diff options
Diffstat (limited to 'application.rb')
| -rw-r--r-- | application.rb | 471 |
1 files changed, 270 insertions, 201 deletions
diff --git a/application.rb b/application.rb index 895b0c2..e23c042 100644 --- a/application.rb +++ b/application.rb @@ -1,20 +1,59 @@ require 'rdiscount' require_relative 'qmrf_report.rb' +require_relative 'task.rb' +require_relative 'helper.rb' include OpenTox +PUBCHEM_CID_URI = PUBCHEM_URI.split("/")[0..-3].join("/")+"/compound/" +[ + "api.rb", + "compound.rb", + "dataset.rb", + "endpoint.rb", + "feature.rb", + "model.rb", + "report.rb", + "substance.rb", + "swagger.rb", + "validation.rb" +].each{ |f| require_relative "./lib/#{f}" } configure :production do + STDOUT.sync = true $logger = Logger.new(STDOUT) - enable :reloader end configure :development do + STDOUT.sync = true $logger = Logger.new(STDOUT) - enable :reloader + $logger.level = Logger::DEBUG end before do - @version = File.read("VERSION").chomp + # use this hostname method instead to('/') + # allowes to set https for xhr requests + #$host_with_port = request.host =~ /localhost/ ? request.host_with_port : request.host + $host_with_port = request.host_with_port + $paths = [ + "api", + "compound", + "dataset", + "endpoint", + "feature", + "model", + "report", + "substance", + "swagger", + "validation"] + if request.path =~ /predict/ + @accept = request.env['HTTP_ACCEPT'].split(",").first + response['Content-Type'] = @accept + halt 400, "Mime type #{@accept} is not supported." unless @accept == "text/html" or @accept == "*/*" + @version = File.read("VERSION").chomp + else + @accept = request.env['HTTP_ACCEPT'].split(",").first + response['Content-Type'] = @accept + end end not_found do @@ -22,258 +61,279 @@ not_found do end error do - @error = request.env['sinatra.error'] - haml :error + # API errors + if request.path.split("/")[1] == "api" || $paths.include?(request.path.split("/")[2]) + @accept = request.env['HTTP_ACCEPT'] + response['Content-Type'] = @accept + @accept == "text/plain" ? request.env['sinatra.error'] : request.env['sinatra.error'].to_json + # batch dataset error + elsif request.env['sinatra.error.params']['batchfile'] && request.env['REQUEST_METHOD'] == "POST" + @error = request.env['sinatra.error'] + response['Content-Type'] = "text/html" + status 200 + return haml :error + # basic error + else + @error = request.env['sinatra.error'] + return haml :error + end end -get '/?' do - redirect to('/predict') +# https://github.com/britg/sinatra-cross_origin#responding-to-options +options "*" do + response.headers["Allow"] = "HEAD,GET,PUT,POST,DELETE,OPTIONS" + response.headers["Access-Control-Allow-Headers"] = "X-Requested-With, X-HTTP-Method-Override, Content-Type, Cache-Control, Accept" + 200 end get '/predict/?' do + # handle user click on back button while batch prediction + if params[:tpid] + begin + Process.kill(9,params[:tpid].to_i) if !params[:tpid].blank? + rescue + nil + end + # remove data helper method + remove_task_data(params[:tpid]) + end + # regular request on '/predict' page @models = OpenTox::Model::Validation.all - @models = @models.delete_if{|m| m.model.name =~ /\b(Net cell association)\b/} @endpoints = @models.collect{|m| m.endpoint}.sort.uniq - if @models.count > 0 - rodent_index = 0 - @models.each_with_index{|model,idx| rodent_index = idx if model.species =~ /Rodent/} - @models.insert(rodent_index-1,@models.delete_at(rodent_index)) - end @models.count > 0 ? (haml :predict) : (haml :info) end get '/predict/modeldetails/:model' do model = OpenTox::Model::Validation.find params[:model] - crossvalidations = OpenTox::Validation::RepeatedCrossValidation.find(model.repeated_crossvalidation_id).crossvalidations + training_dataset = model.model.training_dataset + data_entries = training_dataset.data_entries + crossvalidations = model.crossvalidations + if model.classification? + crossvalidations.each do |cv| + File.open(File.join('public', "#{cv.id}.png"), 'w') do |file| + file.write(cv.probability_plot(format: "png")) + end unless File.exists? File.join('public', "#{cv.id}.png") + end + else + crossvalidations.each do |cv| + File.open(File.join('public', "#{cv.id}.png"), 'w') do |file| + file.write(cv.correlation_plot(format: "png")) + end unless File.exists? File.join('public', "#{cv.id}.png") + end + end - return haml :model_details, :layout=> false, :locals => {:model => model, :crossvalidations => crossvalidations} + response['Content-Type'] = "text/html" + return haml :model_details, :layout=> false, :locals => {:model => model, + :crossvalidations => crossvalidations, + :training_dataset => training_dataset, + :data_entries => data_entries + } end -# get individual compound details -get '/prediction/:neighbor/details/?' do - @compound = OpenTox::Compound.find params[:neighbor] - @smiles = @compound.smiles - begin - @names = @compound.names.nil? ? "No names for this compound available." : @compound.names - rescue - @names = "No names for this compound available." - end - @inchi = @compound.inchi.gsub("InChI=", "") - - haml :details, :layout => false +get "/predict/report/:id/?" do + prediction_model = Model::Validation.find params[:id] + bad_request_error "model with id: '#{params[:id]}' not found." unless prediction_model + report = qmrf_report params[:id] + # output + t = Tempfile.new + t << report.to_xml + name = prediction_model.species.sub(/\s/,"-")+"-"+prediction_model.endpoint.downcase.sub(/\s/,"-") + send_file t.path, :filename => "QMRF_report_#{name.gsub!(/[^0-9A-Za-z]/, '_')}.xml", :type => "application/xml", :disposition => "attachment" end -get '/jme_help/?' do +get '/predict/jme_help/?' do File.read(File.join('views','jme_help.html')) end +# download training dataset get '/predict/dataset/:name' do - response['Content-Type'] = "text/csv" dataset = Dataset.find_by(:name=>params[:name]) - csv = dataset.to_csv - csv + csv = File.read dataset.source + name = params[:name] + ".csv" + t = Tempfile.new + t << csv + t.rewind + response['Content-Type'] = "text/csv" + send_file t.path, :filename => name, :type => "text/csv", :disposition => "attachment" end -get '/predict/:tmppath/:filename/?' do +# download batch predicton file +get '/predict/batch/download/?' do + task = Task.find params[:tid] + dataset = Dataset.find task.dataset_id + name = dataset.name + ".csv" + t = Tempfile.new + # to_prediction_csv takes too much time; use task.csv instead which is the same + #t << dataset.to_prediction_csv + t << task.csv + t.rewind response['Content-Type'] = "text/csv" - path = "/tmp/#{params[:tmppath]}" - send_file path, :filename => "lazar_batch_prediction_#{params[:filename]}", :type => "text/csv", :disposition => "attachment" + send_file t.path, :filename => "#{Time.now.strftime("%Y-%m-%d")}_lazar_batch_prediction_#{name}", :type => "text/csv", :disposition => "attachment" end post '/predict/?' do - # process batch prediction - if !params[:fileselect].blank? + unless params[:fileselect].blank? if params[:fileselect][:filename] !~ /\.csv$/ - bad_request_error "Please submit a csv file." - end - File.open('tmp/' + params[:fileselect][:filename], "w") do |f| - f.write(params[:fileselect][:tempfile].read) + raise "Wrong file extension for '#{params[:fileselect][:filename]}'. Please upload a CSV file." end @filename = params[:fileselect][:filename] - begin - input = OpenTox::Dataset.from_csv_file File.join("tmp", params[:fileselect][:filename]), true - if input.class == OpenTox::Dataset - dataset = OpenTox::Dataset.find input - else - bad_request_error "Could not serialize file '#{@filename}'." - end - rescue - bad_request_error "Could not serialize file '#{@filename}'." - end - @compounds = dataset.compounds - if @compounds.size == 0 - message = dataset[:warnings] - dataset.delete - bad_request_error message + File.open('tmp/' + @filename, "w") do |f| + f.write(params[:fileselect][:tempfile].read) end + # check CSV structure by parsing and header check + csv = CSV.read File.join("tmp", @filename) + header = csv.shift + accepted = ["SMILES","InChI"] + raise "CSV header does not include 'SMILES' or 'InChI'. Please read the <a href='https://dg.in-silico.ch/predict/help' rel='external'> HELP </a> page." unless header.any?(/smiles|inchi/i) + @models = params[:selection].keys.join(",") + return haml :upload + end - # for csv export - @batch = {} - # for haml table - @view = {} + unless params[:batchfile].blank? + dataset = Dataset.from_csv_file File.join("tmp", params[:batchfile]) + raise "No compounds in Dataset. Please read the <a href='https://dg.in-silico.ch/predict/help' rel='external'> HELP </a> page." if dataset.compounds.size == 0 + response['Content-Type'] = "application/json" + return {:dataset_id => dataset.id.to_s, :models => params[:models]}.to_json + end - @compounds.each{|c| @view[c] = []} - params[:selection].keys.each do |model_id| - model = OpenTox::Model::Validation.find model_id - @batch[model] = [] - @compounds.each_with_index do |compound,idx| - prediction = model.predict(compound) - @batch[model] << [compound, prediction] - @view[compound] << [model,prediction] - end - end + unless params[:models].blank? + dataset = Dataset.find params[:dataset_id] + @compounds_size = dataset.compounds.size + @models = params[:models].split(",") + @tasks = [] + @models.each{|m| t = Task.new; t.save; @tasks << t} + @predictions = {} - @csvhash = {} - @warnings = dataset[:warnings] - dupEntries = {} - delEntries = "" - - # split duplicates and deleted entries - @warnings.each do |w| - substring = w.match(/line .* of/) - unless substring.nil? - delEntries += "\"#{w.sub(/\b(tmp\/)\b/,"")}\"\n" - end - substring = w.match(/rows .* Entries/) - unless substring.nil? - lines = [] - substring[0].split(",").each{|s| lines << s[/\d+/]} - lines.shift - lines.each{|l| dupEntries[l.to_i] = w.split(".").first} + maintask = Task.run do + @models.each_with_index do |model_id,idx| + t = @tasks[idx] + t.update_percent(1) + prediction = {} + model = Model::Validation.find model_id + t.update_percent(10) + prediction_dataset = model.predict dataset + t.update_percent(70) + t[:dataset_id] = prediction_dataset.id + t.update_percent(75) + prediction[model_id] = prediction_dataset.id.to_s + t.update_percent(80) + t[:predictions] = prediction + t.update_percent(90) + t[:csv] = prediction_dataset.to_prediction_csv + t.update_percent(100) + t.save end end - - @batch.each_with_index do |hash, idx| - @csvhash[idx] = "" - model = hash[0] - # create header - if model.regression? - predAunit = "(#{model.unit})" - predBunit = "(#{model.unit =~ /mmol\/L/ ? "(mol/L)" : "(mg/kg_bw/day)"})" - @csvhash[idx] = "\"ID\",\"Endpoint\",\"Type\",\"Unique SMILES\",\"Prediction #{predAunit}\",\"Prediction #{predBunit}\",\"95% Prediction interval (low) #{predAunit}\",\"95% Prediction interval (high) #{predAunit}\",\"95% Prediction interval (low) #{predBunit}\",\"95% Prediction interval (high) #{predBunit}\",\"inApplicabilityDomain\",\"inTrainningSet\",\"Note\"\n" - else #classification - av = model.prediction_feature.accept_values - probFirst = av[0].capitalize - probLast = av[1].capitalize - @csvhash[idx] = "\"ID\",\"Endpoint\",\"Type\",\"Unique SMILES\",\"Prediction\",\"predProbability#{probFirst}\",\"predProbability#{probLast}\",\"inApplicabilityDomain\",\"inTrainningSet\",\"Note\"\n" + maintask[:subTasks] = @tasks.collect{|t| t.id} + maintask.save + @pid = maintask.pid + response['Content-Type'] = "text/html" + return haml :batch + else + # single compound prediction + # validate identifier input + if !params[:identifier].blank? + @identifier = params[:identifier].strip + $logger.debug "input:#{@identifier}" + # get compound from SMILES + begin + @compound = Compound.from_smiles @identifier + rescue + @error = "'#{@identifier}' is not a valid SMILES string." unless @compound + return haml :error end - values = hash[1] - dupEntries.keys.each{|k| values.insert(k-1, dupEntries[k])}.compact! - - values.each_with_index do |array, id| - type = (model.regression? ? "Regression" : "Classification") - endpoint = "#{model.endpoint.gsub('_', ' ')} (#{model.species})" - - if id == 0 - @csvhash[idx] += delEntries unless delEntries.blank? - end - unless array.kind_of? String - compound = array[0] - prediction = array[1] - smiles = compound.smiles - - if prediction[:neighbors] - if prediction[:value] - pred = prediction[:value].numeric? ? "#{prediction[:value].delog10.signif(3)}" : prediction[:value] - predA = prediction[:value].numeric? ? "#{prediction[:value].delog10.signif(3)}" : prediction[:value] - predAunit = prediction[:value].numeric? ? "(#{model.unit})" : "" - predB = prediction[:value].numeric? ? "#{compound.mmol_to_mg(prediction[:value].delog10).signif(3)}" : prediction[:value] - predBunit = prediction[:value].numeric? ? "#{model.unit =~ /\b(mmol\/L)\b/ ? "(mg/L)" : "(mg/kg_bw/day)"}" : "" - int = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval]) - intervalLow = (int.nil? ? "" : "#{int[1].delog10.signif(3)}") - intervalHigh = (int.nil? ? "" : "#{int[0].delog10.signif(3)}") - intervalLowMg = (int.nil? ? "" : "#{compound.mmol_to_mg(int[1].delog10).signif(3)}") - intervalHighMg = (int.nil? ? "" : "#{compound.mmol_to_mg(int[0].delog10).signif(3)}") - inApp = "yes" - inT = prediction[:info] =~ /\b(identical)\b/i ? "yes" : "no" - note = prediction[:warnings].join("\n") + ( prediction[:info] ? prediction[:info].sub(/\'.*\'/,"") : "\n" ) - - unless prediction[:probabilities].nil? - av = model.prediction_feature.accept_values - propA = "#{prediction[:probabilities][av[0]].to_f.signif(3)}" - propB = "#{prediction[:probabilities][av[1]].to_f.signif(3)}" - end - else - # no prediction value only one neighbor - inApp = "no" - inT = prediction[:info] =~ /\b(identical)\b/i ? "yes" : "no" - note = prediction[:warnings].join("\n") + ( prediction[:info] ? prediction[:info].sub(/\'.*\'/,"") : "\n" ) - end - else - # no prediction value - inApp = "no" - inT = prediction[:info] =~ /\b(identical)\b/i ? "yes" : "no" - note = prediction[:warnings].join("\n") + ( prediction[:info] ? prediction[:info].sub(/\'.*\'/,"") : "\n" ) - end - if @warnings - @warnings.each do |w| - note += (w.split(".").first + ".") if /\b(#{Regexp.escape(smiles)})\b/ === w - end - end - else - # string note for duplicates - endpoint = type = smiles = pred = predA = predB = propA = propB = intervalLow = intervalHigh = intervalLowMg = intervalHighMg = inApp = inT = "" - note = array - end - if model.regression? - @csvhash[idx] += "\"#{id+1}\",\"#{endpoint}\",\"#{type}\",\"#{smiles}\",\"#{predA}\",\"#{predB}\",\"#{intervalLow}\",\"#{intervalHigh}\",\"#{intervalLowMg}\",\"#{intervalHighMg}\",\"#{inApp}\",\"#{inT}\",\"#{note.chomp}\"\n" - else - @csvhash[idx] += "\"#{id+1}\",\"#{endpoint}\",\"#{type}\",\"#{smiles}\",\"#{pred}\",\"#{propA}\",\"#{propB}\",\"#{inApp}\",\"#{inT}\",\"#{note.chomp}\"\n" - end + @models = [] + @predictions = [] + params[:selection].keys.each do |model_id| + model = Model::Validation.find model_id + @models << model + prediction = model.predict(@compound) + @predictions << prediction end + haml :prediction end - t = Tempfile.new - @csvhash.each do |model, csv| - t.write(csv) - t.write("\n") - end - t.rewind - @tmppath = t.path.split("/").last - - dataset.delete - File.delete