post data, :content_type => content_type
 			dataset = Dataset.new
+<<<<<<< HEAD
 			dataset.read uri.to_s
 			dataset
 		end
@@ -96,6 +132,9 @@ module OpenTox
 			#LOGGER.debug data
 			#data = RestClient.get(uri, :accept => 'application/rdf+xml') # unclear why this does not work for complex uris, Dataset.find works from irb
 			dataset.rdf = data
+=======
+			dataset.read uri.chomp.to_s
+>>>>>>> helma/development
 			dataset
 		end
 
@@ -107,6 +146,7 @@ module OpenTox
 			features
 		end
 
+<<<<<<< HEAD
 		def data
 			data = {}
 			@model.subjects(RDF['type'], OT['DataEntry']).each do |data_entry|
@@ -158,6 +198,8 @@ module OpenTox
 			end
 			data
 		end
+=======
+>>>>>>> helma/development
 
 		def compounds
 			compounds = []
@@ -173,35 +215,13 @@ module OpenTox
       resource.delete
     end
 
-		def save
-			LOGGER.debug "Saving dataset"
-			#task_uri = RestClient.post(@@config[:services]["opentox-dataset"], self.rdf, :content_type =>  "application/rdf+xml").to_s
-      task_uri = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]).post(self.rdf, :content_type =>  "application/rdf+xml").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
+		def to_owl
 		end
 
-		def to_yaml
-			{
-				: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 => self.data
-			}.to_yaml
+		def from_owl
 		end
 
+=end
 	end
 
 end
diff --git a/lib/model.rb b/lib/model.rb
index b4ef86c..8877b84 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -1,44 +1,47 @@
 module OpenTox
 	module Model
+
+		class Generic
+
+			attr_accessor :predicted_variables, :independent_variables, :dependent_variables, :activity_dataset_uri, :feature_dataset_uri, :effects, :activities, :p_values, :fingerprints, :features, :algorithm
+
+			def self.find(uri)
+				owl = OpenTox::Owl.from_uri(uri)
+				@title = owl.title
+				@source = owl.source
+				@identifier = owl.identifier.sub(/^\[/,'').sub(/\]$/,'')
+				@uri = @identifier
+				@algorithm = owl.algorithm
+				@dependent_variables = owl.dependentVariables
+				@independent_variables = owl.independentVariables
+				@predicted_variables = owl.predictedVariables
+			end
+			
+		end
    
-		class Lazar
-    	include Owl
-      
-      PREDICTION_FEATURE_MODIFIER = "_lazar_prediction"
+		class Lazar < Generic
 
-			# Create a new prediction model from a dataset
 			def initialize
-				super
-				self.source = "http://github.com/helma/opentox-model"
-				self.algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
-				self.independentVariables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative") # TODO read this from dataset
+				@source = "http://github.com/helma/opentox-model"
+				@algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
+				#@independent_variables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative")
+				@features = []
+				@effects = {}
+				@activities = {}
+				@p_values = {}
+				@fingerprints = {}
 			end
 
-			def self.from_yaml(yaml)
-				yaml = YAML.load yaml
-				lazar = Lazar.new
-				lazar.title = "lazar model for #{yaml[:endpoint]}"
-				lazar.parameters = {
-					"Dataset URI" => { :scope => "mandatory", :value => "dataset_uri=#{yaml[:activity_dataset]}" },
-					"Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri=#{yaml[:endpoint]}" },
-					"Feature generation URI" => { :scope => "mandatory", :value => "feature_generation_uri=#{File.join(@@config[:services]["opentox-algorithm"],"fminer")}"} #TODO write to yaml
-				}
-				lazar.algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
-				lazar.trainingDataset = yaml[:activity_dataset]
-				lazar.dependentVariables = yaml[:endpoint]
-				lazar.predictedVariables = yaml[:endpoint] + PREDICTION_FEATURE_MODIFIER
-				lazar
+			def save
+				@features.uniq!
+			  resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			  resource.post(self.to_yaml, :content_type => "application/x-yaml").chomp.to_s
 			end
 
 			def self.find_all
-				RestClient.get(@@config[:services]["opentox-model"]).split("\n")
+				RestClient.get(@@config[:services]["opentox-model"]).chomp.split("\n")
 			end
-
-			def self.find(uri)
-				yaml = RestClient.get(uri, :accept => "application/x-yaml")
-				OpenTox::Model::Lazar.from_yaml(yaml)
-  		end
-    
+=begin
 			
