diff options
Diffstat (limited to 'application.rb')
| -rw-r--r-- | application.rb | 188 |
1 files changed, 22 insertions, 166 deletions
diff --git a/application.rb b/application.rb index e4b9e38..0957d71 100644 --- a/application.rb +++ b/application.rb @@ -1,3 +1,6 @@ +require_relative 'task.rb' +require_relative 'prediction.rb' +require_relative 'helper.rb' include OpenTox configure :production do @@ -23,171 +26,15 @@ error do haml :error end -helpers do - def embedded_svg image, options={} - doc = Nokogiri::HTML::DocumentFragment.parse image - svg = doc.at_css 'svg' - title = doc.at_css 'title' - if options[:class].present? - svg['class'] = options[:class] - end - if options[:title].present? - title.children.remove - text_node = Nokogiri::XML::Text.new(options[:title], doc) - title.add_child(text_node) - end - doc.to_html.html_safe - end - - def to_csv(m,predictions,compounds) - model = (m != "Cramer" ? Model::Validation.find(m.to_s) : "Cramer") - csv = "" - if model == "Cramer" - compounds = compounds.collect{|c| c.smiles} - - prediction = [Toxtree.predict(compounds, "Cramer rules"), Toxtree.predict(compounds, "Cramer rules with extensions")] - output = {} - output["model_name"] = "Oral toxicity (Cramer rules)" - output["model_type"] = false - output["model_unit"] = false - ["measurements", "converted_measurements", "prediction_value", "converted_value", "interval", "converted_interval", "probability", "db_hit", "warnings", "info", "toxtree", "sa_prediction", "sa_matches", "confidence"].each do |key| - output["#{key}"] = false - end - output["toxtree"] = true - output["cramer_rules"] = prediction.collect{|array| array.collect{|hash| hash["Cramer rules"]}}.flatten.compact - output["cramer_rules_extensions"] = prediction.collect{|array| array.collect{|hash| hash["Cramer rules, with extensions"]}}.flatten.compact - - # header - csv = "ID,Endpoint,Unique SMILES,Cramer rules,Cramer rules with extensions\n" - - compounds.each_with_index do |smiles, idx| - csv << "#{idx+1},#{output["model_name"]},#{smiles},"\ - "#{output["cramer_rules"][idx] != "nil" ? output["cramer_rules"][idx] : "none" },"\ - "#{output["cramer_rules_extensions"][idx] != "nil" ? output["cramer_rules_extensions"][idx] : "none"}\n" - end - - else - output = {} - predictions.each_with_index do |prediction,idx| - compound = compounds[idx] - line = "" - output["model_name"] = "#{model.endpoint.gsub('_', ' ')} (#{model.species})" - output["model_type"] = model.model.class.to_s.match("Classification") ? type = "Classification" : type = "Regression" - output["model_unit"] = (type == "Regression") ? "(#{model.unit})" : "" - output["converted_model_unit"] = (type == "Regression") ? "#{model.unit =~ /\b(mmol\/L)\b/ ? "(mg/L)" : "(mg/kg_bw/day)"}" : "" - ["measurements", "converted_measurements", "prediction_value", "converted_value", "interval", "converted_interval", "probability", "db_hit", "warnings", "info", "toxtree", "sa_prediction", "sa_matches", "confidence"].each do |key| - output["#{key}"] = false - end - - if prediction[:value] - inApp = (prediction[:warnings].join(" ") =~ /Cannot/ ? "no" : (prediction[:warnings].join(" ") =~ /may|Insufficient/ ? "maybe" : "yes")) - if prediction[:info] =~ /\b(identical)\b/i - prediction[:info] = "This compound was part of the training dataset. All information "\ - "from this compound was removed from the training data before the "\ - "prediction, to obtain unbiased results." - end - note = "\"#{prediction[:warnings].uniq.join(" ")}\"" - - output["prediction_value"] = (type == "Regression") ? "#{prediction[:value].delog10.signif(3)}" : "#{prediction[:value]}" - output["converted_value"] = "#{compound.mmol_to_mg(prediction[:value].delog10).signif(3)}" if type == "Regression" - - output["db_hit"] = prediction[:info] if prediction[:info] - - if prediction[:measurements].is_a?(Array) - output["measurements"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)} (#{model.unit})"} : prediction[:measurements].collect{|value| "#{value}"} - output["converted_measurements"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{compound.mmol_to_mg(value.delog10).signif(3)} #{model.unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"} : false - else - output["measurements"] = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} (#{model.unit})}" : "#{prediction[:measurements]}" - output["converted_measurements"] = (type == "Regression") ? "#{compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(model.unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : false - - end #db_hit - - if type == "Regression" - - if !prediction[:prediction_interval].nil? - interval = prediction[:prediction_interval] - output['interval'] = "#{interval[1].delog10.signif(3)} - #{interval[0].delog10.signif(3)}" - output['converted_interval'] = "#{compound.mmol_to_mg(interval[1].delog10).signif(3)} - #{compound.mmol_to_mg(interval[0].delog10).signif(3)}" - end #prediction interval - - line += "#{idx+1},#{output['model_name']},#{compound.smiles},"\ - "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{prediction[:measurements].join("; ") if prediction[:info]}\","\ - "#{output['prediction_value'] != false ? output['prediction_value'] : ""},"\ - "#{output['converted_value'] != false ? output['converted_value'] : ""},"\ - "#{output['interval'].split(" - ").first.strip unless output['interval'] == false},"\ - "#{output['interval'].split(" - ").last.strip unless output['interval'] == false},"\ - "#{output['converted_interval'].split(" - ").first.strip unless output['converted_interval'] == false},"\ - "#{output['converted_interval'].split(" - ").last.strip unless output['converted_interval'] == false},"\ - "#{inApp},#{note.nil? ? "" : note.chomp}\n" - else # Classification - - # consensus mutagenicity - sa_prediction = KaziusAlerts.predict(compound.smiles) - lazar_mutagenicity = prediction - confidence = 0 - lazar_mutagenicity_val = (lazar_mutagenicity[:value] == "non-mutagenic" ? false : true) - if sa_prediction[:prediction] == false && lazar_mutagenicity_val == false - confidence = 0.85 - elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == true - confidence = 0.85 * ( 1 - sa_prediction[:error_product] ) - elsif sa_prediction[:prediction] == false && lazar_mutagenicity_val == true - confidence = 0.11 - elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == false - confidence = ( 1 - sa_prediction[:error_product] ) - 0.57 - end - output['sa_prediction'] = sa_prediction - output['sa_matches'] = sa_prediction[:matches].collect{|a| a.first}.join("; ") unless sa_prediction[:matches].blank? - output['confidence'] = confidence.signif(3) - output['model_name'] = "Lazar #{model.endpoint.gsub('_', ' ').downcase} (#{model.species}):" - output['probability'] = prediction[:probabilities] ? prediction[:probabilities].collect{|k,v| "#{k}: #{v.signif(3)}"} : false - - line += "#{idx+1},Consensus mutagenicity,#{compound.smiles},"\ - "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{prediction[:measurements].join("; ") if prediction[:info]}\","\ - "#{sa_prediction[:prediction] == false ? "non-mutagenic" : "mutagenic"},"\ - "#{output['confidence']},#{output['sa_matches'] != false ? "\"#{output['sa_matches']}\"" : "none"},"\ - "#{output['prediction_value']},"\ - "#{output['probability'][0] != false ? output['probability'][0].split(":").last : ""},"\ - "#{output['probability'][1] != false ? output['probability'][1].split(":").last : ""},"\ - "#{inApp},#{note.nil? ? "" : note}\n" - - end - - output["warnings"] = prediction[:warnings] if prediction[:warnings] - - else #no prediction value - inApp = "no" - if prediction[:info] =~ /\b(identical)\b/i - prediction[:info] = "This compound was part of the training dataset. All information "\ - "from this compound was removed from the training data before the "\ - "prediction, to obtain unbiased results." - end - note = "\"#{prediction[:warnings].join(" ")}\"" - - output["warnings"] = prediction[:warnings] - output["info"] = prediction[:info] if prediction[:info] - - if type == "Regression" - line += "#{idx+1},#{output['model_name']},#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\ - "#{prediction[:measurements] if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n" - else - line += "#{idx+1},Consensus mutagenicity,#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\ - "#{prediction[:measurements] if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n" - end - - end - csv += line - end - csv - end - end - -end - get '/?' do redirect to('/predict') end get '/predict/?' do + if params[:tpid] && !params[:tpid].blank? + pid = params[:tpid].to_i + Process.kill(9,pid) #if (Process.getpgid(pid) rescue nil).present? + end @models = Model::Validation.all @models = @models.delete_if{|m| m.model.name =~ /\b(Net cell association)\b/} @endpoints = @models.collect{|m| m.endpoint}.sort.uniq @@ -222,7 +69,6 @@ get '/task/?' do string = "<td><table class=\"table\">" prediction = task.predictions[params[:model]][pageNumber.to_i] sorter = [] - $logger.debug prediction if prediction[:info] sorter << {"Info" => prediction[:info]} if prediction[:measurements_string].kind_of?(Array) @@ -357,7 +203,18 @@ post '/predict/?' do counter = 1 predictions = [] @compounds.each do |compound| - prediction = m.predict(compound) + if Prediction.where(compound: compound.id, model: m.id).exists? + $logger.debug "prediction already exists !" + prediction = Prediction.find_by(compound: compound.id, model: m.id).prediction + else + prediction = m.predict(compound) + # save prediction object + prediction_object = Prediction.new + prediction_object[:compound] = compound.id + prediction_object[:model] = m.id + prediction_object[:prediction] = prediction + prediction_object.save + end if type == "Classification"# consensus mutagenicity sa_prediction = KaziusAlerts.predict(compound.smiles) lazar_mutagenicity = prediction @@ -421,9 +278,6 @@ post '/predict/?' do "#{output["cramer_rules"][idx] != "nil" ? output["cramer_rules"][idx] : "none" },"\ "#{output["cramer_rules_extensions"][idx] != "nil" ? output["cramer_rules_extensions"][idx] : "none"}\n" end - #predictions = [] - #predictions << {"Cramer rules" => output["cramer_rules"]} - #predictions << {"Cramer rules, with extensions" => output["cramer_rules_extensions"]} predictions = {} predictions["Cramer rules"] = output["cramer_rules"].collect{|rule| rule != "nil" ? rule : "none"} predictions["Cramer rules, with extensions"] = output["cramer_rules_extensions"].collect{|rule| rule != "nil" ? rule : "none"} @@ -442,9 +296,11 @@ post '/predict/?' do end#models end#main task + @pid = task.pid + $logger.debug "application pid: #{@pid}" File.delete File.join("tmp", params[:fileselect][:filename]) - return haml :task + return haml :batch end # single compound prediction |