resolved merge conflict

4 files changed, 28 insertions, 17 deletions

diff --git a/README b/README
index c4d3375..81c96e4 100644
--- a/README
+++ b/README
@@ -21,22 +21,22 @@ Supported MIME formats (http://chemical-mime.sourceforge.net/):
 Examples:
 
 List all lazar models
-  curl http://webservices.in-silico.ch/test/model
+  curl http://webservices.in-silico.ch/model
 
 Get the representation of a lazar model
-  curl -H "Accept:application/rdf+xml" http://webservices.in-silico.ch/test/model/{id}
+  curl -H "Accept:application/rdf+xml" http://webservices.in-silico.ch/model/{id}
 
 Predict a compound
-  curl -X POST -d compound_uri={compound_uri} http://webservices.in-silico.ch/test/model/{id}
+  curl -X POST -d compound_uri={compound_uri} http://webservices.in-silico.ch/model/{id}
 
 Predict a compound and get the result as YAML
-  curl -X POST -H "Accept:application/x-yaml" -d compound_uri={compound_uri} http://webservices.in-silico.ch/test/model/{id}
+  curl -X POST -H "Accept:application/x-yaml" -d compound_uri={compound_uri} http://webservices.in-silico.ch/model/{id}
 
 Predict a dataset
-  curl -X POST -d dataset_uri={dataset_uri} http://webservices.in-silico.ch/test/model/{id}
+  curl -X POST -d dataset_uri={dataset_uri} http://webservices.in-silico.ch/model/{id}
 
 Delete a model
-  curl -X DELETE http://webservices.in-silico.ch/test/model/{id}
+  curl -X DELETE http://webservices.in-silico.ch/model/{id}
 
 More documentation: Source code (application.rb, lazar.rb)
 
diff --git a/application.rb b/application.rb
index a04b60d..7538196 100644
--- a/application.rb
+++ b/application.rb
@@ -1,5 +1,5 @@
 require 'rubygems'
-gem 'opentox-ruby-api-wrapper', '= 1.4.4.4'
+gem "opentox-ruby-api-wrapper", "= 1.5.6"
 require 'opentox-ruby-api-wrapper'
 LOGGER.progname = File.expand_path(__FILE__)
 
diff --git a/lazar.rb b/lazar.rb
index 9880292..d4d6235 100755
--- a/lazar.rb
+++ b/lazar.rb
@@ -3,8 +3,6 @@ class Lazar < Model
 	attr_accessor :prediction_dataset
 
 	def classify(compound_uri,prediction)
-   
-		prediction.title += " lazar classification"
     
 		lazar = YAML.load self.yaml
 		compound = OpenTox::Compound.new(:uri => compound_uri)
@@ -46,6 +44,11 @@ class Lazar < Model
 					:confidence => conf,
 					:similarities => similarities,
 					:features => compound_matches
+					# uncomment to enable owl-dl serialisation of predictions
+					# url_for("/lazar#classification") => classification,
+					# url_for("/lazar#confidence") => conf,
+					# url_for("/lazar#similarities") => similarities,
+					# url_for("/lazar#features") => compound_matches
 			}
 			prediction.data[compound_uri] << {feature_uri => tuple}
 		end
@@ -57,16 +60,17 @@ class Lazar < Model
 		lazar = YAML.load self.yaml
 		db_activities = lazar.activities[compound_uri]
 		if db_activities
-			prediction.source = lazar.trainingDataset
+			prediction.creator = lazar.trainingDataset
 			feature_uri = lazar.dependentVariables
 			prediction.compounds << compound_uri
 			prediction.features << feature_uri
 			prediction.data[compound_uri] = [] unless prediction.data[compound_uri]
 			db_activities.each do |act|
-        tuple = { 
-          :classification => act,
-          :confidence => 1}
-				prediction.data[compound_uri] << {feature_uri => tuple}
+				prediction.data[compound_uri] << {feature_uri => act}
+        #tuple = { 
+        #  :classification => act}
+          #:confidence => "experimental"}
+				#prediction.data[compound_uri] << {feature_uri => tuple}
 			end
 			true
 		else
@@ -136,9 +140,9 @@ get '/:id/algorithm/?' do
 	YAML.load(Lazar.get(params[:id]).yaml).algorithm
 end
 
-get '/:id/training_dataset/?' do
+get '/:id/trainingDataset/?' do
 	response['Content-Type'] = 'text/plain'
-	YAML.load(Lazar.get(params[:id]).yaml).activity_dataset_uri
+	YAML.load(Lazar.get(params[:id]).yaml).trainingDataset
 end
 
 get '/:id/feature_dataset/?' do
@@ -165,6 +169,7 @@ post '/:id/?' do # create prediction
 	prediction = OpenTox::Dataset.new 
 	prediction.creator = lazar.uri
 	prediction.title = URI.decode YAML.load(lazar.yaml).dependentVariables.split(/#/).last
+	prediction.title += " lazar classification"
 
 	if compound_uri
 		lazar.classify(compound_uri,prediction) unless lazar.database_activity?(compound_uri,prediction) 
@@ -185,7 +190,11 @@ elsif dataset_uri
 			input_dataset.compounds.each do |compound_uri|
 				lazar.classify(compound_uri,prediction) unless lazar.database_activity?(compound_uri,prediction)
 			end
-			uri = prediction.save.chomp
+			begin
+				uri = prediction.save.chomp
+			rescue
+				halt 500, "Could not save prediction dataset"
+			end
 	  end
     halt 202,task_uri
 	end
diff --git a/public/robots.txt b/public/robots.txt
new file mode 100644
index 0000000..1f53798
--- /dev/null
+++ b/public/robots.txt
@@ -0,0 +1,2 @@
+User-agent: *
+Disallow: /