Class: GeneValidator::Output

Inherits:
Object
  • Object
show all
Defined in:
lib/genevalidator/output.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(mutex, mutex_yaml, mutex_html, filename, html_path, yaml_path, idx = 0, start_idx = 0) ⇒ Output

Initilizes the object Params: mutex: Mutex for exclusive access to the console mutex_yaml: Mutex for exclusive access to the YAML file mutex_html: Mutex for exclusive access to the HTML file filename: name of the fasta input file html_path: path of the html folder yaml_path: path where the yaml output wil be saved idx: idnex of the current query start_idx: number of the sequence from the file to start with



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# File 'lib/genevalidator/output.rb', line 40

def initialize(mutex, mutex_yaml, mutex_html, filename, html_path,
               yaml_path, idx = 0, start_idx = 0)
  @prediction_len = 0
  @prediction_def = 'no_definition'
  @nr_hits        = 0

  @filename       = filename
  @html_path      = html_path
  @yaml_path      = yaml_path
  @idx            = idx
  @start_idx      = start_idx

  @mutex          = mutex
  @mutex_yaml     = mutex_yaml
  @mutex_html     = mutex_html
end

Instance Attribute Details

#fails ⇒ Object

Returns the value of attribute fails.



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# File 'lib/genevalidator/output.rb', line 22

def fails
  @fails
end

#filename ⇒ Object

Returns the value of attribute filename.



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# File 'lib/genevalidator/output.rb', line 15

def filename
  @filename
end

#html_path ⇒ Object

Returns the value of attribute html_path.



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# File 'lib/genevalidator/output.rb', line 16

def html_path
  @html_path
end

#idx ⇒ Object

Returns the value of attribute idx.



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# File 'lib/genevalidator/output.rb', line 18

def idx
  @idx
end

#mutex ⇒ Object

Returns the value of attribute mutex.



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# File 'lib/genevalidator/output.rb', line 25

def mutex
  @mutex
end

#mutex_html ⇒ Object

Returns the value of attribute mutex_html.



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# File 'lib/genevalidator/output.rb', line 27

def mutex_html
  @mutex_html
end

#mutex_yaml ⇒ Object

Returns the value of attribute mutex_yaml.



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# File 'lib/genevalidator/output.rb', line 26

def mutex_yaml
  @mutex_yaml
end

#nr_hits ⇒ Object

Returns the value of attribute nr_hits.



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# File 'lib/genevalidator/output.rb', line 10

def nr_hits
  @nr_hits
end

#overall_score ⇒ Object

Returns the value of attribute overall_score.



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# File 'lib/genevalidator/output.rb', line 21

def overall_score
  @overall_score
end

#prediction_def ⇒ Object

Returns the value of attribute prediction_def.



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# File 'lib/genevalidator/output.rb', line 9

def prediction_def
  @prediction_def
end

#prediction_len ⇒ Object

Returns the value of attribute prediction_len.



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# File 'lib/genevalidator/output.rb', line 8

def prediction_len
  @prediction_len
end

#start_idx ⇒ Object

Returns the value of attribute start_idx.



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# File 'lib/genevalidator/output.rb', line 19

def start_idx
  @start_idx
end

#successes ⇒ Object

Returns the value of attribute successes.



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# File 'lib/genevalidator/output.rb', line 23

def successes
  @successes
end

#validations ⇒ Object

list of ValidationReport objects



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# File 'lib/genevalidator/output.rb', line 13

def validations
  @validations
end

#yaml_path ⇒ Object

Returns the value of attribute yaml_path.



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

def yaml_path
  @yaml_path
end

Class Method Details

.overall_evaluation(no_queries, good_scores, bad_scores, no_evidence, no_mafft, no_internet, map_errors, running_times) ⇒ Object

Calculates an overall evaluation of the output Params: all_query_outputs: Array of ValidationTest objects Output Array of Strigs with the reports



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# File 'lib/genevalidator/output.rb', line 228

def self.overall_evaluation(no_queries, good_scores, bad_scores,
                            no_evidence, no_mafft, no_internet, map_errors,
                            running_times)
  good_pred = (good_scores == 1) ? 'One' : "#{good_scores} are"
  bad_pred  = (bad_scores == 1) ? 'One' : "#{bad_scores} are"

  eval = "Overall Query Score Evaluation:\n" \
         "#{no_queries} predictions were validated, from which there" \
         " were:\n" \
         "#{good_pred} good prediction(s),\n" \
         "#{bad_pred} possibly weak prediction(s).\n"

  if no_evidence != 0
    eval << "#{no_evidence} could not be evaluated due to the lack of" \
            ' evidence.'
  end

  # errors per validation
  error_eval = ''
  map_errors.each do |k, v|
    error_eval << "\nWe couldn't run #{k} Validation for #{v} queries"
  end

  if no_mafft >= (no_queries - no_evidence)
    error_eval << "\nWe couldn't run MAFFT multiple alignment"
  end
  if no_internet >= (no_queries - no_evidence)
    error_eval << "\nWe couldn't make use of your internet connection"
  end

  time_eval = ''
  running_times.each do |key, value|
    average_time = value.x / (value.y + 0.0)
    time_eval << "\nAverage running time for #{key} Validation:" \
                 " #{average_time.round(3)}s per validation"
  end

  overall_evaluation = [eval, error_eval, time_eval]
  overall_evaluation.select { |e| e != '' }
end

