trying to speed up bbrc parsing

11 files changed, 253 insertions, 204 deletions

diff --git a/Gemfile b/Gemfile
index 4e3c41b..e3002f8 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,4 +1,4 @@
 source "http://rubygems.org"
 gemspec
-gem 'opentox-server', :path => "../opentox-server"
+#gem 'opentox-server', :path => "../opentox-server"
 gem "opentox-client", :path => "../opentox-client"
diff --git a/algorithm.gemspec b/algorithm.gemspec
index 3bda834..c3119e6 100644
--- a/algorithm.gemspec
+++ b/algorithm.gemspec
@@ -13,11 +13,12 @@ Gem::Specification.new do |s|
 
   s.rubyforge_project = "algorithm"
 
-  s.files         = `git ls-files`.split("\n")
+  s.files         = ["lib/algorithm.rb"]
+  #s.files         = `git ls-files`.split("\n")
   s.required_ruby_version = '>= 1.9.2'
 
   # specify any dependencies here; for example:
-  s.add_runtime_dependency "opentox-server"
+  #s.add_runtime_dependency "opentox-server"
   s.add_runtime_dependency "opentox-client"
   s.add_runtime_dependency 'rinruby'#, "~>2.0.2"
   s.add_runtime_dependency 'nokogiri'#, "~>1.4.4"
diff --git a/fminer.rb b/fminer.rb
index b429250..bfc6879 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -107,178 +107,6 @@ module OpenTox
     end
     
