opentox-ruby-api-wrapper 1.2.3 → 1.2.4

data/Rakefile

@@ -10,13 +10,9 @@ begin
     gem.email = "helma@in-silico.ch"
     gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper"
     gem.authors = ["Christoph Helma"]
-		gem.add_dependency "rest-client"
-		gem.add_dependency "sinatra"
-		gem.add_dependency "rack"
-		gem.add_dependency "rack-contrib"
-		gem.add_dependency "thin"
-		gem.add_dependency "emk-sinatra-url-for"
-		gem.add_dependency "cehoffman-sinatra-respond_to"
+		["sinatra", "rest-client", "rack", "rack-contrib", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core"].each do |dep|
+			gem.add_dependency dep
+		end
 		gem.add_development_dependency "cucumber"
 		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/*)

data/VERSION

@@ -1 +1 @@
-1.2.3
+1.2.4

data/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
@@ -37,10 +37,14 @@ 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
-
 			def self.weighted_tanimoto(fp_a,fp_b,p)
 				common_features = fp_a & fp_b
 				all_features = fp_a + fp_b
@@ -54,7 +58,6 @@ module OpenTox
 					0.0
 				end
 			end
-
 		end
 
 	end

data/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

data/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
@@ -157,46 +158,6 @@ module OpenTox
 			features
 		end
 
-=begin
-		def tuples
-			tuples = []
-			@model.subjects(RDF['type'], OT["Tuple"]).each do |t|
-				tuple = {}
-				compounds = []
-				@model.subjects(OT['values'], t).each do |data_entry|
-					compound_node = @model.object(data_entry,OT['compound'])
-					compounds << @model.object(compound_node,  DC["identifier"]).to_s
-				end
-				@model.find(t, OT['tuple'],nil) do |s,p,pair|
-					feature_node = @model.object(pair, OT['feature'])
-					feature_name = @model.object(feature_node, DC['title']).to_s
-					value_node = @model.object(pair, OT['value'])
-					value = @model.object(value_node, OT['value']).to_s
-					value = value.to_f if value.match(/^[\d\.]+$/)
-					tuple[feature_name.to_sym] = value
-				end
-				tuple[:compounds] = compounds
-				tuples << tuple
-			end
-			tuples
-		end
-
-		def tuple(compound_uri)
-			compound_node = @model.subject(DC["identifier"],compound_uri)
-			#puts compound_uri
-			@model.subjects(OT['compound'], compound_node).each do |data_entry|
-				values_node = @model.object(data_entry, OT['values'])
-				@model.find(values_node, OT['tuple'], nil) do |s,p,tuple| 
-					@model.find(tuple, OT['feature'], nil) do |s,p,feature|
-						name = @model.object(feature,DC['title']).to_s
-						#puts name
-					end
-				end
-				#puts values_node
-			end
-		end
-=end
-
 		def compounds
 			compounds = []
 			@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
@@ -222,8 +183,7 @@ 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
 

data/lib/model.rb

@@ -1,43 +1,31 @@
 module OpenTox
 	module Model
-
+   
 		class Lazar
 			include Owl
 
-			attr_accessor :dataset, :predictions
-			
 			# Create a new prediction model from a dataset
-			def initialize(yaml)
-				super()
-				id = File.basename(yaml,'.yaml')
-				# TODO Untyped Individual: http://localhost:4003/lazar/{id} ????
-				@lazar = YAML.load_file yaml
-				self.uri = File.join(@@config[:services]["opentox-model"],'lazar',id)
-				self.title = "lazar model for #{@lazar[:endpoint]}"
+			def initialize
+				super
 				self.source = "http://github.com/helma/opentox-model"
-				self.parameters = {
-					"Dataset URI" => { :scope => "mandatory", :value => "dataset_uri=#{@lazar[:activity_dataset]}" },
-					"Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri=#{@lazar[:endpoint]}" },
-					"Feature generation URI" => { :scope => "mandatory", :value => "feature_generation_uri=" } #TODO write to yaml
-				}
 				self.algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
-				self.trainingDataset = @lazar[:activity_dataset]
-				self.dependentVariables = @lazar[:endpoint]
-				self.independentVariables = "http://localhost:4002/fminer#BBRC_representative" # TODO read this from dataset
-				self.predictedVariables = @lazar[:endpoint] #+ " lazar prediction"
-				@dataset = OpenTox::Dataset.new
-				@predictions = {}
+				self.independentVariables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative") # TODO read this from dataset
 			end
 
-			def self.find(uri)
-=begin
-				begin
-					YAML.load(RestClient.get uri)
-					Lazar.new uri
-				rescue
-					halt 404, "Model #{uri} not found."
-				end
-=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] #+ " lazar prediction"
+				lazar
 			end
 
 			def self.find_all
@@ -49,65 +37,6 @@ module OpenTox
 				RestClient.post(@uri, :compound_uri => compound.uri)
 			end
 
