ohm/redis backend

5 files changed, 159 insertions, 109 deletions

diff --git a/application.rb b/application.rb
index 88763d9..13248e6 100644
--- a/application.rb
+++ b/application.rb
@@ -19,11 +19,8 @@ set :lock, true
 helpers do 
 
   def error(message)
-    @model.error_messages = message
     LOGGER.error message
-    @model.status = "Error"
-    @model.save
-    #@dataset.delete
+    @model.update :status => "Error", :error_messages => message
     flash[:notice] = message
     redirect url_for('/create')
   end
@@ -60,13 +57,9 @@ helpers do
 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
@@ -78,7 +71,7 @@ get '/login' do
 end
 
 get '/models/?' do
-  @models = ToxCreateModel.all(:order => [ :created_at.desc ])
+  @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}
@@ -135,8 +128,8 @@ put '/model/:id/?' do
   model = ToxCreateModel.get(params[:id])
   begin
     if params[:name] && model.name != params[:name]
-      model.name = params[:name]
-      model.save
+      model.update :name => params[:name]
+      #model.save
     end
     redirect url_for("/model/#{model.id}/name?mode=show")
   rescue
@@ -166,7 +159,7 @@ get '/model/:id/:view/?' do
 end
 
 get '/predict/?' do 
-  @models = ToxCreateModel.all(:order => [ :created_at.desc ])
+  @models = ToxCreateModel.all#(:order => [ :created_at.desc ])
   @models = @models.collect{|m| m if m.status == 'Completed'}.compact
   haml :predict
 end
@@ -204,9 +197,10 @@ 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
+  #@model.save
   task = OpenTox::Task.create("Uploading dataset and creating lazar model",url_for("/models",:full)) do |task|
 
+    task.progress(5)
     @model.update :status => "Uploading and saving dataset"
     begin
       @dataset = OpenTox::Dataset.create(nil, subjectid)
@@ -214,7 +208,7 @@ post '/models' do # create a new model
       case File.extname(params[:file][:filename])
       when ".csv"
         csv = params[:file][:tempfile].read
-        LOGGER.debug csv
+        #LOGGER.debug csv
         @dataset.load_csv(csv, subjectid)
       when ".xls", ".xlsx"
         @dataset.load_spreadsheet(Excel.new params[:file][:tempfile].path, subjectid)
@@ -235,12 +229,14 @@ post '/models' do # create a new model
     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"
+    @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)
@@ -248,17 +244,16 @@ 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
+    #@model.feature_dataset = lazar.metadata[OT.featureDataset]
+    #@model.uri = lazar.uri
+    type = "unknown"
     case lazar.metadata[OT.isA]
     when /Classification/
-      @model.type = "classification"
+      type = "classification"
     when /Regression/
-      @model.type = "regression"
-    else
-      @model.type = "unknown"
+      type = "regression"
     end
-    @model.save
+    @model.update :type => type, :feature_dataset => lazar.metadata[OT.featureDataset], :uri => lazar.uri
 
     unless url_for("",:full).match(/localhost/)
       @model.update :status => "Validating model"
@@ -272,37 +267,43 @@ post '/models' do # create a new model
          nil, OpenTox::SubTask.new(task,25,80))
         @model.update(:validation_uri => validation.uri)
         LOGGER.debug "Validation URI: #{@model.validation_uri}"
+
+        # create summary
+        validation.summary(subjectid).each do |k,v|
+          #LOGGER.debug "mr ::: k: #{k.inspect} - v: #{v.inspect}" 
+          begin
+            eval "@model.update :#{k.to_s} => v" if v
+          rescue
+            eval "@model.update :#{k.to_s} => 0"
+          end
+        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"
+
       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
+        @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
+      #@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
 
 
@@ -311,11 +312,10 @@ post '/models' do # create a new model
     #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
+  #@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')
@@ -356,7 +356,7 @@ 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
+      #LOGGER.debug prediction.to_yaml
       if prediction.metadata[OT.error]
         @predictions << {
           :title => model.name,
@@ -403,7 +403,7 @@ post '/predict/?' do # post chemical name to model
     end
 =end
   end
-  LOGGER.debug @predictions.inspect
+  #LOGGER.debug @predictions.inspect
 
   haml :prediction
 end
@@ -491,7 +491,24 @@ delete '/model/:id/?' do
 end
 
 delete '/?' do
-  DataMapper.auto_migrate!
+  #DataMapper.auto_migrate!
+  ToxCreateModel.all.each do |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
+#      LOGGER.debug "#{model.name} model deleted."
+#    rescue
+#      LOGGER.error "#{model.name} model delete error."
+#    end
+  end
   response['Content-Type'] = 'text/plain'
   "All Models deleted."
 end
diff --git a/helper.rb b/helper.rb
index 3fbd06f..d2c5593 100644
--- a/helper.rb
+++ b/helper.rb
@@ -53,7 +53,7 @@ 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
+    #LOGGER.debug features.to_yaml
     features
   end
 
