From 7947128ea346ef96aa703fc5070bd9b00588d425 Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 22 Aug 2011 12:49:09 +0200 Subject: merge from development -> lazar-gui --- application.rb | 91 ++++++++++++++++++------------------ helper.rb | 30 ------------ model.rb | 2 +- public/javascripts/toxcreate.js | 4 +- views/classification_validation.haml | 4 +- views/help.haml | 28 +++++------ views/model.haml | 4 +- 7 files changed, 67 insertions(+), 96 deletions(-) diff --git a/application.rb b/application.rb index ee851d9..104003e 100644 --- a/application.rb +++ b/application.rb @@ -9,8 +9,9 @@ require 'ftools' require File.join(File.dirname(__FILE__),'model.rb') require File.join(File.dirname(__FILE__),'helper.rb') -use Rack::Session::Cookie, :expire_after => 28800, - :secret => "ui6vaiNi-change_me" +#moved to wrapper->environment +#use Rack::Session::Cookie, :expire_after => 28800, +# :secret => "ui6vaiNi-change_me" use Rack::Flash set :lock, true @@ -31,7 +32,7 @@ helpers do private def delete_model(model, subjectid=nil) - task = OpenTox::Task.create("Deleting model: #{model.uri}",url_for("/delete",:full)) do |task| + task = OpenTox::Task.create("Deleting model: #{model.web_uri}", url_for("/delete",:full)) do |task| begin OpenTox::RestClientWrapper.put(File.join(model.task_uri, "Cancelled"), "Cancelled",{:subjectid => subjectid}) if model.task_uri rescue LOGGER.warn "Cannot cancel task #{model.task_uri}" end task.progress(15) delete_dependent(model.uri, subjectid) if model.uri @@ -49,15 +50,25 @@ helpers do if model.feature_dataset delete_dependent(model.feature_dataset, subjectid) if model.feature_dataset.match(CONFIG[:services]["opentox-dataset"]) end + task.progress(95) + model.delete + unless ToxCreateModel.get(model.id) + begin + aa = OpenTox::Authorization.delete_policies_from_uri(model.web_uri, @subjectid) + LOGGER.debug "Policy deleted for ToxCreateModel URI: #{model.web_uri} with result: #{aa}" + rescue + LOGGER.warn "Policy delete error for ToxCreateModel URI: #{model.web_uri}" + end + end task.progress(100) - "" + url_for("/models",:full) end end def delete_dependent(uri, subjectid=nil) begin - RestClient.delete(uri, :subjectid => subjectid) if subjectid - RestClient.delete(uri) if !subjectid + OpenTox::RestClientWrapper.delete(uri, :subjectid => subjectid) if subjectid + OpenTox::RestClientWrapper.delete(uri) if !subjectid rescue LOGGER.warn "Can not delete uri: #{uri}" end @@ -81,7 +92,7 @@ end get '/models/?' do @models = ToxCreateModel.all.sort(:order => "DESC") @models.each{|m| raise "internal redis error: model is nil" unless m} - subjectstring = session[:subjectid] ? "?subjectid=#{CGI.escape(session[:subjectid])}" : "" + subjectstring = @subjectid ? "?subjectid=#{CGI.escape(@subjectid)}" : "" haml :models, :locals=>{:models=>@models, :subjectstring => subjectstring} end @@ -145,7 +156,7 @@ end get '/model/:id/:view/?' do response['Content-Type'] = 'text/plain' model = ToxCreateModel.get(params[:id]) - subjectstring = session[:subjectid] ? "?subjectid=#{CGI.escape(session[:subjectid])}" : "" + subjectstring = @subjectid ? "?subjectid=#{CGI.escape(@subjectid)}" : "" begin case params[:view] when "model" @@ -199,7 +210,7 @@ end post '/feature' do session[:dataset] = params[:dataset] @features = [] - OpenTox::Dataset.new(params[:dataset]).load_features.each do |uri,metadata| + OpenTox::Dataset.new(params[:dataset], @subjectid).load_features(@subjectid).each do |uri,metadata| @features << OpenTox::Feature.find(uri, @subjectid) if metadata[OWL.sameAs].match(/#{session[:echa]}/) end haml :feature @@ -218,18 +229,16 @@ post '/models' do # create a new model redirect url_for('/create') end - subjectid = session[:subjectid] ? session[:subjectid] : nil - if params[:dataset] and params[:prediction_feature] - @dataset = OpenTox::Dataset.new(params[:dataset],subjectid) + @dataset = OpenTox::Dataset.new(params[:dataset], @subjectid) name = @dataset.load_metadata[DC.title] - @prediction_feature = OpenTox::Feature.find params[:prediction_feature], subjectid + @prediction_feature = OpenTox::Feature.find params[:prediction_feature], @subjectid @dataset.load_compounds elsif params[:file][:filename] name = params[:file][:filename].sub(/\..