diff options
| -rw-r--r-- | application.rb | 150 | ||||
| -rw-r--r-- | helper.rb | 1 |
2 files changed, 25 insertions, 126 deletions
diff --git a/application.rb b/application.rb index 13248e6..1771661 100644 --- a/application.rb +++ b/application.rb @@ -1,14 +1,13 @@ ['rubygems', "haml", "sass", "rack-flash"].each do |lib| require lib end -gem "opentox-ruby", "~> 0" +gem "opentox-ruby", "~> 1" require 'opentox-ruby' gem 'sinatra-static-assets' require 'sinatra/static_assets' require 'ftools' require File.join(File.dirname(__FILE__),'model.rb') require File.join(File.dirname(__FILE__),'helper.rb') -#require File.join(File.dirname(__FILE__),'parser.rb') use Rack::Session::Cookie, :expire_after => 28800, :secret => "ui6vaiNi-change_me" @@ -28,7 +27,7 @@ helpers do private def delete_model(model, subjectid=nil) task = OpenTox::Task.create("Deleting model: #{model.uri}",url_for("/delete",:full)) do |task| - begin RestClient.put(File.join(model.task_uri, 'Cancelled'),subjectid) if model.task_uri rescue LOGGER.warn "Can not cancel task #{model.task_uri}" end + begin RestClient.put(File.join(model.task_uri, 'Cancelled'),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 task.progress(30) @@ -71,20 +70,18 @@ get '/login' do end get '/models/?' do - @models = ToxCreateModel.all#(:order => [ :created_at.desc ]) + @models = ToxCreateModel.all.reverse subjectstring = session[:subjectid] ? "?subjectid=#{CGI.escape(session[:subjectid])}" : "" - #@models.each { |model| model.process } haml :models, :locals=>{:models=>@models, :subjectstring => subjectstring} end get '/model/:id/status/?' do response['Content-Type'] = 'text/plain' model = ToxCreateModel.get(params[:id]) - #percentage_completed = task.metadata[OT.percentageCompleted] if (task = OpenTox::Task.exist?(model.task_uri)) begin haml :model_status, :locals=>{:model=>model}, :layout => false rescue - return "unavailable" + return "Model #{params[:id]} not available" end end @@ -127,10 +124,7 @@ put '/model/:id/?' do response['Content-Type'] = 'text/plain' model = ToxCreateModel.get(params[:id]) begin - if params[:name] && model.name != params[:name] - model.update :name => params[:name] - #model.save - end + model.update :name => params[:name] if params[:name] && model.name != params[:name] redirect url_for("/model/#{model.id}/name?mode=show") rescue return "unavailable" @@ -143,8 +137,6 @@ get '/model/:id/:view/?' do model = ToxCreateModel.get(params[:id]) subjectstring = session[:subjectid] ? "?subjectid=#{CGI.escape(session[:subjectid])}" : "" begin - #model.process - #model.save case params[:view] when "model" haml :model, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false @@ -159,7 +151,7 @@ get '/model/:id/:view/?' do end get '/predict/?' do - @models = ToxCreateModel.all#(:order => [ :created_at.desc ]) + @models = ToxCreateModel.all.reverse @models = @models.collect{|m| m if m.status == 'Completed'}.compact haml :predict end @@ -197,7 +189,6 @@ post '/models' do # create a new model subjectid = session[:subjectid] ? session[:subjectid] : nil @model = ToxCreateModel.create(:name => params[:file][:filename].sub(/\..*$/,""), :subjectid => subjectid) @model.update :web_uri => url_for("/model/#{@model.id}", :full), :warnings => "" - #@model.save task = OpenTox::Task.create("Uploading dataset and creating lazar model",url_for("/models",:full)) do |task| task.progress(5) @@ -208,7 +199,6 @@ post '/models' do # create a new model case File.extname(params[:file][:filename]) when ".csv" csv = params[:file][:tempfile].read - #LOGGER.debug csv @dataset.load_csv(csv, subjectid) when ".xls", ".xlsx" @dataset.load_spreadsheet(Excel.new params[:file][:tempfile].path, subjectid) @@ -231,12 +221,6 @@ post '/models' do # create a new model end @model.update :training_dataset => @dataset.uri, :nr_compounds => @dataset.compounds.size, :status => "Creating prediction model" @model.update :warnings => @dataset.metadata[OT.Warnings] unless @dataset.metadata[OT.Warnings].empty? - #@model.training_dataset = @dataset.uri - #@model.nr_compounds = @dataset.compounds.size - #@model.warnings = @dataset.metadata[OT.Warnings] unless @dataset.metadata[OT.Warnings].empty? - #@model.save - - #@model.update :status => "Creating prediction model" task.progress(15) begin lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :subjectid => subjectid) @@ -244,8 +228,6 @@ post '/models' do # create a new model error "Model creation failed with '#{e.message}'. Please check if the input file is in a valid #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} format." end task.progress(25) - #@model.feature_dataset = lazar.metadata[OT.featureDataset] - #@model.uri = lazar.uri type = "unknown" case lazar.metadata[OT.isA] when /Classification/ @@ -279,30 +261,16 @@ post '/models' do # create a new model end @model.update :status => "Creating validation report" - #begin - validation_report_uri = validation.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" - #rescue => e - #LOGGER.debug "Validation report generation failed with #{e.message}." - #@model.update :warnings => @model.warnings + "\nValidation report generation failed with #{e.message}." - #end - #@model.update :status => "Creating QMRF report" - #begin - #@model.update(:validation_qmrf_report_uri => validation.create_qmrf_report(subjectid)) unless @model.dirty? - 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 - #LOGGER.debug "Validation QMRF report generation failed with #{e.message}." - #@model.update :warnings => @model.warnings + "\nValidation QMRF report generation failed with #{e.message}." - #end - #@model.update :status => "Completed" + validation_report_uri = validation.