diff options
Diffstat (limited to 'application.rb')
| -rw-r--r-- | application.rb | 84 |
1 files changed, 79 insertions, 5 deletions
diff --git a/application.rb b/application.rb index ee7837f..fdb7086 100644 --- a/application.rb +++ b/application.rb @@ -38,8 +38,11 @@ get '/predict/?' do @existing_datasets = dataset_storage @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 - @endpoints << "Oral toxicity (Cramer rules)" + #endpoints = @models.collect{|m| m.endpoint =~ /LOAEL/ ? m.endpoint+" (lazar)" : m.endpoint} + endpoints = @models.collect{|m| m.endpoint} + endpoints << "Oral toxicity (Cramer rules)" + endpoints << "Lowest observed adverse effect level (LOAEL) (Mazzatorta)" + @endpoints = endpoints.sort.uniq @models.count <= 0 ? (haml :info) : (haml :predict) end @@ -63,6 +66,22 @@ get '/task/?' do string += "<tr><td>Cramer rules, with extensions:</td><td>#{prediction["Cramer rules, with extensions"][pageNumber.to_i]}</td>" string += "</table></td>" html += "#{string}</tr></table>" + elsif params[:model] == "Mazzatorta" + prediction = task.predictions[params[:model]] + compound = Compound.find prediction["compounds"][pageNumber] + image = compound.svg + smiles = compound.smiles + html = "<table class=\"table table-bordered single-batch\"><tr>" + html += "<td>#{image}</br>#{smiles}</br></td>" + string = "<td><table class=\"table\">" + if prediction["mazzatorta"][pageNumber.to_i][:prediction] + string += "<tr class=\"hide-top\"><td>Prediction:</td><td>#{prediction["mazzatorta"][pageNumber.to_i][:mmol_prediction]} (mmol/kg_bw/day)</td>" + string += "<tr class=\"hide-top\"><td></td><td>#{prediction["mazzatorta"][pageNumber.to_i][:prediction]} (mg/kg_bw/day)</td>" + else + string += "<tr><td>Warnings:</td><td>#{prediction["mazzatorta"][pageNumber.to_i][:warnings]}</td>" + end + string += "</table></td>" + html += "#{string}</tr></table>" else predictions = task.predictions[params[:model]].collect{|hash| hash.values[0]} prediction_object = Prediction.find predictions[pageNumber] @@ -188,9 +207,13 @@ get '/predict/csv/:task/:model/:filename/?' do end end end - endpoint = (params[:model] == "Cramer") ? "Oral_toxicity_(Cramer_rules)" : (m.endpoint =~ /Mutagenicity/i ? "Consensus_mutagenicity" : "#{m.endpoint}_(#{m.species})") + if params[:model] == "Mazzatorta" + endpoint = "Lowest observed adverse effect level (LOAEL) (Rats) (Mazzatorta)" + else + endpoint = (params[:model] == "Cramer") ? "Oral_toxicity_(Cramer_rules)" : (m.endpoint =~ /Mutagenicity/i ? "Consensus_mutagenicity" : "#{m.endpoint}_(#{m.species})") + end tempfile = Tempfile.new - if params[:model] == "Cramer" + if params[:model] == "Cramer" || params[:model] == "Mazzatorta" # add duplicate warning at the end of a line if ID matches if @dups lines = task.csv.split("\n") @@ -309,7 +332,7 @@ post '/predict/?' do task = Task.run do @models.each_with_index do |model,idx| t = @tasks[idx] - unless model == "Cramer" + if model !~ /Cramer|Mazzatorta/ m = Model::Validation.find model type = (m.regression? ? "Regression" : "Classification") # add header for regression @@ -420,6 +443,47 @@ post '/predict/?' do t[:csv] = header # write predictions @predictions["#{model}"] = predictions + elsif model == "Mazzatorta" + compounds = @compounds.collect{|cid| c = Compound.find cid; c.smiles} + prediction = LoaelMazzatorta.predict(compounds) + output = {} + output["model_name"] = "Lowest observed adverse effect level (LOAEL) (Rats) (Mazzatorta)" + output["mazzatorta"] = [] + #output["mazzatorta"] = prediction + # header + if @ids.blank? + csv = "ID,Input,Endpoint,Unique SMILES,Prediction (mmol/kg_bw/day),Prediction (mg/kg_bw/day),Notes\n" + else + csv = "ID,Original ID,Input,Endpoint,Unique SMILES,Prediction (mmol/kg_bw/day),Prediction (mg/kg_bw/day),Notes\n" + end + # content + compounds.each_with_index do |smiles, idx| + compound = Compound.find @compounds[idx] + if prediction[idx]["value"] + output["mazzatorta"][idx] = {:mmol_prediction => compound.mg_to_mmol(prediction[idx]["value"].delog10p).signif(3),:prediction => prediction[idx]["value"].delog10p.signif(3)} + else + output["mazzatorta"][idx] = {:warnings => prediction[idx]["warnings"][0].split("\t").first} + end + if @ids.blank? + csv << "#{idx+1},#{@identifiers[idx]},#{output["model_name"]},#{smiles},"\ + "#{output["mazzatorta"][idx][:mmol_prediction] if output["mazzatorta"][idx][:mmol_prediction]},"\ + "#{output["mazzatorta"][idx][:prediction] if output["mazzatorta"][idx][:prediction]},"\ + "#{output["mazzatorta"][idx][:warnings] if output["mazzatorta"][idx][:warnings]}\n" + else + csv << "#{idx+1},#{@ids[idx]},#{@identifiers[idx]},#{output["model_name"]},#{smiles},"\ + "#{output["mazzatorta"][idx][:mmol_prediction] if output["mazzatorta"][idx][:mmol_prediction]},"\ + "#{output["mazzatorta"][idx][:prediction] if output["mazzatorta"][idx][:prediction]},"\ + "#{output["mazzatorta"][idx][:warnings] if output["mazzatorta"][idx][:warnings]}\n" + end + end + predictions = {} + predictions["mazzatorta"] = output["mazzatorta"] + #predictions["compounds"] = @compounds + # write csv + t[:csv] = csv + # write predictions + @predictions["#{model}"] = predictions + t.update_percent(100) else # Cramer model compounds = @compounds.collect{|cid| c = Compound.find cid; c.smiles} prediction = [Toxtree.predict(compounds, "Cramer rules"), Toxtree.predict(compounds, "Cramer rules with extensions")] @@ -486,6 +550,16 @@ post '/predict/?' do if model_id == "Cramer" @toxtree = true @predictions << [Toxtree.predict(@compound.smiles, "Cramer rules"), Toxtree.predict(@compound.smiles, "Cramer rules with extensions")] + elsif model_id == "Mazzatorta" + prediction = LoaelMazzatorta.predict(@compound.smiles) + output = {} + $logger.debug prediction + if prediction["value"] + output["mazzatorta"] = {:mmol_prediction => @compound.mg_to_mmol(prediction["value"].delog10p).signif(3),:prediction => prediction["value"].delog10p.signif(3)} + else + output["mazzatorta"] << {:warnings => prediction["warnings"][0].split("\t").first} + end + @predictions << output else model = Model::Validation.find model_id @models << model |