application.rb added again

1 files changed, 501 insertions, 0 deletions

diff --git a/application.rb b/application.rb
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+['rubygems', "haml", "sass", "rack-flash"].each do |lib|
+  require lib
+end
+gem "opentox-ruby", "~> 0"
+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"
+use Rack::Flash
+
+helpers do 
+
+  def error(message)
+    @model.error_messages = message
+    LOGGER.error message
+    @model.status = "Error"
+    @model.save
+    #@dataset.delete
+    flash[:notice] = message
+    redirect url_for('/create')
+  end
+
+  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
+      task.progress(15)
+      delete_dependent(model.uri, subjectid) if model.uri
+      task.progress(30)
+      delete_dependent(model.validation_uri, subjectid) if model.validation_uri
+      task.progress(45)
+      delete_dependent(model.validation_report_uri, subjectid) if model.validation_report_uri
+      task.progress(60)
+      delete_dependent(model.validation_qmrf_uri, subjectid) if model.validation_qmrf_uri
+      task.progress(75)
+      delete_dependent(model.training_dataset, subjectid) if model.training_dataset
+      task.progress(90)
+      delete_dependent(model.feature_dataset, subjectid) if model.feature_dataset
+      task.progress(100)
+      ""
+    end
+  end
+
+  def delete_dependent(uri, subjectid=nil)
+    begin
+      RestClient.delete(uri, :subjectid => subjectid) if subjectid
+      RestClient.delete(uri) if !subjectid
+    rescue
+      LOGGER.warn "Can not delete uri: #{uri}"
+    end
+  end
+end
+
+before do
+  #unless env['REQUEST_METHOD'] == "GET" or ( env['REQUEST_URI'] =~ /\/login$/ and env['REQUEST_METHOD'] == "POST" ) or !AA_SERVER
+    if !logged_in and !( env['REQUEST_URI'] =~ /\/login$/ and env['REQUEST_METHOD'] == "POST" ) #or !AA_SERVER
+      login("guest","guest")
+      #flash[:notice] = "You have to login first to do this."
+      #redirect url_for('/login')
+    end
+  #end
+end
+
+get '/?' do
+  redirect url_for('/create')
+end
+
+get '/login' do
+  haml :login
+end
+
+get '/models/?' do
+  @models = ToxCreateModel.all(:order => [ :created_at.desc ])
+  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"
+  end
+end
+
+get '/model/:id/progress/?' do
+  response['Content-Type'] = 'text/plain'
+  model = ToxCreateModel.get(params[:id])
+  if model.task_uri 
+    if (OpenTox::Task.exist?(model.task_uri))
+      task = OpenTox::Task.exist?(model.task_uri) 
+      percentage_completed = task.percentageCompleted
+    end 
+    begin
+      haml :model_progress, :locals=>{:percentage_completed=>percentage_completed}, :layout => false
+    rescue
+      return "unavailable"
+    end
+  else
+    return ""
+  end
+end
+
+get '/model/:id/name/?' do
+  response['Content-Type'] = 'text/plain'
+  model = ToxCreateModel.get(params[:id])
+  begin
+    case params[:mode]
+      when 'edit'
+        haml :model_name_edit, :locals=>{:model=>model}, :layout => false
+      when 'show'
+        haml :model_name, :locals=>{:model=>model}, :layout => false
+      else
+        params.inspect
+      end
+  rescue
+    return "unavailable"
+  end
+end
+
+put '/model/:id/?' do
+  response['Content-Type'] = 'text/plain'
+  model = ToxCreateModel.get(params[:id])
+  begin
+    if params[:name] && model.name != params[:name]
+      model.name = params[:name]
+      model.save
+    end
+    redirect url_for("/model/#{model.id}/name?mode=show")
+  rescue
+    return "unavailable"
+  end
+end
+
+
+get '/model/:id/:view/?' do
+  response['Content-Type'] = 'text/plain'
+  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
+      when /validation/
+        haml :validation, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false
+      else
+        return "unable to render model: id #{params[:id]}, view #{params[:view]}"
+    end
+  rescue
+    return "unable to render model: id #{params[:id]}, view #{params[:view]}"
+  end
+end
+
+get '/predict/?' do 
+  @models = ToxCreateModel.all(:order => [ :created_at.desc ])
+  @models = @models.collect{|m| m if m.status == 'Completed'}.compact
+  haml :predict
+end
+
+get '/create' do
+  haml :create
+end
+
+get '/help' do
+  haml :help
+end
+
+get "/confidence" do
+  haml :confidence
+end
+
+# proxy to get data from compound service
+# (jQuery load does not work with external URIs)
+get %r{/compound/(.*)} do |inchi|
+  inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'')
+  OpenTox::Compound.from_inchi(inchi).to_names.join(', ')
+end
+
+post '/models' do # create a new model
+  unless params[:file] and params[:file][:tempfile] #params[:endpoint] and 
+    flash[:notice] = "Please upload a Excel or CSV file."
+    redirect url_for('/create')
+  end
+
+  unless logged_in()
+    logout
+    flash[:notice] = "Please login to create a new model."
+    redirect url_for('/create')
+  end
+  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|
+
+    @model.update :status => "Uploading and saving dataset"
+    begin
+      @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
+        LOGGER.debug csv
+        @dataset.load_csv(csv, subjectid)
+      when ".xls", ".xlsx"
+        @dataset.load_spreadsheet(Excel.new params[:file][:tempfile].path, subjectid)
+      else
+        error "#{params[:file][:filename]} has a unsupported file type."
