From 3b74791450ecc1bd89f6ddf84fd1976403188231 Mon Sep 17 00:00:00 2001 From: davor Date: Fri, 23 Dec 2011 11:06:58 +0100 Subject: Fixed Bug and improving clarity --- lazar.rb | 129 +++++++++++++++++++++++++-------------------------------------- 1 file changed, 52 insertions(+), 77 deletions(-) diff --git a/lazar.rb b/lazar.rb index 0d6b704..89e66c6 100644 --- a/lazar.rb +++ b/lazar.rb @@ -45,40 +45,55 @@ post '/lazar/?' do task = OpenTox::Task.create("Create lazar model",url_for('/lazar',:full)) do |task| + + # # # Dataset present, prediction feature present? raise OpenTox::NotFoundError.new "Dataset #{dataset_uri} not found." unless training_activities = OpenTox::Dataset.new(dataset_uri) training_activities.load_all(@subjectid) + # Prediction Feature prediction_feature = OpenTox::Feature.find(params[:prediction_feature],@subjectid) unless params[:prediction_feature] # try to read prediction_feature from dataset raise OpenTox::NotFoundError.new "#{training_activities.features.size} features in dataset #{dataset_uri}. Please provide a prediction_feature parameter." unless training_activities.features.size == 1 prediction_feature = OpenTox::Feature.find(training_activities.features.keys.first,@subjectid) params[:prediction_feature] = prediction_feature.uri # pass to feature mining service end + raise OpenTox::NotFoundError.new "No feature #{prediction_feature.uri} in dataset #{params[:dataset_uri]}. (features: "+ training_activities.features.inspect+")" unless training_activities.features and training_activities.features.include?(prediction_feature.uri) - feature_generation_uri = @@feature_generation_default unless feature_generation_uri = params[:feature_generation_uri] - - raise OpenTox::NotFoundError.new "No feature #{prediction_feature.uri} in dataset #{params[:dataset_uri]}. (features: "+ - training_activities.features.inspect+")" unless training_activities.features and training_activities.features.include?(prediction_feature.uri) + # Feature Generation URI + feature_generation_uri = @@feature_generation_default unless ( (feature_generation_uri = params[:feature_generation_uri]) || (params[:feature_dataset_uri]) ) + # Create instance lazar = OpenTox::Model::Lazar.new - lazar.min_sim = params[:min_sim].to_f if params[:min_sim] - # AM: Manage endpoint related variables. + # # # ENDPOINT RELATED + + # Default Values + # Classification: Weighted Majority, Substructure.match if prediction_feature.feature_type == "classification" @training_classes = training_activities.accept_values(prediction_feature.uri).sort @training_classes.each_with_index { |c,i| lazar.value_map[i+1] = c # don't use '0': we must take the weighted mean later. params[:value_map] = lazar.value_map } + # Regression: SVM, Substructure.match_hits elsif prediction_feature.feature_type == "regression" - lazar.nr_hits = true + lazar.nr_hits = true # AM: Brauchen wir die Variable noch? Kann man an feature_calculation_algorithm auch ablesen (nĂchste Zeile) lazar.feature_calculation_algorithm = "Substructure.match_hits" lazar.prediction_algorithm = "Neighbors.local_svm_regression" end + + + + # # # USER VALUES + + # Min Sim + lazar.min_sim = params[:min_sim].to_f if params[:min_sim] + + # Nr Hits if params[:nr_hits] == "false" # if nr_hits is set optional to true/false it will return as String (but should be True/FalseClass) lazar.nr_hits = false lazar.feature_calculation_algorithm = "Substructure.match" @@ -86,7 +101,18 @@ post '/lazar/?' do lazar.nr_hits = true lazar.feature_calculation_algorithm = "Substructure.match_hits" end - params[:nr_hits] = "true" if lazar.nr_hits + params[:nr_hits] = "true" if lazar.nr_hits + + # Algorithm + lazar.prediction_algorithm = "Neighbors.