output.rb in genevalidator-1.6.3

- old
+ new

@@ -32,12 +32,10 @@
       @config[:run_no] += 1
 
       @prediction_def = definition
       @nr_hits        = no_of_hits
       @idx            = current_idx
-
-      @app_html       = File.join(@config[:html_path], 'files/table.html')
     end
 
     def print_output_console
       mutex.synchronize do
         print_console_header unless @config[:console_header_printed]
@@ -48,37 +46,35 @@
       end
     end
 
     def print_console_header
       @config[:console_header_printed] = true
-      print format("%3s\t%5s\t%20s\t%7s\t", 'No', 'Score', 'Identifier', 'No_Hits')
+      print format("%3s\t%5s\t%20s\t%7s\t", 'No', 'Score', 'Identifier',
+                   'No_Hits')
       puts validations.map(&:short_header).join("\t")
     end
 
     def generate_html
       mutex_html.synchronize do
-        output_html = output_filename
+        output_html   = output_filename
         query_erb     = File.join(@config[:aux], 'template_query.erb')
         template_file = File.open(query_erb, 'r').read
         erb           = ERB.new(template_file, 0, '>')
         File.open(output_html, 'a') { |f| f.write(erb.result(binding)) }
-        File.open(@app_html, 'a') { |f| f.write(erb.result(binding)) }
       end
     end
 
     def output_filename
-      i = (@config[:run_no].to_f / @config[:output_max]).ceil
-      output_html = File.join(@config[:html_path], "results#{i}.html")
+      idx         = (@config[:run_no].to_f / @config[:output_max]).ceil
+      output_html = File.join(@config[:html_path], "results#{idx}.html")
       write_html_header(output_html)
       output_html
     end
 
     def write_html_header(output_html)
       head_erb       = File.join(@config[:aux], 'template_header.erb')
-      head_table_erb = File.join(@config[:aux], 'app_template_header.erb')
       set_up_html(head_erb, output_html) unless File.exist?(output_html)
-      set_up_html(head_table_erb, @app_html) unless File.exist?(@app_html)
     end
 
     def set_up_html(erb_file, output_file)
       return if File.exist?(output_file)
       template_contents = File.open(erb_file, 'r').read
@@ -97,29 +93,35 @@
     end
 
     def create_validation_hashes(row)
       row[:validations] = {}
       @validations.each do |item|
-        val = { header: item.header, description: item.description,
-                status: item.color, print: item.print.gsub('&nbsp;', ' ') }
-        if item.color != 'warning'
-          explain = { approach: item.approach, explanation: item.explanation,
-                      conclusion: item.conclusion }
-          val.merge!(explain)
-        end
+        val     = add_basic_validation_info(item)
+        explain = add_explanation_data(item) if item.color != 'warning'
+        val.merge!(explain) if explain
         val[:graphs] = create_graphs_hash(item) unless item.plot_files.nil?
         row[:validations][item.short_header] = val
       end
       row
     end
 
+    def add_basic_validation_info(item)
+      { header: item.header, description: item.description, status: item.color,
+        print: item.print.gsub('&nbsp;', ' ') }
+    end
+
+    def add_explanation_data(item)
+      { approach: item.approach, explanation: item.explanation,
+        conclusion: item.conclusion }
+    end
+
     def create_graphs_hash(item)
       graphs = []
       item.plot_files.each do |g|
         graphs << { data: g.data, type: g.type, title: g.title,
-                    footer: g.footer, xtitle: g.xtitle,
-                    ytitle: g.ytitle, aux1: g.aux1, aux2: g.aux2 }
+                    footer: g.footer, xtitle: g.xtitle, ytitle: g.ytitle,
+                    aux1: g.aux1, aux2: g.aux2 }
       end
       graphs
     end
 
     def write_row_json(row)
@@ -138,21 +140,14 @@
     # Param:
     # +all_query_outputs+: array with +ValidationTest+ objects
     # +html_path+: path of the html folder
     # +filemane+: name of the fasta input file
     def self.print_footer(overview, config)
-      overall_evaluation = overview(overview)
+      set_overall_evaluation(overview, config)
 