     
-    # Run bbrc algorithm on dataset
-    #
-    # @param [String] dataset_uri URI of the training dataset
-    # @param [String] prediction_feature URI of the prediction feature (i.e. dependent variable)
-    # @param [optional] parameters BBRC parameters, accepted parameters are
-    #   - min_frequency  Minimum frequency (default 5)
-    #   - feature_type Feature type, can be 'paths' or 'trees' (default "trees")
-    #   - backbone BBRC classes, pass 'false' to switch off mining for BBRC representatives. (default "true")
-    #   - min_chisq_significance Significance threshold (between 0 and 1)
-    #   - nr_hits Set to "true" to get hit count instead of presence
-    #   - get_target Set to "true" to obtain target variable as feature
-    # @return [text/uri-list] Task URI
-    post '/fminer/bbrc/?' do
-    
-      @@fminer=OpenTox::Algorithm::Fminer.new(to('/fminer/bbrc',:full))
-      @@fminer.check_params(params,5)
-    
-      task = OpenTox::Task.run("Mining BBRC features", uri('/fminer/bbrc')) do |task|
-
-        time = Time.now
-
-        @@bbrc.Reset
-        if @@fminer.prediction_feature.feature_type == "regression"
-          @@bbrc.SetRegression(true) # AM: DO NOT MOVE DOWN! Must happen before the other Set... operations!
-        else
-          bad_request_error "No accept values for "\
-                            "dataset '#{@@fminer.training_dataset.uri}' and "\
-                            "feature '#{@@fminer.prediction_feature.uri}'" unless 
-                             @@fminer.prediction_feature.accept_values
-          value_map=@@fminer.prediction_feature.value_map
-        end
-        @@bbrc.SetMinfreq(@@fminer.minfreq)
-        @@bbrc.SetType(1) if params[:feature_type] == "paths"
-        @@bbrc.SetBackbone(false) if params[:backbone] == "false"
-        @@bbrc.SetChisqSig(params[:min_chisq_significance].to_f) if params[:min_chisq_significance]
-        @@bbrc.SetConsoleOut(false)
-
-        feature_dataset = OpenTox::Dataset.new
-        feature_dataset.metadata = {
-          RDF::DC.title => "BBRC representatives",
-          RDF::DC.creator => to('/fminer/bbrc',:full),
-          RDF::OT.hasSource => to('/fminer/bbrc', :full),
-        }
-        feature_dataset.parameters = [
-            { RDF::DC.title => "dataset_uri", RDF::OT.paramValue => params[:dataset_uri] },
-            { RDF::DC.title => "prediction_feature", RDF::OT.paramValue => params[:prediction_feature] },
-            { RDF::DC.title => "min_frequency", RDF::OT.paramValue => @@fminer.minfreq },
-            { RDF::DC.title => "nr_hits", RDF::OT.paramValue => (params[:nr_hits] == "true" ? "true" : "false") },
-            { RDF::DC.title => "backbone", RDF::OT.paramValue => (params[:backbone] == "false" ? "false" : "true") }
-        ]
-
-        @@fminer.compounds = []
-        @@fminer.db_class_sizes = Array.new # AM: effect
-        @@fminer.all_activities = Hash.new # DV: for effect calculation in regression part
-        @@fminer.smi = [] # AM LAST: needed for matching the patterns back
-  
-        # Add data to fminer
-        @@fminer.add_fminer_data(@@bbrc, value_map)
-        g_median=@@fminer.all_activities.values.to_scale.median
-
-        #task.progress 10
-        step_width = 80 / @@bbrc.GetNoRootNodes().to_f
-        features_smarts = Set.new
-        features = Array.new
-
-        puts "Setup: #{Time.now-time}"
-        time = Time.now
-        ftime = 0
-  
-        # run @@bbrc
-        
-        # prepare to receive results as hash { c => [ [f,v], ... ] }
-        fminer_results = {}
-
-        (0 .. @@bbrc.GetNoRootNodes()-1).each do |j|
-          results = @@bbrc.MineRoot(j)
-          #task.progress 10+step_width*(j+1)
-          results.each do |result|
-            f = YAML.load(result)[0]
-            smarts = f[0]
-            p_value = f[1]
-  
-            if (!@@bbrc.GetRegression)
-              id_arrs = f[2..-1].flatten
-              max = OpenTox::Algorithm::Fminer.effect(f[2..-1].reverse, @@fminer.db_class_sizes) # f needs reversal for bbrc
-              effect = max+1
-            else #regression part
-              id_arrs = f[2]
-              # DV: effect calculation
-              f_arr=Array.new
-              f[2].each do |id|
-                id=id.keys[0] # extract id from hit count hash
-                f_arr.push(@@fminer.all_activities[id])
-              end
-              f_median=f_arr.to_scale.median
-              if g_median >= f_median
-                effect = 'activating'
-              else
-                effect = 'deactivating'
-              end
-            end
-  
-            ft = Time.now
-            unless features_smarts.include? smarts
-              features_smarts << smarts
-              feature = OpenTox::Feature.find_or_create({
-                RDF::DC.title => smarts.dup,
-                RDF::OT.hasSource => to('/fminer/bbrc', :full),
-                RDF.type => [RDF::OT.Feature, RDF::OT.Substructure, RDF::OT.NumericFeature],
-                RDF::OT.smarts => smarts.dup,
-                RDF::OT.pValue => p_value.to_f.abs.round(5),
-                RDF::OT.effect => effect
-              })
-              features << feature
-            end
-            ftime += Time.now - ft
-
-            id_arrs.each { |id_count_hash|
-              id=id_count_hash.keys[0].to_i
-              count=id_count_hash.values[0].to_i
-              fminer_results[@@fminer.compounds[id]] || fminer_results[@@fminer.compounds[id]] = {}
-              if params[:nr_hits] == "true"
-                fminer_results[@@fminer.compounds[id]][feature.uri] = count
-              else
-                fminer_results[@@fminer.compounds[id]][feature.uri] = 1
-              end
-            }
-  
-          end # end of
-        end   # feature parsing
-
-
-        puts "Fminer: #{Time.now-time} (find/create Features: #{ftime})"
-        time = Time.now
-
-        fminer_compounds = @@fminer.training_dataset.compounds
-        prediction_feature_idx = @@fminer.training_dataset.features.collect{|f| f.uri}.index @@fminer.prediction_feature.uri
-        prediction_feature_all_acts = fminer_compounds.each_with_index.collect { |c,idx| 
-          @@fminer.training_dataset.data_entries[idx][prediction_feature_idx] 
-        }
-        fminer_noact_compounds = fminer_compounds - @@fminer.compounds
-
-        feature_dataset.features = features
-        feature_dataset.features = [ @@fminer.prediction_feature ] + feature_dataset.features if params[:get_target] == "true"
-        feature_dataset.compounds = fminer_compounds
-        fminer_compounds.each_with_index { |c,idx|
-          # TODO: reenable option
-          #if (params[:get_target] == "true")
-            #row = row + [ prediction_feature_all_acts[idx] ]
-          #end
-          features.each { |f|
-            v = fminer_results[c][f.uri] if fminer_results[c] 
-            unless fminer_noact_compounds.include? c
-              v = 0 if v.nil?
-            end
-            feature_dataset.add_data_entry c, f, v.to_i
-          }
-        }
-
-        puts "Prepare save: #{Time.now-time}"
-        time = Time.now
-        feature_dataset.put 
-
-        puts "Save: #{Time.now-time}"
-        feature_dataset.uri
-
-  
-      end
-      response['Content-Type'] = 'text/uri-list'
-      halt 202,task.uri
-    end
-    
    
