diff options
Diffstat (limited to 'validation/validation_service.rb')
| -rwxr-xr-x | validation/validation_service.rb | 75 |
1 files changed, 37 insertions, 38 deletions
diff --git a/validation/validation_service.rb b/validation/validation_service.rb index a1efba5..dcfb8d7 100755 --- a/validation/validation_service.rb +++ b/validation/validation_service.rb @@ -30,7 +30,7 @@ end module Validation - class Validation < Lib::Validation + class Validation # constructs a validation object, Rsets id und uri #def initialize( params={} ) @@ -43,7 +43,7 @@ module Validation # deletes a validation # PENDING: model and referenced datasets are deleted as well, keep it that way? - def delete( delete_all=true ) + def delete_validation( delete_all=true ) if (delete_all) to_delete = [:model_uri, :training_dataset_uri, :test_dataset_uri, :test_target_dataset_uri, :prediction_dataset_uri ] case self.validation_type @@ -72,7 +72,7 @@ module Validation end end end - self.destroy + self.delete if (subjectid) begin res = OpenTox::Authorization.delete_policies_from_uri(validation_uri, subjectid) @@ -222,17 +222,13 @@ module Validation # :percent_unpredicted => prediction.percent_unpredicted, # :finished => true} # self.save! - self.attributes= {:num_instances => prediction.num_instances, + self.update :num_instances => prediction.num_instances, :num_without_class => prediction.num_without_class, :percent_without_class => prediction.percent_without_class, :num_unpredicted => prediction.num_unpredicted, :percent_unpredicted => prediction.percent_unpredicted, - :finished => true} - begin - self.save - rescue DataMapper::SaveFailureError => e - raise "could not save validation: "+e.resource.errors.inspect - end + :finished => true + raise unless self.valid? end task.progress(100) if task @@ -240,7 +236,7 @@ module Validation end end - class Crossvalidation < Lib::Crossvalidation + class Crossvalidation # constructs a crossvalidation, id and uri are set #def initialize( params={} ) @@ -262,12 +258,12 @@ module Validation end # deletes a crossvalidation, all validations are deleted as well - def delete - Validation.all(:crossvalidation_id => self.id).each do |v| + def delete_crossvalidation + Validation.find(:crossvalidation_id => self.id).each do |v| v.subjectid = self.subjectid - v.delete + v.delete_validation end - self.destroy + self.delete if (subjectid) begin res = OpenTox::Authorization.delete_policies_from_uri(crossvalidation_uri, subjectid) @@ -281,6 +277,9 @@ module Validation # creates the cv folds def create_cv_datasets( prediction_feature, task=nil ) + self.random_seed = 1 unless self.random_seed + self.num_folds = 10 unless self.num_folds + self.stratified = false unless self.stratified if copy_cv_datasets( prediction_feature ) # dataset folds of a previous crossvalidaiton could be used task.progress(100) if task @@ -296,7 +295,7 @@ module Validation i = 0 task_step = 100 / self.num_folds.to_f; @tmp_validations.each do | val | - validation = Validation.new val + validation = Validation.create val validation.subjectid = self.subjectid validation.validate_algorithm( algorithm_params, OpenTox::SubTask.create(task, i * task_step, ( i + 1 ) * task_step) ) @@ -316,8 +315,7 @@ module Validation # copies datasets from an older crossvalidation on the same dataset and the same folds # returns true if successfull, false otherwise def copy_cv_datasets( prediction_feature ) - - cvs = Crossvalidation.all( { + cvs = Crossvalidation.find( { :dataset_uri => self.dataset_uri, :num_folds => self.num_folds, :stratified => self.stratified, @@ -326,13 +324,13 @@ module Validation cvs.each do |cv| next if AA_SERVER and !OpenTox::Authorization.authorized?(cv.crossvalidation_uri,"GET",self.subjectid) tmp_val = [] - Validation.all( :crossvalidation_id => cv.id ).each do |v| + Validation.find( :crossvalidation_id => cv.id ).each do |v| break unless v.prediction_feature == prediction_feature and OpenTox::Dataset.exist?(v.training_dataset_uri,self.subjectid) and OpenTox::Dataset.exist?