add/adjust/remove log messages

6 files changed, 30 insertions, 13 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index b921b9c..37c7931 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -20,7 +20,7 @@ module OpenTox
     # @param [optional,OpenTox::Task] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
     # @return [String] URI of new resource (dataset, model, ...)
     def run(params=nil, waiting_task=nil)
-      LOGGER.info "Running algorithm '"+@uri.to_s+"' with params: "+params.inspect
+      LOGGER.debug "Running algorithm '"+@uri.to_s+"' with params: "+params.inspect
       RestClientWrapper.post(@uri, params, {:accept => 'text/uri-list'}, waiting_task).to_s
     end
 
diff --git a/lib/authorization.rb b/lib/authorization.rb
index a9744e9..ecb78b3 100644
--- a/lib/authorization.rb
+++ b/lib/authorization.rb
@@ -306,7 +306,7 @@ module OpenTox
     def self.check_policy(uri, subjectid)
       return true unless uri and subjectid
       token_valid = OpenTox::Authorization.is_token_valid(subjectid)      
-      LOGGER.debug "OpenTox::Authorization.check_policy with uri: #{uri}, subjectid: #{subjectid} is valid: #{token_valid}"
+      #LOGGER.debug "OpenTox::Authorization.check_policy with uri: #{uri}, subjectid: #{subjectid} is valid: #{token_valid}"
       # check if subjectid is valid
       unless token_valid
         # abort if invalid
diff --git a/lib/model.rb b/lib/model.rb
index c9d367e..cab1b4c 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -16,7 +16,7 @@ module OpenTox
           accept_header = 'application/rdf+xml'
         end
       end
-      LOGGER.info "running model "+@uri.to_s+", params: "+params.inspect+", accept: "+accept_header.to_s
+      LOGGER.debug "running model "+@uri.to_s+", params: "+params.inspect+", accept: "+accept_header.to_s
       RestClientWrapper.post(@uri,params,{:accept => accept_header},waiting_task).to_s
     end
 
diff --git a/lib/r-util.rb b/lib/r-util.rb
index 463a145..f9591d5 100644
--- a/lib/r-util.rb
+++ b/lib/r-util.rb
@@ -326,6 +326,8 @@ module OpenTox
         end
       end
 
+      #LOGGER.debug "converting to array"
+      
       # values into 2D array, then to dataframe
       d_values = []
       dataset.compounds.each do |c|
@@ -345,14 +347,24 @@ module OpenTox
           d_values << c_values
         end
       end  
+      
+      #LOGGER.debug "assigning"
+      
       df_name = "df_#{dataset.uri.split("/")[-1].split("?")[0]}"
       assign_dataframe(df_name,d_values,compound_names,features)
       
+      #LOGGER.debug "setting types"
+      
       # set dataframe column types accordingly
       f_count = 1 #R starts at 1
       features.each do |f|
-        feat = OpenTox::Feature.find(f,subjectid)
-        nominal = feat.metadata[RDF.type].to_a.flatten.include?(OT.NominalFeature)
+        type = dataset.features[f][RDF.type]
+        unless type
+          LOGGER.debug "derive feature type by rest-call"
+          feat = OpenTox::Feature.find(f,subjectid)
+          type = feat.metadata[RDF.type]
+        end
+        nominal = type.to_a.flatten.include?(OT.NominalFeature)
         if nominal
           @r.eval "#{df_name}[,#{f_count}] <- as.character(#{df_name}[,#{f_count}])"
         else
@@ -388,8 +400,13 @@ module OpenTox
       compounds.size.times{|i| dataset.add_compound(compounds[i]) if compound_indices==nil or compound_indices.include?(i)}
       features.each{|f| dataset.add_feature(f,@@feats[df][f])}
       features.size.times do |c|
-        feat = OpenTox::Feature.find(features[c],subjectid)
-        nominal = feat.metadata[RDF.type].to_a.flatten.include?(OT.NominalFeature)
+        type = @@feats[df][features[c]][RDF.type]
+        unless type
+          LOGGER.debug "derive feature type by rest-call"
+          feat = OpenTox::Feature.find(features[c],subjectid)
+          type = feat.metadata[RDF.type]
+        end
+        nominal = type.to_a.flatten.include?(OT.NominalFeature)
         compounds.size.times do |r|
           if compound_indices==nil or compound_indices.include?(r)
             dataset.add(compounds[r],features[c],nominal ? values[r][c] : values[r][c].to_f) if values[r][c]!="NA"
diff --git a/lib/spork.rb b/lib/spork.rb
index c77b5b5..40b78ed 100644
--- a/lib/spork.rb
+++ b/lib/spork.rb
@@ -36,12 +36,12 @@ module Spork
   # :no_detach => true if you want to keep the child process under the parent control. usually you do NOT want this
   def self.spork(options={})
     logger = options[:logger]
-    logger.debug "spork> parent PID = #{Process.pid}" if logger
+    #logger.debug "spork> parent PID = #{Process.pid}" if logger
     
     child = fork do
       begin
         start = Time.now
-        logger.debug "spork> child PID = #{Process.pid}" if logger
+        #logger.debug "spork> child PID = #{Process.pid}" if logger
 
         # set the nice priority if needed
         Process.setpriority(Process::PRIO_PROCESS, 0, options[:priority]) if options[:priority]
@@ -56,7 +56,7 @@ module Spork
         #raise ex
         logger.error "spork> Exception in child[#{Process.pid}] - #{ex.class}: #{ex.message}" if logger
       ensure
-        logger.info "spork> child[#{Process.pid}] took #{Time.now - start} sec" if logger
+        #logger.info "spork> child[#{Process.pid}] took #{Time.now - start} sec" if logger
         # this form of exit doesn't call at_exit handlers
         exit!(0)
       end
diff --git a/lib/task.rb b/lib/task.rb
index d8f0ba6..86d3d5f 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -72,7 +72,7 @@ module OpenTox
         end
       end  
       task.pid = task_pid
-      LOGGER.debug "Started task: "+task.uri.to_s
+      #LOGGER.debug "Started task: "+task.uri.to_s
       task
     end  
   
@@ -248,7 +248,7 @@ module OpenTox
       due_to_time = Time.new + DEFAULT_TASK_MAX_DURATION
       start_time = Time.new
       dur = 0
-      LOGGER.debug "start waiting for task "+@uri.to_s+" at: "+Time.new.to_s+", waiting at least until "+due_to_time.to_s
+      LOGGER.debug "start waiting for task "+@uri.to_s.chomp+" at: "+Time.new.to_s+", waiting at least until "+due_to_time.to_s
       
       load_metadata # for extremely fast tasks
       check_state
@@ -265,7 +265,7 @@ module OpenTox
         end
       end
       waiting_task.waiting_for(nil) if waiting_task
-      LOGGER.debug "Task '"+@metadata[OT.hasStatus].to_s+"': "+@uri.to_s+", Result: "+@metadata[OT.resultURI].to_s
+      LOGGER.debug "Task '"+@metadata[OT.hasStatus].to_s+"': "+@uri.to_s.chomp+", Result: "+@metadata[OT.resultURI].to_s
     end
     
     # updates percentageCompleted value (can only be increased)