owl-dl (temporarily) removed, switched to YAML representation

2 files changed, 27 insertions, 45 deletions

diff --git a/application.rb b/application.rb
index 641c28d..9c50383 100644
--- a/application.rb
+++ b/application.rb
@@ -1,6 +1,7 @@
 require 'rubygems'
 gem 'opentox-ruby-api-wrapper', '= 1.3.1'
 require 'opentox-ruby-api-wrapper'
+LOGGER.progname = File.expand_path(__FILE__)
 
 class Model
 	include DataMapper::Resource
diff --git a/lazar.rb b/lazar.rb
index 9014d3b..8966527 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -4,24 +4,25 @@ class Lazar < Model
 
 	def classify(compound_uri)
   
-    unless @dataset
-		  @dataset = OpenTox::Dataset.new
+    #unless @dataset
+		  #@dataset = OpenTox::Dataset.new
 		  @predictions = {}
-    end
-		lazar = YAML.load yaml
+    #end
+		lazar = YAML.load self.yaml
 		compound = OpenTox::Compound.new(:uri => compound_uri)
-		compound_matches = compound.match lazar[:features]
+		compound_matches = compound.match lazar.features
 
 		conf = 0.0
-		neighbors = []
+		similarities = {}
 		classification = nil
 
-		lazar[:fingerprints].each do |uri,matches|
+		lazar.fingerprints.each do |uri,matches|
 
-			sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(compound_matches,matches,lazar[:p_values])
-			if sim > 0.3
-				neighbors << uri
-				lazar[:activities][uri].each do |act|
+			sim = OpenTox::Algorithm::Similarity.weighted_tanimoto(compound_matches,matches,lazar.p_values)
+			LOGGER.debug sim
+			if sim > 0#.3
+				similarities[uri] = sim
+				lazar.activities[uri].each do |act|
 					case act.to_s
 					when 'true'
 						conf += OpenTox::Utils.gauss(sim)
@@ -32,23 +33,24 @@ class Lazar < Model
 			end
 		end
 	
-		conf = conf/neighbors.size
+		conf = conf/similarities.size
 		if conf > 0.0
 			classification = true
 		elsif conf < 0.0
 			classification = false
 		end
+		LOGGER.debug conf
 		
-		compound = @dataset.find_or_create_compound(compound_uri)
-		feature = @dataset.find_or_create_feature(lazar[:endpoint])
+		#compound = @dataset.compounds[compound_uri]
+		#feature = @dataset.features[lazar.endpoint]
 
 		if (classification != nil)
-			tuple = @dataset.create_tuple(feature,{ 'lazar#classification' => classification, 'lazar#confidence' => conf})
-			@dataset.add_tuple compound,tuple
-			@predictions[compound_uri] = { lazar[:endpoint] => { :lazar_prediction => {
+			#tuple = @dataset.create_tuple(feature,{ 'lazar#classification' => classification, 'lazar#confidence' => conf})
+			#@dataset.add_tuple compound,tuple
+			@predictions[compound_uri] = { lazar.dependent_variable => { :lazar_prediction => {
 					:classification => classification,
 					:confidence => conf,
-					:neighbors => neighbors,
+					:similarities => similarities,
 					:features => compound_matches
 				} } }
 		end
@@ -58,15 +60,9 @@ class Lazar < Model
 	def database_activity?(compound_uri)
 		# find database activities
 		lazar = YAML.load self.yaml
-		db_activities = lazar[:activities][compound_uri]
+		db_activities = lazar.activities[compound_uri]
 		if db_activities
-			@dataset = OpenTox::Dataset.new
-			@predictions = {}
-			c = @dataset.find_or_create_compound(compound_uri)
-			f = @dataset.find_or_create_feature(lazar[:endpoint])
-			v = db_activities.join(',')
-			@dataset.add c,f,v
-			@predictions[compound_uri] = { lazar[:endpoint] => {:measured_activities => db_activities}}
+			@predictions = {:compound_uri => { lazar.dependent_variable => {:measured_activities => db_activities}}}
 			true
 		else
 			false
@@ -76,27 +72,12 @@ class Lazar < Model
 end
 
 post '/?' do # create model
-	#model = Lazar.new(:task_uri => params[:task_uri])
-	#model.uri = url_for("/#{model.id}", :full)
+	halt 400, "MIME type \"#{request.content_type}\" not supported." unless request.content_type.match(/yaml/)
 	model = Lazar.new
 	model.save
 	model.uri = url_for("/#{model.id}", :full)
-#	model.uri
-#end
-#
-#put '/:id/?' do # create model from yaml representation
-#	model = Lazar.first(params[:id])
-	case request.content_type
-	when /yaml/
-		input =	request.env["rack.input"].read
-		model.yaml = input
-		lazar = OpenTox::Model::Lazar.from_yaml(input)
-		lazar.uri = model.uri
-		model.owl = lazar.rdf
-		model.save
-	else
-		halt 400, "MIME type \"#{request.content_type}\" not supported."
-	end
+	model.yaml =	request.env["rack.input"].read
+	model.save
 	model.uri
 end
 
@@ -107,7 +88,7 @@ post '/:id/?' do # create prediction
 	halt 404, "No compound_uri or dataset_uri parameter." unless compound_uri = params[:compound_uri] or dataset_uri = params[:dataset_uri]
 
 	if compound_uri
-		lazar.classify(compound_uri) unless lazar.database_activity?(compound_uri) # FEHLER
+		lazar.classify(compound_uri) unless lazar.database_activity?(compound_uri) 
 	elsif dataset_uri
 		input_dataset = OpenTox::Dataset.find(dataset_uri)
 		input_dataset.compounds.each do |compound_uri|