major change: using literal datatypes in owl

1 files changed, 31 insertions, 9 deletions

diff --git a/lib/model.rb b/lib/model.rb
index dfd5886..684873b 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -3,13 +3,22 @@ module OpenTox
 
 		class Generic
 
-			attr_accessor :uri, :title, :creator, :date, :format, :predictedVariables, :independentVariables, :dependentVariables, :trainingDataset, :feature_dataset_uri, :effects, :activities, :p_values, :fingerprints, :features, :algorithm
+      MODEL_ATTRIBS = [:uri, :title, :creator, :date, :format, :predictedVariables, :independentVariables, :dependentVariables, :trainingDataset, :algorithm]
+      MODEL_ATTRIBS.each{ |a| attr_accessor(a) }
 
 			def self.find(uri)
 				owl = OpenTox::Owl.from_uri(uri, "Model")
         return self.new(owl)
       end
       
+      def self.to_rdf(model)
+        owl = OpenTox::Owl.create 'Model', model.uri
+        (MODEL_ATTRIBS - [:uri]).each do |a|
+          owl.set(a.to_s,model.send(a.to_s))
+        end
+        owl.rdf
+      end
+      
       protected
       def initialize(owl)
         [:date, :creator, :title, :format, :algorithm, :dependentVariables, 
@@ -17,9 +26,17 @@ module OpenTox
             self.send("#{a.to_s}=".to_sym, owl.get(a.to_s))
         end
         @uri = owl.uri 
-        RestClientWrapper.raise_uri_error "invalid model:\n"+
-          self.to_yaml+"\n",@uri.to_s unless (Utils.is_uri?(@uri) and 
-          @dependentVariables and @independentVariables and @predictedVariables) if ENV['RACK_ENV'] =~ /test|debug/
+        if ENV['RACK_ENV'] =~ /test|debug/
+          begin
+            raise "uri invalid" unless Utils.is_uri?(@uri)
+            raise "no algorithm" unless @algorithm and @algorithm.size>0
+            raise "no dependent variables" unless @dependentVariables and @dependentVariables.size>0 
+            raise "no indenpendent variables" unless @independentVariables
+            raise "no predicted variables" unless @predictedVariables and @predictedVariables.size>0
+          rescue => ex
+            RestClientWrapper.raise_uri_error "invalid model: '"+ex.message+"'\n"+self.to_yaml+"\n",@uri.to_s    
+          end
+        end
 			end
 	 end
   
@@ -35,6 +52,7 @@ module OpenTox
        
        LOGGER.debug "Build model, algorithm_uri:"+algorithm_uri.to_s+", algorithm_parms: "+algorithm_params.inspect.to_s
        uri = OpenTox::RestClientWrapper.post(algorithm_uri,algorithm_params).to_s
+       LOGGER.debug "Build model done: "+uri.to_s
        RestClientWrapper.raise_uri_error("Invalid build model result: '"+uri.to_s+"'", algorithm_uri, algorithm_params ) unless Utils.model_uri?(uri)
        return PredictionModel.find(uri)
      end
@@ -57,6 +75,8 @@ module OpenTox
          return false
        elsif @uri =~/ambit2/ and @title =~ /pKa/
          return false
+       elsif @uri =~/majority/
+         return @uri =~ /class/
        else
          raise "unknown model, uri:'"+@uri.to_s+"' title:'"+@title.to_s+"'"
        end
@@ -65,7 +85,9 @@ module OpenTox
   
    
 		class Lazar < Generic
-
+      
+      attr_accessor :feature_dataset_uri, :effects, :activities, :p_values, :fingerprints, :features
+      
 			def initialize
 				@source = "http://github.com/helma/opentox-model"
 				@algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
@@ -80,11 +102,11 @@ module OpenTox
 			def save
 				@features.uniq!
 			  resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-			  resource.post(self.to_yaml, :content_type => "application/x-yaml").chomp.to_s
+			  resource.post(self.to_yaml, :content_type => "text/x-yaml").chomp.to_s
 			end
 
 			def self.find_all
-				RestClient.get(@@config[:services]["opentox-model"]).chomp.split("\n")
+				RestClientWrapper.get(@@config[:services]["opentox-model"]).chomp.split("\n")
 			end
 =begin
 			
@@ -101,7 +123,7 @@ module OpenTox
 
 			def self.create(data)
 			  resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-			  resource.post(data, :content_type => "application/x-yaml").chomp.to_s
+			  resource.post(data, :content_type => "text/x-yaml").chomp.to_s
 			end
 
 			def delete
@@ -116,7 +138,7 @@ module OpenTox
 #			end
 
 #			def yaml=(data)
-#				RestClient.put(@@uri, data, :content_type => "application/x-yaml").to_s
+#				RestClient.put(@@uri, data, :content_type => "text/x-yaml").to_s
 #			end
 
 			def endpoint