*$/,"") end - @model = ToxCreateModel.create(:name => name, :subjectid => subjectid) + @model = ToxCreateModel.create(:name => name, :subjectid => @subjectid) @model.update :web_uri => url_for("/model/#{@model.id}", :full), :warnings => "" task = OpenTox::Task.create("Toxcreate Task - Uploading dataset and creating lazar model",url_for("/models",:full)) do |task| @@ -238,33 +247,33 @@ post '/models' do # create a new model unless params[:dataset] and params[:prediction_feature] begin - @dataset = OpenTox::Dataset.create(nil, subjectid) + @dataset = OpenTox::Dataset.create(nil, @subjectid) # check format by extension - not all browsers provide correct content-type]) case File.extname(params[:file][:filename]) when ".csv" csv = params[:file][:tempfile].read - @dataset.load_csv(csv, subjectid) + @dataset.load_csv(csv, @subjectid) when ".xls", ".xlsx" excel_file = params[:file][:tempfile].path + File.extname(params[:file][:filename]) File.rename(params[:file][:tempfile].path, excel_file) # add extension, spreadsheet does not read files without extensions - @dataset.load_spreadsheet(Excel.new excel_file, subjectid) + @dataset.load_spreadsheet(Excel.new excel_file, @subjectid) if @dataset.metadata[OT.Errors] raise "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/help"} or #{link_to "CSV", "/help"} formats." end when ".sdf" sdf = params[:file][:tempfile].read - @dataset.load_sdf(sdf, subjectid) + @dataset.load_sdf(sdf, @subjectid) else raise "#{params[:file][:filename]} has an unsupported file type." end - @dataset.save(subjectid) + @dataset.save(@subjectid) rescue => e error "Dataset creation failed '#{e.message}'",e end if @dataset.features.keys.size != 1 error "More than one feature in dataset #{params[:file][:filename]}. Please delete irrelvant columns and try again." else - @prediction_feature = OpenTox::Feature.find(@dataset.features.keys.first,subjectid) + @prediction_feature = OpenTox::Feature.find(@dataset.features.keys.first,@subjectid) end end @@ -276,7 +285,7 @@ post '/models' do # create a new model @model.update :warnings => @dataset.metadata[OT.Warnings] unless @dataset.metadata[OT.Warnings] and @dataset.metadata[OT.Warnings].empty? task.progress(15) begin - lazar = OpenTox::Model::Lazar.create( {:dataset_uri => @dataset.uri, :prediction_feature => @prediction_feature.uri, :subjectid => subjectid}, + lazar = OpenTox::Model::Lazar.create( {:dataset_uri => @dataset.uri, :prediction_feature => @prediction_feature.uri, :subjectid => @subjectid}, OpenTox::SubTask.new(task,15,25)) rescue => e error "Model creation failed",e # Please check if the input file is in a valid #{link_to "Excel", "/help"} or #{link_to "CSV", "/help"} format." @@ -297,7 +306,7 @@ post '/models' do # create a new model crossvalidation = OpenTox::Crossvalidation.create( { :algorithm_uri => lazar.metadata[OT.algorithm], :dataset_uri => lazar.parameter("dataset_uri"), - :subjectid => subjectid, + :subjectid => @subjectid, :prediction_feature => lazar.parameter("prediction_feature"), :algorithm_params => "feature_generation_uri=#{lazar.parameter("feature_generation_uri")}" }, nil, OpenTox::SubTask.new(task,25,80)) @@ -306,12 +315,12 @@ post '/models' do # create a new model LOGGER.debug "Validation URI: #{@model.validation_uri}" # create summary - validation = crossvalidation.statistics(subjectid) + validation = crossvalidation.statistics(@subjectid) @model.update(:nr_predictions => validation.metadata[OT.numInstances].to_i - validation.metadata[OT.numUnpredicted].to_i) if validation.metadata[OT.classificationStatistics] @model.update(:correct_predictions => validation.metadata[OT.classificationStatistics][OT.percentCorrect].to_f) @model.update(:confusion_matrix => validation.confusion_matrix.to_yaml) - @model.update(:weighted_area_under_roc => validation.metadata[OT.classificationStatistics][OT.weightedAreaUnderRoc].to_f) + @model.update(:average_area_under_roc => validation.metadata[OT.classificationStatistics][OT.averageAreaUnderRoc].to_f) validation.metadata[OT.classificationStatistics][OT.classValueStatistics].each do |m| if m[OT.classValue] =~ TRUE_REGEXP #HACK: estimate true feature value correctly @@ -332,9 +341,9 @@ post '/models' do # create a new model begin @model.update :status => "Creating validation report" - validation_report_uri = crossvalidation.find_or_create_report(subjectid, OpenTox::SubTask.new(task,80,90)) #unless @model.dirty? + validation_report_uri = crossvalidation.find_or_create_report(@subjectid, OpenTox::SubTask.new(task,80,90)) #unless @model.dirty? @model.update :validation_report_uri => validation_report_uri, :status => "Creating QMRF report" - qmrf_report = OpenTox::Crossvalidation::QMRFReport.create(@model.uri, subjectid, OpenTox::SubTask.new(task,90,99)) + qmrf_report = OpenTox::Crossvalidation::QMRFReport.create(@model.uri, @subjectid, OpenTox::SubTask.new(task,90,99)) @model.update(:validation_qmrf_uri => qmrf_report.uri, :status => "Completed") rescue => e error "Model report creation failed",e @@ -353,14 +362,14 @@ post '/models' do # create a new model end post '/predict/?' do # post chemical name to model - subjectid = session[:subjectid] ? session[:subjectid] : nil + @identifier = params[:identifier] unless params[:selection] and params[:identifier] != '' flash[:notice] = "Please enter a compound identifier and select an endpoint from the list." redirect url_for('/predict') end begin - @compound = OpenTox::Compound.from_name(params[:identifier]) + @compound = OpenTox::Compound.from_smiles(params[:identifier]) rescue flash[:notice] = "Could not find a structure for '#{@identifier}'. Please try again." redirect url_for('/predict') @@ -372,15 +381,15 @@ post '/predict/?' do # post chemical name to model confidence = nil title = nil db_activities = [] - lazar = OpenTox::Model::Lazar.find model.uri - prediction_dataset_uri = lazar.run({:compound_uri => @compound.uri, :subjectid => subjectid}) + lazar = OpenTox::Model::Lazar.find model.uri, @subjectid + prediction_dataset_uri = lazar.run({:compound_uri => @compound.uri, :subjectid => @subjectid}) LOGGER.debug "Prediction dataset_uri: #{prediction_dataset_uri}" if lazar.value_map @value_map = lazar.value_map else @value_map = nil end - prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri, subjectid) + prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri, @subjectid) if prediction_dataset.metadata[OT.hasSource].match(/dataset/) @predictions << { :title => model.name, @@ -388,7 +397,7 @@ post '/predict/?' do # post chemical name to model } else predicted_feature = prediction_dataset.metadata[OT.dependentVariables] - prediction = OpenTox::Feature.find(predicted_feature, subjectid) + prediction = OpenTox::Feature.find(predicted_feature, @subjectid) if prediction.metadata[OT.error] @predictions << { :title => model.name, @@ -418,14 +427,14 @@ post "/lazar/?" do # get detailed prediction @page = 0 @page = params[:page].to_i if params[:page] @model_uri = params[:model_uri] - lazar = OpenTox::Model::Lazar.find @model_uri - prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => session[:subjectid]) + lazar = OpenTox::Model::Lazar.find @model_uri, @subjectid + prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => @subjectid) if lazar.value_map @value_map = lazar.value_map else @value_map = nil end - @prediction = OpenTox::LazarPrediction.find(prediction_dataset_uri, session[:subjectid]) + @prediction = OpenTox::LazarPrediction.find(prediction_dataset_uri, @subjectid) @compound = OpenTox::Compound.new(params[:compound_uri]) haml :lazar end @@ -453,18 +462,10 @@ delete '/model/:id/?' do model = ToxCreateModel.get(params[:id]) raise OpenTox::NotFoundError.new("Model with id: #{params[:id]} not found!") unless model begin - delete_model(model, @subjectid) - model.delete - unless ToxCreateModel.get(params[:id]) - begin - aa = OpenTox::Authorization.delete_policies_from_uri(model.web_uri, @subjectid) - LOGGER.debug "Policy deleted for Dataset URI: #{uri} with result: #{aa}" - rescue - LOGGER.warn "Policy delete error for Dataset URI: #{uri}" - end - end + delete_model(model, @subjectid) flash[:notice] = "#{model.name} model deleted." rescue + LOGGER.error "#{model.name} model delete error." flash[:notice] = "#{model.name} model delete error." end redirect url_for('/models') diff --git a/helper.rb b/helper.rb index 698fd3e..80707c3 100644 --- a/helper.rb +++ b/helper.rb @@ -1,35 +1,5 @@ helpers do - def login(username, password) - logout - session[:subjectid] = OpenTox::Authorization.authenticate(username, password) - #LOGGER.debug "ToxCreate login user #{username} with subjectid: " + session[:subjectid].to_s - if session[:subjectid] != nil - session[:username] = username - return true - else - session[:username] = "" - return false - end - end - - def logout - if session[:subjectid] != nil - session[:subjectid] = nil - session[:username] = "" - return true - end - return false - end - - def logged_in() - return true if !AA_SERVER - if session[:subjectid] != nil - return OpenTox::Authorization.is_token_valid(session[:subjectid]) - end - return false - end - def is_authorized(uri, action) if OpenTox::Authorization.server && session[:subjectid] != nil return OpenTox::Authorization.authorized?