move plotting

9 files changed, 247 insertions, 100 deletions

diff --git a/application.rb b/application.rb
index 2cc433c..0bb75b5 100755
--- a/application.rb
+++ b/application.rb
@@ -4,6 +4,7 @@ require 'opentox-server'
 
 require "./test/test_application.rb"
 require "./report/report_application.rb"
+require "./report/plot_application.rb"
 require "./validation/validation_application.rb"
 
 
diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb
index e9da980..42dd572 100755
--- a/lib/ot_predictions.rb
+++ b/lib/ot_predictions.rb
@@ -4,12 +4,15 @@ require "./lib/predictions.rb"
 module Lib
   
   class OTPredictions < Predictions
-  
-    def initialize(data, compounds=nil, training_values=nil)
+
+    attr_reader :training_values, :prediction_feature_title
+    
+    def initialize(data, compounds=nil, training_values=nil, prediction_feature_title=nil)
       internal_server_error unless data.is_a?(Hash)
       super(data)
       @compounds = compounds
       @training_values = training_values
+      @prediction_feature_title = prediction_feature_title
     end
     
     def identifier(instance_index)
@@ -20,10 +23,6 @@ module Lib
       @compounds[instance_index]
     end
 
-    def training_values()
-      @training_values
-    end
-    
     def compute_stats()
       res = {}
       case feature_type
@@ -39,7 +38,7 @@ module Lib
       OTPredictions.to_array( [self] )
     end
 
-    def self.to_array( predictions, add_pic=false, format=false, validation_uris=nil )
+    def self.to_array( predictions, format=false, validation_uris=nil )
   
       confidence_available = false
       training_data_available = false
@@ -57,6 +56,7 @@ module Lib
         p.num_instances.times do |i|
           a = {}
           a["Compound"] = p.identifier(i)+"?media=image/png&size=150"
+          a["Compound URI"] = p.identifier(i)
           a["Training value"] = p.training_values[p.identifier(i)] if training_data_available
           a["Test value"] = p.actual_value(i)
           a["Predicted value"] = p.predicted_value(i)
@@ -75,7 +75,6 @@ module Lib
           end
           a["Confidence value"] = p.confidence_value(i) if confidence_available
           a["Validation URI"] = v_uris[i] if validation_uris
-          a["Compound URI"] = p.identifier(i)
 
           idx = join_map["#{p.identifier(i)}#{v_uris ? v_uris[i] : ''}"]
           if (idx!=nil and format) # join equal compounds unless formatting is disabled
@@ -91,7 +90,7 @@ module Lib
         end
       end
 
-      unless predictions[0].feature_type=="classification"
+      unless predictions.first.feature_type=="classification"
         # compute horziontal line step-width to make boxplots inter-comparable
         # step 1: compute max delta
         delta = 0
@@ -103,41 +102,50 @@ module Lib
         # e.g. delta > 100 -> stepwidth = 100, delta within [10-99.9] -> stepwidth = 10, delta within [1-9.99] -> stepwidth = 1
         hline = 10**Math.log(delta,10).floor
       end
-      
+
+      transformer = PredictionTransformer.new(res.collect{|r| r["Compound URI"]},predictions.first.prediction_feature_title)
+
       res.size.times do |r|
-        unless predictions[0].feature_type=="classification"
+        # add boxplot
+        unless predictions.first.feature_type=="classification"
           # add boxplots including training, test and predicted values
           val_str = training_data_available ? "training=#{[res[r]["Training value"]].join(",")};" : ""
           val_str << "test=#{[res[r]["Test value"]].join(",")};predicted=#{[res[r]["Predicted value"]].join(",")}"
-          res[r]["Boxplot"] = File.join($validation[:uri],"/report/boxplot/#{val_str}?hline=#{hline}")
+          res[r]["Boxplot"] = File.join($validation[:uri],"/boxplot/#{val_str}?hline=#{hline}&size=150")
         end
-        # format values
+        # render missing values
         if format
           res[r]["Test value"] = "'missing'" unless res[r]["Test value"]
-          res[r]["Predicted value"] = (res[r]["Training value"] ? "'not-predicted'" : "'prediction-failed'") unless res[r]["Predicted value"]
+          res[r]["Predicted value"] = (res[r]["Training value"] ? "'in-training-data'" : "'outside-AD'") unless res[r]["Predicted value"]
         end
+        # handle arrays
+        # add transformed values
         ["Training value","Test value","Predicted value","Error","Confidence value","Validation URI"].each do |v|
           next unless res[r].has_key?(v)
-          if [res[r][v]].flatten.size==1 # if single value
-            res[r][v] = res[r][v].to_nice_s if format
-          else # else if multiple values (-> format is enabled)
-            unless predictions[0].feature_type=="classification"
-              # for regression, compute mean (to fix table sorting)
-              mean = res[r][v].inject(0.0) { |sum, el| sum + el } / res[r][v].size
-              res[r][v] = mean.to_nice_s + " (" + res[r][v].collect{|v| v.to_nice_s}.join(", ")+")"
-            else
-              res[r][v] = res[r][v].join(", ")
-            end
+          vals = [res[r][v]].flatten
+          do_transform = (transformer.do_transform? and ["Training value","Test value","Predicted value"].include?(v))
+          if predictions.first.feature_type=="classification" or vals.any?{|x| !x.is_a?(Numeric)}
+            res[r][v] = vals.join(", ")
+          elsif vals.size==1
+            res[r][v] = vals.first.to_nice_s
+            res[r][v] += "\n#{transformer.transform(vals.first,res[r]["Compound URI"])}" if do_transform
+          else # vals.size > 1
+            mean = vals.inject(0.0) { |sum, el| sum + el } / vals.size
+            res[r][v] = "#{mean.to_nice_s} (mean)"
+            res[r][v] += "\n#{transformer.transform(mean,res[r]["Compound URI"])}" if do_transform
+            res[r][v] += "\n("+vals.collect{|v| v.to_nice_s}.join(", ")
+            res[r][v] += "\n#{transformer.transform(vals,res[r]["Compound URI"])}" if do_transform
+            res[r][v] += ")"
           end
         end
       end
 
