diff options
Diffstat (limited to 'lib/lazar.rb')
| -rw-r--r-- | lib/lazar.rb | 32 |
1 files changed, 16 insertions, 16 deletions
diff --git a/lib/lazar.rb b/lib/lazar.rb index 34d868c..edfee43 100644 --- a/lib/lazar.rb +++ b/lib/lazar.rb @@ -12,7 +12,6 @@ module OpenTox attr_accessor :prediction_dataset def initialize(params) - puts "prediction started" @prediction_dataset = OpenTox::Dataset.new(nil, @subjectid) # set instance variables and prediction dataset parameters from parameters params.each {|k,v| @@ -25,7 +24,7 @@ module OpenTox instance_variable_set("@#{k}", []) } - @prediction_feature = OpenTox::Feature.new(@prediction_feature_uri,@subjectid) + @prediction_feature = OpenTox::Feature.new @prediction_feature_uri, @subjectid @predicted_variable = OpenTox::Feature.new @predicted_variable_uri, @subjectid @predicted_confidence = OpenTox::Feature.new @predicted_confidence_uri, @subjectid @prediction_dataset.metadata = { @@ -36,8 +35,6 @@ module OpenTox RDF::OT.predictedVariables => [@predicted_variable_uri,@predicted_confidence_uri] } - puts "metadata set" - @training_dataset = OpenTox::Dataset.new(@training_dataset_uri,@subjectid) @feature_dataset = OpenTox::Dataset.new(@feature_dataset_uri, @subjectid) @@ -50,18 +47,16 @@ module OpenTox prediction_feature_pos = @training_dataset.features.collect{|f| f.uri}.index @prediction_feature.uri if @dataset_uri - compounds = OpenTox::Dataset.new(@dataset_uri,@subjectid).compounds + compounds = OpenTox::Dataset.new(@dataset_uri, @subjectid).compounds else - compounds = [ OpenTox::Compound.new(@compound_uri,@subjectid) ] + compounds = [ OpenTox::Compound.new(@compound_uri, @subjectid) ] end - puts "compounds started" compounds.each do |compound| #database_activity = @training_dataset.database_activity(params) database_activities = @training_dataset.values(compound,@prediction_feature) - puts "checking dataset activity" if database_activities and !database_activities.empty? database_activities.each do |database_activity| @prediction_dataset.add_data_entry compound, @prediction_feature, database_activity @@ -75,15 +70,10 @@ module OpenTox :compound => compound, :feature_dataset => @feature_dataset, } - puts "fingerprints" - puts @feature_calculation_algorithm - puts compound_params #compound_fingerprints = OpenTox::Algorithm::FeatureValues.send( @feature_calculation_algorithm, compound_params, @subjectid ) # TODO: fix for pc descriptors #compound_fingerprints = OpenTox::Algorithm::Descriptor.send( @feature_calculation_algorithm, compound, @feature_dataset.features.collect{ |f| f[RDF::DC.title] } ) compound_fingerprints = eval("#{@feature_calculation_algorithm}(compound, @feature_dataset.features.collect{ |f| f[RDF::DC.title] } )") - puts "Fingerprints" - puts compound_fingerprints.inspect @training_dataset.compounds.each_with_index { |cmpd, idx| act = @training_dataset.data_entries[idx][prediction_feature_pos] @acts << (@prediction_feature.feature_type=="classification" ? @prediction_feature.value_map.invert[act] : nil) @@ -99,12 +89,10 @@ module OpenTox } # query structure =end @q_prop = compound_fingerprints.first.collect{|v| v.to_f} - puts @q_prop.inspect mtf = OpenTox::Algorithm::Transform::ModelTransformer.new(self) mtf.transform - puts "Prediction" prediction = OpenTox::Algorithm::Neighbors.send(@prediction_algorithm, { :props => mtf.props, :acts => mtf.acts, @@ -127,7 +115,7 @@ module OpenTox if @compound_uri # add neighbors only for compound predictions @neighbors.each do |neighbor| - n = OpenTox::Compound.new(neighbor[:compound]) + n = OpenTox::Compound.new(neighbor[:compound], @subjectid) @prediction_dataset.add_data_entry n, @prediction_feature, @prediction_feature.value_map[neighbor[:activity]] @prediction_dataset.add_data_entry n, @similarity_feature, neighbor[:similarity] #@prediction_dataset << [ n, @prediction_feature.value_map[neighbor[:activity]], nil, nil, neighbor[:similarity] ] @@ -218,6 +206,18 @@ module OpenTox put @uri +<<<<<<< HEAD +======= + if params[:feature_dataset_uri] + bad_request_error "Feature dataset #{params[:feature_dataset_uri]} does not exist." unless URI.accessible? params[:feature_dataset_uri], @subjectid + @parameters << {RDF::DC.title => "feature_dataset_uri", RDF::OT.paramValue => params[:feature_dataset_uri]} + self[RDF::OT.featureDataset] = params["feature_dataset_uri"] + else + # run feature generation algorithm + feature_dataset_uri = OpenTox::Algorithm.new(params[:feature_generation_uri], @subjectid).run(params) + @parameters << {RDF::DC.title => "feature_dataset_uri", RDF::OT.paramValue => feature_dataset_uri} + self[RDF::OT.featureDataset] = feature_dataset_uri +>>>>>>> ad386110267ecc3e0c5301769b4880a7e555a44e end end |