Merge branch 'release/v3.1.0' into development

6 files changed, 31 insertions, 28 deletions

diff --git a/ChangeLog b/ChangeLog
index de9e01b..5872d56 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,11 @@
+v3.1.0 2012-02-24
+		* utils.rb: added for special routines (e.g. descriptor calculation)
+		* task.rb: Polling with increasing interval
+		* parser.rb: CSV up and download fixed
+		* transform.rb: routines to create machine learning data matrices
+		* algorithm.rb: SVM parameter grid search, cos similarity as algorithm,
+		gauss() removed
+
 v3.0.1 2011-10-19
     * feature: model registration to ontology service
     * ontology lib gets endpoints from ontology service
diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index db21c46..c026c56 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -527,7 +527,7 @@ module OpenTox
       # @param [Hash] required keys: compound, features, feature_dataset_uri, pc_type
       # @return [Hash] Hash with matching Smarts and number of hits 
       def self.lookup(params)
-        params[:compound].lookup(params[:features], params[:feature_dataset_uri],params[:pc_type])
+        params[:compound].lookup(params[:features], params[:feature_dataset_uri],params[:pc_type],params[:subjectid])
       end  
     end
 
diff --git a/lib/authorization.rb b/lib/authorization.rb
index 5d57781..a9744e9 100644
--- a/lib/authorization.rb
+++ b/lib/authorization.rb
@@ -37,13 +37,15 @@ module OpenTox
       
       #Loads and sends Policyfile(XML) to open-sso server
       # @param [String] URI to create a policy for      
-      def send(uri)    
+      def send(uri)
         xml = get_xml(uri)
         ret = false
-        ret = Authorization.create_policy(xml, @subjectid) 
+        ret = Authorization.create_policy(xml, @subjectid)
+        LOGGER.warn "Create policy on openSSO failed for URI: #{uri} subjectid: #{@subjectid}. Will try again." if !ret
+        ret = Authorization.create_policy(xml, @subjectid) if !ret
         LOGGER.debug "Policy send with subjectid: #{@subjectid}"
         LOGGER.warn "Not created Policy is: #{xml}" if !ret
-        ret  
+        ret
       end
       
     end
@@ -337,7 +339,7 @@ module OpenTox
     # @param [String] subjectid
     # @return [Boolean] true if access granted, else otherwise
     def self.authorized?(uri, request_method, subjectid)
-      if CONFIG[:authorization][:free_request].include?(request_method)  
+      if CONFIG[:authorization][:free_request].include?(request_method)
         #LOGGER.debug "authorized? >>true<< (request is free), method: #{request_method}, URI: #{uri}, subjectid: #{subjectid}"
         true
       elsif OpenTox::Authorization.free_uri?(uri, request_method)
@@ -360,7 +362,7 @@ module OpenTox
         false
       end
     end
-    
+
     private
     def self.free_uri?(uri, request_method)
       if CONFIG[:authorization][:free_uris]
@@ -374,7 +376,7 @@ module OpenTox
       end    
       return false
     end
-    
+
     def self.authorize_exception?(uri, request_method)
       if CONFIG[:authorization][:authorize_exceptions]
         CONFIG[:authorization][:authorize_exceptions].each do |request_methods,uris|
@@ -387,6 +389,6 @@ module OpenTox
       end    
       return false
     end    
-    
+
   end
-end
\ No newline at end of file
+end
diff --git a/lib/compound.rb b/lib/compound.rb
index a2b7e48..c25125b 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -198,9 +198,8 @@ module OpenTox
     # @param [Array] Array of feature names
     # @param [String] Feature dataset uri
     # @return [Hash] Hash with feature name as key and value as value
-		def lookup(feature_array,feature_dataset_uri,pc_type)
-      ds = OpenTox::Dataset.find(feature_dataset_uri)
-
+    def lookup(feature_array,feature_dataset_uri,pc_type,subjectid=nil)
+      ds = OpenTox::Dataset.find(feature_dataset_uri,subjectid)
       #entry = ds.data_entries[self.uri]
       entry = nil 
       ds.data_entries.each { |c_uri, values| 
@@ -209,17 +208,15 @@ module OpenTox
           break
         end
       }
-
       LOGGER.debug "#{entry.size} entries in feature ds for query." unless entry.nil?
 
