diff options
Diffstat (limited to 'validation/validation_service.rb')
| -rwxr-xr-x | validation/validation_service.rb | 43 |
1 files changed, 23 insertions, 20 deletions
diff --git a/validation/validation_service.rb b/validation/validation_service.rb index 3dd06c0..8609f85 100755 --- a/validation/validation_service.rb +++ b/validation/validation_service.rb @@ -172,12 +172,12 @@ module Validation model.get unless self.algorithm_uri - self.algorithm_uri = model.metadata[OT.algorithm.to_s] + self.algorithm_uri = model.metadata[RDF::OT.algorithm.to_s] end if self.prediction_feature.to_s.size==0 - dependentVariables = model.metadata[OT.dependentVariables.to_s] + dependentVariables = model.metadata[RDF::OT.dependentVariables.to_s] internal_server_error "model has no dependentVariables specified, please give prediction_feature for model validation" unless dependentVariables - self.prediction_feature = model.metadata[OT.dependentVariables.to_s] + self.prediction_feature = model.metadata[RDF::OT.dependentVariables.to_s] end prediction_dataset_uri = "" @@ -219,9 +219,9 @@ module Validation model.get feature_type = model.feature_type(self.subjectid) - dependentVariables = model.metadata[OT.dependentVariables.to_s] + dependentVariables = model.metadata[RDF::OT.dependentVariables.to_s] prediction_feature = self.prediction_feature ? nil : dependentVariables - algorithm_uri = self.algorithm_uri ? nil : model.metadata[OT.algorithm.to_s] + algorithm_uri = self.algorithm_uri ? nil : model.metadata[RDF::OT.algorithm.to_s] predicted_variable = model.predicted_variable(self.subjectid) predicted_confidence = model.predicted_confidence(self.subjectid) internal_server_error "cannot determine whether model '"+model.uri.to_s+"' performs classification or regression: '#{feature_type}', "+ @@ -327,9 +327,9 @@ module Validation if (delete_feature_datasets) begin model = OpenTox::Model::Generic.find(v.model_uri) - if model.metadata[OT.featureDataset.to_s] - $logger.debug "loo-cleanup> delete feature dataset "+model.metadata[OT.featureDataset.to_s] - OpenTox::RestClientWrapper.delete model.metadata[OT.featureDataset.to_s],subjectid + if model.metadata[RDF::OT.featureDataset.to_s] + $logger.debug "loo-cleanup> delete feature dataset "+model.metadata[RDF::OT.featureDataset.to_s] + OpenTox::RestClientWrapper.delete model.metadata[RDF::OT.featureDataset.to_s],subjectid end rescue end @@ -425,8 +425,11 @@ module Validation Validation.find( :crossvalidation_id => cv.id, :validation_type => "crossvalidation" ).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) + URI.accessible?(v.training_dataset_uri,self.subjectid) and + URI.accessible?(v.test_dataset_uri,self.subjectid) + # CH: Dataset.exist? has been removed, URI.accessible? is cheaper because it needs only HEAD requests + #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? tmp_val << { :validation_type => "crossvalidation", @@ -457,7 +460,7 @@ module Validation train_dataset_uris = [] test_dataset_uris = [] - meta = { DC.creator => self.crossvalidation_uri } + meta = { RDF::DC.creator => self.crossvalidation_uri } case stratified when "false" if self.loo=="true" @@ -485,11 +488,11 @@ module Validation internal_server_error "internal error, num train compounds not correct, should be '"+(shuffled_compound_indices.size-test_compound_indices.size).to_s+ "', is '"+train_compound_indices.size.to_s+"'" unless shuffled_compound_indices.size - test_compound_indices.size == train_compound_indices.size datasetname = 'dataset fold '+(n+1).to_s+' of '+self.num_folds.to_s - meta[DC.title] = "training "+datasetname + meta[RDF::DC.title] = "training "+datasetname $logger.debug "training set: "+datasetname+"_train, compounds: "+train_compound_indices.size.to_s train_dataset_uri = orig_dataset.split( train_compound_indices, orig_dataset.features, meta, self.subjectid ).uri train_dataset_uris << train_dataset_uri - meta[DC.title] = "test "+datasetname + meta[RDF::DC.title] = "test "+datasetname $logger.debug "test set: "+datasetname+"_test, compounds: "+test_compound_indices.size.to_s test_dataset_uri = orig_dataset.split( test_compound_indices, orig_dataset.features, meta, self.subjectid ).uri test_dataset_uris << test_dataset_uri @@ -573,14 +576,14 @@ module Validation result = {} result[:training_dataset_uri] = orig_dataset.split( training_compound_indices, orig_dataset.features, - { DC.title => "Bootstrapping training dataset of "+orig_dataset.title.to_s, - DC.creator => $url_provider.to('/validation/bootstrapping',:full) }, + { RDF::DC.title => "Bootstrapping training dataset of "+orig_dataset.title.to_s, + RDF::DC.creator => $url_provider.to('/validation/bootstrapping',:full) }, subjectid ).uri task.progress(66) if task result[:test_dataset_uri] = orig_dataset.split( test_compound_indices, orig_dataset.features, - { DC.title => "Bootstrapping test dataset of "+orig_dataset.title.to_s, - DC.creator => $url_provider.to('/validation/bootstrapping',:full)} , + { RDF::DC.title => "Bootstrapping test dataset of "+orig_dataset.title.to_s, + RDF::DC.creator => $url_provider.to('/validation/bootstrapping',:full)} , subjectid ).uri task.progress(100) if task @@ -616,7 +619,7 @@ module Validation bad_request_error "prediction feature required for stratified splits" unless prediction_feature end - meta = { DC.creator => creator_uri } + meta = { RDF::DC.creator => creator_uri } case stratified when /true|super/ @@ -643,7 +646,7 @@ module Validation test_compound_indices = compound_indices[split..-1] task.progress(33) if task - meta[DC.title] = "Training dataset split of "+orig_dataset.uri + meta[RDF::DC.title] = "Training dataset split of "+orig_dataset.uri result = {} train_data = orig_dataset.split( training_compound_indices, orig_dataset.features, meta, subjectid ) est_num_train_compounds = (orig_dataset.compounds.size*split_ratio).round @@ -652,7 +655,7 @@ module Validation result[:training_dataset_uri] = train_data.uri task.progress(66) if task - meta[DC.title] = "Test dataset split of "+orig_dataset.uri + meta[RDF::DC.title] = "Test dataset split of "+orig_dataset.uri test_data = orig_dataset.split( test_compound_indices, orig_dataset.features, meta, subjectid ) est_num_test_compounds = orig_dataset.compounds.size-est_num_train_compounds internal_server_error "Test dataset num coumpounds != #{est_num_test_compounds}, instead: "+test_data.compounds.size.to_s unless |