 
 
diff --git a/java/CdkDescriptorInfo.class b/java/CdkDescriptorInfo.class
index 922c779..687d68c 100644
--- a/java/CdkDescriptorInfo.class
+++ b/java/CdkDescriptorInfo.class
diff --git a/java/CdkDescriptors.class b/java/CdkDescriptors.class
index 34b973f..9785405 100644
--- a/java/CdkDescriptors.class
+++ b/java/CdkDescriptors.class
diff --git a/java/JoelibDescriptorInfo.class b/java/JoelibDescriptorInfo.class
index 0ee67bf..c091e54 100644
--- a/java/JoelibDescriptorInfo.class
+++ b/java/JoelibDescriptorInfo.class
diff --git a/java/JoelibDescriptors.class b/java/JoelibDescriptors.class
index d88ac63..a49018d 100644
--- a/java/JoelibDescriptors.class
+++ b/java/JoelibDescriptors.class
diff --git a/lib/bbrc.rb b/lib/bbrc.rb
new file mode 100644
index 0000000..740a763
--- /dev/null
+++ b/lib/bbrc.rb
@@ -0,0 +1,183 @@
+ENV['FMINER_SMARTS'] = 'true'
+ENV['FMINER_NO_AROMATIC'] = 'true'
+ENV['FMINER_PVALUES'] = 'true'
+ENV['FMINER_SILENT'] = 'true'
+ENV['FMINER_NR_HITS'] = 'true'
+
+module OpenTox
+  module Algorithm
+    class Fminer
+      # Run bbrc algorithm on dataset
+      #
+      # @param [String] dataset_uri URI of the training dataset
+      # @param [String] prediction_feature URI of the prediction feature (i.e. dependent variable)
+      # @param [optional] parameters BBRC parameters, accepted parameters are
+      #   - min_frequency  Minimum frequency (default 5)
+      #   - feature_type Feature type, can be 'paths' or 'trees' (default "trees")
+      #   - backbone BBRC classes, pass 'false' to switch off mining for BBRC representatives. (default "true")
+      #   - min_chisq_significance Significance threshold (between 0 and 1)
+      #   - nr_hits Set to "true" to get hit count instead of presence
+      #   - get_target Set to "true" to obtain target variable as feature
+      # @return [text/uri-list] Task URI
+      def self.bbrc params
+        
+        @fminer=OpenTox::Algorithm::Fminer.new
+        @fminer.check_params(params,5)
+      
+        #task = OpenTox::Task.run("Mining BBRC features", __FILE__ ) do |task|
+
+          time = Time.now
+
+          @bbrc = Bbrc::Bbrc.new
+          @bbrc.Reset
+          if @fminer.prediction_feature.feature_type == "regression"
+            @bbrc.SetRegression(true) # AM: DO NOT MOVE DOWN! Must happen before the other Set... operations!
+          else
+            bad_request_error "No accept values for "\
+                              "dataset '#{@fminer.training_dataset.uri}' and "\
+                              "feature '#{@fminer.prediction_feature.uri}'" unless 
+                               @fminer.prediction_feature.accept_values
+            value_map=@fminer.prediction_feature.value_map
+          end
+          @bbrc.SetMinfreq(@fminer.minfreq)
+          @bbrc.SetType(1) if params[:feature_type] == "paths"
+          @bbrc.SetBackbone(false) if params[:backbone] == "false"
+          @bbrc.SetChisqSig(params[:min_chisq_significance].to_f) if params[:min_chisq_significance]
+          @bbrc.SetConsoleOut(false)
+
+          feature_dataset = OpenTox::Dataset.new
+          feature_dataset.title = "BBRC representatives"
+          feature_dataset.creator = __FILE__
+          feature_dataset.parameters = [
+              { "title" => "dataset_id", "paramValue" => params[:dataset].id },
+              { "title" => "prediction_feature", "paramValue" => params[:prediction_feature].id },
+              { "title" => "min_frequency", "paramValue" => @fminer.minfreq },
+              { "title" => "nr_hits", "paramValue" => (params[:nr_hits] == "true" ? "true" : "false") },
+              { "title" => "backbone", "paramValue" => (params[:backbone] == "false" ? "false" : "true") }
+          ] 
+
+          @fminer.compounds = []
+          @fminer.db_class_sizes = Array.new # AM: effect
+          @fminer.all_activities = Hash.new # DV: for effect calculation in regression part
+          @fminer.smi = [] # AM LAST: needed for matching the patterns back
+    
+          # Add data to fminer
+          @fminer.add_fminer_data(@bbrc, value_map)
+          g_median=@fminer.all_activities.values.to_scale.median
+
+          #task.progress 10
+          step_width = 80 / @bbrc.GetNoRootNodes().to_f
+          features_smarts = Set.new
+          features = Array.new
+
+          puts "Setup: #{Time.now-time}"
+          time = Time.now
+          ftime = 0
