internal authorization with first user of users.yaml

7 files changed, 82 insertions, 67 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 6ae9e72..d5f85c7 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -1,66 +1,66 @@
 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)
-			  resource = RestClient::Resource.new(params[:feature_generation_uri], :user => request.username, :password => request.password)
-			  resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri]
-			end
-		end
+      def self.create_feature_dataset(params)
+        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
-				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)
-			  resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => request.username, :password => request.password)
-				@uri = resource.post :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
-			end
+      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)
+        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
index 6abbc91..372d52b 100644
--- a/lib/authorization.rb
+++ b/lib/authorization.rb
@@ -20,5 +20,5 @@ helpers do
 end
  
 before do
-  #protected! unless env['REQUEST_METHOD'] == "GET"
+  protected! unless env['REQUEST_METHOD'] == "GET"
 end
\ No newline at end of file
diff --git a/lib/dataset.rb b/lib/dataset.rb
index f4372be..1aa3469 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -78,7 +78,8 @@ module OpenTox
 		end
 
 		def self.create(data, content_type = 'application/rdf+xml')
-		  uri = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => request.username, :password => request.password).post 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
@@ -168,12 +169,12 @@ module OpenTox
 
 		# Delete a dataset
 		def delete
-  		resource = RestClient::Resource.new(@uri, :user => request.username, :password => request.password)
+  		resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
       resource.delete
     end
 
 		def save
-      RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => request.username, :password => request.password).post(self.rdf, :content_type =>  "application/rdf+xml").to_s		
+      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		
 		end
 
 		def to_yaml
diff --git a/lib/environment.rb b/lib/environment.rb
index f7513c5..ee36366 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -25,6 +25,10 @@ else
   puts "Please edit #{user_file} and restart your application."
   exit
 end
+if @@users.length < 1 or !@@users
+  puts "Please edit #{user_file} and restart your application."
+  exit
+end
 
 # RDF namespaces
 RDF = Redland::Namespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'
diff --git a/lib/model.rb b/lib/model.rb
index b86b3fc..6bdbfd2 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -34,7 +34,8 @@ module OpenTox
 			
 			# Predict a compound
 			def predict(compound)
-				RestClient::Resource.new(@uri, :user => request.username, :password => request.password).post(:compound_uri => compound.uri)
+				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
@@ -42,7 +43,8 @@ module OpenTox
 			end
 
 			def self.create(data)
-			  RestClient::Resource.new(@@config[:services]["opentox-model"], :user => request.username, :password => request.password).post(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 endpoint
diff --git a/lib/task.rb b/lib/task.rb
index 5dd5e4c..23795dc 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -10,7 +10,8 @@ module OpenTox
 		end
 
 		def self.create
-			uri = RestClient::Resource.new(@@config[:services]["opentox-task"], :user => request.username, :password => request.password).post nil
+      resource = RestClient::Resource.new(@@config[:services]["opentox-task"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			uri = resource.post(nil)
 			Task.new(uri)
 		end
 
@@ -23,16 +24,19 @@ module OpenTox
 		end
 
 		def started
-			#LOGGER.info File.join(@uri,'started')
-			RestClient::Resource.new(@uri, :user => request.username, :password => request.password).put File.join(@uri,'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
-			RestClient::Resource.new(@uri, :user => request.username, :password => request.password).put File.join(@uri,'cancelled'), {}
+			resource = RestClient::Resource.new(@File.join(@uri,'cancelled'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			resource.put({})
 		end
 
 		def completed(uri)
-			RestClient::Resource.new(@uri, :user => request.username, :password => request.password).put File.join(@uri,'completed'), :resource => uri
+			resource = RestClient::Resource.new(File.join(@uri,'completed'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
+			resource.put :resource => uri
 		end
 		 
 		def status
diff --git a/lib/templates/config.ru b/lib/templates/config.ru
index 63dd2ce..ffccbc1 100644
--- a/lib/templates/config.ru
+++ b/lib/templates/config.ru
@@ -8,6 +8,9 @@ FileUtils.mkdir_p 'log' unless File.exists?('log')
 log = File.new("log/#{ENV["RACK_ENV"]}.log", "a")
 $stdout.reopen(log)
 $stderr.reopen(log)
+$stdout.sync = true
+$stderr.sync = true
+
  
 if ENV['RACK_ENV'] == 'production'
 	use Rack::MailExceptions do |mail|
@@ -21,3 +24,4 @@ end
 
 run Sinatra::Application
 
+set :raise_errors, true
\ No newline at end of file