added report examples and example tests, new module Validation

1 files changed, 16 insertions, 10 deletions

diff --git a/report/report_factory.rb b/report/report_factory.rb
index 5120a51..2d7de03 100644
--- a/report/report_factory.rb
+++ b/report/report_factory.rb
@@ -19,7 +19,7 @@ module Reports::ReportFactory
   RT_CV = "crossvalidation"
   RT_ALG_COMP = "algorithm_comparison"
   
-  REPORT_TYPES = [RT_FASTTOX, RT_VALIDATION, RT_CV, RT_ALG_COMP ]
+  REPORT_TYPES = [RT_VALIDATION, RT_CV, RT_ALG_COMP ] #,RT_FASTTOX
   
   # creates a report of a certain type according to the validation data in validation_set 
   #
@@ -220,17 +220,17 @@ class Reports::ReportContent
                             split_set_attribute = nil,
                             plot_file_name="roc-plot.svg", 
                             section_title="Roc Plot",
-                            section_text="This section contains the roc plot.",
+                            section_text=nil,
                             image_title=nil,
                             image_caption=nil)
-    unless image_title
-      if class_value
-        image_title = "Roc Plot for class-value '"+class_value+"'"
-      else
-        image_title = "Roc Plot for all classes"
-      end
-    end
     
+    if class_value
+      section_text = "This section contains the roc plot for class '"+class_value+"'." unless section_text
+      image_title = "Roc Plot for class-value '"+class_value+"'" unless image_title
+    else
+      section_text = "This section contains the roc plot." unless section_text
+      image_title = "Roc Plot for all classes" unless image_title
+    end
     
     section_roc = @xml_report.add_section(@xml_report.get_root_element, section_title)
     if validation_set.first.get_predictions
@@ -241,7 +241,9 @@ class Reports::ReportContent
         Reports::RPlotFactory.create_roc_plot( plot_file_path, validation_set, class_value, split_set_attribute, validation_set.size>1 )
         @xml_report.add_imagefigure(section_roc, image_title, plot_file_name, "SVG", image_caption)
       rescue RuntimeError => ex
-        LOGGER.error("could not create roc plot: "+ex.message)   
+        LOGGER.error("could not create roc plot: "+ex.message)
+        LOGGER.debug("if R cannot find your libs, try adding R_LIBS='<lib>' to your ~/.Renviron file")
+        rm_tmp_file(plot_file_name)
         @xml_report.add_paragraph(section_roc, "could not create roc plot: "+ex.message)
       end  
     else
@@ -307,4 +309,8 @@ class Reports::ReportContent
     return tmp_file_path
   end
   
+  def rm_tmp_file(tmp_file_name)
+    @tmp_files.delete(tmp_file_name) if @tmp_files.has_key?(tmp_file_name)
+  end
+  
 end
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