+    
+          # run @bbrc
+          
+          # prepare to receive results as hash { c => [ [f,v], ... ] }
+          fminer_results = {}
+
+          (0 .. @bbrc.GetNoRootNodes()-1).each do |j|
+            results = @bbrc.MineRoot(j)
+            #task.progress 10+step_width*(j+1)
+            results.each do |result|
+              f = YAML.load(result)[0]
+              smarts = f[0]
+              p_value = f[1]
+    
+              if (!@bbrc.GetRegression)
+                id_arrs = f[2..-1].flatten
+                max = OpenTox::Algorithm::Fminer.effect(f[2..-1].reverse, @fminer.db_class_sizes) # f needs reversal for bbrc
+                effect = max+1
+              else #regression part
+                id_arrs = f[2]
+                # DV: effect calculation
+                f_arr=Array.new
+                f[2].each do |id|
+                  id=id.keys[0] # extract id from hit count hash
+                  f_arr.push(@fminer.all_activities[id])
+                end
+                f_median=f_arr.to_scale.median
+                if g_median >= f_median
+                  effect = 'activating'
+                else
+                  effect = 'deactivating'
+                end
+              end
+    
+              ft = Time.now
+              unless features_smarts.include? smarts
+                features_smarts << smarts
+                feature = OpenTox::Feature.find_or_create_by({
+                  "title" => smarts.dup,
+                  "numeric" => true,
+                  "substructure" => true,
+                  "smarts" => smarts.dup,
+                  "pValue" => p_value.to_f.abs.round(5),
+                  "effect" => effect
+                })
+                features << feature
+              end
+              ftime += Time.now - ft
+
+              id_arrs.each { |id_count_hash|
+                id=id_count_hash.keys[0].to_i
+                count=id_count_hash.values[0].to_i
+                fminer_results[@fminer.compounds[id]] || fminer_results[@fminer.compounds[id]] = {}
+                if params[:nr_hits] == "true"
+                  fminer_results[@fminer.compounds[id]][feature] = count
+                else
+                  fminer_results[@fminer.compounds[id]][feature] = 1
+                end
+              }
+    
+            end # end of
+          end   # feature parsing
+
+
+          puts "Fminer: #{Time.now-time} (find/create Features: #{ftime})"
+          time = Time.now
+          puts JSON.pretty_generate(fminer_results)
+
+          fminer_compounds = @fminer.training_dataset.compounds
+          prediction_feature_idx = @fminer.training_dataset.features.index @fminer.prediction_feature
+          prediction_feature_all_acts = fminer_compounds.each_with_index.collect { |c,idx| 
+            @fminer.training_dataset.data_entries[idx][prediction_feature_idx] 
+          }
+          fminer_noact_compounds = fminer_compounds - @fminer.compounds
+
+          feature_dataset.features = features
+          feature_dataset.features = [ @fminer.prediction_feature ] + feature_dataset.features if params[:get_target] == "true"
+          feature_dataset.compounds = fminer_compounds
+          fminer_compounds.each_with_index { |c,idx|
+            # TODO: reenable option
+            #if (params[:get_target] == "true")
+              #row = row + [ prediction_feature_all_acts[idx] ]
+            #end
+            features.each { |f|
+              v = fminer_results[c][f.uri] if fminer_results[c] 
+              unless fminer_noact_compounds.include? c
+                v = 0 if v.nil?
+              end
+              feature_dataset.add_data_entry c, f, v.to_i
+            }
+          }
+
+          puts "Prepare save: #{Time.now-time}"
+          time = Time.now
+          feature_dataset.save
+
+          puts "Save: #{Time.now-time}"
+          feature_dataset
+
+    
+        end
+      #end
+    end
+  end
+end
+    
+
+
diff --git a/lib/descriptor.rb b/lib/descriptor.rb
index a8f5123..9a93b32 100644
--- a/lib/descriptor.rb
+++ b/lib/descriptor.rb
@@ -1,6 +1,8 @@
 require 'digest/md5'
 ENV["JAVA_HOME"] ||= "/usr/lib/jvm/java-7-openjdk" 
-BABEL_3D_CACHE_DIR = File.join(Dir.pwd,'/babel_3d_cache')
+BABEL_3D_CACHE_DIR = File.join(File.dirname(__FILE__),"..",'/babel_3d_cache')
+# TODO store 3D structures in mongodb
+# TODO store descriptors in mongodb
 
