diff options
Diffstat (limited to 'application.rb')
| -rw-r--r-- | application.rb | 44 |
1 files changed, 26 insertions, 18 deletions
diff --git a/application.rb b/application.rb index fbebc66..b0357e8 100644 --- a/application.rb +++ b/application.rb @@ -189,16 +189,27 @@ get '/predict/csv/:task/:model/:filename/?' do response['Content-Type'] = "text/csv" filename = params[:filename] =~ /\.csv$/ ? params[:filename].gsub(/\.csv$/,"") : params[:filename] task = Task.find params[:task].to_s - m = Model::Validation.find params[:model].to_s unless params[:model] == "Cramer" + m = Model::Validation.find params[:model].to_s unless params[:model] =~ /Cramer|Mazzatorta/ dataset = Batch.find_by(:name => filename) + $logger.debug dataset.inspect @ids = dataset.ids warnings = dataset.warnings.blank? ? nil : dataset.warnings.join("\n") unless warnings.nil? + @parse = [] + warnings.split("\n").each do |warning| + if warning =~ /^Cannot/ + smi = warning.split("SMILES compound").last.split("at").first + line = warning.split("SMILES compound").last.split("at line").last.split("of").first.strip.to_i + @parse << "Cannot parse SMILES compound#{smi}at line #{line} of #{dataset.source.split("/").last}\n" + end + end keys_array = [] warnings.split("\n").each do |warning| - text = warning.split("ID").first - numbers = warning.split("ID").last.split("and") - keys_array << numbers.collect{|n| n.strip.to_i} + if warning =~ /^Duplicate/ + text = warning.split("ID").first + numbers = warning.split("ID").last.split("and") + keys_array << numbers.collect{|n| n.strip.to_i} + end end @dups = {} keys_array.each do |keys| @@ -209,13 +220,15 @@ get '/predict/csv/:task/:model/:filename/?' do end if params[:model] == "Mazzatorta" endpoint = "Lowest observed adverse effect level (LOAEL) (Rats) (Mazzatorta)" + elsif params[:model] == "Cramer" + endpoint = "Oral_toxicity_(Cramer_rules)" else - endpoint = (params[:model] == "Cramer") ? "Oral_toxicity_(Cramer_rules)" : (m.endpoint =~ /Mutagenicity/i ? "Consensus_mutagenicity" : "#{m.endpoint}_(#{m.species})") + endpoint = "#{m.endpoint}_(#{m.species})" end tempfile = Tempfile.new - if params[:model] == "Cramer" || params[:model] == "Mazzatorta" - # add duplicate warning at the end of a line if ID matches - if @dups + if params[:model] =~ /Cramer|Mazzatorta/ + # add duplicate and parse warnings + unless warnings.nil? lines = task.csv.split("\n") header = lines.shift out = "" @@ -226,7 +239,8 @@ get '/predict/csv/:task/:model/:filename/?' do out << line+"\n" end end - tempfile.write(header+"\n"+out) + (@parse && !@parse.blank?) ? tempfile.write(header+"\n"+out+"\n"+@parse.join("\n")) : tempfile.write(header+"\n"+out) + #tempfile.write(header+"\n"+out) else tempfile.write(task.csv) end @@ -244,12 +258,6 @@ get '/predict/csv/:task/:model/:filename/?' do else lines << "#{idx+1},#{@ids[idx]},#{identifier},#{Prediction.find(prediction_id).csv.tr("\n","")},#{@dups[idx+1]}" end - else - if @ids.blank? - lines << "#{idx+1},#{identifier},#{p},#{@dups[idx+1]}" - else - lines << "#{idx+1},#{@ids[idx]},#{identifier},#{p},#{@dups[idx+1]}" - end end else if prediction_id.is_a? BSON::ObjectId @@ -267,8 +275,8 @@ get '/predict/csv/:task/:model/:filename/?' do end end end - csv = header + lines.join("") - tempfile.write(csv) + (@parse && !@parse.blank?) ? tempfile.write(header+lines.join("")+"\n"+@parse.join("\n")) : tempfile.write(header+lines.join("")) + #tempfile.write(header+lines.join("")) end tempfile.rewind send_file tempfile, :filename => "#{Time.now.strftime("%Y-%m-%d")}_lazar_batch_prediction_#{endpoint}_#{filename}.csv", :type => "text/csv", :disposition => "attachment" @@ -278,6 +286,7 @@ post '/predict/?' do # process batch prediction if !params[:fileselect].blank? || !params[:existing].blank? if !params[:existing].blank? + $logger.debug "Take file from database." @dataset = Batch.find params[:existing].keys[0] @compounds = @dataset.compounds @identifiers = @dataset.identifiers @@ -553,7 +562,6 @@ post '/predict/?' do 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 |