diff options
Diffstat (limited to 'lib/dataset.rb')
| -rw-r--r-- | lib/dataset.rb | 41 |
1 files changed, 38 insertions, 3 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb index 95c1918..c916722 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -197,7 +197,12 @@ module OpenTox accept_values end - # Detect feature type(s) in the dataset + # Detect feature type (reduced to one across all features) + # Classification takes precedence over regression + # DEPRECATED -- + # HAS NO SENSE FOR DATASETS WITH MORE THAN 1 FEATURE + # FEATURES CAN HAVE MULTIPLE TYPES + # Replacement: see feature_types() # @return [String] `classification", "regression", "mixed" or unknown` def feature_type(subjectid=nil) load_features(subjectid) @@ -210,6 +215,24 @@ module OpenTox "unknown" end end + + + # Detect feature types. A feature can have multiple types. + # Returns types hashed by feature URI, with missing features omitted. + # Example (YAML): + # http://toxcreate3.in-silico.ch:8082/dataset/152/feature/nHal: + # - http://www.opentox.org/api/1.1#NumericFeature + # - http://www.opentox.org/api/1.1#NominalFeature + # ... + # + # @return [Hash] Keys: feature URIs, Values: Array of types + def feature_types(subjectid=nil) + load_features(subjectid) + @features.inject({}){ |h,(f,metadata)| + h[f]=metadata[RDF.type] unless metadata[RDF.type][0].include? "MissingFeature" + h + } + end =begin =end @@ -316,11 +339,14 @@ module OpenTox end # Complete feature values by adding zeroes - def complete_data_entries + # @param [Hash] key: compound, value: duplicate sizes + def complete_data_entries(compound_sizes) all_features = @features.keys @data_entries.each { |c, e| (Set.new(all_features.collect)).subtract(Set.new e.keys).to_a.each { |f| - self.add(c,f,0) + compound_sizes[c].times { + self.add(c,f,0) + } } } end @@ -454,6 +480,14 @@ module OpenTox end end + def value_map(prediction_feature_uri) + training_classes = accept_values(prediction_feature_uri).sort + value_map=Hash.new + training_classes.each_with_index { |c,i| value_map[i+1] = c } + value_map + end + + private # Copy a dataset (rewrites URI) def copy(dataset) @@ -504,6 +538,7 @@ module OpenTox @data_entries[compound.uri].collect{|f,v| @features[f] if f.match(/neighbor/)}.compact if @data_entries[compound.uri] end + # def errors(compound) # features = @data_entries[compound.uri].keys # features.collect{|f| @features[f][OT.error]}.join(" ") if features |