opentox-ruby-api-wrapper 1.3.1 → 1.4.0

data/VERSION

@@ -1 +1 @@
-1.3.1
+1.4.0

data/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"
@@ -29,29 +17,12 @@ 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
 				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

data/lib/dataset.rb

@@ -3,12 +3,27 @@ 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)
+			YAML.load RestClient.get(uri, :accept => 'application/x-yaml').to_s 
+		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
@@ -87,17 +102,7 @@ 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
-			dataset.read uri.to_s
-			dataset
-		end
-
-		def self.find(uri)
-			dataset = Dataset.new
-			LOGGER.debug "Getting data from #{uri}"
-			data = `curl "#{uri}"`
-			#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
 			dataset
 		end
 
@@ -165,35 +170,13 @@ 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

data/lib/model.rb

@@ -2,6 +2,31 @@ module OpenTox
 	module Model
    
 		class Lazar
+
+			attr_accessor :dependent_variable, :activity_dataset_uri, :feature_dataset_uri, :effects, :activities, :p_values, :fingerprints, :features, :algorithm
+			
+			def initialize
+				@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 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"]).chomp.split("\n")
+			end
+=begin
 			include Owl
 
 			# Create a new prediction model from a dataset
@@ -28,10 +53,6 @@ module OpenTox
 				lazar
 			end
 
-			def self.find_all
-				RestClient.get(@@config[:services]["opentox-model"]).split("\n")
-			end
-
 			def self.find(uri)
 				yaml = RestClient.get(uri, :accept => "application/x-yaml")
 				OpenTox::Model::Lazar.from_yaml(yaml)
@@ -50,7 +71,7 @@ module OpenTox
 
 			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
@@ -101,6 +122,7 @@ module OpenTox
 				@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

data/lib/owl.rb

@@ -1,31 +1,127 @@
 module OpenTox
 
-	module Owl
+	class Owl
 
-		attr_reader :uri
-
-		def initialize
+		attr_reader :uri, :ot_class
 
+		def initialize(ot_class,uri)
 			@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]
+			@ot_class = ot_class
+			@uri = Redland::Uri.new(uri.chomp)
+			@model.add @uri, RDF['type'], OT[@ot_class]
+			@model.add @uri, DC['identifier'], @uri
+		end
+
+		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['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
-			uri = Redland::Uri.new(uri)
+			@uri = uri.chomp
 			# 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 +133,18 @@ 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 +153,8 @@ 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 +163,19 @@ 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

data/lib/task.rb

@@ -7,16 +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)
@@ -28,7 +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
 
@@ -64,22 +61,7 @@ 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.put({})
 		end
@@ -104,9 +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
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: opentox-ruby-api-wrapper
 version: !ruby/object:Gem::Version 
-  version: 1.3.1
+  version: 1.4.0
 platform: ruby
 authors: 
 - Christoph Helma
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-03-02 00:00:00 +01:00
+date: 2010-03-18 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency