diff options
Diffstat (limited to 'validation/validation_application.rb')
| -rwxr-xr-x | validation/validation_application.rb | 47 |
1 files changed, 32 insertions, 15 deletions
diff --git a/validation/validation_application.rb b/validation/validation_application.rb index 32ca971..1bc55f6 100755 --- a/validation/validation_application.rb +++ b/validation/validation_application.rb @@ -6,8 +6,16 @@ end require 'lib/dataset_cache.rb' require 'validation/validation_service.rb' +helpers do + def check_stratified(params) + params[:stratified] = "false" unless params[:stratified] + raise OpenTox::BadRequestError.new "stratified != true|false|super, is #{params[:stratified]}" unless + params[:stratified]=~/true|false|super/ + end +end + get '/crossvalidation/?' do - LOGGER.info "list all crossvalidations" + LOGGER.info "list all crossvalidations "+params.inspect model_uri = params.delete("model") || params.delete("model_uri") if model_uri model = OpenTox::Model::Generic.find(model_uri, @subjectid) @@ -46,17 +54,20 @@ post '/crossvalidation/?' do raise OpenTox::BadRequestError.new "prediction_feature missing" unless params[:prediction_feature].to_s.size>0 raise OpenTox::BadRequestError.new "illegal param-value num_folds: '"+params[:num_folds].to_s+"', must be integer >1" unless params[:num_folds]==nil or params[:num_folds].to_i>1 - + check_stratified(params) + task = OpenTox::Task.create( "Perform crossvalidation", url_for("/crossvalidation", :full) ) do |task| #, params cv_params = { :dataset_uri => params[:dataset_uri], :algorithm_uri => params[:algorithm_uri], + :algorithm_params => params[:algorithm_params], + :prediction_feature => params[:prediction_feature], + :stratified => params[:stratified], :loo => "false", :subjectid => @subjectid } [ :num_folds, :random_seed ].each{ |sym| cv_params[sym] = params[sym] if params[sym] } - cv_params[:stratified] = (params[:stratified].size>0 && params[:stratified]!="false" && params[:stratified]!="0") if params[:stratified] cv = Validation::Crossvalidation.create cv_params cv.subjectid = @subjectid - cv.perform_cv( params[:prediction_feature], params[:algorithm_params], OpenTox::SubTask.create(task,0,95)) + cv.perform_cv( OpenTox::SubTask.create(task,0,95) ) # computation of stats is cheap as dataset are already loaded into the memory Validation::Validation.from_cv_statistics( cv.id, @subjectid, OpenTox::SubTask.create(task,95,100) ) cv.crossvalidation_uri @@ -87,16 +98,19 @@ post '/crossvalidation/loo/?' do raise OpenTox::BadRequestError.new "algorithm_uri missing" unless params[:algorithm_uri].to_s.size>0 raise OpenTox::BadRequestError.new "prediction_feature missing" unless params[:prediction_feature].to_s.size>0 raise OpenTox::BadRequestError.new "illegal param: num_folds, stratified, random_seed not allowed for loo-crossvalidation" if params[:num_folds] or - params[:stratifed] or params[:random_seed] + params[:stratified] or params[:random_seed] task = OpenTox::Task.create( "Perform loo-crossvalidation", url_for("/crossvalidation/loo", :full) ) do |task| #, params - cv_params = { :dataset_uri => params[:dataset_uri], + cv_params = { :dataset_uri => params[:dataset_uri], + :algorithm_params => params[:algorithm_params], + :prediction_feature => params[:prediction_feature], :algorithm_uri => params[:algorithm_uri], :loo => "true" } cv = Validation::Crossvalidation.create cv_params cv.subjectid = @subjectid - cv.perform_cv( params[:prediction_feature], params[:algorithm_params], OpenTox::SubTask.create(task,0,95)) + cv.perform_cv( OpenTox::SubTask.create(task,0,95)) # computation of stats is cheap as dataset are already loaded into the memory Validation::Validation.from_cv_statistics( cv.id, @subjectid, OpenTox::SubTask.create(task,95,100) ) + cv.clean_loo_files( !