 			# Predict a compound
 			def predict(compound)
@@ -48,12 +51,12 @@ module OpenTox
 			end
 
 			def self.base_uri
-				@@config[:services]["opentox-model"]
+				File.join @@config[:services]["opentox-model"],'lazar'
 			end
 
 			def self.create(data)
 			  resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-			  resource.post(data, :content_type => "application/x-yaml").to_s
+			  resource.post(data, :content_type => "application/x-yaml").chomp.to_s
 			end
 
 			def delete
@@ -103,8 +106,8 @@ module OpenTox
 				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
 end
diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb
index 03838e8..849043c 100644
--- a/lib/opentox-ruby-api-wrapper.rb
+++ b/lib/opentox-ruby-api-wrapper.rb
@@ -8,6 +8,6 @@ rescue LoadError
 	puts "Please install Openbabel with 'rake openbabel:install' in the compound component"
 end
 
-['owl', 'compound','dataset','algorithm','model','task','utils','authorization'].each do |lib|
+['owl', 'compound','dataset','algorithm','model','task','validation','utils','authorization'].each do |lib|
 	require lib
 end
diff --git a/lib/owl.rb b/lib/owl.rb
index 82d6e0e..1d47d2c 100644
--- a/lib/owl.rb
+++ b/lib/owl.rb
@@ -1,101 +1,55 @@
 module OpenTox
 
-	module Owl
+	class Owl
 
-		attr_reader :uri
+		attr_accessor :uri, :ot_class, :model
 
 		def initialize
-
 			@model = Redland::Model.new Redland::MemoryStore.new
-			@parser = Redland::Parser.new
-			@serializer = Redland::Serializer.ntriples
-			
-			# 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]
-		end
-
-		def uri=(uri)
-			@uri = uri
-			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])
-				id = @model.object(me, DC['identifier'])
-				@model.delete me, DC['identifier'], id
-				# find/replace metadata
-				@model.find(me, nil, nil) do |s,p,o|
-					@model.delete s,p,o
-					@model.add uri,p,o
-				end
-				@model.add uri, DC['identifier'], @uri 
-			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 self.create(ot_class,uri)
+			owl = OpenTox::Owl.new
+			owl.ot_class = ot_class
+			owl.uri = Redland::Uri.new(uri.chomp)
+			owl.model.add owl.uri, RDF['type'], OT[owl.ot_class]
+			owl.model.add owl.uri, DC['identifier'], owl.uri
+			owl
 		end
 
-		def title=(title)
-			me = @model.subject(RDF['type'],OT[self.owl_class])
+		def self.from_uri(uri)
+			owl = OpenTox::Owl.new
+			parser = Redland::Parser.new
 			begin
-				t = @model.object(me, DC['title'])
-				@model.delete me, DC['title'], t
-			rescue
+				parser.parse_into_model(owl.model,uri)
+			rescue => e
+				raise "Error parsing #{uri}: #{e.message + e.backtrace}"
 			end
-			@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])
-			begin
-				t = @model.object(me, DC['source'])
-				@model.delete me, DC['source'], t
-			rescue
-			end
-			@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)
+			owl.uri =  Redland::Uri.new(uri.chomp)
+			owl
 		end
 
 		def rdf
 			@model.to_string
 		end
 
-		def to_ntriples
-			@serializer.model_to_string(Redland::Uri.new(@uri), @model)
+		def method_missing(name, *args)
+			methods = ['title', 'source', 'identifier', 'algorithm', 'independentVariables', 'dependentVariables', 'predictedVariables', 'date','trainingDataset' ]
+			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[name.to_s]).to_s
+				end
+			else
+				raise "Method '#{name.to_s}' not found."
+			end
 		end
 
