handle confidence nil values, and fix prediction confidence sorting, improved prediction table

7 files changed, 22 insertions, 13 deletions

diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb
index 644168f..93581d8 100755
--- a/lib/ot_predictions.rb
+++ b/lib/ot_predictions.rb
@@ -146,11 +146,11 @@ module Lib
                 predicted_values << regression_value(prediction_dataset, c, no_prediction_feature ? nil : predicted_variable)
               end
               # TODO confidence_values << prediction_dataset.get_prediction_confidence(c, predicted_variable)
-              conf = predicted_values[count]!=nil ? 1 : 0 
+              conf = predicted_values[count]!=nil ? 1 : nil 
               begin
                 feature = prediction_dataset.data_entries[c].keys[0]
                 feature_data = prediction_dataset.features[feature]
-                conf = feature_data[OT.confidence] if feature_data[OT.confidence]!=nil 
+                conf = feature_data[OT.confidence].to_f if feature_data[OT.confidence]!=nil 
               rescue
                 LOGGER.warn "could not get confidence"
               end
@@ -259,13 +259,17 @@ module Lib
           a << (format ? p.predicted_value(i).to_nice_s : p.predicted_value(i))
           if p.feature_type=="classification"
             if (p.predicted_value(i)!=nil and p.actual_value(i)!=nil)
-              a << (p.classification_miss?(i) ? 1 : 0)
+              if p.classification_miss?(i)
+                a << (format ? ICON_ERROR : 1)
+              else
+                a << (format ? ICON_OK : 0)
+              end
             else
               a << nil
             end
           end
           if p.confidence_values_available?
-            conf_column = a.size
+            conf_column = a.size if conf_column==nil
             a << p.confidence_value(i) #(format ? p.confidence_value(i).to_nice_s : p.confidence_value(i))
           end
           a << p.identifier(i)
@@ -274,10 +278,10 @@ module Lib
       end
       
       if conf_column!=nil
-        res.sort!{ |x,y| y[4] <=> x[4] }
+        res = res.sort_by{ |n| n[conf_column] || 0 }.reverse
         if format
           res.each do |a|
-            a[4] = a[4].to_nice_s
+            a[conf_column] = a[conf_column].to_nice_s
           end
         end
       end
@@ -291,7 +295,6 @@ module Lib
       res.insert(0, header)
       
       return res
-  end
-    
+    end
   end
 end
diff --git a/report/environment.rb b/report/environment.rb
index 59465aa..bdb4a04 100755
--- a/report/environment.rb
+++ b/report/environment.rb
@@ -27,6 +27,8 @@ require "report/validation_data.rb"
 require "report/util.rb"
 require "report/statistical_test.rb"
 
+ICON_ERROR = File.join(CONFIG[:services]["opentox-validation"],"resources/error.png")
+ICON_OK = File.join(CONFIG[:services]["opentox-validation"],"resources/ok.png")
 
 
 
diff --git a/report/report_application.rb b/report/report_application.rb
index 1637ead..3c8670a 100755
--- a/report/report_application.rb
+++ b/report/report_application.rb
@@ -23,6 +23,10 @@ get '/'+ENV['DOCBOOK_DIRECTORY']+'/:resource' do
   get_docbook_resource ENV['DOCBOOK_DIRECTORY']+"/"+request.env['REQUEST_URI'].split("/")[-1]
 end
 
+get '/resources/:resource' do
+  get_docbook_resource "resources/"+request.env['REQUEST_URI'].split("/")[-1]
+end
+
 get '/report/:type/css_style_sheet/?' do
   perform do |rs|
     "@import \""+params[:css_style_sheet]+"\";"
diff --git a/report/xml_report.rb b/report/xml_report.rb
index b308c01..cf30e3b 100755
--- a/report/xml_report.rb
+++ b/report/xml_report.rb
@@ -159,16 +159,16 @@ module Reports
       table
     end
     
-    def add_image( element, url )
+    def add_image( element, url ) #, scale=false )
       image = Element.new("imageobject")
-      imagedata = Reports::XMLReportUtil.attribute_element("imagedata",
-        {"fileref" => url, "format"=>"PNG", "contentwidth" => "2in" }) #PENDING: do not hardcode size
+      params = {"fileref" => url, "format"=>"PNG"}
+      #params["contentwidth"] = "2in"
+      imagedata = Reports::XMLReportUtil.attribute_element("imagedata",params) 
       image << imagedata
       element << image
       return image    
     end
     
-    
     # adds a table to a REXML:Element, _table_values_ should be a multi-dimensional-array, returns the table as element
     # 
     # call-seq:
@@ -216,7 +216,7 @@ 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\/png$/ #PENDING 
+          if auto_link_urls && v.to_s =~ /depict/ || v.to_s =~ /png$/ #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)
diff --git a/resources/error.png b/resources/error.png
new file mode 100644
index 0000000..e051534
--- /dev/null
+++ b/resources/error.png
diff --git a/resources/ok.png b/resources/ok.png
new file mode 100644
index 0000000..31bd433
--- /dev/null
+++ b/resources/ok.png
diff --git a/resources/ot-logo.png b/resources/ot-logo.png
new file mode 100644
index 0000000..248a853
--- /dev/null
+++ b/resources/ot-logo.png