       header = []
-      header << "Compound" if add_pic
+      header << "Compound" if format
       header << "Training value" if training_data_available
       header << "Test value"
       header << "Predicted value"
-      if predictions[0].feature_type=="classification"
+      if predictions.first.feature_type=="classification"
         header << "Classification" 
       else 
         header << "Error"
@@ -152,7 +160,66 @@ module Lib
       res.each do |a|
         array << header.collect{|h| a[h]}
       end
+
+      if transformer.do_transform?
+        array[0].each_with_index do |v,i|
+          array[0][i] += "\n[#{transformer.unit}]" if ["Training value","Test value","Predicted value","Error"].include?(v)
+        end
+      end
+
       array
     end
   end
+
+  ########## HACK FOR LOEAL MODELS ##############################
+  
+  class PredictionTransformer
+
+    def initialize(compounds, prediction_feature_title)
+      @prediction_feature_title = prediction_feature_title
+      case prediction_feature_title
+      when "LOAEL_log_mmol_kg_bw_day"
+        @mw = {}
+        OpenTox::Algorithm::Descriptor.physchem(compounds.collect{|c| OpenTox::Compound.new(c)},["Openbabel.mw"]).each do |uri,hash|
+          @mw[uri] = hash["Openbabel.mw"].to_f
+        end
+      end
+    end
+
+    def do_transform?
+      case @prediction_feature_title
+      when /LOAEL_log_.mol_kg_bw_day/, "LOAEL_log_mg_kg_bw_day"
+        true
+      else
+        false
+      end
+    end
+
+    def unit
+      case @prediction_feature_title
+      when /LOAEL_log_.mol_kg_bw_day/
+        "-log mol/kg bw/day"
+      when "LOAEL_log_mg_kg_bw_day"
+        "log mg/kg bw/day"
+      else
+        nil
+      end
+    end
+
+    def transform_single(val, c_uri)
+      case @prediction_feature_title
+      when /LOAEL_log_.mol_kg_bw_day/
+        val = (10**(-1*val)) * (@mw[c_uri]*1000)
+      when "LOAEL_log_mg_kg_bw_day"
+        val = 10**val
+      else
+        nil
+      end
+      val ? (val*10).round/10.0 : nil
+    end
+
+    def transform(val, c_uri)
+      "["+[val].flatten.collect{|v| transform_single(v,c_uri)}.join(", ")+" mg/kg bw/day]"
+    end
+  end
 end
diff --git a/lib/prediction_data.rb b/lib/prediction_data.rb
index a6e79c6..58c5570 100644
--- a/lib/prediction_data.rb
+++ b/lib/prediction_data.rb
@@ -9,7 +9,7 @@ module Lib
     def self.filter_data( data, compounds, min_confidence, min_num_predictions, max_num_predictions, prediction_index=nil )
       