.print_footer(no_queries, scores, good_predictions, bad_predictions, nee, no_mafft, no_internet, map_errors, running_times, html_path, filename) ⇒ Object

Method that closes the gas in the html file and writes the overall evaluation 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(all_query_outputs, html_path, filename)



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# File 'lib/genevalidator/output.rb', line 162

def self.print_footer(no_queries, scores, good_predictions, bad_predictions,
                      nee, no_mafft, no_internet, map_errors, running_times,
                      html_path, filename)
  # compute the statistics
  # overall_evaluation = overall_evaluation(all_query_outputs, filename)
  overall_evaluation = overall_evaluation(no_queries, good_predictions,
                                          bad_predictions, nee, no_mafft,
                                          no_internet, map_errors,
                                          running_times)

  less = overall_evaluation[0]
  less = less.gsub("\n", '<br>').gsub("'", %q(\\\'))

  # print to console
  evaluation = ''
  overall_evaluation.each { |e| evaluation << "\n#{e}" }
  puts evaluation
  puts ''

  # print to html
  # make the historgram with the resulted scores
  statistics_filename = "#{html_path}/files/json/#{filename}_statistics.json"
  f = File.open(statistics_filename, 'w')

  f.write(
    [scores.group_by { |a| a }.map { |k, vs| { 'key' => k,
                                               'value' => vs.length,
                                               'main' => false } }].to_json)
  f.close

  plot_statistics = Plot.new("files/json/#{filename}_statistics.json",
                             :simplebars,
                             'Overall evaluation',
                             '',
                             'validation score',
                             'number of queries',
                             10)

  evaluation = evaluation.gsub("\n", '<br>').gsub("'", %q(\\\'))

  index_file = "#{html_path}/results.html"
  table_file = "#{html_path}/files/table.html"
  aux_dir = File.join(File.dirname(File.expand_path(__FILE__)), '../../aux')

  template_footer     = File.join(aux_dir, 'template_footer.erb')
  app_template_footer = File.join(aux_dir, 'app_template_footer.erb')

  template_file = File.open(template_footer, 'r').read
  erb = ERB.new(template_file, 0, '>')
  File.open(index_file, 'a+') do |file|
    file.write(erb.result(binding))
  end

  table_footer_template = File.open(app_template_footer, 'r').read
  table_erb = ERB.new(table_footer_template, 0, '>')
  File.open(table_file, 'a+') do |file|
    file.write(table_erb.result(binding))
  end
end

Instance Method Details

#generate_html ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 103

def generate_html
  if @fails == 0
    bg_icon = 'success'
  else
    bg_icon = 'danger'
  end

  index_file = "#{@html_path}/results.html"
  table_file = "#{@html_path}/files/table.html"

  aux_dir = File.join(File.dirname(File.expand_path(__FILE__)), '../../aux')

  # if it's the first time I write in the html file
  if @idx == @start_idx
    @mutex_html.synchronize do
      template_header     = File.join(aux_dir, 'template_header.erb')
      template_file       = File.open(template_header, 'r').read
      erb                 = ERB.new(template_file, 0, '>')

      #  Creating a Separate output file for the web app
      app_template_header = File.join(aux_dir, 'app_template_header.erb')
      table_template_file = File.open(app_template_header, 'r').read
      erb_table           = ERB.new(table_template_file, 0, '>')

      File.open(index_file, 'w+') do |file|
        file.write(erb.result(binding))
      end

      File.open(table_file, 'w+') do |file|
        file.write(erb_table.result(binding))
      end
    end
  end

  toggle = "toggle#{@idx}"

  @mutex_yaml.synchronize do
    template_query = File.join(aux_dir, 'template_query.erb')
    template_file = File.open(template_query, 'r').read
    erb = ERB.new(template_file, 0, '>')

    File.open(index_file, 'a') do |file|
      file.write(erb.result(binding))
    end

    File.open(table_file, 'a') do |file|
      file.write(erb.result(binding))
    end
  end
end

#print_output_console ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 57

def print_output_console
  if @idx == @start_idx
    header = sprintf('%3s|%s|%20s|%5s', 'No', 'Score', 'Identifier',
                     'No_Hits')
    validations.map do |v|
      header << "|#{v.short_header}"
    end
    puts header
  end

  short_def          = @prediction_def.scan(/([^ ]+)/)[0][0]
  validation_outputs = validations.map(&:print)

  output             = sprintf('%3s|%d|%20s|%5s|', @idx, @overall_score,
                               short_def, @nr_hits)
  validation_outputs.each do |item|
    output << item
    output << '|'
  end

  @mutex.synchronize do
    puts output.gsub('&nbsp;', ' ')
  end
end

#print_output_file_yaml ⇒ Object 



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# File 'lib/genevalidator/output.rb', line 82

def print_output_file_yaml
  file_yaml = "#{@yaml_path}/#{@filename}.yaml"
  report = validations
  if @idx == @start_idx
    @mutex_yaml.synchronize do
      File.open(file_yaml, 'w') do |f|
        YAML.dump({ @prediction_def.scan(/([^ ]+)/)[0][0] => report }, f)
      end
    end
  else
    @mutex_yaml.synchronize do
      hash = {} # YAML.load_file(file_yaml)
      hash[@prediction_def.scan(/([^ ]+)/)[0][0]] = report
      File.open(file_yaml, 'a') do |f|
        new_report =  hash.to_yaml
        f.write(new_report[4..new_report.length - 1])
      end
    end
  end
end