diff --git a/model.rb b/model.rb
index eb459b3..7d22a4d 100644
--- a/model.rb
+++ b/model.rb
@@ -1,51 +1,84 @@
-class ToxCreateModel
-
-	include DataMapper::Resource
-
-	property :id, Serial
-	property :name, String, :length => 255
-	property :warnings, Text, :length => 2**32-1 
-	property :error_messages, Text, :length => 2**32-1  # :errors interferes with datamapper validation
-	property :type, String
-  property :status, String, :length => 255
-	property :created_at, DateTime
-
-	property :task_uri, String, :length => 255
-	property :uri, String, :length => 255
-
-	property :training_dataset, String, :length => 255
-	property :feature_dataset, String, :length => 255
-	#property :validation_task_uri, String, :length => 255
-	property :validation_uri, String, :length => 255
-
-	#property :validation_report_task_uri, String, :length => 255
-	property :validation_report_uri, String, :length => 255
-
-	#property :validation_qmrf_task_uri, String, :length => 255
-	property :validation_qmrf_uri, String, :length => 255
-
-	property :nr_compounds, Integer
-	property :nr_predictions, Integer
-	property :true_positives, Integer
-	property :false_positives, Integer
-	property :true_negatives, Integer
-	property :false_negatives, Integer
-	property :correct_predictions, Integer
-	property :weighted_area_under_roc, Float
-	property :sensitivity, Float
-	property :specificity, Float
-	property :r_square, Float
-	property :root_mean_squared_error, Float
-	property :mean_absolute_error, Float
-
-  property :web_uri, String, :length => 255
+require 'ohm'
+#require 'redis/objects'
+#@@redis = Redis.new(:thread_safe=>true)#(:host => '127.0.0.1', :port => 6379)
+
+class ToxCreateModel < Ohm::Model
+
+  #include Redis::Objects
+	#include DataMapper::Resource
+	#attribute :id
+	attribute :name
+	attribute :warnings
+	attribute :error_messages
+	attribute :type
+  attribute :status
+	attribute :created_at
+
+	attribute :task_uri
+	attribute :uri
+
+	attribute :training_dataset
+	attribute :feature_dataset
+	#attributey :validation_task_uri
+	attribute :validation_uri
+
+	#attributey :validation_report_task_uri
+	attribute :validation_report_uri
+
+	#attributey :validation_qmrf_task_uri
+	attribute :validation_qmrf_uri
+
+	attribute :nr_compounds
+	attribute :nr_predictions
+	attribute :true_positives
+	attribute :false_positives
+	attribute :true_negatives
+	attribute :false_negatives
+	attribute :correct_predictions
+	attribute :weighted_area_under_roc
+	attribute :sensitivity
+	attribute :specificity
+	attribute :r_square
+	attribute :root_mean_squared_error
+	attribute :mean_absolute_error
+
+  attribute :web_uri
 
   attr_accessor :subjectid
   @subjectid = nil
 
-  after :save, :check_policy
+  #after :save, :check_policy
 
 =begin
+  attr_accessor :id, :name, :warnings, :error_messages, :type, :status, :created_at, :task_uri, :uri, :training_dataset, :feature_dataset, :validation_task_uri, :validation_uri, :validation_report_task_uri, :validation_report_uri, :validation_qmrf_task_uri, :validation_qmrf_uri, :nr_compounds, :nr_predictions, :true_positives, :false_positives, :true_negatives, :false_negatives, :correct_predictions, :weighted_area_under_roc, :sensitivity, :specificity, :r_square, :root_mean_squared_error, :mean_absolute_error, :web_uri
+
+  def self.all
+  end
+
+  def self.get(id)
+  end
+  
+  def self.create(params)
+    @id = @@redis.incr "toxcreate"
+    params.each { |k,v| @@redis.hset "toxcreate:#{@id}", k, v }
+    self.get(@id)
+  end
+
+  def update(params)
+  end
+
+  def method_missing
+    begin
+    rescue
+      raise "Unknown method"
+    end
+  end
+
+  attr_accessor :subjectid
+  @subjectid = nil
+
+  after :save, :check_policy
+
 def status
 		#begin
 			RestClient.get(File.join(@task_uri, 'hasStatus')).body
@@ -195,4 +228,4 @@ def status
 
 end
 
-DataMapper.auto_upgrade!
+#DataMapper.auto_upgrade!
diff --git a/views/classification_validation.haml b/views/classification_validation.haml
index 94ba8f9..41362ba 100644
--- a/views/classification_validation.haml
+++ b/views/classification_validation.haml
@@ -1,17 +1,17 @@
 %dt Correct predictions:
 %dd
-	= sprintf("%.2f", model.correct_predictions) if model.correct_predictions
+	= sprintf("%.2f", model.correct_predictions.to_f) if model.correct_predictions
 	= '%'
 %dt
 	%a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :target => "_blank"} Weighted area under ROC:
 %dd 
-	= sprintf("%.3f", model.weighted_area_under_roc) if model.weighted_area_under_roc
+	= sprintf("%.3f", model.weighted_area_under_roc.to_f) if model.weighted_area_under_roc
 %dt
 	%a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :target => "_blank"} Specificity:
-%dd= sprintf("%.3f", model.specificity) if model.specificity
+%dd= sprintf("%.3f", model.specificity.to_f) if model.specificity
 %dt
 	%a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :target => "_blank"} Sensitivity:
-%dd= sprintf("%.3f", model.sensitivity) if model.sensitivity
+%dd= sprintf("%.3f", model.sensitivity.to_f) if model.sensitivity
 %dt
 	%a{:href => "http://en.wikipedia.org/wiki/Confusion_matrix", :target => "_blank"} Confusion Matrix:
 %dd
diff --git a/views/model.haml b/views/model.haml
index 8112dd6..e1bdd99 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -35,8 +35,8 @@
         %span
           %br
         
-      %dt Started:
-      %dd= model.created_at.strftime("%m/%d/%Y - %I:%M:%S%p")
+      -#%dt Started:
+      -#%dd= model.created_at.strftime("%m/%d/%Y - %I:%M:%S%p")
       - if model.nr_compounds
         %dt Training compounds:
         %dd= model.nr_compounds