working predictions for toxcreate

1 files changed, 13 insertions, 52 deletions

diff --git a/lazar.rb b/lazar.rb
index 3b8a0cf..8ad9fed 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -1,8 +1,3 @@
-# R integration
-# workaround to initialize R non-interactively (former rinruby versions did this by default)
-# avoids compiling R with X
-R = nil
-require "rinruby" 
 require "haml" 
 #require "lazar-helper"
 
@@ -36,23 +31,6 @@ get '/:id/?' do
 	end
 end
 
-=begin
-get '/:id/algorithm/?' do
-	response['Content-Type'] = 'text/plain'
-	YAML.load(ModelStore.get(params[:id]).yaml).algorithm
-end
-
-get '/:id/trainingDataset/?' do
-	response['Content-Type'] = 'text/plain'
-	YAML.load(ModelStore.get(params[:id]).yaml).trainingDataset
-end
-
-get '/:id/feature_dataset/?' do
-	response['Content-Type'] = 'text/plain'
-	YAML.load(ModelStore.get(params[:id]).yaml).feature_dataset_uri
-end
-=end
-
 # Store a lazar model. This method should not be called directly, use OpenTox::Algorithm::Lazr to create a lazar model
 # @param [Body] lazar Model representation in YAML format
 # @return [String] Model URI
@@ -71,47 +49,30 @@ end
 # @param [optional,String] dataset_uri URI of the dataset to be predicted
 # @param [optional,String] compound_uri URI of the compound to be predicted
 # @param [optional,Header] Accept Content-type of prediction, can be either `application/rdf+xml or application/x-yaml`
-# @return [text/uri-list,application/rdf+xml,application/x-yaml] URI of prediction task (dataset prediction) or prediction in requested representation
+# @return [text/uri-list] URI of prediction task (dataset prediction) or prediction dataset (compound prediction)
 post '/:id/?' do
 
-  start = Time.now
 	@lazar = YAML.load ModelStore.get(params[:id]).yaml
   
 	halt 404, "Model #{params[:id]} does not exist." unless @lazar
 	halt 404, "No compound_uri or dataset_uri parameter." unless compound_uri = params[:compound_uri] or dataset_uri = params[:dataset_uri]
 
-  s = Time.now
+  response['Content-Type'] = 'text/uri-list'
 	if compound_uri
-    #begin
-      @prediction = @lazar.predict(compound_uri,true) 
-    #rescue
-      #LOGGER.error "Lazar prediction failed for #{compound_uri} with #{$!} "
-      #halt 500, "Prediction of #{compound_uri} with #{@lazar.uri} failed."
-    #end
-    #accept = request.env['HTTP_ACCEPT']
-    #accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil?
-    LOGGER.debug "Total: #{Time.now - start} seconds"
-		#case accept
-		#when /yaml/ 
-			@prediction.uri
-    #else # RestClientWrapper does not send accept header
-		#when /application\/rdf\+xml/
-			#@prediction.to_rdfxml
-    #else
-      #halt 400, "MIME type \"#{request.env['HTTP_ACCEPT']}\" not supported." 
-		#end
+    begin
+      cache = PredictionCache.first(:model_uri => @lazar.uri, :compound_uri => compound_uri)
+      return cache.dataset_uri if cache
+      prediction_uri = @lazar.predict(compound_uri,true).uri
+      PredictionCache.create(:model_uri => @lazar.uri, :compound_uri => compound_uri, :dataset_uri => prediction_uri)
+      prediction_uri
+    rescue
+      LOGGER.error "Lazar prediction failed for #{compound_uri} with #{$!} "
+      halt 500, "Prediction of #{compound_uri} with #{@lazar.uri} failed."
+    end
 
 	elsif dataset_uri
-    response['Content-Type'] = 'text/uri-list'
 		task_uri = OpenTox::Task.as_task("Predict dataset",url_for("/#{lazar.id}", :full)) do
-			OpenTox::Dataset.find(dataset_uri).compounds.each do |compound_uri|
-				#begin
-          predict(compound_uri,true) 
-				#rescue
-					#LOGGER.error "#{prediction_type} failed for #{compound_uri} with #{$!} "
-				#end
-			end
-      @prediction.save
+      @lazar.predict(dataset_uri).uri
 	  end
     halt 202,task_uri
 	end