Merge remote branch 'helma/test' into test

10 files changed, 153 insertions, 58 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 25ae4cb..2a781d8 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -1,27 +1,29 @@
 module OpenTox
-	module Algorithm 
+  module Algorithm 
 
-		class Fminer 
-			include Owl
+    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 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)
-				RestClient.post params[:feature_generation_uri], :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri] 
-			end
-		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
+    end
 
-		class Lazar 
-			include Owl
+    class Lazar 
+      include Owl
 
 			def initialize
 				super
@@ -40,26 +42,29 @@ module OpenTox
 			
 			def self.create_model(params)
 				LOGGER.debug 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")
+				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")
 			end
 
-		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
-				common_p_sum = 0.0
-				if common_features.size > 0
-					common_features.each{|f| common_p_sum += p[f]}
-					all_p_sum = 0.0
-					all_features.each{|f| all_p_sum += p[f]}
-					common_p_sum/all_p_sum
-				else
-					0.0
-				end
-			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
+        common_p_sum = 0.0
+        if common_features.size > 0
+          common_features.each{|f| common_p_sum += p[f]}
+          all_p_sum = 0.0
+          all_features.each{|f| all_p_sum += p[f]}
+          common_p_sum/all_p_sum
+        else
+          0.0
+        end
+      end
+    end
 
-	end
+  end
 end
diff --git a/lib/authorization.rb b/lib/authorization.rb
new file mode 100644
index 0000000..9a1760a
--- /dev/null
+++ b/lib/authorization.rb
@@ -0,0 +1,24 @@
+helpers do
+ 
+  def protected!
+    response['WWW-Authenticate'] = %(Basic realm="Opentox Webservice Authentication") and \
+    throw(:halt, [401, "Not authorized\n"]) and \
+    return unless authorized?
+  end
+ 
+  def authorized?
+    @auth ||= Rack::Auth::Basic::Request.new(request.env)
+    @auth.provided? && @auth.basic? && @auth.credentials && valid_user?
+  end
+  
+  def valid_user?
+    users = @@users[:users]
+    return @auth.credentials == [@auth.username, users.fetch(@auth.username)] if users.has_key?(@auth.username)
+    return false
+  end
+ 
+end
+ 
+before do
+  #protected! unless env['REQUEST_METHOD'] == "GET"
+end
diff --git a/lib/compound.rb b/lib/compound.rb
index 56646c0..0ee853d 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -17,7 +17,8 @@ module OpenTox
 				@inchi = sdf2inchi(params[:sdf])
 				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:name]
-				@inchi = RestClient.get("#{@@cactus_uri}#{params[:name]}/stdinchi").chomp
+				# paranoid URI encoding to keep SMILES charges and brackets
+				@inchi = RestClient.get("#{@@cactus_uri}#{URI.encode(params[:name], Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").chomp
 				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:uri]
 				@uri = params[:uri]
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 962a576..bbadd2d 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -14,6 +14,8 @@ module OpenTox
 			data_entry = @model.subject OT['compound'], compound
 			if data_entry.nil?
 				data_entry = @model.create_resource
+				dataset = @model.subject(RDF['type'],OT[self.owl_class])
+				@model.add dataset, OT['dataEntry'], data_entry
 				@model.add data_entry, RDF['type'], OT["DataEntry"]
 				@model.add data_entry, OT['compound'], compound
 			end
@@ -29,6 +31,8 @@ module OpenTox
 			data_entry = @model.subject OT['compound'], compound
 			if data_entry.nil?
 				data_entry = @model.create_resource
+				dataset = @model.subject(RDF['type'],OT[self.owl_class])
+				@model.add dataset, OT['dataEntry'], data_entry
 				@model.add data_entry, RDF['type'], OT["DataEntry"]
 				@model.add data_entry, OT['compound'], compound
 			end
@@ -57,7 +61,7 @@ module OpenTox
 		def find_or_create_compound(uri)
 			compound = @model.subject(DC["identifier"], uri)
 			if compound.nil?
-				compound = @model.create_resource
+				compound = @model.create_resource(uri)
 				@model.add compound, RDF['type'], OT["Compound"]
 				@model.add compound, DC["identifier"], uri
 			end
@@ -68,7 +72,7 @@ module OpenTox
 		def find_or_create_feature(uri)
 			feature = @model.subject(DC["identifier"], uri)
 			if feature.nil?
-				feature = @model.create_resource
+				feature = @model.create_resource(uri)
 				@model.add feature, RDF['type'], OT["Feature"]
 				@model.add feature, DC["identifier"], uri
 				@model.add feature, DC["title"], File.basename(uri).split(/#/)[1]
@@ -78,7 +82,8 @@ module OpenTox
 		end
 
 		def self.create(data, content_type = 'application/rdf+xml')
-      uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => content_type
+      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
@@ -154,12 +159,14 @@ module OpenTox
 
 		# Delete a dataset
 		def delete
-			RestClient.delete @uri
-		end
+  		resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+      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.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
diff --git a/lib/environment.rb b/lib/environment.rb
index c4de0b5..27da072 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -6,6 +6,7 @@ ENV['RACK_ENV'] = 'test' unless ENV['RACK_ENV']
 basedir = File.join(ENV['HOME'], ".opentox")
 config_dir = File.join(basedir, "config")
 config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml")
+user_file = File.join(config_dir, "users.yaml")
 