-			def database_activity?(compound_uri)
-				# find database activities
-				db_activities = @lazar[:activities][compound_uri]
-				if db_activities
-					c = @dataset.find_or_create_compound(compound_uri)
-					f = @dataset.find_or_create_feature(@lazar[:endpoint])
-					v = db_activities.join(',')
-					@dataset.add c,f,v
-					@predictions[compound_uri] = { @lazar[:endpoint] => {:measured_activities => db_activities}}
-					true
-				else
-					false
-				end
-			end
-
-			def classify(compound_uri)
-
-				compound = OpenTox::Compound.new(:uri => compound_uri)
-				compound_matches = compound.match @lazar[:features]
-
-				conf = 0.0
-				neighbors = []
-				classification = nil
-
-				@lazar[:fingerprints].each do |uri,matches|
-
-					sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(compound_matches,matches,@lazar[:p_values])
-					if sim > 0.3
-						neighbors << uri
-						@lazar[:activities][uri].each do |act|
-							case act.to_s
-							when 'true'
-								conf += OpenTox::Utils.gauss(sim)
-							when 'false'
-								conf -= OpenTox::Utils.gauss(sim)
-							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
-					} } }
-			end
-
 			def self.base_uri
 				@@config[:services]["opentox-model"]
 			end

data/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

data/lib/task.rb

@@ -1,20 +1,21 @@
 module OpenTox
 
-	class Task #< OpenTox
+	class Task
+
+		attr_accessor :uri
 
 		def initialize(uri)
-			super(uri)
+			#super()
+			@uri = uri
 		end
 
-		#def self.create(uri)
 		def self.create
-			puts @@config[:services]["opentox-task"]
-			uri = RestClient.post @@config[:services]["opentox-task"], ''#, :dataset_uri => uri
+			uri = RestClient.post @@config[:services]["opentox-task"], nil
 			Task.new(uri)
 		end
 
-		def self.find(params)
-			Task.new(params[:uri])
+		def self.find(uri)
+			Task.new(uri)
 		end
 
 		def self.base_uri
@@ -22,32 +23,32 @@ module OpenTox
 		end
 
 		def start
-			RestClient.put @uri, :status => 'started'
+			RestClient.put File.join(@uri,'started'), nil
 		end
 
-		def stop
-			RestClient.put @uri, :status => 'stopped'
+		def cancel
+			RestClient.put File.join(@uri,'cancelled'), nil
 		end
 
-		def completed
-			RestClient.put @uri, :status => 'completed'
+		def completed(uri)
+			RestClient.put File.join(@uri,'completed'), :resource => uri
 		end
 		 
 		def status
 			RestClient.get File.join(@uri, 'status')
 		end
-
-		def completed?
-			self.status == 'completed'
+		 
+		def resource
+			RestClient.get File.join(@uri, 'resource')
 		end
 
-		def resource
-			RestClient.get @uri
+		def completed?
+			self.status.to_s == 'completed'
 		end
 
 		def wait_for_completion
 			until self.completed?
-				sleep 1
+				sleep 0.1
 			end
 		end
 

data/lib/tasks/opentox.rb

@@ -1,24 +1,4 @@
 require File.join(File.dirname(__FILE__), '..', 'opentox-ruby-api-wrapper.rb')
-require File.join(File.dirname(__FILE__), 'redis.rb')
-
-namespace :redis do
-
-	desc "Flush Redis testing database"
-	task :flush do
-		require 'redis'
-		r = Redis.new :db => 2
-		r.flush_db
-	end
-
-	desc "Flush all Redis databases"
-	task :flushall do
-		require 'redis'
-		r = Redis.new
-		r.flush_all
-	end
-
-
-end
 
 namespace :opentox do
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: opentox-ruby-api-wrapper
 version: !ruby/object:Gem::Version 
-  version: 1.2.3
+  version: 1.2.4
 platform: ruby
 authors: 
 - Christoph Helma
@@ -9,11 +9,11 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-12-21 00:00:00 +01:00
+date: 2010-01-09 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: rest-client
+  name: sinatra
   type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
@@ -23,7 +23,7 @@ dependencies:
         version: "0"
     version: 
 - !ruby/object:Gem::Dependency 
-  name: sinatra
+  name: rest-client
   type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
@@ -82,6 +82,26 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: "0"
     version: 
+- !ruby/object:Gem::Dependency 
+  name: dm-more
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: dm-core
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
 - !ruby/object:Gem::Dependency 
   name: cucumber
   type: :development