       internal_server_error "cannot filter anything, no confidence values available" if data[:confidence_values][0]==nil
-      bad_request_error "please specify either min_confidence or max_num_predictions" if 
+      bad_request_error "please specify either min_confidence XOR max_num_predictions" if 
         (min_confidence!=nil and max_num_predictions!=nil) || (min_confidence==nil and max_num_predictions==nil)
       bad_request_error "min_num_predictions only valid for min_confidence" if 
         (min_confidence==nil and min_num_predictions!=nil)
diff --git a/report/plot_application.rb b/report/plot_application.rb
new file mode 100644
index 0000000..c3c4d4f
--- /dev/null
+++ b/report/plot_application.rb
@@ -0,0 +1,105 @@
+require 'digest/md5'
+
+class Validation::Application < OpenTox::Application
+
+  helpers do
+    def eval_r(r, cmd)
+      $logger.debug cmd
+      r.eval cmd
+    end
+  end
+
+  # produces a boxplot
+  # params should be given in URI, e.g. : ..boxplot/test_values=5.8,5.6,5.3;predicted=5.9
+  # ; separates series (or categories)
+  # = seperates key and values for each series
+  # , seperates values for each series
+  # 'hline=<float>' can be given as optional param (with '?') to draw horizontal lines with the given stepwidth
+  # (default: no horizontal lines, lines allow to compare different plots)
+  get '/validation/boxplot/:vals' do
+
+    filename = "#{Digest::MD5.hexdigest(params[:vals].inspect+params[:hline].inspect+params[:size].inspect)}.png"
+    unless (File.exists?("/tmp/#{filename}"))
+      # retrieve values
+      vals = {}
+      params[:vals].split(";").collect do |x|
+          y = x.split("=")
+          vals[y[0]] = (y[1] ? y[1].split(",").collect{|z| z.to_f} : nil)
+      end
+      names = "c(\""+vals.keys.join("\",\"")+"\")"
+      values = vals.values.collect{|a| "c("+(a ? a.join(",") : "")+")"}.join(",")
+      
+      # the min range is set to hline*2 to draw at least two horizontal lines
+      hline = params[:hline] ? params[:hline].to_f : nil
+      unless hline
+        ylim = ""
+      else
+        min = vals.values.flatten.compact.min
+        max = vals.values.flatten.compact.max
+        if (max-min<(hline*2))
+          to_add = (hline*2)-(max-min)
+          min -= to_add/2.0
+          max += to_add/2.0
+        end
+        range = "c(#{min},#{max})"
+        ylim = ",ylim=#{range}"
+      end
+
+      # return "boxplot(#{values},col=c('red','blue','green'),names=#{names}#{ylim})"
+      @r = RinRuby.new(true,false)
+      size = (params[:size] ? params[:size].to_i : 300)
+      eval_r(@r,"png(\"/tmp/#{filename}\",width=#{2*size},height=#{size})")
+      eval_r(@r,"par(mai=c(0.5,0.5,0.2,0.2))")
+      eval_r(@r,"boxplot(#{values},col=c('red','blue','green'),names=#{names}#{ylim})")
+      if hline
+        # seq defines were to draw hline
+        # example: min -9.5, max 10.5, hline = 2 -> seq(-10,12,by=2) -> produces lines from -10 to 12 with step-width 2
+        eval_r(@r,"abline(h=seq(floor(#{min}/#{hline})*#{hline}, round(#{max}/#{hline})*#{hline}, by=#{hline}),lty=2,col='dimgrey')")
+      end
+      eval_r(@r,'dev.off()')
+      @r.quit
+    end
+    send_file("/tmp/#{filename}",:filename=>"#{params[:vals]}.png",:type=>'image/png',:disposition => 'inline')
+  end
+
+  get '/validation/binplot/:vals' do
+
+    filename = "#{Digest::MD5.hexdigest(params[:vals].inspect+params[:size].inspect)}.png"
+    unless (File.exists?("/tmp/#{filename}")) and false
+
+      @r = RinRuby.new(true,false)
+      size = (params[:size] ? params[:size].to_i : 300)
+
+      # each bin is given as x1,x2,y
+      xvals = []
+      yvals = []
+      params[:vals].split(";").each do |bin|
+        x1,x2,y = bin.split(",")
+        if xvals.size==0 # first add point at y=0 to add a vertrical line from 0 to x1
+          xvals << x1.to_f
+          yvals << 0
+        end
+        # for each bin, add an additional point at y=0 to draw a vertrical line to 0
+        xvals += [x1.to_f, x2.to_f, x2.to_f]
+        yvals += [y.to_f,  y.to_f, 0]
+      end
+      # add first point again to draw horizontal line at y=0
+      xvals << xvals[0]
+      yvals << yvals[0]
+
+      eval_r(@r,"x <- c(#{xvals.join(",")})")
+      eval_r(@r,"y <- c(#{yvals.join(",")})")
+      eval_r(@r,"png(\"/tmp/#{filename}\",width=#{2*size},height=#{size})")
+#      eval_r(@r,"par(mai=c(0.5,0.5,0.2,0.2))")
+#      eval_r(@r,"par(mfrow=c(2,4))")
+      eval_r(@r,"plot(x,y,type='n', xlim=rev(range(x)), ylim=c(0,max(y)), xlab='#{params[:xlab]}', ylab='#{params[:ylab]}')")# type='n',
+#      eval_r(@r,"par(pch=22, col='red')")
+      eval_r(@r,"lines(x,y, type='l', col='red')")
+      eval_r(@r,"title(main='#{params[:title]}')")
+      eval_r(@r,'dev.off()')
+      @r.quit
+    end
+    send_file("/tmp/#{filename}",:filename=>"#{params[:vals]}.png",:type=>'image/png',:disposition => 'inline')
+  end
+
+end
diff --git a/report/report_application.rb b/report/report_application.rb
index 2bddf97..4c2fe29 100755
--- a/report/report_application.rb
+++ b/report/report_application.rb
@@ -35,51 +35,6 @@ class Validation::Application < OpenTox::Application
     end
   end
 
