Hotfix: p_value and SMARTS matching

1 files changed, 3 insertions, 4 deletions

diff --git a/fminer.rb b/fminer.rb
index d706063..e0a0054 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -288,7 +288,7 @@ post '/fminer/last/?' do
     smi = [] # AM LAST: needed for matching the patterns back
     nr_active=0
     nr_inactive=0
-    all_activities = Hash.new# DV: for effect calculation in regression part
+    all_activities = Hash.new #DV: for effect calculation (class and regr)
 
     training_dataset.data_entries.each do |compound,entry|
       begin
@@ -332,6 +332,7 @@ post '/fminer/last/?' do
                 @@last.AddActivity(activity, id)
                 all_activities[id]=activity # DV: insert global information
                 compounds[id] = compound
+		smi[id] = smiles # AM LAST: changed this to store SMILES.
                 id += 1
               rescue
                 LOGGER.warn "Could not add " + smiles + "\t" + value.to_s + " to fminer"
@@ -342,8 +343,6 @@ post '/fminer/last/?' do
       end
     end
 
-    g_array=all_activities.values # DV: calculation of global median for effect calculation
-    g_median=OpenTox::Algorithm.median(g_array)
     
     raise "No compounds in dataset #{training_dataset.uri}" if compounds.size==0
 
@@ -375,7 +374,7 @@ post '/fminer/last/?' do
           RDF.type => [OT.Substructure],
           OT.hasSource => feature_dataset.uri,
           OT.smarts => smarts,
-          OT.pValue => p_value.to_f,
+          OT.pValue => p_value.to_f.abs,
           OT.effect => effect,
           OT.parameters => [
             { DC.title => "dataset_uri", OT.paramValue => params[:dataset_uri] },