 TMP_DIR = File.join(basedir, "tmp")
 LOG_DIR = File.join(basedir, "log")
@@ -15,6 +16,7 @@ if File.exist?(config_file)
 else
 	FileUtils.mkdir_p TMP_DIR
 	FileUtils.mkdir_p LOG_DIR
+	FileUtils.mkdir_p config_dir
 	FileUtils.cp(File.join(File.dirname(__FILE__), 'templates/config.yaml'), config_file)
 	puts "Please edit #{config_file} and restart your application."
 	exit
@@ -100,6 +102,21 @@ LOGGER = MyLogger.new(logfile,'daily') # daily rotation
 
 LOGGER.level = Logger::DEBUG
 
+if File.exist?(user_file)
+  @@users = YAML.load_file(user_file)
+else
+  FileUtils.cp(File.join(File.dirname(__FILE__), 'templates/users.yaml'), user_file)
+  puts "Please edit #{user_file} and restart your application."
+  exit
+end
+
+begin
+  0 < @@users[:users].keys.length
+rescue
+  puts "Please edit #{user_file} and restart your application. Create at least one user with password."
+  exit
+end
+
 # RDF namespaces
 RDF = Redland::Namespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
 OWL = Redland::Namespace.new 'http://www.w3.org/2002/07/owl#'
diff --git a/lib/model.rb b/lib/model.rb
index a585b59..6c48734 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -24,7 +24,7 @@ module OpenTox
 				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.predictedVariables = yaml[:endpoint] + "_lazar_prediction"
 				lazar
 			end
 
@@ -39,7 +39,9 @@ module OpenTox
 			
 			# Predict a compound
 			def predict(compound)
-				RestClient.post(@uri, :compound_uri => compound.uri)
+				# nicht absichern??
+				resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+				resource.post(:compound_uri => compound.uri)
 			end
 
 			def self.base_uri
@@ -47,7 +49,15 @@ module OpenTox
 			end
 
 			def self.create(data)
-				RestClient.post(@@config[:services]["opentox-model"], data, :content_type => "application/x-yaml").to_s
+			  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
+			end
+
+			def delete
+			  resource = RestClient::Resource.new(self.uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+				resource.delete
+				#RestClient.delete @uri if @uri
+				#RestClient.delete model.task_uri if model.task_uri
 			end
 
 #			def self.create(task)
diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb
index ca57fc9..03838e8 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'].each do |lib|
+['owl', 'compound','dataset','algorithm','model','task','utils','authorization'].each do |lib|
 	require lib
 end
diff --git a/lib/owl.rb b/lib/owl.rb
index a843e59..82d6e0e 100644
--- a/lib/owl.rb
+++ b/lib/owl.rb
@@ -16,7 +16,6 @@ module OpenTox
 			# 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'], OWL['Ontology']
 			@model.add tmp, RDF['type'], OT[self.owl_class]
 		end
 
diff --git a/lib/task.rb b/lib/task.rb
index 70d22bf..c5cddf7 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -10,7 +10,10 @@ module OpenTox
 		end
 
 		def self.create
-			uri = RestClient.post @@config[:services]["opentox-task"], {}
+			#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)
 		end
 
@@ -26,7 +29,7 @@ module OpenTox
 			task_uris = RestClient.get(@@config[:services]["opentox-task"]).split(/\n/)
 			task_uris.collect{|uri| Task.new(uri)}
 		end
-		 
+
 		def created_at
 			RestClient.get File.join(@uri, 'created_at')
 		end
@@ -42,7 +45,24 @@ module OpenTox
 		def resource
 			RestClient.get File.join(@uri, 'resource')
 		end
+		 
+		def started
+      LOGGER.info File.join(@uri,'started')
+      resource = RestClient::Resource.new(File.join(@uri,'started'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+      resource.put({}) 
+		end
 
+		def cancel
+			resource = RestClient::Resource.new(@File.join(@uri,'cancelled'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			resource.put({})
+		end
+
+		def completed(uri)
+			resource = RestClient::Resource.new(File.join(@uri,'completed'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			resource.put :resource => uri
+		end
+
+=begin
 		def started
 			RestClient.put File.join(@uri,'started'), {}
 		end
@@ -51,20 +71,27 @@ module OpenTox
 			RestClient.put File.join(@uri,'cancelled'), {}
 		end
 
-		def failed
-			RestClient.put File.join(@uri,'failed'), {}
+		def completed(uri)
+			RestClient.put File.join(@uri,'completed'), :resource => uri
 		end
 
-		def parent=(task)
-			RestClient.put File.join(@uri,'parent'), {:uri => task.uri}
+=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
 
-		def completed(uri)
-			RestClient.put File.join(@uri,'completed'), :resource => uri
+		def parent=(task)
+			#RestClient.put File.join(@uri,'parent'), {:uri => task.uri}
+			resource = RestClient::Resource.new(File.join(@uri,'parent'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			LOGGER.debug "task.rb: #{resource}"
+			resource.put :uri => task.uri
 		end
 		 
 		def pid=(pid)
-			RestClient.put File.join(@uri, 'pid'), :pid => pid
+		  resource = RestClient::Resource.new(File.join(@uri,'pid'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			resource.put :pid => pid
 		end
 
 		def completed?
diff --git a/lib/templates/users.yaml b/lib/templates/users.yaml
new file mode 100644
index 0000000..483fd7b
--- /dev/null
+++ b/lib/templates/users.yaml
@@ -0,0 +1,5 @@
+# please insert users and passwords here.
+# one user and password each line. uncomment the line.
+:users:
+# username: "secretpassword"
+# exampleuser: "ih9aiTog"
\ No newline at end of file