#{params[:prediction_algorithm]}" unless params[:prediction_algorithm].nil? + + # Propositionalization + lazar.prop_kernel = true if (params[:local_svm_kernel] == "propositionalized" || params[:prediction_algorithm] == "local_mlr_prop") + + # Conf_stdev + lazar.conf_stdev = ( (params[:conf_stdev] == "true") ? true : false ) + + @@ -99,29 +125,20 @@ post '/lazar/?' do - # - # AM: features - # - # - # + # # # Features - # READ OR CREATE + # Read Features if params[:feature_dataset_uri] + lazar.feature_calculation_algorithm = "" # TODO: Implement lookup in feature dataset feature_dataset_uri = params[:feature_dataset_uri] training_features = OpenTox::Dataset.new(feature_dataset_uri) - case training_features.feature_type(@subjectid) - when "classification" - lazar.similarity_algorithm = "Similarity.tanimoto" - when "regression" - lazar.similarity_algorithm = "Similarity.euclid" + if training_features.feature_type(@subjectid) == "regression" + lazar.similarity_algorithm = "Similarity.cosine" end - else # create features + + # Create Features + else params[:feature_generation_uri] = feature_generation_uri - #if feature_generation_uri.match(/fminer/) - # lazar.feature_calculation_algorithm = "Substructure.match" - #else - # raise OpenTox::NotFoundError.new "External feature generation services not yet supported" - #end params[:subjectid] = @subjectid prediction_feature = OpenTox::Feature.find params[:prediction_feature], @subjectid if prediction_feature.feature_type == "regression" && feature_generation_uri.match(/fminer/) @@ -133,20 +150,16 @@ post '/lazar/?' do - # WRITE IN MODEL + # # # Write fingerprints training_features.load_all(@subjectid) raise OpenTox::NotFoundError.new "Dataset #{feature_dataset_uri} not found." if training_features.nil? - # sorted features for index lookups - - lazar.features = training_features.features.sort if prediction_feature.feature_type == "regression" and lazar.feature_calculation_algorithm != "Substructure.match" || "Substructure.match_hits" - training_features.data_entries.each do |compound,entry| lazar.fingerprints[compound] = {} unless lazar.fingerprints[compound] entry.keys.each do |feature| # CASE 1: Substructure - if lazar.feature_calculation_algorithm == "Substructure.match" || "Substructure.match_hits" + if lazar.feature_calculation_algorithm == "Substructure.match" || lazar.feature_calculation_algorithm == "Substructure.match_hits" if training_features.features[feature] smarts = training_features.features[feature][OT.smarts] #lazar.fingerprints[compound] << smarts @@ -163,26 +176,11 @@ post '/lazar/?' do end # CASE 2: Others + elsif entry[feature].flatten.size == 1 + lazar.fingerprints[compound][feature] = entry[feature].flatten.first + lazar.features << feature unless lazar.features.include? feature else - case training_features.feature_type(@subjectid) - when "classification" - # fingerprints are sets - if entry[feature].flatten.size == 1 - #lazar.fingerprints[compound] << feature if entry[feature].flatten.first.to_s.match(TRUE_REGEXP) - lazar.fingerprints[compound][feature] = entry[feature].flatten.first if entry[feature].flatten.first.to_s.match(TRUE_REGEXP) - lazar.features << feature unless lazar.features.include? feature - else - LOGGER.warn "More than one entry (#{entry[feature].inspect}) for compound #{compound}, feature #{feature}" - end - when "regression" - # fingerprints are arrays - if entry[feature].flatten.size == 1 - lazar.fingerprints[compound][lazar.features.index(feature)] = entry[feature].flatten.first - #lazar.fingerprints[compound][feature] = entry[feature].flatten.first - else - LOGGER.warn "More than one entry (#{entry[feature].inspect}) for compound #{compound}, feature #{feature}" - end - end + LOGGER.warn "More than one entry (#{entry[feature].inspect}) for compound #{compound}, feature #{feature}" end end end @@ -191,28 +189,8 @@ post '/lazar/?' do - - # - # AM: SETTINGS - # - # - # - - # AM: allow settings override by user - lazar.prediction_algorithm = "Neighbors.#{params[:prediction_algorithm]}" unless params[:prediction_algorithm].nil? - lazar.prop_kernel = true if (params[:local_svm_kernel] == "propositionalized" || params[:prediction_algorithm] == "local_mlr_prop") - lazar.conf_stdev = false - lazar.conf_stdev = true if params[:conf_stdev] == "true" - - - - - - # - # AM: Feed data - # - # - # + + # # # Activities if prediction_feature.feature_type == "regression" training_activities.data_entries.each do |compound,entry| @@ -238,11 +216,7 @@ post '/lazar/?' do - # - # AM: Metadata - # - # - # + # Metadata lazar.metadata[DC.title] = "lazar model for #{URI.decode(File.basename(prediction_feature.uri))}" lazar.metadata[OT.dependentVariables] = prediction_feature.uri @@ -264,6 +238,7 @@ post '/lazar/?' do model_uri = lazar.save(@subjectid) LOGGER.info model_uri + " created #{Time.now}" model_uri + end response['Content-Type'] = 'text/uri-list' raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled" -- cgit v1.2.3