-  # produces a boxplot
-  # params should be given in URI, e.g. : ..boxplot/test_values=5.8,5.6,5.3;predicted=5.9
-  # ; separates series (or categories)
-  # = seperates key and values for each series
-  # , seperates values for each series
-  # 'hline=<float>' can be given as optional param (with '?') to specifiy the stepwidth of horizontal lines
-  # (default is 1.0, horizontal lines allow to compare different plots)
-  get '/validation/report/boxplot/:vals' do
-
-    filename = "#{Base64.encode64(params[:vals].inspect+params[:hline].inspect)}.png"
-    unless (File.exists?("/tmp/#{filename}"))
-      # retrieve values
-      vals = {}
-      params[:vals].split(";").collect do |x|
-          y = x.split("=")
-          vals[y[0]] = (y[1] ? y[1].split(",").collect{|z| z.to_f} : nil)
-      end
-      names = "c(\""+vals.keys.join("\",\"")+"\")"
-      values = vals.values.collect{|a| "c("+(a ? a.join(",") : "")+")"}.join(",")
-      
-      # the min range is set to hline*2 to draw at least two horizontal lines
-      hline = params[:hline] ? params[:hline].to_f : 1.0
-      min = vals.values.flatten.compact.min
-      max = vals.values.flatten.compact.max
-      if (max-min<(hline*2))
-        to_add = (hline*2)-(max-min)
-        min -= to_add/2.0
-        max += to_add/2.0
-      end
-      range = "c(#{min},#{max})"
-
-      # return "boxplot(#{values},col=c('red','blue','green'),names=#{names},ylim=#{range})"
-      @r = RinRuby.new(true,false)
-      @r.eval "png(\"/tmp/#{filename}\",width=300,height=150)"
-      @r.eval "par(mai=c(0.5,0.5,0.2,0.2))"
-      @r.eval "boxplot(#{values},col=c('red','blue','green'),names=#{names},ylim=#{range})"
-      # seq defines were to draw hline
-      # example: min -9.5, max 10.5, hline = 2 -> seq(-10,12,by=2) -> produces lines from -10 to 12 with step-width 2
-      @r.eval "abline(h=seq(floor(#{min}/#{hline})*#{hline}, round(#{max}/#{hline})*#{hline}, by=#{hline}),lty=2,col='dimgrey')" 
-      @r.eval 'dev.off()'
-      @r.quit
-    end
-    send_file("/tmp/#{filename}",:filename=>"#{params[:vals]}.png",:type=>'image/png',:disposition => 'inline')
-  end
-  
   get '/validation/report/?' do
     perform do |rs|
       case request.env['HTTP_ACCEPT'].to_s
diff --git a/report/report_content.rb b/report/report_content.rb
index eac44a3..98d8cbb 100755
--- a/report/report_content.rb
+++ b/report/report_content.rb
@@ -73,7 +73,7 @@ class Reports::ReportContent
       @xml_report.add_paragraph(section_table, section_text) if section_text
       v_uris = validation_set.validations.collect{|v| Array.new(v.num_instances.to_i,v.validation_uri)} if add_validation_uris
       @xml_report.add_table(section_table, table_title, Lib::OTPredictions.to_array(validation_set.validations.collect{|v| v.get_predictions}, 
-        true, true, v_uris))
+        true, v_uris))
     else
       @xml_report.add_paragraph(section_table, "No prediction info available.")
     end
@@ -412,4 +412,4 @@ class Reports::ReportContent
     @tmp_files.delete(tmp_file_name) if @tmp_files.has_key?(tmp_file_name)
   end
   