 module OpenTox
 
@@ -35,6 +37,7 @@ module OpenTox
 
       DESCRIPTORS = OBDESCRIPTORS.merge(CDKDESCRIPTORS.merge(JOELIBDESCRIPTORS))
       DESCRIPTOR_VALUES = OBDESCRIPTORS.keys + CDKDESCRIPTOR_VALUES + JOELIBDESCRIPTORS.keys
+
       require_relative "unique_descriptors.rb"
 
       def self.description descriptor
@@ -53,6 +56,7 @@ module OpenTox
       end
 
       def self.smarts_match compounds, smarts, count=false
+        compounds = parse compounds
         obconversion = OpenBabel::OBConversion.new
         obmol = OpenBabel::OBMol.new
         obconversion.set_in_format('inchi')
@@ -80,7 +84,8 @@ module OpenTox
         smarts_match compounds,smarts,true
       end
 
-      def self.physchem compounds, descriptors
+      def self.physchem compounds, descriptors=UNIQUEDESCRIPTORS
+        compounds = parse compounds
         des = {}
         descriptors.each do |d|
           lib, descriptor = d.split(".",2)
@@ -99,6 +104,7 @@ module OpenTox
       end
 
       def self.openbabel compounds, descriptors
+        compounds = parse compounds
         $logger.debug "compute #{descriptors.size} openbabel descriptors for #{compounds.size} compounds"
         obdescriptors = descriptors.collect{|d| OpenBabel::OBDescriptor.find_type d}
         obmol = OpenBabel::OBMol.new
@@ -115,19 +121,8 @@ module OpenTox
         fingerprint
       end
 
-      def self.run_cmd cmd
-        cmd = "#{cmd} 2>&1"
-        $logger.debug "running external cmd: '#{cmd}'"
-        p = IO.popen(cmd) do |io|
-          while line = io.gets
-            $logger.debug "> #{line.chomp}"
-          end
-          io.close
-          raise "external cmd failed '#{cmd}' (see log file for error msg)" unless $?.to_i == 0
-        end
-      end
-
       def self.cdk compounds, descriptors
+        compounds = parse compounds
         $logger.debug "compute #{descriptors.size} cdk descriptors for #{compounds.size} compounds"
         sdf = sdf_3d compounds
         # use java system call (rjb blocks within tasks)
@@ -135,7 +130,7 @@ module OpenTox
         run_cmd "java -classpath #{CDK_JAR}:#{JAVA_DIR}  CdkDescriptors #{sdf} #{descriptors.join(" ")}"
         fingerprint = {}
         YAML.load_file(sdf+"cdk.yaml").each_with_index do |calculation,i|
-          $logger.error "Descriptor calculation failed for compound #{compounds[i].uri}." if calculation.empty?
+          $logger.error "Descriptor calculation failed for compound #{compounds[i].inchi}." if calculation.empty?
           descriptors.each do |descriptor|
             fingerprint[compounds[i]] = calculation
           end
@@ -145,6 +140,7 @@ module OpenTox
       end
 