-      create_plot_json(overview[:scores], config[:plot_dir])
+      footer_erb          = File.join(config[:aux], 'template_footer.erb')
 
-      less = overall_evaluation[0].gsub("\n", '<br>').gsub("'", %q(\\\'))
-
-      eval = print_summary_to_console(overall_evaluation, config[:summary])
-      evaluation     = eval.gsub("\n", '<br>').gsub("'", %q(\\\'))
-
-      footer_erb     = File.join(config[:aux], 'template_footer.erb')
-
       no_of_results_files = (config[:run_no].to_f / config[:output_max]).ceil
       template_file       = File.open(footer_erb, 'r').read
       erb                 = ERB.new(template_file, 0, '>')
 
       output_files = []
@@ -162,44 +157,48 @@
         results_html = File.join(config[:html_path], "results#{i}.html")
         File.open(results_html, 'a+') { |f| f.write(erb.result(binding)) }
       end
 
       turn_off_sorting(config[:html_path]) if no_of_results_files > 1
+    end
 
-      # write footer for the app
-      app_footer_erb = File.join(config[:aux], 'app_template_footer.erb')
-      table_html     = File.join(config[:html_path], 'files/table.html')
-      table_footer_template = File.open(app_footer_erb, 'r').read
-      table_erb             = ERB.new(table_footer_template, 0, '>')
-      File.open(table_html, 'a+') { |f| f.write(table_erb.result(binding)) }
+    def self.set_overall_evaluation(overview, config)
+      overall_evaluation = overview(overview)
+      less = overall_evaluation[0].gsub("\n", '<br>').gsub("'", %q(\\\'))
+
+      eval = print_summary_to_console(overall_evaluation, config[:summary])
+      evaluation     = eval.gsub("\n", '<br>').gsub("'", %q(\\\'))
+
+      create_overview_json(overview[:scores], config[:plot_dir], less,
+                           evaluation)
     end
 
     def self.turn_off_sorting(html_path)
       script_file = File.join(html_path, 'files/js/script.js')
-      temp_file   = File.join(html_path, 'files/js/script.temp.js')
-      File.open(temp_file, 'w') do |out_file|
-        out_file.puts File.readlines(script_file)[30..-1].join
+      File.open("#{script_file}.tmp", 'w') do |f|
+        f.puts File.readlines(script_file)[30..-1].join
       end
-      FileUtils.mv(temp_file, script_file)
+      FileUtils.mv("#{script_file}.tmp", script_file)
     end
 
     def self.print_summary_to_console(overall_evaluation, summary)
       # print to console
       eval = ''
-      overall_evaluation.each { |e| eval << "\n#{e}" }
+      overall_evaluation.each { |e| eval << "#{e}\n" }
       $stderr.puts eval if summary
       $stderr.puts ''
       eval
     end
 
     # make the historgram with the resulted scores
-    def self.create_plot_json(scores, plot_dir)
+    def self.create_overview_json(scores, plot_dir, less, evaluation)
       plot_file = File.join(plot_dir, 'overview.json')
       data = [scores.group_by { |a| a }.map { |k, vs| { 'key' => k, 'value' => vs.length, 'main' => false } }]
       hash = { data: data, type: :simplebars, title: 'Overall Evaluation',
                footer: '', xtitle: 'Validation Score',
-               ytitle: 'Number of Queries', aux1: 10, aux2: '' }
+               ytitle: 'Number of Queries', aux1: 10, aux2: '', less: less,
+               evaluation: evaluation }
       File.open(plot_file, 'w') { |f| f.write hash.to_json }
     end
 
     ##
     # Calculates an overall evaluation of the output
@@ -231,11 +230,11 @@
                 ' evidence.'
       end
       eval
     end
 
+    # errors per validation
     def self.errors_overview(o)
-      # errors per validation
       error_eval = ''
       o[:map_errors].each do |k, v|
         error_eval << "\nWe couldn't run #{k} Validation for #{v} queries"
       end
       if o[:no_mafft] >= (o[:no_queries] - o[:nee])