       if entry.nil?
         uri, smiles_to_inchi = OpenTox::Algorithm.get_pc_descriptors({:compounds => [self.uri], :pc_type => pc_type})
-        uri = OpenTox::Algorithm.load_ds_csv(uri, smiles_to_inchi)
-        ds = OpenTox::Dataset.find(uri)
+        uri = OpenTox::Algorithm.load_ds_csv(uri, smiles_to_inchi, subjectid)
+        ds = OpenTox::Dataset.find(uri,subjectid)
         entry = ds.data_entries[self.uri]
-        ds.delete
+        ds.delete(subjectid)
       end
-
       features = entry.keys
       features.each { |feature| 
         new_feature = File.join(feature_dataset_uri, "feature", feature.split("/").last) 
diff --git a/lib/model.rb b/lib/model.rb
index b3de1a3..a858a0f 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -237,7 +237,6 @@ module OpenTox
 
         @compound = Compound.new compound_uri
         features = {}
-
         #LOGGER.debug self.to_yaml
         unless @prediction_dataset
           @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid)
@@ -248,22 +247,19 @@ module OpenTox
             OT.parameters => [{DC.title => "compound_uri", OT.paramValue => compound_uri}]
           } )
         end
-
         if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "regression"
           all_activities = [] 
           all_activities = @activities.values.flatten.collect! { |i| i.to_f }
         end
-
         unless database_activity(subjectid) # adds database activity to @prediction_dataset
-
           # Calculation of needed values for query compound
           @compound_features = eval("#{@feature_calculation_algorithm}({
                                     :compound => @compound, 
                                     :features => @features, 
                                     :feature_dataset_uri => @metadata[OT.featureDataset],
-                                    :pc_type => self.parameter(\"pc_type\")
+                                    :pc_type => self.parameter(\"pc_type\"),
+                                    :subjectid => subjectid
                                     })")
-          
           # Adding fingerprint of query compound with features and values(p_value*nr_hits)
           @compound_fingerprints = {}
           @compound_features.each do |feature, value| # value is nil if "Substructure.match"
diff --git a/lib/utils.rb b/lib/utils.rb
index c9e9eca..d9d7b4b 100644
--- a/lib/utils.rb
+++ b/lib/utils.rb
@@ -104,13 +104,13 @@ module OpenTox
     # Load dataset via CSV
     # @param[Array] Ambit result uri, piecewise (1st: base, 2nd: SMILES, 3rd+: features
     # @return[String] dataset uri 
-    def self.load_ds_csv(ambit_result_uri, smiles_to_inchi)
+    def self.load_ds_csv(ambit_result_uri, smiles_to_inchi, subjectid=nil)
       
       master=nil
       (1...ambit_result_uri.size).collect { |idx|
         curr_uri = ambit_result_uri[0] + ambit_result_uri[idx]
         LOGGER.debug "Requesting #{curr_uri}"
-        csv_data = CSV.parse( OpenTox::RestClientWrapper.get(curr_uri, {:accept => "text/csv"}) )
+        csv_data = CSV.parse( OpenTox::RestClientWrapper.get(curr_uri, {:accept => "text/csv", :subjectid => subjectid}) )
         if csv_data[0] && csv_data[0].size>1
           if master.nil? # This is the smiles entry
             (1...csv_data.size).each{ |idx| csv_data[idx][1] = smiles_to_inchi[csv_data[idx][1]] }
@@ -145,11 +145,11 @@ module OpenTox
       #File.open("/tmp/test.csv", 'w') {|f| f.write( master.collect {|r| r.join(",")}.join("\n") ) }
      
       parser = OpenTox::Parser::Spreadsheets.new
-      ds = OpenTox::Dataset.new
-      ds.save
+      ds = OpenTox::Dataset.new(nil,subjectid)
+      ds.save(subjectid)
       parser.dataset = ds
       ds = parser.load_csv(master.collect{|r| r.join(",")}.join("\n"))
-      ds.save
+      ds.save(subjectid)
     end