       def self.joelib compounds, descriptors
+        compounds = parse compounds
         $logger.debug "compute #{descriptors.size} joelib descriptors for #{compounds.size} compounds"
         # use java system call (rjb blocks within tasks)
         # use Tempfiles to avoid "Argument list too long" error 
@@ -152,7 +148,7 @@ module OpenTox
         run_cmd "java -classpath #{JOELIB_JAR}:#{JMOL_JAR}:#{LOG4J_JAR}:#{JAVA_DIR}  JoelibDescriptors  #{sdf} #{descriptors.join(' ')}"
         fingerprint = {}
         YAML.load_file(sdf+"joelib.yaml").each_with_index do |calculation,i|
-          $logger.error "Descriptor calculation failed for compound #{compounds[i].uri}." if calculation.empty?
+          $logger.error "Descriptor calculation failed for compound #{compounds[i].inchi}." if calculation.empty?
           descriptors.each do |descriptor|
             fingerprint[compounds[i]] = calculation
           end
@@ -162,6 +158,7 @@ module OpenTox
       end
 
       def self.lookup compounds, features, dataset
+        compounds = parse compounds
         fingerprint = []
         compounds.each do |compound|
           fingerprint << []
@@ -170,13 +167,26 @@ module OpenTox
         end
       end
 
+      def self.run_cmd cmd
+        cmd = "#{cmd} 2>&1"
+        $logger.debug "running external cmd: '#{cmd}'"
+        p = IO.popen(cmd) do |io|
+          while line = io.gets
+            $logger.debug "> #{line.chomp}"
+          end
+          io.close
+          raise "external cmd failed '#{cmd}' (see log file for error msg)" unless $?.to_i == 0
+        end
+      end
+
       def self.sdf_3d compounds
+        compounds = parse compounds
         obconversion = OpenBabel::OBConversion.new
         obmol = OpenBabel::OBMol.new
         obconversion.set_in_format 'inchi' 
         obconversion.set_out_format 'sdf'
 
-        digest = Digest::MD5.hexdigest compounds.collect{|c| c.uri}.inspect
+        digest = Digest::MD5.hexdigest compounds.collect{|c| c.inchi}.inspect
         sdf_file = "/tmp/#{digest}.sdf"
         if File.exists? sdf_file # do not recreate existing 3d sdfs
           $logger.debug "re-using cached 3d structures from #{sdf_file}"
@@ -200,11 +210,11 @@ module OpenTox
               sdf_2d = obconversion.write_string(obmol)  
               error = nil
               if compound.inchi.include?(";") # component includes multiple compounds (; in inchi, . in smiles)
-                error = "OpenBabel 3D generation failes for multi-compound #{compound.uri}, trying to calculate descriptors from 2D structure."
+                error = "OpenBabel 3D generation failes for multi-compound #{compound.inchi}, trying to calculate descriptors from 2D structure."
               else
                 OpenBabel::OBOp.find_type("Gen3D").do(obmol) 
                 sdf_3d = obconversion.write_string(obmol)  
-                error = "3D generation failed for compound #{compound.uri}, trying to calculate descriptors from 2D structure." if sdf_3d.match(/.nan/)
+                error = "3D generation failed for compound #{compound.inchi}, trying to calculate descriptors from 2D structure." if sdf_3d.match(/.nan/)
               end
               if error
                 $logger.warn error
@@ -226,6 +236,19 @@ module OpenTox
         sdf_file
       end
 
+      def self.parse compounds
+        case compounds.class.to_s
+        when "OpenTox::Compound"
+          compounds = [compounds]
+        when "Array"
+          compounds
+        when "OpenTox::Dataset"
+          compounds = compounds.compounds
+        else
+          bad_request_error "Cannot calculate descriptors for #{compounds.class} objects."
+        end
+      end
+
       def self.fix_value val
         val = val.first if val.is_a? Array and val.size == 1
         if val.numeric?
@@ -236,7 +259,7 @@ module OpenTox
         end
         val
       end
-      private_class_method :sdf_3d, :fix_value
+      private_class_method :sdf_3d, :fix_value, :parse, :run_cmd
     end
   end
 end
diff --git a/lib/fminer.rb b/lib/fminer.rb
index 8023bdd..3333517 100644
--- a/lib/fminer.rb
+++ b/lib/fminer.rb
@@ -1,3 +1,4 @@
+require_relative 'bbrc'
 =begin
 * Name: fminer.rb
 * Description: Fminer library 
@@ -10,6 +11,7 @@ module OpenTox
 
