move to ruby-plot 0.0.3, use png instead of svg, use ?media for compound images

6 files changed, 21 insertions, 20 deletions

diff --git a/lib/ohm_util.rb b/lib/ohm_util.rb
index 21d7978..856f9d2 100644
--- a/lib/ohm_util.rb
+++ b/lib/ohm_util.rb
@@ -6,7 +6,7 @@ module Lib
       prop_names = model.attributes.collect{|p| p.to_s}
       params.keys.each do |k|
         key = k.to_s
-        if (key == "subjectid")
+        if (key == "subjectid" || key == "media")
           params.delete(k)
         else
           unless prop_names.include?(key)
@@ -28,10 +28,11 @@ module Lib
     end
     
     def self.find(model, filter_params)
-      if (filter_params.size==0)
+      params = check_params(model,filter_params)
+      if (params.size==0)
         model.all
       else
-        model.find(check_params(model,filter_params))
+        model.find(params)
       end
     end
     
diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb
index 1fd601c..22f9b20 100755
--- a/lib/ot_predictions.rb
+++ b/lib/ot_predictions.rb
@@ -213,7 +213,7 @@ module Lib
           begin
             #a.push( "http://ambit.uni-plovdiv.bg:8080/ambit2/depict/cdk?search="+
             #  URI.encode(OpenTox::Compound.new(:uri=>p.identifier(i)).smiles) ) if add_pic
-            a << p.identifier(i)+"/image"
+            a << p.identifier(i)+"?media=image/png"
           rescue => ex
             raise ex
             #a.push("Could not add pic: "+ex.message)
diff --git a/report/environment.rb b/report/environment.rb
index 4729dc8..a149a1d 100755
--- a/report/environment.rb
+++ b/report/environment.rb
@@ -4,7 +4,7 @@
   'rexml/document',  'ruby-plot', 'opentox-ruby' ].each do |g|
     require g
 end
-gem 'ruby-plot', '= 0.0.2'
+gem 'ruby-plot', '= 0.0.3'
 
 #R.quit
 
diff --git a/report/plot_factory.rb b/report/plot_factory.rb
index 43c45fc..deb1880 100644
--- a/report/plot_factory.rb
+++ b/report/plot_factory.rb
@@ -161,7 +161,7 @@ module Reports
     end
     
     
-    def self.create_ranking_plot( svg_out_file, validation_set, compare_attribute, equal_attribute, rank_attribute, class_value=nil )
+    def self.create_ranking_plot( out_file, validation_set, compare_attribute, equal_attribute, rank_attribute, class_value=nil )
 
       #compute ranks
       #puts "rank attibute is "+rank_attribute.to_s
@@ -184,14 +184,14 @@ module Reports
                     ranks, 
                     nil, #0.1, 
                     validation_set.num_different_values(equal_attribute), 
-                    svg_out_file) 
+                    out_file) 
     end
   
     protected
-    def self.plot_ranking( title, comparables_array, ranks_array, confidence = nil, numdatasets = nil, svg_out_file = nil )
+    def self.plot_ranking( title, comparables_array, ranks_array, confidence = nil, numdatasets = nil, out_file = nil )
       
       (confidence and numdatasets) ? conf = "-q "+confidence.to_s+" -k "+numdatasets.to_s : conf = ""
-      svg_out_file ? show = "-o" : show = ""  
+      out_file ? show = "-o" : show = ""  
       (title and title.length > 0) ? tit = '-t "'+title+'"' : tit = ""  
       #title = "-t \""+ranking_value_prop+"-Ranking ("+comparables.size.to_s+" "+comparable_prop+"s, "+num_groups.to_s+" "+ranking_group_prop+"s, p < "+p.to_s+")\" "
       
@@ -208,12 +208,12 @@ module Reports
       end
       raise "rank plot failed" unless $?==0
       
-      if svg_out_file
-        f = File.new(svg_out_file, "w")
+      if out_file
+        f = File.new(out_file, "w")
         f.puts res
       end
         
