From 31f1217be7162aac06aa262376f432f676928749 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 9 Nov 2017 14:28:30 +0000 Subject: cleanup and reorder code;save prediction object also for single prediction --- helper.rb | 228 ++++++++++++++++++++++++++------------------------------------ 1 file changed, 97 insertions(+), 131 deletions(-) (limited to 'helper.rb') diff --git a/helper.rb b/helper.rb index 3bd1755..d423285 100644 --- a/helper.rb +++ b/helper.rb @@ -1,4 +1,5 @@ helpers do + def embedded_svg image, options={} doc = Nokogiri::HTML::DocumentFragment.parse image svg = doc.at_css 'svg' @@ -14,146 +15,111 @@ helpers do doc.to_html.html_safe end - def to_csv(m,predictions,compounds) - model = (m != "Cramer" ? Model::Validation.find(m.to_s) : "Cramer") + def prediction_to_csv(m,c,p) + #model = Model::Validation.find(m.to_s) + model = m + model_name = "#{model.endpoint.gsub('_', ' ')} (#{model.species})" + model_unit = model.regression? ? "(#{model.unit})" : "" + converted_model_unit = model.regression? ? "#{model.unit =~ /\b(mmol\/L)\b/ ? "(mg/L)" : "(mg/kg_bw/day)"}" : "" + + #predictions = predictions_ids.collect{|prediction_id| Prediction.find prediction_id} 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 + compound = c#Compound.find prediction_object.compound + prediction = p#prediction_object.prediction + #prediction.delete_if{|k,v| k =~ /neighbors|prediction_feature_id/} + output = {} + line = "" + output["model_name"] = model_name + output["model_unit"] = model_unit + output["converted_model_unit"] = converted_model_unit + + 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 - 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 + note = "\"#{prediction[:warnings].uniq.join(" ")}\"" + + output["prediction_value"] = model.regression? ? "#{prediction[:value].delog10.signif(3)}" : "#{prediction[:value]}" + output["converted_value"] = model.regression? ? "#{compound.mmol_to_mg(prediction[:value].delog10).signif(3)}" : nil + + if prediction[:measurements].is_a?(Array) + output["measurements"] = model.regression? ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)}"} : prediction[:measurements].collect{|value| "#{value}"} + output["converted_measurements"] = model.regression? ? prediction[:measurements].collect{|value| "#{compound.mmol_to_mg(value.delog10).signif(3)}"} : false + else + output["measurements"] = model.regression? ? "#{prediction[:measurements].delog10.signif(3)}" : "#{prediction[:measurements]}" + output["converted_measurements"] = model.regression? ? "#{compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)}" : false + + end #db_hit + + if model.regression? + + if !prediction[:prediction_interval].blank? + interval = prediction[:prediction_interval] + output['interval'] = [] + output['converted_interval'] = [] + output['interval'] << interval[1].delog10.signif(3) + output['interval'] << interval[0].delog10.signif(3) + output['converted_interval'] << compound.mmol_to_mg(interval[1].delog10).signif(3) + output['converted_interval'] << compound.mmol_to_mg(interval[0].delog10).signif(3) + end #prediction interval + + line += "#{output['model_name']},#{compound.smiles},"\ + "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{output['measurements'].join("; ") if prediction[:info]}\","\ + "#{!output['prediction_value'].blank? ? output['prediction_value'] : ""},"\ + "#{!output['converted_value'].blank? ? output['converted_value'] : ""},"\ + "#{!prediction[:prediction_interval].blank? ? output['interval'].first : ""},"\ + "#{!prediction[:prediction_interval].blank? ? output['interval'].last : ""},"\ + "#{!prediction[:prediction_interval].blank? ? output['converted_interval'].first : ""},"\ + "#{!prediction[:prediction_interval].blank? ? output['converted_interval'].last : ""},"\ + "#{inApp},#{note.nil? ? "" : note.chomp}\n" + else # Classification + + if !prediction[:probabilities].blank? + output['probabilities'] = [] + prediction[:probabilities].each{|k,v| output['probabilities'] << v.signif(3)} + end + + line += "Consensus mutagenicity,#{compound.smiles},"\ + "\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{output['measurements'].join("; ") if prediction[:info]}\","\ + "#{prediction['Consensus prediction']},"\ + "#{prediction['Consensus confidence']},"\ + "#{prediction['Structural alerts for mutagenicity']},"\ + "#{output['prediction_value']},"\ + "#{!prediction[:probabilities].blank? ? output['probabilities'].first : ""},"\ + "#{!prediction[:probabilities].blank? ? output['probabilities'].last : ""},"\ + "#{inApp},#{note.nil? ? "" : note}\n" - # header - csv = "ID,Endpoint,Unique SMILES,Cramer rules,Cramer rules with extensions\n" + end - 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" + 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(" ")}\"" - 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)}"} : prediction[:measurements].collect{|value| "#{value}"} - output["converted_measurements"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{compound.mmol_to_mg(value.delog10).signif(3)}"} : false - else - output["measurements"] = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)}" : "#{prediction[:measurements]}" - output["converted_measurements"] = (type == "Regression") ? "#{compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)}" : 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"}\",\"#{output['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"}\",\"#{output['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].collect{|m| m.delog10.signif(3)}.join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n" - else - line += "#{idx+1},Consensus mutagenicity,#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\ - "#{prediction[:measurements].join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n" - end + output['warnings'] = prediction[:warnings] + output['info'] = prediction[:info] if prediction[:info] - end - csv += line + if model.regression? + line += "#{output['model_name']},#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\ + "#{prediction[:measurements].collect{|m| m.delog10.signif(3)}.join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n" + else + line += "Consensus mutagenicity,#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\ + "#{prediction[:measurements].join("; ") if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n" end - csv + end + csv += line + # output + csv end end -- cgit v1.2.3