diff options
Diffstat (limited to 'lib/dataset.rb')
| -rw-r--r-- | lib/dataset.rb | 42 |
1 files changed, 27 insertions, 15 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb index 78f5633..4543e42 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -41,12 +41,14 @@ module OpenTox end # Get all values for a given substance and feature - # @param [OpenTox::Substance,BSON::ObjectId] substance or substance id - # @param [OpenTox::Feature,BSON::ObjectId] feature or feature id + # @param [OpenTox::Substance,BSON::ObjectId,String] substance or substance id + # @param [OpenTox::Feature,BSON::ObjectId,String] feature or feature id # @return [Array<TrueClass,FalseClass,Float>] values def values substance,feature substance = substance.id if substance.is_a? Substance feature = feature.id if feature.is_a? Feature + substance = BSON::ObjectId.from_string(substance) if substance.is_a? String + feature = BSON::ObjectId.from_string(feature) if feature.is_a? String data_entries.select{|row| row[0] == substance and row[1] == feature}.collect{|row| row[2]} end @@ -86,6 +88,8 @@ module OpenTox features.select{|f| f._type.match("SubstanceProperty")} end + # Get nominal and numeric prediction features + # @return [Array<OpenTox::NominalLazarPrediction,OpenTox::NumericLazarPrediction>] def prediction_features features.select{|f| f._type.match("Prediction")} end @@ -377,19 +381,6 @@ module OpenTox # Dataset operations - # Merge an array of datasets - # @param [Array<OpenTox::Dataset>] datasets to be merged - # @return [OpenTox::Dataset] merged dataset - def self.merge datasets - dataset = self.create(:source => datasets.collect{|d| d.id.to_s}.join(", "), :name => datasets.collect{|d| d.name}.uniq.join(", ")) - datasets.each do |d| - dataset.data_entries += d.data_entries - dataset.warnings += d.warnings - end - dataset.save - dataset - end - # Copy a dataset # @return OpenTox::Dataset dataset copy def copy @@ -434,6 +425,27 @@ module OpenTox end chunks end +=begin + # Merge an array of datasets + # @param [Array<OpenTox::Dataset>] datasets to be merged + # @return [OpenTox::Dataset] merged dataset + def self.merge datasets: datasets, features: features, value_maps: value_maps, keep_original_features: keep_original_features, remove_duplicates: remove_duplicates + dataset = self.create(:source => datasets.collect{|d| d.id.to_s}.join(", "), :name => datasets.collect{|d| d.name}.uniq.join(", ")+" merged") + datasets.each_with_index do |d,i| + dataset.data_entries += d.data_entries + dataset.warnings += d.warnings + end + feature_classes = features.collect{|f| f.class}.uniq + if feature_classes.size == 1 + if features.first.nominal? + merged_feature = MergedNominalBioActivity.find_or_create_by(:name => features.collect{|f| f.name} + " (merged)", :original_feature_id => feature.id, :transformation => map, :accept_values => map.values.sort) + compounds.each do |c| + values(c,feature).each { |v| dataset.add c, new_feature, map[v] } + end + dataset.save + dataset + end +=end # Change nominal feature values # @param [NominalFeature] Original feature |