File.join("tmp", params[:fileselect][:filename]) - return haml :batch end +end - # validate identifier input - if !params[:identifier].blank? - @identifier = params[:identifier] - $logger.debug "input:#{@identifier}" - # get compound from SMILES - @compound = Compound.from_smiles @identifier - bad_request_error "'#{@identifier}' is not a valid SMILES string." if @compound.blank? - - @models = [] - @predictions = [] - params[:selection].keys.each do |model_id| - model = OpenTox::Model::Validation.find model_id - @models << model - @predictions << model.predict(@compound) +get '/prediction/task/?' do + # returns task progress in percent + if params[:turi] + task = Task.find(params[:turi].to_s) + response['Content-Type'] = "application/json" + return JSON.pretty_generate(:percent => task.percent) + # kills task process id + elsif params[:ktpid] + begin + Process.kill(9,params[:ktpid].to_i) if !params[:ktpid].blank? + rescue + nil + end + #remove_task_data(params[:ktpid]) deletes also the source file + response['Content-Type'] = "application/json" + return JSON.pretty_generate(:ktpid => params[:ktpid]) + # returns task details + elsif params[:predictions] + task = Task.find(params[:predictions]) + pageSize = params[:pageSize].to_i - 1 + pageNumber= params[:pageNumber].to_i - 1 + csv = CSV.parse(task.csv) + header = csv.shift + string = "<td><table class=\"table table-bordered\">" + # find canonical smiles column + cansmi = 0 + header.each_with_index do |h,idx| + cansmi = idx if h =~ /Canonical SMILES/ + string += "<th class=\"fit\">#{h}</th>" + end + string += "</tr>" + string += "<tr>" + csv[pageNumber].each_with_index do |line,idx| + if idx == cansmi + c = Compound.from_smiles line + string += "<td class=\"fit\">#{line}</br>" \ + "<a class=\"btn btn-link\" data-id=\"link\" " \ + "data-remote=\"#{to("/prediction/#{c.id}/details")}\" data-toggle=\"modal\" " \ + "href=#details>" \ + "#{embedded_svg(c.svg, title: "click for details")}" \ + "</td>" + else + string += "<td nowrap>#{line.numeric? && line.include?(".") ? line.to_f.signif(3) : (line.nil? ? line : line.gsub(" ","<br />"))}</td>" + end end - haml :prediction + string += "</tr>" + string += "</table></td>" + response['Content-Type'] = "application/json" + return JSON.pretty_generate(:prediction => [string]) end end -get "/report/:id/?" do - prediction_model = Model::Validation.find params[:id] - bad_request_error "model with id: '#{params[:id]}' not found." unless prediction_model - report = qmrf_report params[:id] - # output - t = Tempfile.new - t << report.to_xml - name = prediction_model.species.sub(/\s/,"-")+"-"+prediction_model.endpoint.downcase.sub(/\s/,"-") - send_file t.path, :filename => "QMRF_report_#{name.gsub!(/[^0-9A-Za-z]/, '_')}.xml", :type => "application/xml", :disposition => "attachment" +# get individual compound details +get '/prediction/:neighbor/details/?' do + @compound = OpenTox::Compound.find params[:neighbor] + @smiles = @compound.smiles + begin + @names = @compound.names.nil? ? "No names for this compound available." : @compound.names + rescue + @names = "No names for this compound available." + end + @inchi = @compound.inchi + + haml :details, :layout => false end -get '/license' do +get '/predict/license' do @license = RDiscount.new(File.read("LICENSE.md")).to_html haml :license, :layout => false end -get '/faq' do +get '/predict/faq' do @faq = RDiscount.new(File.read("FAQ.md")).to_html - haml :faq, :layout => false + haml :faq#, :layout => false +end + +get '/predict/help' do + haml :help end get '/style.css' do @@ -281,3 +341,12 @@ get '/style.css' do scss :style end +# for swagger representation +get '/api/swagger-ui.css' do + headers 'Content-Type' => 'text/css; charset=utf-8' + scss :style +end + +get '/IST_logo_s.png' do + redirect to('/images/IST_logo_s.png') +end |