first attempt at installing openbabel from github

4 files changed, 9 insertions, 142 deletions

diff --git a/ChangeLog b/ChangeLog
deleted file mode 100644
index 08d2402..0000000
--- a/ChangeLog
+++ /dev/null
@@ -1,2 +0,0 @@
-v0.0.3 2012-05-07
-* switch from v0.0.2pre to v0.0.3
diff --git a/ext/lazar/extconf.rb b/ext/lazar/extconf.rb
index c37b40b..0c86985 100644
--- a/ext/lazar/extconf.rb
+++ b/ext/lazar/extconf.rb
@@ -22,8 +22,7 @@ rescue
   nr_processors = 1
 end
 
-#FileUtils.mkdir_p openbabel_dir
-=begin
+FileUtils.mkdir_p openbabel_dir
 Dir.chdir main_dir do
   FileUtils.rm_rf src_dir
   puts "Downloading OpenBabel sources"
@@ -48,26 +47,26 @@ Dir.chdir build_dir do
   system "make install"
   ENV["PKG_CONFIG_PATH"] = File.dirname(File.expand_path(Dir["#{install_dir}/**/openbabel*pc"].first))
 end
-=end
 
 # get include and lib from pkg-config
 ob_include= File.expand_path "../../openbabel/include/openbabel-2.0"
 ob_lib= File.expand_path "../../openbabel/lib"
 
-=begin
 # compile ruby bindings
 puts "Compiling and installing OpenBabel Ruby bindings."
 Dir.chdir ruby_src_dir do
+  #p `pwd`
   # fix rpath
   system "sed -i 's|with_ldflags.*$|with_ldflags(\"#\$LDFLAGS -dynamic -Wl,-rpath,#{install_lib_dir}\") do|' #{File.join(ruby_src_dir,'extconf.rb')}"
   system "#{RbConfig.ruby} extconf.rb --with-openbabel-include=#{ob_include} --with-openbabel-lib=#{ob_lib}"
   system "make -j#{nr_processors}"
 end
+
+#p(ruby_src_dir+"/openbabel.#{RbConfig::CONFIG["DLEXT"]}", "./")
 #FileUtils.cp(ruby_src_dir+"/openbabel.#{RbConfig::CONFIG["DLEXT"]}", "./")
-#FileUtils.mkdir_p lib_dir
-#FileUtils.mv "openbabel.#{RbConfig::CONFIG["DLEXT"]}", lib_dir
+FileUtils.mkdir_p lib_dir
+FileUtils.mv "openbabel.#{RbConfig::CONFIG["DLEXT"]}", lib_dir
 #FileUtils.remove_entry_secure src_dir, build_dir
-=end
 
 # install fminer
 fminer_dir = File.join main_dir, "libfminer"
diff --git a/lazar.gemspec b/lazar.gemspec
index 6fe3f5b..8da29b7 100644
--- a/lazar.gemspec
+++ b/lazar.gemspec
@@ -22,7 +22,7 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency "bundler"
   s.add_runtime_dependency "rest-client"
   s.add_runtime_dependency 'nokogiri'
-  #s.add_runtime_dependency "openbabel"
+  s.add_runtime_dependency "openbabel"
   s.add_runtime_dependency 'rserve-client'
   s.add_runtime_dependency "mongoid", '~> 5.0beta'  
 
diff --git a/lib/lazar-model.rb b/lib/lazar-model.rb
index aeaa515..1970401 100644
--- a/lib/lazar-model.rb
+++ b/lib/lazar-model.rb
@@ -129,8 +129,6 @@ module OpenTox
     end
 
     class LazarFminerClassification < LazarClassification
-      #field :feature_dataset_id, type: BSON::ObjectId
-      #field :feature_calculation_algorithm, type: String
 