 		def parameters=(params)
@@ -108,26 +62,110 @@ module OpenTox
 			end
 		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
-			#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
+		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 method_missing(name, *args)
-			# create magic setter methods
-			if /=/ =~ name.to_s
-				create_owl_statement name.to_s.sub(/=/,''), args.first
-			else
-				raise "No method #{name}"
+		def data
+			data = {}
+			@model.subjects(RDF['type'], OT['DataEntry']).each do |data_entry|
+				compound_node  = @model.object(data_entry, OT['compound'])
+				compound_uri = @model.object(compound_node, DC['identifier']).to_s
+				@model.find(data_entry, OT['values'], nil) do |s,p,values|
+					feature_node = @model.object values, OT['feature']
+					feature_uri = @model.object(feature_node, DC['identifier']).to_s.sub(/\^\^.*$/,'') # remove XML datatype
+					type = @model.object(values, RDF['type'])
+					if type == OT['FeatureValue']
+						value = @model.object(values, OT['value']).to_s
+						case value.to_s
+						when TRUE_REGEXP # defined in environment.rb
+							value = true
+						when FALSE_REGEXP # defined in environment.rb
+							value = false
+						else
+							LOGGER.warn compound_uri + " has value '" + value.to_s + "' for feature " + feature_uri
+							value = nil
+						end
+						data[compound_uri] = [] unless data[compound_uri]
+						data[compound_uri] << {feature_uri => value} unless value.nil?
+					elsif type == OT['Tuple']
+						entry = {}
+						data[compound_uri] = [] unless data[compound_uri]
+						#data[compound_uri][feature_uri] = [] unless data[compound_uri][feature_uri]
+						@model.find(values, OT['complexValue'],nil) do |s,p,complex_value|
+							name_node = @model.object complex_value, OT['feature']
+							name = @model.object(name_node, DC['title']).to_s
+							value = @model.object(complex_value, OT['value']).to_s
+							v = value.sub(/\^\^.*$/,'') # remove XML datatype
+							v = v.to_f if v.match(/^[\.|\d]+$/) # guess numeric datatype
+							entry[name] = v
+						end
+						data[compound_uri] << {feature_uri => entry} unless entry.empty?
+					end
+				end
 			end
+			data
 		end
-=end
 
 	end
-
 end
diff --git a/lib/task.rb b/lib/task.rb
index c5cddf7..5591a34 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -1,3 +1,5 @@
+LOGGER.progname = File.expand_path(__FILE__)
+
 module OpenTox
 
 	class Task
@@ -5,16 +7,13 @@ module OpenTox
 		attr_accessor :uri
 
 		def initialize(uri)
-			#super()
-			@uri = uri
+			@uri = uri.chomp
 		end
 
 		def self.create
-			#uri = RestClient.post @@config[:services]["opentox-task"], {}
       resource = RestClient::Resource.new(@@config[:services]["opentox-task"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-			#uri = resource.post(nil)
-			uri = resource.post({})
-			Task.new(uri)
+			uri = resource.post({}).chomp
+			Task.new(uri.chomp)
 		end
 
 		def self.find(uri)
@@ -26,7 +25,7 @@ module OpenTox
 		end
 
 		def self.all
-			task_uris = RestClient.get(@@config[:services]["opentox-task"]).split(/\n/)
+			task_uris = RestClient.get(@@config[:services]["opentox-task"]).chomp.split(/\n/)
 			task_uris.collect{|uri| Task.new(uri)}
 		end
 
@@ -53,7 +52,7 @@ module OpenTox
 		end
 
 		def cancel
-			resource = RestClient::Resource.new(@File.join(@uri,'cancelled'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			resource = RestClient::Resource.new(File.join(@uri,'cancelled'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
 			resource.put({})
 		end
 
@@ -62,23 +61,8 @@ module OpenTox
 			resource.put :resource => uri
 		end
 
-=begin
-		def started
-			RestClient.put File.join(@uri,'started'), {}
-		end
-
-		def cancel
-			RestClient.put File.join(@uri,'cancelled'), {}
-		end
-
-		def completed(uri)
-			RestClient.put File.join(@uri,'completed'), :resource => uri
-		end
-
-=end
 		def failed
-			#RestClient.put File.join(@uri,'failed'), {}
-			resource = RestClient::Resource.new(@File.join(@uri,'failed'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			resource = RestClient::Resource.new(File.join(@uri,'failed'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
 			resource.put({})
 		end
 
@@ -102,9 +86,9 @@ module OpenTox
 			self.status.to_s == 'failed'
 		end
 
-		def wait_for_completion
+		def wait_for_completion(dur=0.1)
 			until self.completed? or self.failed?
-				sleep 1
+				sleep dur
 			end
 		end
 
