diff options
-rw-r--r-- | lib/algorithm.rb | 2 | ||||
-rw-r--r-- | lib/authorization.rb | 4 | ||||
-rw-r--r-- | lib/compound.rb | 3 | ||||
-rw-r--r-- | lib/model.rb | 8 | ||||
-rw-r--r-- | lib/task.rb | 3 |
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 |