fminer.rb

1 files changed, 55 insertions, 28 deletions

diff --git a/fminer.rb b/fminer.rb
index 79b0d06..b9c8b5b 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -70,8 +70,7 @@ post '/fminer/bbrc/?' do
 
   halt 404, "Please submit a dataset_uri." unless params[:dataset_uri] and  !params[:dataset_uri].nil?
   halt 404, "Please submit a prediction_feature." unless params[:prediction_feature] and  !params[:prediction_feature].nil?
-  prediction_feature = params[:prediction_feature]
-
+  prediction_feature = OpenTox::Feature.find params[:prediction_feature], @subjectid
   training_dataset = OpenTox::Dataset.find "#{params[:dataset_uri]}", @subjectid
   halt 404, "No feature #{params[:prediction_feature]} in dataset #{params[:dataset_uri]}" unless training_dataset.features and training_dataset.features.include?(params[:prediction_feature])
 
@@ -89,8 +88,13 @@ post '/fminer/bbrc/?' do
     @@bbrc.SetMinfreq(minfreq)
     @@bbrc.SetType(1) if params[:feature_type] == "paths"
     @@bbrc.SetBackbone(eval params[:backbone]) if params[:backbone] and ( params[:backbone] == "true" or params[:backbone] == "false" ) # convert string to boolean
-    @@bbrc.SetChisqSig(params[:min_chisq_significance]) if params[:min_chisq_significance]
+    @@bbrc.SetChisqSig(params[:min_chisq_significance].to_f) if params[:min_chisq_significance]
     @@bbrc.SetConsoleOut(false)
+    if prediction_feature.feature_type == "regression"
+      @@bbrc.SetRegression(true)
+    else
+      @training_classes = training_dataset.feature_classes(prediction_feature.uri, @subjectid)
+    end
 
     feature_dataset = OpenTox::Dataset.new(nil, @subjectid)
     feature_dataset.add_metadata({
@@ -122,21 +126,30 @@ post '/fminer/bbrc/?' do
         next
       end
       entry.each do |feature,values|
-        if feature == prediction_feature
+        if feature == prediction_feature.uri
           values.each do |value|
             if value.nil? 
               LOGGER.warn "No #{feature} activiity for #{compound.to_s}."
             else
-              case value.to_s
-              when "true"
-                nr_active += 1
-                activity = 1
-              when "false"
-                nr_inactive += 1
-                activity = 0
-              else
-                activity = value.to_f
-                @@bbrc.SetRegression(true)
+              if prediction_feature.feature_type == "classification"
+                case value.to_s
+                when "true"
+                  nr_active += 1
+                  activity = 1
+                when "false"
+                  nr_inactive += 1
+                  activity = 0
+                when /#{@training_classes.last}/
+                  nr_active += 1
+                  activity = 1
+                when /#{@training_classes.first}/
+                  nr_inactive += 1
+                  activity = 0
+                else
+                  LOGGER.warn "Unknown class \"#{value.to_s}\"."
+                end
+              elsif prediction_feature.feature_type == "regression"
+                activity = Math.log10(value.to_f)
               end
               begin
                 @@bbrc.AddCompound(smiles,id)
@@ -232,7 +245,7 @@ post '/fminer/last/?' do
 
   halt 404, "Please submit a dataset_uri." unless params[:dataset_uri] and  !params[:dataset_uri].nil?
   halt 404, "Please submit a prediction_feature." unless params[:prediction_feature] and  !params[:prediction_feature].nil?
-  prediction_feature = params[:prediction_feature]
+  prediction_feature = OpenTox::Feature.find params[:prediction_feature], @subjectid
   training_dataset = OpenTox::Dataset.new "#{params[:dataset_uri]}", @subjectid
   training_dataset.load_all(@subjectid)
   halt 404, "No feature #{params[:prediction_feature]} in dataset #{params[:dataset_uri]}" unless training_dataset.features and training_dataset.features.include?(params[:prediction_feature])
@@ -252,8 +265,13 @@ post '/fminer/last/?' do
     @@last.SetType(1) if params[:feature_type] == "paths"
     @@last.SetMaxHops(params[:hops]) if params[:hops]
     @@last.SetConsoleOut(false)
+    if prediction_feature.feature_type == "regression"
+      @@last.SetRegression(true)
+    else
+      @training_classes = training_dataset.feature_classes(prediction_feature.uri)
+    end
 
-    feature_dataset = OpenTox::Dataset.new
+    feature_dataset = OpenTox::Dataset.new(nil, @subjectid)
     feature_dataset.add_metadata({
       DC.title => "LAST representatives for " + training_dataset.metadata[DC.title].to_s,
       DC.creator => url_for('/fminer/last',:full),
@@ -284,28 +302,37 @@ post '/fminer/last/?' do
         next
       end
       entry.each do |feature,values|
-        if feature == prediction_feature
+        if feature == prediction_feature.uri
           values.each do |value|
             if value.nil? 
               LOGGER.warn "No #{feature} activiity for #{compound.to_s}."
             else
-              case value.to_s
-              when "true"
-                nr_active += 1
-                activity = 1
-              when "false"
-                nr_inactive += 1
-                activity = 0
-              else
+              if prediction_feature.feature_type == "classification"
+                case value.to_s
+                when "true"
+                  nr_active += 1
+                  activity = 1
+                when "false"
+                  nr_inactive += 1
+                  activity = 0
+                when /#{@training_classes.last}/
+                  nr_active += 1
+                  activity = 1
+                when /#{@training_classes.first}/
+                  nr_inactive += 1
+                  activity = 0
+                else
+                  LOGGER.warn "Unknown class \"#{value.to_s}."
+                end
+              elsif prediction_feature.feature_type == "regression"
                 activity = value.to_f
-                @@last.SetRegression(true)
               end
               begin
                 @@last.AddCompound(smiles,id)
                 @@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.
+		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"
@@ -330,7 +357,7 @@ post '/fminer/last/?' do
     end
 
     lu = LU.new                             # AM LAST: uses last-utils here
-    dom=lu.read(xml)                        # AM LAST: parse GraphML (needs hpricot, @ch: to be included in wrapper!)
+    dom=lu.read(xml)                        # AM LAST: parse GraphML 
     smarts=lu.smarts_rb(dom,'nls')          # AM LAST: converts patterns to LAST-SMARTS using msa variant (see last-pm.maunz.de)
     instances=lu.match_rb(smi,smarts)       # AM LAST: creates instantiations
     instances.each do |smarts, ids|