       def self.create training_dataset
         model = super(training_dataset)
@@ -145,136 +143,6 @@ module OpenTox
         model.save
         model
       end
-
-=begin
-      def predict object
-
-        t = Time.now
-        at = Time.now
-
-        @training_dataset = OpenTox::Dataset.find(training_dataset_id)
-        @feature_dataset = OpenTox::Dataset.find(feature_dataset_id)
-
-        compounds = []
-        case object.class.to_s
-        when "OpenTox::Compound"
-          compounds = [object] 
-        when "Array"
-          compounds = object
-        when "OpenTox::Dataset"
-          compounds = object.compounds
-        else 
-          bad_request_error "Please provide a OpenTox::Compound an Array of OpenTox::Compounds or an OpenTox::Dataset as parameter."
-        end
-
-        $logger.debug "Setup: #{Time.now-t}"
-        t = Time.now
-
-        @query_fingerprint = Algorithm.run(feature_calculation_algorithm, compounds, @feature_dataset.features.collect{|f| f.name} )
-
-        $logger.debug "Query fingerprint calculation: #{Time.now-t}"
-        t = Time.now
-
-        predictions = []
-        prediction_feature = OpenTox::Feature.find prediction_feature_id
-        tt = 0
-        pt = 0
-        nt = 0
-        st = 0
-        nit = 0
-        @training_fingerprints ||= @feature_dataset.data_entries
-        compounds.each_with_index do |compound,c|
-          t = Time.new
-
-          $logger.debug "predict compound #{c+1}/#{compounds.size} #{compound.inchi}"
-
-          database_activities = @training_dataset.values(compound,prediction_feature)
-          if database_activities and !database_activities.empty?
-            database_activities = database_activities.first if database_activities.size == 1
-            $logger.debug "Compound #{compound.inchi} occurs in training dataset with activity #{database_activities}"
-            predictions << {:compound => compound, :value => database_activities, :confidence => "measured"}
-            next
-          else
-
-            #training_fingerprints = @feature_dataset.data_entries
-            query_fingerprint = @query_fingerprint[c]
-            neighbors = []
-            tt += Time.now-t
-            t = Time.new
-            
-
-            # find neighbors
-            @training_fingerprints.each_with_index do |fingerprint, i|
-              ts = Time.new
-              sim = Algorithm.run(similarity_algorithm,fingerprint, query_fingerprint)
-              st += Time.now-ts
-              ts = Time.new
-              if sim > self.min_sim
-                if prediction_algorithm =~ /Regression/
-                  neighbors << [@feature_dataset.compound_ids[i],sim,training_activities[i], fingerprint]
-                else
-                  neighbors << [@feature_dataset.compound_ids[i],sim,training_activities[i]] # use compound_ids, instantiation of Compounds is too time consuming
-                end
-              end
-              nit += Time.now-ts
-            end
-
-            if neighbors.empty?
-              predictions << {:compound => compound, :value => nil, :confidence => nil, :warning => "No neighbors with similarity > #{min_sim} in dataset #{training_dataset.id}"}
-              next
-            end
-            nt += Time.now-t
-            t = Time.new
-
-            if prediction_algorithm =~ /Regression/
-              prediction = Algorithm.run(prediction_algorithm, neighbors, :min_train_performance => self.min_train_performance)
-            else
-              prediction = Algorithm.run(prediction_algorithm, neighbors)
-            end
-            prediction[:compound] = compound
-            prediction[:neighbors] = neighbors.sort{|a,b| b[1] <=> a[1]} # sort with ascending similarities
-
-
-            # AM: transform to original space (TODO)
-            #confidence_value = ((confidence_value+1.0)/2.0).abs if prediction.first and similarity_algorithm =~ /cosine/
-
-
-            $logger.debug "predicted value: #{prediction[:value]}, confidence: #{prediction[:confidence]}"
-            predictions << prediction
-            pt += Time.now-t
-          end
-
-        end 
-        $logger.debug "Transform time: #{tt}"
-        $logger.debug "Neighbor search time: #{nt} (Similarity calculation: #{st}, Neighbor insert: #{nit})"
-        $logger.debug "Prediction time: #{pt}"
-        $logger.debug "Total prediction time: #{Time.now-at}"
-
-        # serialize result
-        case object.class.to_s
-        when "OpenTox::Compound"
-          return predictions.first
-        when "Array"
-          return predictions
-        when "OpenTox::Dataset"
-          # prepare prediction dataset
-          prediction_dataset = LazarPrediction.new(
-            :title => "Lazar prediction for #{prediction_feature.title}",
-            :creator =>  __FILE__,
-            :prediction_feature_id => prediction_feature.id
-
-          )
-          confidence_feature = OpenTox::NumericFeature.find_or_create_by( "title" => "Prediction confidence" )
-          warning_feature = OpenTox::NominalFeature.find_or_create_by("title" => "Warnings")
-          prediction_dataset.features = [ prediction_feature, confidence_feature, warning_feature ]
-          prediction_dataset.compounds = compounds
-          prediction_dataset.data_entries = predictions.collect{|p| [p[:value], p[:confidence],p[:warning]]}
-          prediction_dataset.save_all
-          return prediction_dataset
-        end
-
-      end
-=end
     end
 
     class LazarRegression < Lazar
@@ -291,6 +159,8 @@ module OpenTox
     class PredictionModel < Lazar
       field :category, type: String
       field :endpoint, type: String
+      field :unit, type: String
+      field :model_id, type: BSON::ObjectId
       field :crossvalidation_id, type: BSON::ObjectId
     end