Activating property calculation for regression

2 files changed, 32 insertions, 17 deletions

diff --git a/fminer.rb b/fminer.rb
index 9242f9f..3554dbb 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -21,7 +21,7 @@ get '/fminer/?' do
 end
 
 post '/fminer/?' do
-
+    
 	halt 404, "Please submit a dataset_uri." unless params[:dataset_uri] and  !params[:dataset_uri].nil?
 	halt 404, "Please submit a feature_uri." unless params[:feature_uri] and  !params[:feature_uri].nil?
 	LOGGER.debug "Dataset: " + params[:dataset_uri]
@@ -48,9 +48,10 @@ post '/fminer/?' do
 		id = 1 # fminer start id is not 0
 		compounds = []
 
+        g_hash = Hash.new# DV: for effect calculation in regression part
 		@@fminer.Reset
 		LOGGER.debug "Fminer: initialising ..."
-		training_dataset.data.each do |c,features|
+        training_dataset.data.each do |c,features|
 			begin
 				smiles = OpenTox::Compound.new(:uri => c.to_s).smiles
 			rescue
@@ -82,6 +83,7 @@ post '/fminer/?' do
 						begin
 							@@fminer.AddCompound(smiles,id)
 							@@fminer.AddActivity(activity, id)
+                            g_hash[id]=activity # DV: insert global information
 						rescue
 							LOGGER.warn "Could not add " + smiles + "\t" + act.to_s + " to fminer"
 						end
@@ -90,6 +92,8 @@ post '/fminer/?' do
 				id += 1
 			end
 		end
+        g_array=g_hash.values # DV: calculation of global median for effect calculation
+        g_median=OpenTox::Utils.median(g_array)
 		minfreq = (0.06*id).round
 		@@fminer.SetMinfreq(minfreq)
 		LOGGER.debug "Fminer: initialised with #{id} compounds, minimum frequency #{minfreq}"
@@ -113,9 +117,19 @@ post '/fminer/?' do
 					else
 						effect = 'deactivating'
 					end
-				else
+				else #regression part
 					ids = f[2]
-					effect = 'activating' # AM: Pending: needs analysis of median act
+                    # DV: effect calculation
+                    f_arr=Array.new
+                    f[2].each do |id|
+                        f_arr.push(g_hash[id]) 
+                    end 
+                    f_median=OpenTox::Utils.median(f_arr)
+                    if g_median >= f_median 
+						effect = 'activating'
+					else
+						effect = 'deactivating'
+                    end
 				end
 
 				tuple = {
diff --git a/similarity.rb b/similarity.rb
index 672c03b..060bd2b 100644
--- a/similarity.rb
+++ b/similarity.rb
@@ -1,25 +1,26 @@
 require File.join(File.dirname(__FILE__),'dataset.rb')
 
 helpers do
-	def find
-		# + charges are dropped
-		uri = uri(params[:splat].first.gsub(/(InChI.*) (.*)/,'\1+\2')) # reinsert dropped '+' signs in InChIs
-		halt 404, "Dataset \"#{uri}\" not found." unless @set = Dataset.find(uri)
-	end
+def find
+# + charges are dropped
+uri = uri(params[:splat].first.gsub(/(InChI.*) (.*)/,'\1+\2')) # reinsert dropped '+' signs in InChIs
+halt 404, "Dataset \"#{uri}\" not found." unless @set = Dataset.find(uri)
+end
 
-	def uri(name)
-		name = URI.encode(name)
-		uri = File.join Dataset.base_uri, name
-	end
+def uri(name)
+name = URI.encode(name)
+uri = File.join Dataset.base_uri, name
+end
 end
 
 get '/tanimoto/dataset/*/dataset/*/?' do
-	find
-	@set.tanimoto(uri(params[:splat][1]))
+find
+@set.tanimoto(uri(params[:splat][1]))
 end
 
 get '/weighted_tanimoto/dataset/*/dataset/*/?' do
-	find
-	@set.weighted_tanimoto(uri(params[:splat][1]))
+find
+@set.weighted_tanimoto(uri(params[:splat][1]))
 end
 
+