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)) + @model.update(:validation_qmrf_uri => qmrf_report.uri, :status => "Completed") rescue => e LOGGER.debug "Model validation failed with #{e.message}." @model.save # to avoid dirty models @model.update :warnings => @model.warnings + "\nModel validation failed with #{e.message}.", :status => "Error", :error_messages => e.message end - #@model.save end @@ -315,13 +283,10 @@ post '/models' do # create a new model lazar.uri end @model.update(:task_uri => task.uri) - #@model.save flash[:notice] = "Model creation and validation started - this may last up to several hours depending on the number and size of the training compounds." redirect url_for('/models') -=begin -=end end post '/predict/?' do # post chemical name to model @@ -340,7 +305,6 @@ post '/predict/?' do # post chemical name to model @predictions = [] params[:selection].keys.each do |id| model = ToxCreateModel.get(id.to_i) - #model.process unless model.uri prediction = nil confidence = nil title = nil @@ -356,7 +320,6 @@ post '/predict/?' do # post chemical name to model else predicted_feature = prediction_dataset.metadata[OT.dependentVariables] prediction = OpenTox::Feature.find(predicted_feature) - #LOGGER.debug prediction.to_yaml if prediction.metadata[OT.error] @predictions << { :title => model.name, @@ -372,38 +335,7 @@ post '/predict/?' do # post chemical name to model end end # TODO failed/unavailable predictions -=begin - source = prediction.creator - if prediction.data[@compound.uri] - if source.to_s.match(/model/) # real prediction - prediction = prediction.data[@compound.uri].first.values.first - #LOGGER.debug prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#classification")] - #LOGGER.debug prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#confidence")] - if !prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#classification")].nil? - @predictions << { - :title => model.name, - :model_uri => model.uri, - :prediction => prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#classification")], - :confidence => prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#confidence")] - } - elsif !prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#regression")].nil? - @predictions << { - :title => model.name, - :model_uri => model.uri, - :prediction => prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#regression")], - :confidence => prediction[File.join(CONFIG[:services]["opentox-model"],"lazar#confidence")] - } - end - else # database value - prediction = prediction.data[@compound.uri].first.values - @predictions << {:title => model.name, :measured_activities => prediction} - end - else - @predictions << {:title => model.name, :prediction => "not available (not enough similar compounds in the training dataset)"} - end -=end end - #LOGGER.debug @predictions.inspect haml :prediction end @@ -416,40 +348,10 @@ post "/lazar/?" do # get detailed prediction prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => params[:subjectid]) @prediction = OpenTox::LazarPrediction.find(prediction_dataset_uri, session[:subjectid]) @compound = OpenTox::Compound.new(params[:compound_uri]) - #@title = prediction.metadata[DC.title] - # TODO dataset activity - #@activity = prediction.metadata[OT.prediction] - #@confidence = prediction.metadata[OT.confidence] - #@neighbors = [] - #@features = [] -# if @prediction.data[@compound.uri] -# if @prediction.creator.to_s.match(/model/) # real prediction -# p = @prediction.data[@compound.uri].first.values.first -# if !p[File.join(CONFIG[:services]["opentox-model"],"lazar#classification")].nil? -# feature = File.join(CONFIG[:services]["opentox-model"],"lazar#classification") -# elsif !p[File.join(CONFIG[:services]["opentox-model"],"lazar#regression")].nil? -# feature = File.join(CONFIG[:services]["opentox-model"],"lazar#regression") -# end -# @activity = p[feature] -# @confidence = p[File.join(CONFIG[:services]["opentox-model"],"lazar#confidence")] -# @neighbors = p[File.join(CONFIG[:services]["opentox-model"],"lazar#neighbors")] -# @features = p[File.join(CONFIG[:services]["opentox-model"],"lazar#features")] -# else # database value -# @measured_activities = @prediction.data[@compound.uri].first.values -# end -# else -# @activity = "not available (no similar compounds in the training dataset)" -# end haml :lazar end post '/login' do -=begin - if session[:subjectid] != nil - flash[:notice] = "You are already logged in as user: #{session[:username]}. Please log out first." - redirect url_for('/login') - end -=end if params[:username] == '' || params[:password] == '' flash[:notice] = "Please enter username and password." redirect url_for('/login') @@ -457,7 +359,6 @@ post '/login' do if login(params[:username], params[:password]) flash[:notice] = "Welcome #{session[:username]}!" redirect url_for('/create') - #haml :create else flash[:notice] = "Login failed. Please try again." haml :login @@ -474,7 +375,7 @@ delete '/model/:id/?' do raise OpenTox::NotFoundError.new("Model with id: #{params[:id]} not found!") unless model begin delete_model(model, @subjectid) - model.destroy + model.delete unless ToxCreateModel.get(params[:id]) begin aa = OpenTox::Authorization.delete_policies_from_uri(model.web_uri, @subjectid) @@ -491,23 +392,22 @@ delete '/model/:id/?' do end delete '/?' do - #DataMapper.auto_migrate! ToxCreateModel.all.each do |model| -# begin -# delete_model(model, @subjectid) + 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 -# LOGGER.debug "#{model.name} model deleted." -# rescue -# LOGGER.error "#{model.name} model delete error." -# end + 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 + LOGGER.debug "#{model.name} model deleted." + rescue + LOGGER.error "#{model.name} model delete error." + end end response['Content-Type'] = 'text/plain' "All Models deleted." @@ -53,7 +53,6 @@ helpers do features = {:activating => [], :deactivating => []} descriptors.each { |d| LOGGER.debug d.inspect; features[d[OT.effect].to_sym] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} } - #LOGGER.debug features.to_yaml features end |