diff options
Diffstat (limited to 'lib/model.rb')
| -rw-r--r-- | lib/model.rb | 49 |
1 files changed, 36 insertions, 13 deletions
diff --git a/lib/model.rb b/lib/model.rb index a858a0f..c9d367e 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -103,7 +103,7 @@ module OpenTox include Model - attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :subjectid, :value_map, :compound_fingerprints, :feature_calculation_algorithm, :neighbors + attr_accessor :compound, :prediction_dataset, :features, :effects, :activities, :p_values, :fingerprints, :feature_calculation_algorithm, :similarity_algorithm, :prediction_algorithm, :subjectid, :value_map, :compound_fingerprints, :feature_calculation_algorithm, :neighbors, :compounds def initialize(uri=nil) if uri @@ -169,12 +169,13 @@ module OpenTox lazar.prediction_algorithm = hash["prediction_algorithm"] if hash["prediction_algorithm"] lazar.subjectid = hash["subjectid"] if hash["subjectid"] lazar.value_map = hash["value_map"] if hash["value_map"] + lazar.compounds = hash["compounds"] if hash["compounds"] lazar end def to_json - Yajl::Encoder.encode({:uri => @uri,:metadata => @metadata, :compound => @compound, :prediction_dataset => @prediction_dataset, :features => @features, :effects => @effects, :activities => @activities, :p_values => @p_values, :fingerprints => @fingerprints, :feature_calculation_algorithm => @feature_calculation_algorithm, :similarity_algorithm => @similarity_algorithm, :prediction_algorithm => @prediction_algorithm, :subjectid => @subjectid, :value_map => @value_map}) + Yajl::Encoder.encode({:uri => @uri,:metadata => @metadata, :compound => @compound, :prediction_dataset => @prediction_dataset, :features => @features, :effects => @effects, :activities => @activities, :p_values => @p_values, :fingerprints => @fingerprints, :feature_calculation_algorithm => @feature_calculation_algorithm, :similarity_algorithm => @similarity_algorithm, :prediction_algorithm => @prediction_algorithm, :subjectid => @subjectid, :value_map => @value_map, :compounds => @compounds}) end def run( params, accept_header=nil, waiting_task=nil ) @@ -237,6 +238,7 @@ module OpenTox @compound = Compound.new compound_uri features = {} + #LOGGER.debug self.to_yaml unless @prediction_dataset @prediction_dataset = Dataset.create(CONFIG[:services]["opentox-dataset"], subjectid) @@ -247,19 +249,19 @@ module OpenTox OT.parameters => [{DC.title => "compound_uri", OT.paramValue => compound_uri}] } ) end - if OpenTox::Feature.find(metadata[OT.dependentVariables], subjectid).feature_type == "regression" - all_activities = [] - all_activities = @activities.values.flatten.collect! { |i| i.to_f } - end + unless database_activity(subjectid) # adds database activity to @prediction_dataset + # Calculation of needed values for query compound @compound_features = eval("#{@feature_calculation_algorithm}({ :compound => @compound, :features => @features, :feature_dataset_uri => @metadata[OT.featureDataset], :pc_type => self.parameter(\"pc_type\"), + :lib => self.parameter(\"lib\"), :subjectid => subjectid })") + # Adding fingerprint of query compound with features and values(p_value*nr_hits) @compound_fingerprints = {} @compound_features.each do |feature, value| # value is nil if "Substructure.match" @@ -314,6 +316,16 @@ module OpenTox @prediction_dataset.add @compound.uri, feature_uri, true f+=1 end + elsif @feature_calculation_algorithm == "Substructure.lookup" + f = 0 + @compound_features.each do |feature, value| + features[feature] = feature + @prediction_dataset.add_feature(feature, { + RDF.type => [OT.NumericFeature] + }) + @prediction_dataset.add @compound.uri, feature, value + f+=1 + end else @compound_features.each do |feature| features[feature] = feature @@ -337,15 +349,26 @@ module OpenTox else feature_uri = feature end - @prediction_dataset.add neighbor[:compound], feature_uri, true + if @feature_calculation_algorithm == "Substructure.lookup" + @prediction_dataset.add neighbor[:compound], feature_uri, @fingerprints[neighbor[:compound]][feature_uri] + else + @prediction_dataset.add neighbor[:compound], feature_uri, true + end + unless features.has_key? feature features[feature] = feature_uri - @prediction_dataset.add_feature(feature_uri, { - RDF.type => [OT.Substructure], - OT.smarts => feature, - OT.pValue => @p_values[feature], - OT.effect => @effects[feature] - }) + if @feature_calculation_algorithm == "Substructure.lookup" + @prediction_dataset.add_feature(feature_uri, { + RDF.type => [OT.NumericFeature] + }) + else + @prediction_dataset.add_feature(feature_uri, { + RDF.type => [OT.Substructure], + OT.smarts => feature, + OT.pValue => @p_values[feature], + OT.effect => @effects[feature] + }) + end f+=1 end end |