diff options
Diffstat (limited to 'lib/lazar.rb')
| -rw-r--r-- | lib/lazar.rb | 16 |
1 files changed, 6 insertions, 10 deletions
diff --git a/lib/lazar.rb b/lib/lazar.rb index 4a59c01..d6a6f47 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -46,13 +46,14 @@ module OpenTox # Prepare lazar object (includes graph mining) # @param[Array] lazar parameters as strings # @param[Hash] REST parameters, as input by user - def self.create feature_dataset, prediction_feature=nil, params={} + def self.create training_dataset, feature_dataset, prediction_feature=nil, params={} lazar = OpenTox::Model::Lazar.new bad_request_error "No features found in feature dataset #{feature_dataset.id}." if feature_dataset.features.empty? lazar.feature_dataset_id = feature_dataset.id - @training_dataset = OpenTox::Dataset.find(feature_dataset.parameters.select{|p| p["title"] == "dataset_id"}.first["paramValue"]) + @training_dataset = training_dataset + #@training_dataset = OpenTox::Dataset.find(feature_dataset.parameters.select{|p| p["title"] == "dataset_id"}.first["paramValue"]) bad_request_error "Training dataset compounds do not match feature dataset compounds. Please ensure that they are in the same order." unless @training_dataset.compounds == feature_dataset.compounds lazar.training_dataset_id = @training_dataset.id @@ -141,19 +142,17 @@ module OpenTox bad_request_error "Please provide one of the parameters: :compound, :compounds, :dataset" end - puts "Setup: #{Time.now-time}" + $logger.debug "Setup: #{Time.now-time}" time = Time.now @query_fingerprint = OpenTox::Algorithm::Descriptor.send( feature_calculation_algorithm, compounds, @feature_dataset.features.collect{|f| f["title"]} ) - puts "Fingerprint calculation: #{Time.now-time}" + $logger.debug "Fingerprint calculation: #{Time.now-time}" time = Time.now # AM: transform to cosine space min_sim = (min_sim.to_f*2.0-1.0).to_s if similarity_algorithm =~ /cosine/ - p compounds.size - i = 0 compounds.each_with_index do |compound,c| $logger.debug "predict compound #{c+1}/#{compounds.size} #{compound.inchi}" @@ -172,9 +171,6 @@ module OpenTox #mtf.transform # - puts "Transform: #{Time.now-time}" - time = Time.now - # find neighbors neighbors = [] @feature_dataset.data_entries.each_with_index do |fingerprint, i| @@ -186,7 +182,7 @@ module OpenTox prediction = OpenTox::Algorithm::Classification.send(prediction_algorithm, neighbors) - puts "Prediction: #{Time.now-time}" + $logger.debug "Prediction: #{Time.now-time}" time = Time.now # AM: transform to original space (TODO) |