-end
\ No newline at end of file
+end
diff --git a/report/report_format.rb b/report/report_format.rb
index 8d9d55e..68781c6 100644
--- a/report/report_format.rb
+++ b/report/report_format.rb
@@ -85,9 +85,11 @@ module Reports::ReportFormat
 
     # HACK to add java script to html file (modifying the xsl would probably be the clean correct solution)
     html_file = File.join(directory,html_filename.to_s)
-    content = File.read(html_file, :encoding=>"ISO-8859-1").gsub(/\<\//, "\n</")
-    content = content.gsub(/\<body\s/,"\n#{JAVASCRIPT}\n<body ")
-    content = content.gsub(/table summary="Predic/,"table class=\"tablesorter\" summary=\"Predic")
+    content = File.read(html_file, :encoding=>"ISO-8859-1")
+    content.gsub!(/\<\//, "\n</") # for better readability of the html source
+    content.gsub!(/&lt;br&gt;/,"<br>") # there is no straightforward way to add line breaks in docbook
+    content.gsub!(/\<body\s/,"\n#{JAVASCRIPT}\n<body ")
+    content.gsub!(/table summary="Predic/,"table class=\"tablesorter\" summary=\"Predic")
     File.open(html_file, 'wb', :encoding=>"ISO-8859-1") { |file| file.write(content) }
   end
   
diff --git a/report/validation_access.rb b/report/validation_access.rb
index 6248ff2..c3a5121 100755
--- a/report/validation_access.rb
+++ b/report/validation_access.rb
@@ -201,11 +201,11 @@ class Reports::ValidationDB
     if validation.training_dataset_uri
       d = Lib::DatasetCache.find(validation.training_dataset_uri)
       data.compounds.each do |c|
-        training_values[c] = (d.compound_indices(c) ? d.compound_indices(c).collect{|idx| d.data_entry_value(idx,validation.prediction_feature)} : nil)
+        training_values[c] = d.compound_indices(c).collect{|idx| d.data_entry_value(idx,validation.prediction_feature)} if d.compound_indices(c)
       end
     end
     task.progress(90) if task
-    Lib::OTPredictions.new( data.data, data.compounds, training_values )
+    Lib::OTPredictions.new( data.data, data.compounds, training_values, OpenTox::Feature.new(validation.prediction_feature).title )
   end
   
   def get_accept_values( validation )
diff --git a/report/xml_report.rb b/report/xml_report.rb
index 2fbbbbe..feb49f8 100755
--- a/report/xml_report.rb
+++ b/report/xml_report.rb
@@ -165,17 +165,29 @@ module Reports
       element << table
       table
     end
-    
-    def add_image( element, url ) #, scale=false )
-      image = Element.new("imageobject")
-      params = {"fileref" => url, "format"=>"PNG"}
+
+    def self.image( image_url, link_url=nil )
+      img = Element.new("imageobject")
+      params = {"fileref" => image_url, "format"=>"PNG"}
       #params["contentwidth"] = "2in"
       imagedata = Reports::XMLReportUtil.attribute_element("imagedata",params) 
-      image << imagedata
-      element << image
-      return image    
+      img << imagedata
+      unless link_url
+        img
+      else
+        ulink = Element.new("ulink")
+        ulink.add_attributes({"url" => link_url })
+        ulink << img
+        ulink
+      end
     end
     
