Class: GeneValidator::JsonToGVResults

Inherits:
Object
  • Object
show all
Extended by:
Forwardable
Defined in:
lib/genevalidator/json_to_gv_results.rb

Overview

produce GV results from a JSON previously produced from GV

Class Method Summary collapse

Class Method Details

.calculate_no_quries_with_no_evidence ⇒ Object

calculate number of queries that had warnings for all validations.



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# File 'lib/genevalidator/json_to_gv_results.rb', line 138

def calculate_no_quries_with_no_evidence
  all_warnings = 0
  @json_array.each do |row|
    status = row['validations'].map { |_, h| h['status'] }
    if status.count { |r| r == 'warning' } == status.length
      all_warnings += 1
    end
  end
  all_warnings
end

.calculate_overall_score ⇒ Object 



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# File 'lib/genevalidator/json_to_gv_results.rb', line 110

def calculate_overall_score
  scores = []
  @json_array.each { |row| scores << row['overall_score'] }
  plot_dir = File.join(@config[:html_path], 'files/json')
  less     =  generate_evaluation(scores)
  Output.create_overview_json(scores, plot_dir, less, less)
end

.create_json_file(row) ⇒ Object 



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# File 'lib/genevalidator/json_to_gv_results.rb', line 49

def create_json_file(row)
  @json_file = File.join(@config[:plot_dir],
                         "#{@config[:filename]}_#{row['idx']}.json")
  File.open(@json_file, 'w') { |f| f.write(row.to_json) }
end

.generate_evaluation(scores) ⇒ Object 



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# File 'lib/genevalidator/json_to_gv_results.rb', line 118

def generate_evaluation(scores)
  no_of_queries = scores.length
  good_scores = scores.count { |s| s >= 75 }
  bad_scores  = scores.count { |s| s < 75 }
  nee         = calculate_no_quries_with_no_evidence # nee = no evidence

  good_pred = (good_scores == 1) ? 'One' : "#{good_scores} are"
  bad_pred  = (bad_scores == 1) ? 'One' : "#{bad_scores} are"
  eval = 'Overall Query Score Evaluation:<br>' \
         "#{no_of_queries} predictions were validated, from which there" \
         ' were:<br>' \
         "#{good_pred} good prediction(s),<br>" \
         "#{bad_pred} possibly weak prediction(s).<br>"
  return eval if nee == 0
  eval << "#{nee} could not be evaluated due to the lack of" \
          ' evidence.<br>'
  eval
end

.generate_html_header(output_html) ⇒ Object 



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# File 'lib/genevalidator/json_to_gv_results.rb', line 60

def generate_html_header(output_html)
  return if File.exist?(output_html)
  json_header_template = File.join(@config[:aux], 'json_header.erb')
  template_contents    = File.open(json_header_template, 'r').read
  erb                  = ERB.new(template_contents, 0, '>')
  File.open(output_html, 'w+') { |f| f.write(erb.result(binding)) }
end

.generate_html_query(output_html, row) ⇒ Object 



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# File 'lib/genevalidator/json_to_gv_results.rb', line 68

def generate_html_query(output_html, row)
  @row = row
  json_query_template = File.join(@config[:aux], 'json_query.erb')
  template_contents   = File.open(json_query_template, 'r').read
  erb                 = ERB.new(template_contents, 0, '>')
  File.open(output_html, 'a') { |f| f.write(erb.result(binding)) }
end

.html_footer ⇒ Object

Add footer to all output files



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# File 'lib/genevalidator/json_to_gv_results.rb', line 77

def html_footer
  no_of_output_files = (@config[:run_no].to_f / @config[:output_max]).ceil

  output_files = []
  (1..no_of_output_files).each { |i| output_files << "results#{i}.html" }

  write_html_footer(no_of_output_files, output_files)
end

.init ⇒ Object 



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# File 'lib/genevalidator/json_to_gv_results.rb', line 17

def init
  @opt    = opt
  @config = {
    html_path: "#{@opt[:json_file]}.html",
    plot_dir: "#{@opt[:json_file]}.html/files/json",
    aux: File.expand_path(File.join(File.dirname(__FILE__), '../../aux')),
    filename: File.basename(@opt[:json_file]),
    output_max: 2500,
    run_no: 0
  }
  @json_array = load_json_file
end

.load_json_file ⇒ Object 



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# File 'lib/genevalidator/json_to_gv_results.rb', line 44

def load_json_file
  json_contents = File.read(File.expand_path(@opt[:json_file]))
  JSON.load(json_contents)
end

.output_filename ⇒ Object 



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# File 'lib/genevalidator/json_to_gv_results.rb', line 55

def output_filename
  i = (@config[:run_no].to_f / @config[:output_max]).ceil
  File.join(@config[:html_path], "results#{i}.html")
end

.run ⇒ Object 



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# File 'lib/genevalidator/json_to_gv_results.rb', line 30

def run
  init
  GeneValidator.create_output_folder(@config[:html_path], @config[:aux])
  @json_array.each do |row|
    @config[:run_no] += 1
    create_json_file(row)
    output_html = output_filename
    generate_html_header(output_html) unless File.exist?(output_html)
    generate_html_query(output_html, row)
  end
  html_footer
  calculate_overall_score
end

.turn_off_automated_sorting ⇒ Object

By default, on page load, the results are automatically sorted by the index. However since the whole idea is that users would sort by JSON, this is not wanted here.



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# File 'lib/genevalidator/json_to_gv_results.rb', line 100

def turn_off_automated_sorting
  script_file = File.join(@config[:html_path],
                          'files/js/genevalidator.compiled.min.js')
  original_content = File.read(script_file)
  # removes the automatic sort on page load
  updated_content = original_content.gsub(',sortList:[[0,0]]', '')
  File.open("#{script_file}.tmp", 'w') { |f| f.puts updated_content }
  FileUtils.mv("#{script_file}.tmp", script_file)
end

.write_html_footer(no_of_output_files, output_files) ⇒ Object 



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# File 'lib/genevalidator/json_to_gv_results.rb', line 86

def write_html_footer(no_of_output_files, output_files)
  turn_off_automated_sorting
  json_footer_template = File.join(@config[:aux], 'json_footer.erb')
  template_contents    = File.open(json_footer_template, 'r').read
  erb                  = ERB.new(template_contents, 0, '>')
  (1..no_of_output_files).each do |i|
    results_html = File.join(@config[:html_path], "results#{i}.html")
    File.open(results_html, 'a+') { |f| f.write(erb.result(binding)) }
  end
end