Class: GeneValidator::JsonToGVResults
- Inherits:
-
Object
- Object
- GeneValidator::JsonToGVResults
- 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
-
.calculate_no_quries_with_no_evidence ⇒ Object
calculate number of queries that had warnings for all validations.
- .calculate_overall_score ⇒ Object
- .create_json_file(row) ⇒ Object
- .generate_evaluation(scores) ⇒ Object
- .generate_html_header(output_html) ⇒ Object
- .generate_html_query(output_html, row) ⇒ Object
-
.html_footer ⇒ Object
Add footer to all output files.
- .init ⇒ Object
- .load_json_file ⇒ Object
- .output_filename ⇒ Object
- .run ⇒ Object
-
.turn_off_automated_sorting ⇒ Object
By default, on page load, the results are automatically sorted by the index.
- .write_html_footer(no_of_output_files, output_files) ⇒ Object
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 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" } (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.(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.(@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 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 (no_of_output_files, output_files) turn_off_automated_sorting = File.join(@config[:aux], 'json_footer.erb') template_contents = File.open(, '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 |