-      svg_out_file ? svg_out_file : res
+      out_file ? out_file : res
     end
     
     def self.demo_ranking_plot
@@ -264,7 +264,7 @@ module Reports
                     :actual_values =>     [0, 1, 0, 0, 1, 1]}
       tp_fp_rates = get_tp_fp_rates(roc_values)
       data = { :names => ["default"], :fp_rate => [tp_fp_rates[:fp_rate]], :tp_rate => [tp_fp_rates[:tp_rate]] }                    
-      RubyPlot::plot_lines("/tmp/plot.svg",
+      RubyPlot::plot_lines("/tmp/plot.png",
         "ROC-Plot", 
         "False positive rate", 
         "True Positive Rate", data[:names], data[:fp_rate], data[:tp_rate], data[:faint] )
diff --git a/report/report_content.rb b/report/report_content.rb
index 674bb13..1e47cee 100755
--- a/report/report_content.rb
+++ b/report/report_content.rb
@@ -155,12 +155,12 @@ class Reports::ReportContent
       
       section_text += "\nWARNING: regression plot information not available for all validation results" if prediction_set.size!=validation_set.size
       @xml_report.add_paragraph(section_regr, section_text) if section_text
-      plot_file_name = "regr_plot"+@tmp_file_count.to_s+".svg"
+      plot_file_name = "regr_plot"+@tmp_file_count.to_s+".png"
       @tmp_file_count += 1
       begin
         plot_file_path = add_tmp_file(plot_file_name)
         Reports::PlotFactory.create_regression_plot( plot_file_path, prediction_set, name_attribute )
-        @xml_report.add_imagefigure(section_regr, image_title, plot_file_name, "SVG", 120, image_caption)
+        @xml_report.add_imagefigure(section_regr, image_title, plot_file_name, "PNG", 100, image_caption)
       rescue RuntimeError => ex
         LOGGER.error("Could not create regression plot: "+ex.message)
         rm_tmp_file(plot_file_name)
@@ -194,12 +194,12 @@ class Reports::ReportContent
         class_value = accept_values[i]
         image_title = image_titles ? image_titles[i] : "ROC Plot for class-value '"+class_value.to_s+"'"
         image_caption = image_captions ? image_captions[i] : nil
-        plot_file_name = "roc_plot"+@tmp_file_count.to_s+".svg"
+        plot_file_name = "roc_plot"+@tmp_file_count.to_s+".png"
         @tmp_file_count += 1
         begin
           plot_file_path = add_tmp_file(plot_file_name)
           Reports::PlotFactory.create_roc_plot( plot_file_path, prediction_set, class_value, split_set_attribute, false )#prediction_set.size>1 )
-          @xml_report.add_imagefigure(section_roc, image_title, plot_file_name, "SVG", 120, image_caption)
+          @xml_report.add_imagefigure(section_roc, image_title, plot_file_name, "PNG", 100, image_caption)
         rescue RuntimeError => ex
           msg = "WARNING could not create roc plot for class value '"+class_value.to_s+"': "+ex.message
           LOGGER.error(msg)
@@ -270,11 +270,11 @@ class Reports::ReportContent
     section_bar = @xml_report.add_section(@current_section, section_title)
     @xml_report.add_paragraph(section_bar, section_text) if section_text
     
-    plot_file_name = "bar_plot"+@tmp_file_count.to_s+".svg"
+    plot_file_name = "bar_plot"+@tmp_file_count.to_s+".png"
     @tmp_file_count += 1
     plot_file_path = add_tmp_file(plot_file_name)
     Reports::PlotFactory.create_bar_plot(plot_file_path, validation_set, title_attribute, value_attributes )
-    @xml_report.add_imagefigure(section_bar, image_title, plot_file_name, "SVG", 120, image_caption)
+    @xml_report.add_imagefigure(section_bar, image_title, plot_file_name, "PNG", 100, image_caption)
   end  
   
   private
diff --git a/report/xml_report.rb b/report/xml_report.rb
index 4b9a11a..4fbfae3 100755
--- a/report/xml_report.rb
+++ b/report/xml_report.rb
@@ -184,7 +184,7 @@ module Reports
         row = Element.new("row")
         r.each do |v|
           entry = Element.new("entry")
-          if auto_link_urls && v.to_s =~ /depict/ || v.to_s =~ /image$/ #PENDING 
+          if auto_link_urls && v.to_s =~ /depict/ || v.to_s =~ /image\/png$/ #PENDING 
             add_image(entry, v.to_s)
           elsif auto_link_urls && v.to_s =~ /^http(s?):\/\//
            add_url(entry, v.to_s, v.to_s)