(uri, action, session[:subjectid]) diff --git a/model.rb b/model.rb index e433893..bab5bde 100644 --- a/model.rb +++ b/model.rb @@ -31,7 +31,7 @@ class ToxCreateModel < Ohm::Model attribute :nr_compounds attribute :nr_predictions attribute :correct_predictions - attribute :weighted_area_under_roc + attribute :average_area_under_roc attribute :sensitivity attribute :specificity attribute :r_square diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js index a5dc44c..ee783ce 100755 --- a/public/javascripts/toxcreate.js +++ b/public/javascripts/toxcreate.js @@ -77,8 +77,7 @@ $(function() { if (progress == "100") return -1; $("div#model_" + id + "_progress").progressbar("value", parseInt(progress)); - $("div#model_" + id + "_progress").attr({title: parseInt(progress) + "%", alt: parseInt(progress) + "%"}); - //$("div#model_" + id + "_progress").attr("alt", parseInt(progress) + "%"); + $("div#model_" + id + "_progress").attr({title: parseInt(progress) + "%"}); }, error: function(data) { id = -1; @@ -208,6 +207,7 @@ jQuery.fn.deleteModel = function(type, options) { if(confirm(opts.confirm_message)) { $("div#model_" + opts.id).fadeTo("slow",0.5); $("span#model_" + opts.id + "_status").html("Deleting"); + $("a#delete_" + opts.id).html(""); $.ajax({ type: opts.method, url: opts.action, diff --git a/views/classification_validation.haml b/views/classification_validation.haml index f25a321..9f5c2c9 100644 --- a/views/classification_validation.haml +++ b/views/classification_validation.haml @@ -3,9 +3,9 @@ = sprintf("%.2f", model.correct_predictions.to_f) if model.correct_predictions = '%' %dt - %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :rel => "external"} Weighted area under ROC: + %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :rel => "external"} Average area under ROC: %dd - = sprintf("%.3f", model.weighted_area_under_roc.to_f) if model.weighted_area_under_roc + = sprintf("%.3f", model.average_area_under_roc.to_f) if model.average_area_under_roc %dt %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :rel => "external"} Specificity: %dd= sprintf("%.3f", model.specificity.to_f) if model.specificity diff --git a/views/help.haml b/views/help.haml index 2b39d6c..f602dff 100644 --- a/views/help.haml +++ b/views/help.haml @@ -87,13 +87,13 @@ %p Excel examples for download: - %ul - %li - = link_to "hamster_carcinogenicity.xls", "/hamster_carcinogenicity.xls" - (classification) - %li - = link_to "EPAFHM.xls", "/EPAFHM.xls" - (regression) +%ul + %li + = link_to "hamster_carcinogenicity.xls", "/hamster_carcinogenicity.xls" + (classification) + %li + = link_to "EPAFHM.xls", "/EPAFHM.xls" + (regression) %h3 CSV example @@ -113,13 +113,13 @@ %p CSV examples for download: - %ul - %li - = link_to "hamster_carcinogenicity.csv", "/hamster_carcinogenicity.csv" - (classification) - %li - = link_to "EPAFHM.csv", "/EPAFHM.csv" - (regression) +%ul + %li + = link_to "hamster_carcinogenicity.csv", "/hamster_carcinogenicity.csv" + (classification) + %li + = link_to "EPAFHM.csv", "/EPAFHM.csv" + (regression) %p You can create CSV files in Excel: Create a sheet with two columns and export them as CSV file with the "Save As" option from the menu, selecting the CSV (comma delimited) format. diff --git a/views/model.haml b/views/model.haml index 899bb6a..266fe19 100644 --- a/views/model.haml +++ b/views/model.haml @@ -24,7 +24,7 @@ #{js} }); - %div{:id => "model_#{model.id}_progress", :class => "model_progress", :title => "#{percentage_completed}%", :alt => "#{percentage_completed}%"} + %div{:id => "model_#{model.id}_progress", :class => "model_progress", :title => "#{percentage_completed}%"} //= haml :model_progress, :locals=>{:percentage_completed=>percentage_completed}, :layout => false %span @@ -41,7 +41,7 @@ - if CONFIG[:logger]=="debug" %dt Task: %dd - %a{:href => "#{model.task_uri}", :rel => "external"} + %a{:href => "#{model.task_uri}", :id => "model_#{model.id}_task_link", :rel => "external"} = model.task_uri - if model.warnings %dt Warnings: -- cgit v1.2.3