+    def add_image( element, image_url, link_url=nil )
+      img = XMLReport.image( image_url, link_url )
+      element << img
+      img    
+    end
+
     # adds a table to a REXML:Element, _table_values_ should be a multi-dimensional-array, returns the table as element
     # 
     # call-seq:
@@ -210,7 +222,7 @@ module Reports
           if auto_link_urls && v.to_s =~ /^http(s?):\/\//
             add_url(entry, v.to_s)
           else
-            entry.text = v.to_s
+            entry.text = v.to_s.gsub(/\n/,"<br>") # will be xml-escaped, post-processing required
           end
           row << entry
         end
@@ -223,8 +235,10 @@ module Reports
         row = Element.new("row")
         r.each do |v|
           entry = Element.new("entry")
-          if auto_link_urls && (v.to_s =~ /depict|boxplot|media=image|.png$/) #PENDING 
-            add_image(entry, v.to_s)
+          if v.is_a?(Element)
+            entry << v
+          elsif auto_link_urls && (v.to_s =~ /depict|boxplot|media=image|.png$/) #PENDING 
+            add_image(entry, v.to_s, (v.to_s=~/\?/ ? v.to_s.split("?").first : nil))
           elsif auto_link_urls && v.to_s =~ /^http(s?):\/\//
            #add_url(entry, v.to_s, v.to_s)
            v.to_s.split(" ").each do |vv|
@@ -236,6 +250,7 @@ module Reports
          else
            text = v.to_s
            text.gsub!(/\+\-/,"&plusmn;")
+           text.gsub!(/\n/,"&lt;br&gt;") # is xml-escaped, post-processing required
            entry << Text.new(text, true, nil, true)
           end
           row << entry
@@ -292,7 +307,8 @@ module Reports
         end
       end
       
-      @doc.write(out) #,2, true, true)
+      @doc.write(out)
+      # @doc.write(out, 2)
       out.flush
     end
   
@@ -303,16 +319,17 @@ module Reports
   
       rep = Reports::XMLReport.new("Demo report", "subtitle" "Fistname", "Surname")
       section1 = rep.add_section(rep.get_root_element, "First Section")
-      rep.add_paragraph(section1, "some text")
-      rep.add_paragraph(section1, "even more text")
-      rep.add_imagefigure(section1, "Figure", "http://upload.wikimedia.org/wikipedia/commons/thumb/e/eb/Siegel_der_Albert-Ludwigs-Universit%C3%A4t_Freiburg.svg/354px-Siegel_der_Albert-Ludwigs-Universit%C3%A4t_Freiburg.svg", "SVG", 100, "this is the logo of freiburg university")
-      section2 = rep.add_section(rep.get_root_element,"Second Section")
-      rep.add_section(section2,"A Subsection")
-      rep.add_section(section2,"Another Subsection")
-      rep.add_url(section2,"www.google.de", "link zu google")
-      sec3 = rep.add_section(rep.get_root_element,"Third Section")
-      rep.add_paragraph(sec3, "some    \n              more text for section 3",true)
-      rep.add_image(sec3, "http://ambit.uni-plovdiv.bg:8080/ambit2/depict/cdk?search=c1ccccc1")
+      rep.add_table(section1, "Table", [["a\n1","b"],["c","d"]])
+#      rep.add_paragraph(section1, "some text")
+#      rep.add_paragraph(section1, "even more text")
+#      rep.add_imagefigure(section1, "Figure", #"http://upload.wikimedia.org/wikipedia/commons/thumb/e/eb/Siegel_der_Albert-Ludwigs-Universit%C3%A4t_Freiburg.svg/354px-Siegel_der_Albert-Ludwigs-Universit%C3%A4t_Freiburg.svg", "SVG", 100, "this is the logo of freiburg university")
+#      section2 = rep.add_section(rep.get_root_element,"Second Section")
+#      rep.add_section(section2,"A Subsection")
+#      rep.add_section(section2,"Another Subsection")
+#      rep.add_url(section2,"www.google.de", "link zu google")
+#      sec3 = rep.add_section(rep.get_root_element,"Third Section")
+#      rep.add_paragraph(sec3, "some    \n              more text for section 3",true)
+#      rep.add_image(sec3, "http://ambit.uni-plovdiv.bg:8080/ambit2/depict/cdk?search=c1ccccc1")
       
       #vals= [["a", "b", "c"],["a2", "b2", "c2"],["1", "2", "http://3"]]
       #rep.add_table(rep.get_root_element, "demo-table", vals)