     # Fminer algorithms (https://github.com/amaunz/fminer2)
     class Fminer 
+      include OpenTox
       
       attr_accessor :prediction_feature, :training_dataset, :minfreq, :compounds, :db_class_sizes, :all_activities, :smi
 
@@ -19,15 +21,16 @@ module OpenTox
       # @param[Integer] per-mil value for min frequency
       
       def check_params(params,per_mil)
-        bad_request_error "Please submit a dataset_uri." unless params[:dataset_uri] and  !params[:dataset_uri].nil?
-        @training_dataset = OpenTox::Dataset.new "#{params[:dataset_uri]}"
+        bad_request_error "Please submit a dataset." unless params[:dataset] and  !params[:dataset].nil?
+        @training_dataset = OpenTox::Dataset.new 
+        @training_dataset = params[:dataset]
         unless params[:prediction_feature] # try to read prediction_feature from dataset
           resource_not_found_error "Please provide a prediction_feature parameter" unless @training_dataset.features.size == 1
-          params[:prediction_feature] = @training_dataset.features.first.uri
+          params[:prediction_feature] = @training_dataset.features.first
         end
-        @prediction_feature = OpenTox::Feature.find params[:prediction_feature]
-        resource_not_found_error "No feature '#{params[:prediction_feature]}' in dataset '#{params[:dataset_uri]}'" unless 
-          @training_dataset.find_feature_uri( params[:prediction_feature] ) 
+        @prediction_feature = params[:prediction_feature]
+        resource_not_found_error "No feature '#{params[:prediction_feature]}' in dataset '#{params[:dataset]}'" unless 
+          @training_dataset.features.include?( params[:prediction_feature] ) 
         unless params[:min_frequency].nil? 
           # check for percentage
           if params[:min_frequency].include? "pc"
@@ -58,7 +61,8 @@ module OpenTox
         end
         if @minfreq.nil?
           @minfreq=min_frequency(@training_dataset,@prediction_feature,per_mil)
-          $logger.debug "min_frequency #{@minfreq} (input was #{per_mil} per-mil)"
+          p "min_frequency #{@minfreq} (input was #{per_mil} per-mil)"
+          #$logger.debug "min_frequency #{@minfreq} (input was #{per_mil} per-mil)"
         end
       end
 
@@ -109,7 +113,7 @@ module OpenTox
           end
 
           if compound_activities.nil?
-            $logger.warn "No activity for '#{compound.uri}' and feature '#{@prediction_feature.uri}'"
+            $logger.warn "No activity for '#{compound.inchi}' and feature '#{@prediction_feature.title}'"
           else
             if @prediction_feature.feature_type == "classification"
               activity= value_map.invert[compound_activities].to_i # activities are mapped to 1..n
@@ -178,7 +182,7 @@ module OpenTox
       # return [Integer] min-frequency
       def min_frequency(training_dataset,prediction_feature,per_mil)
         nr_labeled_cmpds=0
-        f_idx=training_dataset.features.collect{|f| f.uri}.index prediction_feature.uri
+        f_idx=training_dataset.features.index prediction_feature
         training_dataset.compounds.each_with_index { |cmpd, c_idx|
           if ( training_dataset.data_entries[c_idx] )
                unless training_dataset.data_entries[c_idx][f_idx].nil?
diff --git a/lib/opentox-algorithm.rb b/lib/opentox-algorithm.rb
new file mode 100644
index 0000000..4aaad9c
--- /dev/null
+++ b/lib/opentox-algorithm.rb
@@ -0,0 +1,10 @@
+require 'statsample'
+
+# Require sub-Repositories
+require_relative '../libfminer/libbbrc/bbrc' # include before openbabel
+require_relative '../libfminer/liblast/last' # 
+require_relative '../last-utils/lu.rb'
+
+#Dir[File.join(File.dirname(__FILE__),"*.rb")].each{ |f| require_relative f}
+require_relative "descriptor.rb"
+require_relative "fminer.rb"