(v.test_dataset_uri,self.subjectid) #make sure self.id is set - self.save if self.new? + #self.save if self.new? tmp_val << { :validation_type => "crossvalidation", :training_dataset_uri => v.training_dataset_uri, :test_dataset_uri => v.test_dataset_uri, @@ -342,7 +340,7 @@ module Validation :prediction_feature => prediction_feature, :algorithm_uri => self.algorithm_uri } end - if tmp_val.size == self.num_folds + if tmp_val.size == self.num_folds.to_i @tmp_validations = tmp_val LOGGER.debug "copied dataset uris from cv "+cv.crossvalidation_uri.to_s #+":\n"+tmp_val.inspect return true @@ -354,23 +352,22 @@ module Validation # creates cv folds (training and testdatasets) # stores uris in validation objects def create_new_cv_datasets( prediction_feature, task = nil ) - - raise "random seed not set "+self.inspect unless self.random_seed LOGGER.debug "creating datasets for crossvalidation" orig_dataset = OpenTox::Dataset.find(self.dataset_uri,self.subjectid) raise OpenTox::NotFoundError.new "Dataset not found: "+self.dataset_uri.to_s unless orig_dataset shuffled_compounds = orig_dataset.compounds.shuffle( self.random_seed ) - unless self.stratified - split_compounds = shuffled_compounds.chunk( self.num_folds ) + unless self.stratified + split_compounds = shuffled_compounds.chunk( self.num_folds.to_i ) else class_compounds = {} # "inactive" => compounds[], "active" => compounds[] .. - shuffled_compounds.each do |c| - orig_dataset.features(c).each do |a| - value = OpenTox::Feature.new(:uri => a.uri).value(prediction_feature).to_s - class_compounds[value] = [] unless class_compounds.has_key?(value) - class_compounds[value].push(c) + accept_values = orig_dataset.features[prediction_feature][OT.acceptValue] + accept_values.each do |value| + class_compounds[value] = [] + shuffled_compounds.each do |c| + #PENDING accept values are type string, data_entries may be boolean + class_compounds[value] << c if orig_dataset.data_entries[c][prediction_feature].collect{|v| v.to_s}.include?(value) end end LOGGER.debug "stratified cv: different class values: "+class_compounds.keys.join(", ") @@ -378,7 +375,7 @@ module Validation split_class_compounds = [] # inactive_compounds[fold_i][], active_compounds[fold_i][], .. class_compounds.values.each do |compounds| - split_class_compounds.push( compounds.chunk( self.num_folds ) ) + split_class_compounds << compounds.chunk( self.num_folds.to_i ) end LOGGER.debug "stratified cv: splits for class values: "+split_class_compounds.collect{ |c| c.collect{ |cc| cc.size }.join("/") }.join(", ") @@ -389,7 +386,7 @@ module Validation # step 1: sort current split in ascending order split_comp.sort!{|x,y| x.size <=> y.size } # step 2: add splits - (0..self.num_folds-1).each do |i| + (0..self.num_folds.to_i-1).each do |i| unless split_compounds[i] split_compounds[i] = split_comp[i] else @@ -406,7 +403,7 @@ module Validation @tmp_validations = [] - (1..self.num_folds).each do |n| + (1..self.num_folds.to_i).each do |n| datasetname = 'cv'+self.id.to_s + #'_d'+orig_dataset.name.to_s + @@ -418,7 +415,7 @@ module Validation test_compounds = [] train_compounds = [] - (1..self.num_folds).each do |nn| + (1..self.num_folds.to_i).each do |nn| compounds = split_compounds.at(nn-1) if n == nn @@ -428,8 +425,9 @@ module Validation end end - raise "internal error, num test compounds not correct" unless (shuffled_compounds.size/self.num_folds - test_compounds.size).abs <= 1 - raise "internal error, num train compounds not correct" unless shuffled_compounds.size - test_compounds.size == train_compounds.size + raise "internal error, num test compounds not correct" unless (shuffled_compounds.size/self.num_folds.to_i - test_compounds.size).abs <= 1 + raise "internal error, num train compounds not correct, should be '"+(shuffled_compounds.size-test_compounds.size).to_s+ + "', is '"+train_compounds.size.to_s+"'" unless shuffled_compounds.size - test_compounds.size == train_compounds.size LOGGER.debug "training set: "+datasetname+"_train, compounds: "+train_compounds.size.to_s #train_dataset_uri = orig_dataset.create_new_dataset( train_compounds, orig_dataset.features, datasetname + '_train', source ) @@ -442,7 +440,7 @@ module Validation { DC.title => datasetname + '_test', DC.creator => source }, self.subjectid ).uri #make sure self.id is set - self.save if self.new? + #self.save if self.new? tmp_validation = { :validation_type => "crossvalidation", :training_dataset_uri => train_dataset_uri, :test_dataset_uri => test_dataset_uri, @@ -551,9 +549,10 @@ module Validation # splits a dataset into test and training dataset # returns map with training_dataset_uri and test_dataset_uri def self.train_test_dataset_split( orig_dataset_uri, prediction_feature, subjectid, split_ratio=nil, random_seed=nil, task=nil ) - split_ratio=0.67 unless split_ratio + split_ratio = split_ratio.to_f random_seed=1 unless random_seed + random_seed = random_seed.to_i orig_dataset = OpenTox::Dataset.find orig_dataset_uri, subjectid orig_dataset.load_all subjectid |