(params[:algorithm_params] && params[:algorithm_params] =~ /feature_dataset_uri/) ) cv.crossvalidation_uri end return_task(task) @@ -343,12 +357,13 @@ post '/training_test_validation/?' do task = OpenTox::Task.create( "Perform training-test-validation", url_for("/", :full) ) do |task| #, params v = Validation::Validation.create :validation_type => "training_test_validation", :algorithm_uri => params[:algorithm_uri], + :algorithm_params => params[:algorithm_params], :training_dataset_uri => params[:training_dataset_uri], :test_dataset_uri => params[:test_dataset_uri], :test_target_dataset_uri => params[:test_target_dataset_uri], :prediction_feature => params[:prediction_feature] v.subjectid = @subjectid - v.validate_algorithm( params[:algorithm_params], task ) + v.validate_algorithm( task ) v.validation_uri end return_task(task) @@ -402,10 +417,11 @@ post '/bootstrapping' do :test_target_dataset_uri => params[:dataset_uri], :prediction_feature => params[:prediction_feature], :algorithm_uri => params[:algorithm_uri], + :algorithm_params => params[:algorithm_params], :training_dataset_uri => params[:training_dataset_uri], :test_dataset_uri => params[:test_dataset_uri] v.subjectid = @subjectid - v.validate_algorithm( params[:algorithm_params], OpenTox::SubTask.create(task,33,100)) + v.validate_algorithm( OpenTox::SubTask.create(task,33,100)) v.validation_uri end return_task(task) @@ -452,18 +468,19 @@ post '/training_test_split' do raise OpenTox::BadRequestError.new "dataset_uri missing" unless params[:dataset_uri].to_s.size>0 raise OpenTox::BadRequestError.new "algorithm_uri missing" unless params[:algorithm_uri].to_s.size>0 raise OpenTox::BadRequestError.new "prediction_feature missing" unless params[:prediction_feature].to_s.size>0 + check_stratified(params) task = OpenTox::Task.create( "Perform training test split validation", url_for("/training_test_split", :full) ) do |task| #, params - strat = (params[:stratified].size>0 && params[:stratified]!="false" && params[:stratified]!="0") if params[:stratified] params.merge!( Validation::Util.train_test_dataset_split(params[:dataset_uri], params[:prediction_feature], - @subjectid, strat, params[:split_ratio], params[:random_seed], OpenTox::SubTask.create(task,0,33))) + @subjectid, params[:stratified], params[:split_ratio], params[:random_seed], OpenTox::SubTask.create(task,0,33))) v = Validation::Validation.create :validation_type => "training_test_split", :training_dataset_uri => params[:training_dataset_uri], :test_dataset_uri => params[:test_dataset_uri], :test_target_dataset_uri => params[:dataset_uri], :prediction_feature => params[:prediction_feature], - :algorithm_uri => params[:algorithm_uri] + :algorithm_uri => params[:algorithm_uri], + :algorithm_params => params[:algorithm_params] v.subjectid = @subjectid - v.validate_algorithm( params[:algorithm_params], OpenTox::SubTask.create(task,33,100)) + v.validate_algorithm( OpenTox::SubTask.create(task,33,100)) v.validation_uri end return_task(task) @@ -545,10 +562,10 @@ end post '/plain_training_test_split' do LOGGER.info "creating pure training test split "+params.inspect raise OpenTox::BadRequestError.new "dataset_uri missing" unless params[:dataset_uri] + check_stratified(params) task = OpenTox::Task.create( "Create data-split", url_for("/plain_training_test_split", :full) ) do |task| - strat = (params[:stratified].size>0 && params[:stratified]!="false" && params[:stratified]!="0") if params[:stratified] result = Validation::Util.train_test_dataset_split(params[:dataset_uri], params[:prediction_feature], @subjectid, - strat, params[:split_ratio], params[:random_seed]) + params[:stratified], params[:split_ratio], params[:random_seed], task) content_type "text/uri-list" result[:training_dataset_uri]+"\n"+result[:test_dataset_uri]+"\n" end |