diff --git a/lib/validation.rb b/lib/validation.rb
new file mode 100644
index 0000000..6fd5704
--- /dev/null
+++ b/lib/validation.rb
@@ -0,0 +1,21 @@
+module OpenTox
+	class Validation
+
+		attr_accessor :uri
+
+		def initialize(params)
+			resource = RestClient::Resource.new(params[:uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			@uri = resource.post(params).to_s
+		end
+		
+		def self.crossvalidation(params)
+			params[:uri] = File.join(@@config[:services]['opentox-validation'], "crossvalidation")
+      params[:num_folds] = 10 unless params[:num_folds]
+		 	params[:random_seed] = 2 unless params[:random_seed]
+		 	params[:stratified] = false unless params[:stratified]
+			OpenTox::Validation.new(params)
+		end
+
+	end
+end
+
diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec
index 89de270..258ee09 100644
--- a/opentox-ruby-api-wrapper.gemspec
+++ b/opentox-ruby-api-wrapper.gemspec
@@ -5,14 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = %q{opentox-ruby-api-wrapper}
-  s.version = "1.2.7"
+  s.version = "1.4.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Christoph Helma"]
-  s.date = %q{2010-02-09}
+  s.date = %q{2010-03-18}
   s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
   s.email = %q{helma@in-silico.ch}
-  s.executables = ["yaml2owl.rb", "opentox-install-debian.sh"]
+  s.executables = ["opentox-install-ubuntu.sh", "opentox-install-debian.sh", "yaml2owl.rb"]
   s.extra_rdoc_files = [
     "LICENSE",
      "README.rdoc"
@@ -23,8 +23,10 @@ Gem::Specification.new do |s|
      "Rakefile",
      "VERSION",
      "bin/opentox-install-debian.sh",
+     "bin/opentox-install-ubuntu.sh",
      "bin/yaml2owl.rb",
      "lib/algorithm.rb",
+     "lib/authorization.rb",
      "lib/compound.rb",
      "lib/config/config_ru.rb",
      "lib/dataset.rb",
@@ -38,7 +40,9 @@ Gem::Specification.new do |s|
      "lib/task.rb",
      "lib/tasks/opentox.rb",
      "lib/templates/config.yaml",
-     "lib/utils.rb"
+     "lib/templates/users.yaml",
+     "lib/utils.rb",
+     "lib/validation.rb"
   ]
   s.homepage = %q{http://github.com/helma/opentox-ruby-api-wrapper}
   s.rdoc_options = ["--charset=UTF-8"]
@@ -56,28 +60,28 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<rack>, [">= 0"])
       s.add_runtime_dependency(%q<rack-contrib>, [">= 0"])
       s.add_runtime_dependency(%q<rack-flash>, [">= 0"])
-      s.add_runtime_dependency(%q<thin>, [">= 0"])
       s.add_runtime_dependency(%q<emk-sinatra-url-for>, [">= 0"])
       s.add_runtime_dependency(%q<cehoffman-sinatra-respond_to>, [">= 0"])
       s.add_runtime_dependency(%q<dm-more>, [">= 0"])
       s.add_runtime_dependency(%q<dm-core>, [">= 0"])
       s.add_runtime_dependency(%q<sinatra-static-assets>, [">= 0"])
-      s.add_development_dependency(%q<cucmber>, [">= 0"])
+      s.add_development_dependency(%q<cucumber>, [">= 0"])
       s.add_development_dependency(%q<jeweler>, [">= 0"])
+      s.add_development_dependency(%q<thin>, [">= 0"])
     else
       s.add_dependency(%q<sinatra>, [">= 0"])
       s.add_dependency(%q<rest-client>, [">= 0"])
       s.add_dependency(%q<rack>, [">= 0"])
       s.add_dependency(%q<rack-contrib>, [">= 0"])
       s.add_dependency(%q<rack-flash>, [">= 0"])
-      s.add_dependency(%q<thin>, [">= 0"])
       s.add_dependency(%q<emk-sinatra-url-for>, [">= 0"])
       s.add_dependency(%q<cehoffman-sinatra-respond_to>, [">= 0"])
       s.add_dependency(%q<dm-more>, [">= 0"])
       s.add_dependency(%q<dm-core>, [">= 0"])
       s.add_dependency(%q<sinatra-static-assets>, [">= 0"])
-      s.add_dependency(%q<cucmber>, [">= 0"])
+      s.add_dependency(%q<cucumber>, [">= 0"])
       s.add_dependency(%q<jeweler>, [">= 0"])
+      s.add_dependency(%q<thin>, [">= 0"])
     end
   else
     s.add_dependency(%q<sinatra>, [">= 0"])
@@ -85,14 +89,14 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<rack>, [">= 0"])
     s.add_dependency(%q<rack-contrib>, [">= 0"])
     s.add_dependency(%q<rack-flash>, [">= 0"])
-    s.add_dependency(%q<thin>, [">= 0"])
     s.add_dependency(%q<emk-sinatra-url-for>, [">= 0"])
     s.add_dependency(%q<cehoffman-sinatra-respond_to>, [">= 0"])
     s.add_dependency(%q<dm-more>, [">= 0"])
     s.add_dependency(%q<dm-core>, [">= 0"])
     s.add_dependency(%q<sinatra-static-assets>, [">= 0"])
-    s.add_dependency(%q<cucmber>, [">= 0"])
+    s.add_dependency(%q<cucumber>, [">= 0"])
     s.add_dependency(%q<jeweler>, [">= 0"])
+    s.add_dependency(%q<thin>, [">= 0"])
   end
 end