+      end
+    rescue => e
+      error "Dataset creation failed with #{e.message}"
+    end
+    @dataset.save(subjectid)
+    task.progress(10)
+    if @dataset.compounds.size < 10
+      error "Too few compounds to create a prediction model. Did you provide compounds in SMILES format and classification activities as described in the #{link_to "instructions", "/excel_format"}? As a rule of thumb you will need at least 100 training compounds for nongeneric datasets. A lower number could be sufficient for congeneric datasets."
+    end
+    if @dataset.features.keys.size != 1
+      error "More than one feature in dataset #{params[:file][:filename]}. Please delete irrelvant columns and try again."
+    end
+    if @dataset.metadata[OT.Errors]
+      error "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} formats."
+    end
+    @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)
+    rescue => e
+      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
+    case lazar.metadata[OT.isA]
+    when /Classification/
+      @model.type = "classification"
+    when /Regression/
+      @model.type = "regression"
+    else
+      @model.type = "unknown"
+    end
+    @model.save
+
+    unless url_for("",:full).match(/localhost/)
+      @model.update :status => "Validating model"
+      begin
+        validation = OpenTox::Crossvalidation.create(
+          {:algorithm_uri => lazar.metadata[OT.algorithm],
+          :dataset_uri => lazar.parameter("dataset_uri"),
+          :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))
+        @model.update(:validation_uri => validation.uri)
+        LOGGER.debug "Validation URI: #{@model.validation_uri}"
+      rescue => e
+        LOGGER.debug "Model validation failed with #{e.message}."
+        @model.warnings += "Model validation failed with #{e.message}."
+      end
+      # create summary
+      validation.summary(subjectid).each do |k,v|
+        LOGGER.debug "mr ::: k: #{k.inspect} - v: #{v.inspect}" 
+        begin
+          eval "@model.#{k.to_s} = v" if v
+        rescue
+          eval "@model.#{k.to_s} = 0"
+        end
+      end
+      @model.save
+      
+      @model.update :status => "Creating validation report"
+      begin
+        @model.update(:validation_report_uri => validation.find_or_create_report(subjectid, OpenTox::SubTask.new(task,80,90))) unless @model.dirty?
+      rescue => e
+        LOGGER.debug "Validation report generation failed with #{e.message}."
+        @model.warnings += "Validation 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)
+      rescue => e
+        LOGGER.debug "Validation QMRF report generation failed with #{e.message}."
+        @model.warnings += "Validation QMRF report generation failed with #{e.message}."
+      end
+    end
+
+
+    #@model.warnings += "<p>Incorrect Smiles structures (ignored):</p>" + parser.smiles_errors.join("<br/>") unless parser.smiles_errors.empty?
+    #@model.warnings += "<p>Irregular activities (ignored):</p>" + parser.activity_errors.join("<br/>") unless parser.activity_errors.empty?
+    #duplicate_warnings = ''
+    #parser.duplicates.each {|inchi,lines| duplicate_warnings += "<p>#{lines.join('<br/>')}</p>" if lines.size > 1 }
+    #@model.warnings += "<p>Duplicated structures (all structures/activities used for model building, please  make sure, that the results were obtained from <em>independent</em> experiments):</p>" + duplicate_warnings unless duplicate_warnings.empty?
+    @model.update :status => "Completed"
+    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
+  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])
+  rescue
+    flash[:notice] = "Could not find a structure for '#{@identifier}'. Please try again."
+    redirect url_for('/predict')
+  end
+  @predictions = []
+  params[:selection].keys.each do |id|
+    model = ToxCreateModel.get(id.to_i)
+    #model.process unless model.uri
+    prediction = nil
+    confidence = nil
+    title = nil
+    db_activities = []
+    lazar = OpenTox::Model::Lazar.new model.uri
+    prediction_dataset_uri = lazar.run({:compound_uri => @compound.uri, :subjectid => subjectid})
+    prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri, subjectid)
+    if prediction_dataset.metadata[OT.hasSource].match(/dataset/)
+      @predictions << {
+        :title => model.name,
+        :measured_activities => prediction_dataset.measured_activities(@compound)
+      }
+    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,
+          :error => prediction.metadata[OT.error]
+          }
+      else
+        @predictions << {
+          :title => model.name,
+          :model_uri => model.uri,
+          :prediction => prediction.metadata[OT.prediction],
+          :confidence => prediction.metadata[OT.confidence]
+          }
+      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
+
+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.new @model_uri
+  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')
+  end
+  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
+  end
+end
+
+post '/logout' do
+  logout
+  redirect url_for('/login')
+end
+
+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.destroy
+    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
+    flash[:notice] = "#{model.name} model deleted."
+  rescue
+    flash[:notice] = "#{model.name} model delete error."
+  end
+  redirect url_for('/models')
+end
+
+delete '/?' do
+  DataMapper.auto_migrate!
+  response['Content-Type'] = 'text/plain'
+  "All Models deleted."
+end
+
+# SASS stylesheet
+get '/stylesheets/style.css' do
+  headers 'Content-Type' => 'text/css; charset=utf-8'
+  sass :style
+end