some test issues resolved

5 files changed, 16 insertions, 4 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index ed7b629..2a781d8 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -16,6 +16,7 @@ module OpenTox
       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
@@ -41,6 +42,7 @@ module OpenTox
 			
 			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")
diff --git a/lib/authorization.rb b/lib/authorization.rb
index 7cb548e..9a1760a 100644
--- a/lib/authorization.rb
+++ b/lib/authorization.rb
@@ -20,5 +20,5 @@ helpers do
 end
  
 before do
-  protected! unless env['REQUEST_METHOD'] == "GET"
-end
\ No newline at end of file
+  #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/model.rb b/lib/model.rb
index 8abd040..6c48734 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -39,6 +39,7 @@ module OpenTox
 			
 			# Predict a compound
 			def predict(compound)
+				# nicht absichern??
 				resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
 				resource.post(:compound_uri => compound.uri)
 			end
@@ -52,6 +53,13 @@ module OpenTox
 			  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)
 #				@uri = RestClient.post(@@config[:services]["opentox-model"], :task_uri => task.uri)
 #			end
diff --git a/lib/task.rb b/lib/task.rb
index 97b3c1d..c5cddf7 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -84,7 +84,8 @@ module OpenTox
 
 		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])
+			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