initial lazar version for quantitative descriptors

3 files changed, 109 insertions, 76 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index 2fde0eb..d7b57af 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -64,6 +64,18 @@ module OpenTox
           0.0
         end
       end
+      def self.euclidean(prop_a,prop_b)
+        common_properties = prop_a.keys & prop_b.keys
+        if common_properties.size > 1
+          dist_sum = 0
+          common_properties.each do |p|
+            dist_sum += (prop_a[p] - prop_b[p])**2
+          end
+          1/(1+Math.sqrt(dist_sum))
+        else
+          nil
+        end
+      end
     end
 
   end
diff --git a/lib/model.rb b/lib/model.rb
index e8f6048..1cc0825 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -1,13 +1,13 @@
 module OpenTox
-	module Model
+  module Model
 
-		class Generic
+    class Generic
 
       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")
+      def self.find(uri)
+        owl = OpenTox::Owl.from_uri(uri, "Model")
         return self.new(owl)
       end
       
@@ -36,78 +36,108 @@ module OpenTox
             RestClientWrapper.raise_uri_error "invalid model: '"+ex.message+"'\n"+self.to_yaml+"\n",@uri.to_s    
           end
         end
-			end
-	 end
+      end
+    end
   
-   class PredictionModel < Generic
+    class PredictionModel < Generic
+      
+      def self.build( algorithm_uri, algorithm_params )
+         
+        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
      
-     def self.build( algorithm_uri, algorithm_params )
-        
-       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
-    
-     def predict_dataset( dataset_uri )
-
-       LOGGER.debug "Predict dataset: "+dataset_uri.to_s+" with model "+@uri.to_s
-       uri = RestClientWrapper.post(@uri, {:accept => "text/uri-list", :dataset_uri=>dataset_uri})
-       RestClientWrapper.raise_uri_error("Prediciton result no dataset uri: "+uri.to_s, @uri, {:dataset_uri=>dataset_uri} ) unless Utils.dataset_uri?(uri)
-       uri
-     end
-    
-     def classification?
-       #HACK replace with request to ontology server
-       if @title =~ /(?i)classification/
-         return true
-       elsif @title =~ /(?i)regression/
-         return false
-       elsif @uri =~/ntua/ and @title =~ /mlr/
-         return false
-       elsif @uri =~/tu-muenchen/ and @title =~ /regression|M5P|GaussP/
-         return false
-       elsif @uri =~/ambit2/ and @title =~ /pKa/ || @title =~ /Regression|Caco/
-         return false
-       elsif @uri =~/majority/
-         return (@uri =~ /class/) != nil
-       else
-         raise "unknown model, uri:'"+@uri.to_s+"' title:'"+@title.to_s+"'"
-       end
-     end
-   end
-  
+      def predict_dataset( dataset_uri )
+ 
+        LOGGER.debug "Predict dataset: "+dataset_uri.to_s+" with model "+@uri.to_s
+        uri = RestClientWrapper.post(@uri, {:accept => "text/uri-list", :dataset_uri=>dataset_uri})
+        RestClientWrapper.raise_uri_error("Prediciton result no dataset uri: "+uri.to_s, @uri, {:dataset_uri=>dataset_uri} ) unless Utils.dataset_uri?(uri)
+        uri
+      end
+     
+      def classification?
+        #HACK replace with request to ontology server
+        if @title =~ /(?i)classification/
+          return true
+        elsif @title =~ /(?i)regression/
+          return false
+        elsif @uri =~/ntua/ and @title =~ /mlr/
+          return false
+        elsif @uri =~/tu-muenchen/ and @title =~ /regression|M5P|GaussP/
+          return false
+        elsif @uri =~/ambit2/ and @title =~ /pKa/ || @title =~ /Regression|Caco/
+          return false
+        elsif @uri =~/majority/
+          return (@uri =~ /class/) != nil
+        else
+          raise "unknown model, uri:'"+@uri.to_s+"' title:'"+@title.to_s+"'"
+        end
+      end
+    end
    
-		class Lazar < Generic
+    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")
-				#@independent_variables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative")
-				@features = []
-				@effects = {}
-				@activities = {}
-				@p_values = {}
-				@fingerprints = {}
-			end
+      def initialize
+        @source = "http://github.com/helma/opentox-model"
+        @algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
+        #@independent_variables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative")
+        @features = []
+        @effects = {}
+        @activities = {}
+        @p_values = {}
+        @fingerprints = {}
+      end
+
+      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
+      end
+
+      def self.find_all
+        RestClientWrapper.get(@@config[:services]["opentox-model"]).chomp.split("\n")
+      end
+
+      def self.predict(compound_uri,model_uri)
+        #RestClientWrapper.post(model_uri,{:compound_uri => compound_uri, :accept => 'application/x-yaml'})
+        `curl -X POST -d 'compound_uri=#{compound_uri}' -H 'Accept:application/x-yaml' #{model_uri}`
+      end
+    end
+   
+    class PropertyLazar < Generic
+      
+      attr_accessor :feature_dataset_uri, :properties, :features, :activities#, :effects, :p_values
+      
+      def initialize
+        @source = "http://github.com/helma/opentox-model"
+        @algorithm = File.join(@@config[:services]["opentox-algorithm"],"property_lazar")
+        #@independent_variables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative")
+        @features = []
+        #@effects = {}
+        @activities = {}
+        #@p_values = {}
+        @properties = {}
+      end
 
-			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
-			end
+      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
+      end
 
-			def self.find_all
-				RestClientWrapper.get(@@config[:services]["opentox-model"]).chomp.split("\n")
-			end
+      def self.find_all
+        RestClientWrapper.get(@@config[:services]["opentox-model"]).chomp.split("\n")
+      end
 
       def self.predict(compound_uri,model_uri)
         #RestClientWrapper.post(model_uri,{:compound_uri => compound_uri, :accept => 'application/x-yaml'})
-		`curl -X POST -d 'compound_uri=#{compound_uri}' -H 'Accept:application/x-yaml' #{model_uri}`
+        `curl -X POST -d 'compound_uri=#{compound_uri}' -H 'Accept:application/x-yaml' #{model_uri}`
       end
-		end
-	end
+    end
+  end
 end
diff --git a/lib/validation.rb b/lib/validation.rb
index bd38488..89a2a0c 100644
--- a/lib/validation.rb
+++ b/lib/validation.rb
@@ -4,16 +4,7 @@ module OpenTox
 		attr_accessor :uri
 
 		def initialize(params)
-			#resource = RestClient::Resource.new(params[:uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-			#@uri = resource.post(params).body
-			#LOGGER.debug "VALIDATION URI: " + @uri.to_s
-			call = "curl -X POST "
-			params.each do |k,v|
-				call += " -d "+k.to_s+"=\""+URI.encode(v.to_s)+"\"" unless k == :uri
-			end
-			call += " "+params[:uri]
-			LOGGER.debug call
-			@uri = `#{call}`
+      @uri = OpenTox::RestClientWrapper.post(File.join(@@config[:services]["opentox-validation"],"/crossvalidation"),params,nil,false)
 		end
 		
 		def self.crossvalidation(params)