diff options
Diffstat (limited to 'lib/model.rb')
| -rw-r--r-- | lib/model.rb | 63 |
1 files changed, 14 insertions, 49 deletions
diff --git a/lib/model.rb b/lib/model.rb index c6a2cf4..5654bcc 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -80,21 +80,16 @@ module OpenTox OpenTox::Model::Lazar.find(model_uri) end -=begin - # Create a new lazar model and return task - # @param [optional,Hash] params Parameters for the lazar algorithm (OpenTox::Algorithm::Lazar) - # @return [OpenTox::Task] Task for lazar model creation - def self.create_task(params) - task_uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"lazar"), {}, params, false) - Task.find(task_uri) - #model_uri = lazar_algorithm.run(params) - #OpenTox::Model::Lazar.new(model_uri) - end -=end + # Get a parameter value + # @param [String] param Parameter name + # @return [String] Parameter value def parameter(param) @metadata[OT.parameters].collect{|p| p[OT.paramValue] if p[DC.title] == param}.compact.first end + # Predict a dataset + # @param [String] dataset_uri Dataset URI + # @return [OpenTox::Dataset] Dataset with predictions def predict_dataset(dataset_uri) @prediction_dataset = Dataset.create @prediction_dataset.add_metadata({ @@ -145,6 +140,7 @@ module OpenTox if @neighbors.size == 0 @prediction_dataset.add_feature(prediction_feature_uri, { + OT.isA => OT.MeasuredFeature, OT.hasSource => @uri, DC.creator => @uri, DC.title => URI.decode(File.basename( @metadata[OT.dependentVariables] )), @@ -155,6 +151,7 @@ module OpenTox else @prediction_dataset.add_feature(prediction_feature_uri, { + OT.isA => OT.ModelPrediction, OT.hasSource => @uri, DC.creator => @uri, DC.title => URI.decode(File.basename( @metadata[OT.dependentVariables] )), @@ -171,8 +168,9 @@ module OpenTox feature_uri = File.join( @prediction_dataset.uri, "feature", "descriptor", f.to_s) features[feature] = feature_uri @prediction_dataset.add_feature(feature_uri, { + OT.isA => OT.Substructure, OT.smarts => feature, - OT.p_value => @p_values[feature], + OT.pValue => @p_values[feature], OT.effect => @effects[feature] }) @prediction_dataset.add @compound.uri, feature_uri, true @@ -190,7 +188,8 @@ module OpenTox @prediction_dataset.add_feature(neighbor_uri, { OT.compound => neighbor[:compound], OT.similarity => neighbor[:similarity], - OT.activity => neighbor[:activity] + OT.measuredActivity => neighbor[:activity], + OT.isA => OT.Neighbor }) @prediction_dataset.add @compound.uri, neighbor_uri, true f = 0 unless f @@ -204,8 +203,9 @@ module OpenTox unless features.has_key? feature features[feature] = feature_uri @prediction_dataset.add_feature(feature_uri, { + OT.isA => OT.Substructure, OT.smarts => feature, - OT.p_value => @p_values[feature], + OT.pValue => @p_values[feature], OT.effect => @effects[feature] }) f+=1 @@ -228,7 +228,6 @@ module OpenTox @neighbors = [] @fingerprints.each do |training_compound,training_features| - #@activities.each do |training_compound,activities| sim = eval("#{@similarity_algorithm}(@compound_features,training_features,@p_values)") if sim > @min_sim @activities[training_compound].each do |act| @@ -244,17 +243,6 @@ module OpenTox end -=begin - def cached_prediction - dataset_uri = PredictionCache.find(:model_uri => @uri, :compound_uri => @compound.uri).dataset_uri) - return false unless dataset_uri - @prediction_dataset = Dataset.find(dataset_uri) - return false unless @prediction_dataset - LOGGER.debug "Serving cached prediction" - true - end -=end - # Find database activities and store them in @prediction_dataset # @return [Boolean] true if compound has databasse activities, false if not def database_activity @@ -278,29 +266,6 @@ module OpenTox RestClientWrapper.delete @uri unless @uri == CONFIG[:services]["opentox-model"] end -=begin -=end - -=begin - def self.create_from_dataset(dataset_uri,feature_dataset_uri,prediction_feature=nil) - training_activities = OpenTox::Dataset.find(dataset_uri) - training_features = OpenTox::Dataset.find(feature_dataset_uri) - unless prediction_feature # try to read prediction_feature from dataset - raise "#{training_activities.features.size} features in dataset #{dataset_uri}. Please provide a prediction_feature parameter." unless training_activities.features.size == 1 - prediction_feature = training_activities.features.keys.first - params[:prediction_feature] = prediction_feature - end - lazar = Lazar.new - training_features = OpenTox::Dataset.new(feature_dataset_uri) - case training_features.feature_type - when "classification" - lazar.similarity_algorithm = "weighted_tanimoto" - when "regression" - lazar.similarity_algorithm = "weighted_euclid" - end - end -=end - end end end |