Merge remote branch 'helma/master' into development

1 files changed, 95 insertions, 18 deletions

diff --git a/lazar.rb b/lazar.rb
index db29399..64175be 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -1,21 +1,17 @@
 get '/lazar/?' do
-	if File.exists?('public/lazar.owl')
-		rdf = File.read('public/lazar.owl')
-	else
-		owl = OpenTox::Owl.create 'Algorithm', url_for('/lazar',:full)
-		owl.set 'title',"lazar"
-		owl.set 'creator',"http://github.com/helma/opentox-algorithm"
-		owl.parameters = {
-			"Dataset URI" =>
-				{ :scope => "mandatory", :value => "dataset_uri" },
-			"Feature URI for dependent variable" =>
-				{ :scope => "mandatory", :value => "prediction_feature" },
-			"Feature generation URI" =>
-				{ :scope => "mandatory", :value => "feature_generation_uri" }
-		}
-		rdf = owl.rdf
-		File.open('public/lazar.owl', 'w') {|f| f.print rdf}
-	end
+  owl = OpenTox::Owl.create 'Algorithm', url_for('/lazar',:full)
+  owl.set 'title',"lazar"
+  owl.set 'creator',"http://github.com/helma/opentox-algorithm"
+  owl.parameters = {
+    "Dataset URI" =>
+      { :scope => "mandatory", :value => "dataset_uri" },
+    "Feature URI for dependent variable" =>
+      { :scope => "mandatory", :value => "prediction_feature" },
+    "Feature generation URI" =>
+      { :scope => "mandatory", :value => "feature_generation_uri" }
+  }
+  rdf = owl.rdf
+  File.open('public/lazar.owl', 'w') {|f| f.print rdf}
 	response['Content-Type'] = 'application/rdf+xml'
 	rdf
 end
@@ -40,7 +36,7 @@ post '/lazar/?' do # create a model
     training_activities.features.inspect+")" unless training_activities.features and training_activities.features.include?(params[:prediction_feature])
 
   response['Content-Type'] = 'text/uri-list' 
-  task_uri = OpenTox::Task.as_task do |task|
+  task_uri = OpenTox::Task.as_task("Create lazar model",url_for('/lazar',:full)) do |task|
 
 		# create features
 		LOGGER.debug "Starting fminer"
@@ -115,3 +111,84 @@ post '/lazar/?' do # create a model
 	end
   halt 202,task_uri
 end
+
+post '/property_lazar/?' do # create a model
+
+	LOGGER.debug "Dataset: '" + params[:dataset_uri].to_s + "'"
+	LOGGER.debug "Endpoint: '" + params[:prediction_feature].to_s + "'"
+	LOGGER.debug "Feature dataset: '" + params[:feature_dataset_uri].to_s + "'"
+	dataset_uri = "#{params[:dataset_uri]}"
+
+	begin
+		training_activities = OpenTox::Dataset.find(dataset_uri)
+	rescue
+		halt 404, "Dataset #{dataset_uri} not found" 
+  end
+
+  halt 404, "No prediction_feature parameter." unless params[:prediction_feature]
+	halt 404, "No feature_dataset_uri parameter." unless params[:feature_dataset_uri]
+	halt 404, "No feature #{params[:prediction_feature]} in dataset #{params[:dataset_uri]}. (features: "+
+    training_activities.features.inspect+")" unless training_activities.features and training_activities.features.include?(params[:prediction_feature])
+
+  response['Content-Type'] = 'text/uri-list' 
+  task_uri = OpenTox::Task.as_task("Create lazar model",url_for('/property_lazar',:full)) do |task|
+
+		# create features
+		#LOGGER.debug "Starting fminer"
+    #params[:feature_uri] = params[:prediction_feature]
+		#fminer_task_uri = OpenTox::Algorithm::Fminer.create_feature_dataset(params)
+		#fminer_task = OpenTox::Task.find(fminer_task_uri)
+		#fminer_task.wait_for_completion
+		#raise "fminer failed" unless fminer_task.completed?
+    
+		#LOGGER.debug "Fminer finished #{Time.now}"
+		feature_dataset_uri = params[:feature_dataset_uri]
+		training_features = OpenTox::Dataset.find(feature_dataset_uri)
+		halt 404, "Dataset #{feature_dataset_uri} not found." if training_features.nil?
+		lazar = OpenTox::Model::PropertyLazar.new
+		lazar.trainingDataset = dataset_uri
+		lazar.feature_dataset_uri = feature_dataset_uri
+		#halt 404, "More than one descriptor type" unless training_features.features.size == 1
+    lazar.features = training_features.features
+		training_features.data.each do |compound,features|
+			lazar.properties[compound] = {} unless lazar.properties[compound]
+      LOGGER.debug features.inspect
+      if features
+      features.each do |f|
+        f.each do |name,value|
+			#lazar.features.each do |feature|
+          lazar.properties[compound][name] = value
+        #lazar.properties[compound] = features
+        end
+      end
+      end
+    end
+
+		activities = {}
+		classification = true
+		training_activities.data.each do |compound,features|
+			lazar.activities[compound] = [] unless lazar.activities[compound]
+			features.each do |feature|
+				case feature[params[:prediction_feature]].to_s
+				when "true"
+					lazar.activities[compound] << true
+				when "false"
+					lazar.activities[compound] << false
+				else 
+					lazar.activities[compound] << feature[params[:prediction_feature]].to_f
+					classification = false
+				end
+			end
+		end
+		if classification
+			lazar.dependentVariables = params[:prediction_feature]+"_lazar_classification"
+		else
+			lazar.dependentVariables = params[:prediction_feature]+"_lazar_regression"
+		end
+		
+		model_uri = lazar.save
+		LOGGER.info model_uri + " created #{Time.now}"
+    model_uri
+	end
+  halt 202,task_uri
+end