diff options
Diffstat (limited to 'validation/validation_application.rb')
| -rwxr-xr-x | validation/validation_application.rb | 275 |
1 files changed, 169 insertions, 106 deletions
diff --git a/validation/validation_application.rb b/validation/validation_application.rb index 4bcd07d..d2dfef0 100755 --- a/validation/validation_application.rb +++ b/validation/validation_application.rb @@ -3,23 +3,30 @@ require lib end -require 'lib/merge.rb' -#require 'lib/active_record_setup.rb' +require 'lib/dataset_cache.rb' require 'validation/validation_service.rb' get '/crossvalidation/?' do LOGGER.info "list all crossvalidations" - uri_list = Lib::OhmUtil.find( Validation::Crossvalidation, params ).collect{|v| v.crossvalidation_uri}.join("\n") + "\n" + uri_list = Lib::OhmUtil.find( Validation::Crossvalidation, params ).sort.collect{|v| v.crossvalidation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = - "Single validations: "+url_for("/",:full)+"\n"+ - "Crossvalidation reports: "+url_for("/report/crossvalidation",:full) + "Single validations: "+url_for("/",:full)+"\n"+ + "Leave-one-out crossvalidations: "+url_for("/crossvalidation/loo",:full)+"\n"+ + "Crossvalidation reports: "+url_for("/report/crossvalidation",:full) description = "A list of all crossvalidations.\n"+ "Use the POST method to perform a crossvalidation." - post_params = [[:dataset_uri,:algorithm_uri,:prediction_feature,[:num_folds,10],[:random_seed,1],[:stratified,false],[:algorithm_params,""]]] + post_command = OpenTox::PostCommand.new request.url,"Perform crossvalidation" + post_command.attributes << OpenTox::PostAttribute.new("algorithm_uri") + post_command.attributes << OpenTox::PostAttribute.new("dataset_uri") + post_command.attributes << OpenTox::PostAttribute.new("prediction_feature") + post_command.attributes << OpenTox::PostAttribute.new("algorithm_params",false,nil,"Params used for model building, separate with ';', example: param1=v1;param2=v2") + post_command.attributes << OpenTox::PostAttribute.new("num_folds",false,"10") + post_command.attributes << OpenTox::PostAttribute.new("random_seed",false,"1","An equal random seed value ensures the excact same random dataset split.") + post_command.attributes << OpenTox::PostAttribute.new("stratified",false,"false","Stratification ensures an equal class-value spread in folds.") content_type "text/html" - OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_params + OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_command else content_type "text/uri-list" uri_list @@ -27,20 +34,25 @@ get '/crossvalidation/?' do end post '/crossvalidation/?' do - task = OpenTox::Task.create( "Perform crossvalidation", url_for("/crossvalidation", :full) ) do |task| #, params - LOGGER.info "creating crossvalidation "+params.inspect - raise OpenTox::BadRequestError.new "dataset_uri missing" unless params[:dataset_uri] - raise OpenTox::BadRequestError.new "algorithm_uri missing" unless params[:algorithm_uri] - raise OpenTox::BadRequestError.new "prediction_feature missing" unless params[:prediction_feature] - 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 + LOGGER.info "creating crossvalidation "+params.inspect + 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 + 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 + 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] } - [ :num_folds, :random_seed, :stratified ].each{ |sym| cv_params[sym] = params[sym] if params[sym] } + :algorithm_uri => params[:algorithm_uri], + :loo => "false", + :subjectid => params[: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], task ) + cv.perform_cv( params[:prediction_feature], params[:algorithm_params], 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 end return_task(task) @@ -50,28 +62,64 @@ post '/crossvalidation/cleanup/?' do LOGGER.info "crossvalidation cleanup, starting..." content_type "text/uri-list" deleted = [] - #Validation::Crossvalidation.find_like(params).each do |cv| - Validation::Crossvalidation.all( { :finished => false } ).each do |cv| - #num_vals = Validation::Validation.find( :all, :conditions => { :crossvalidation_id => cv.id } ).size - #num_vals = Validation::Validation.all( :crossvalidation_id => cv.id ).size - #if cv.num_folds != num_vals || !cv.finished + Validation::Crossvalidation.all.collect.delete_if{|cv| cv.finished}.each do |cv| + if OpenTox::Authorization.authorized?(cv.crossvalidation_uri,"DELETE",@subjectid) LOGGER.debug "delete cv with id:"+cv.id.to_s+", finished is false" deleted << cv.crossvalidation_uri - #Validation::Crossvalidation.delete(cv.id) cv.subjectid = @subjectid cv.delete_crossvalidation - #end + sleep 1 if AA_SERVER + end end LOGGER.info "crossvalidation cleanup, deleted "+deleted.size.to_s+" cvs" deleted.join("\n")+"\n" end post '/crossvalidation/loo/?' do - raise "not yet implemented" + LOGGER.info "creating loo-crossvalidation "+params.inspect + 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 + 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] + task = OpenTox::Task.create( "Perform loo-crossvalidation", url_for("/crossvalidation/loo", :full) ) do |task| #, params + cv_params = { :dataset_uri => params[:dataset_uri], + :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)) + # 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 + end + return_task(task) end get '/crossvalidation/loo/?' do - raise OpenTox::BadRequestError.new "GET operation not supported, use POST for performing a loo-crossvalidation, see "+url_for("/crossvalidation", :full)+" for crossvalidation results" + LOGGER.info "list all crossvalidations" + params[:loo]="true" + uri_list = Lib::OhmUtil.find( Validation::Crossvalidation, params ).sort.collect{|v| v.crossvalidation_uri}.join("\n") + "\n" + if request.env['HTTP_ACCEPT'] =~ /text\/html/ + related_links = + "Single validations: "+url_for("/",:full)+"\n"+ + "All crossvalidations: "+url_for("/crossvalidation",:full)+"\n"+ + "Crossvalidation reports: "+url_for("/report/crossvalidation",:full) + description = + "A list of all leave one out crossvalidations.\n"+ + "Use the POST method to perform a crossvalidation." + post_command = OpenTox::PostCommand.new request.url,"Perform leave-one-out-crossvalidation" + post_command.attributes << OpenTox::PostAttribute.new("algorithm_uri") + post_command.attributes << OpenTox::PostAttribute.new("dataset_uri") + post_command.attributes << OpenTox::PostAttribute.new("prediction_feature") + post_command.attributes << OpenTox::PostAttribute.new("algorithm_params",false,nil,"Params used for model building, separate with ';', example: param1=v1;param2=v2") + content_type "text/html" + OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_command + else + content_type "text/uri-list" + uri_list + end + end get '/crossvalidation/:id' do @@ -108,33 +156,9 @@ get '/crossvalidation/:id' do end get '/crossvalidation/:id/statistics' do - LOGGER.info "get merged validation-result for crossvalidation with id "+params[:id].to_s -# begin - #crossvalidation = Validation::Crossvalidation.find(params[:id]) -# rescue ActiveRecord::RecordNotFound => ex -# raise OpenTox::NotFoundError.new "Crossvalidation '#{params[:id]}' not found." -# end - #crossvalidation = Validation::Crossvalidation.find(params[:id]) - crossvalidation = Validation::Crossvalidation.get(params[:id]) - - raise OpenTox::NotFoundError.new "Crossvalidation '#{params[:id]}' not found." unless crossvalidation - raise OpenTox::BadRequestError.new "Crossvalidation '"+params[:id].to_s+"' not finished" unless crossvalidation.finished - - Lib::MergeObjects.register_merge_attributes( Validation::Validation, - Validation::VAL_MERGE_AVG,Validation::VAL_MERGE_SUM,Validation::VAL_MERGE_GENERAL-[:date,:validation_uri,:crossvalidation_uri]) unless - Lib::MergeObjects.merge_attributes_registered?(Validation::Validation) - - #v = Lib::MergeObjects.merge_array_objects( Validation::Validation.find( :all, :conditions => { :crossvalidation_id => params[:id] } ) ) - # convert ohm:set into array, as ohm:set[0]=nil(!) - vals = Validation::Validation.find( :crossvalidation_id => params[:id] ).collect{|x| x} -# LOGGER.debug vals.collect{|v| v.validation_uri}.join("\n") -# LOGGER.debug vals.size -# LOGGER.debug vals.class - raise "could not load all validations for crossvalidation" if vals.include?(nil) - v = Lib::MergeObjects.merge_array_objects( vals ) - v.date = nil - #v.id = nil + LOGGER.info "get crossvalidation statistics for crossvalidation with id "+params[:id].to_s + v = Validation::Validation.from_cv_statistics( params[:id], @subjectid ) case request.env['HTTP_ACCEPT'].to_s when /text\/html/ related_links = @@ -143,6 +167,9 @@ get '/crossvalidation/:id/statistics' do "The averaged statistics for the crossvalidation." content_type "text/html" OpenTox.text_to_html v.to_yaml,@subjectid,related_links,description + when "application/rdf+xml" + content_type "application/rdf+xml" + v.to_rdf else content_type "application/x-yaml" v.to_yaml @@ -160,8 +187,8 @@ delete '/crossvalidation/:id/?' do # Validation::Crossvalidation.delete(params[:id]) cv = Validation::Crossvalidation.get(params[:id]) - cv.subjectid = @subjectid raise OpenTox::NotFoundError.new "Crossvalidation '#{params[:id]}' not found." unless cv + cv.subjectid = @subjectid cv.delete_crossvalidation end @@ -187,7 +214,7 @@ get '/crossvalidation/:id/predictions' do raise OpenTox::BadRequestError.new "Crossvalidation '"+params[:id].to_s+"' not finished" unless crossvalidation.finished content_type "application/x-yaml" - validations = Validation::Validation.find( :crossvalidation_id => params[:id] ) + validations = Validation::Validation.find( :crossvalidation_id => params[:id], :validation_type => "crossvalidation" ) p = Lib::OTPredictions.to_array( validations.collect{ |v| v.compute_validation_stats_with_model(nil, true) } ).to_yaml case request.env['HTTP_ACCEPT'].to_s @@ -208,7 +235,7 @@ end get '/?' do LOGGER.info "list all validations, params: "+params.inspect - uri_list = Lib::OhmUtil.find( Validation::Validation, params ).collect{|v| v.validation_uri}.join("\n") + "\n" + uri_list = Lib::OhmUtil.find( Validation::Validation, params ).sort.collect{|v| v.validation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = "To perform a validation:\n"+ @@ -237,7 +264,8 @@ end post '/test_set_validation' do LOGGER.info "creating test-set-validation "+params.inspect - if params[:model_uri] and params[:test_dataset_uri] and !params[:training_dataset_uri] and !params[:algorithm_uri] + if params[:model_uri].to_s.size>0 and params[:test_dataset_uri].to_s.size>0 and + params[:training_dataset_uri].to_s.size==0 and params[:algorithm_uri].to_s.size==0 task = OpenTox::Task.create( "Perform test-set-validation", url_for("/", :full) ) do |task| #, params v = Validation::Validation.create :validation_type => "test_set_validation", :model_uri => params[:model_uri], @@ -262,7 +290,7 @@ get '/test_set_validation' do #uri_list = Validation::Validation.all( :validation_type => "test_set_validation" ).collect{ |v| v.validation_uri }.join("\n")+"\n" #params[:validation_type] = "test_set_validation" #uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" - uri_list = Validation::Validation.find(:validation_type => "test_set_validation").collect{|v| v.validation_uri}.join("\n") + "\n" + uri_list = Validation::Validation.find(:validation_type => "test_set_validation").sort.collect{|v| v.validation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = @@ -271,9 +299,13 @@ get '/test_set_validation' do description = "A list of all test-set-validations.\n"+ "To perform a test-set-validation use the POST method." - post_params = [[:model_uri, :test_dataset_uri, [:test_target_dataset_uri,"same-as-test_dataset_uri"], [:prediction_feature, "dependent-variable-of-model"]]] + post_command = OpenTox::PostCommand.new request.url,"Perform test-set-validation" + post_command.attributes << OpenTox::PostAttribute.new("model_uri") + post_command.attributes << OpenTox::PostAttribute.new("test_dataset_uri") + post_command.attributes << OpenTox::PostAttribute.new("test_target_dataset_uri",false,nil,"Specify if target endpoint values are not available in test dataset.") + post_command.attributes << OpenTox::PostAttribute.new("prediction_feature",false,nil,"Default is 'dependentVariables' of the model.") content_type "text/html" - OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_params + OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_command else content_type "text/uri-list" uri_list @@ -282,7 +314,8 @@ end post '/training_test_validation/?' do LOGGER.info "creating training-test-validation "+params.inspect - if params[:algorithm_uri] and params[:training_dataset_uri] and params[:test_dataset_uri] and params[:prediction_feature] and !params[:model_uri] + if params[:algorithm_uri].to_s.size>0 and params[:training_dataset_uri].to_s.size>0 and + params[:test_dataset_uri].to_s.size>0 and params[:prediction_feature].to_s.size>0 and params[:model_uri].to_s.size==0 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], @@ -307,7 +340,7 @@ get '/training_test_validation' do #uri_list = Validation::Validation.all( :validation_type => "training_test_validation" ).collect{ |v| v.validation_uri }.join("\n")+"\n" #params[:validation_type] = "training_test_validation" #uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" - uri_list = Validation::Validation.find(:validation_type => "training_test_validation").collect{|v| v.validation_uri}.join("\n") + "\n" + uri_list = Validation::Validation.find(:validation_type => "training_test_validation").sort.collect{|v| v.validation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = @@ -316,14 +349,15 @@ get '/training_test_validation' do description = "A list of all training-test-validations.\n"+ "To perform a training-test-validation use the POST method." - post_params = [[:algorithm_uri, - :training_dataset_uri, - :test_dataset_uri, - [:test_target_dataset_uri,"same-as-test_dataset_uri"], - :prediction_feature, - [:algorithm_params, ""]]] + post_command = OpenTox::PostCommand.new request.url,"Perform training-test-validation" + post_command.attributes << OpenTox::PostAttribute.new("algorithm_uri") + post_command.attributes << OpenTox::PostAttribute.new("training_dataset_uri") + post_command.attributes << OpenTox::PostAttribute.new("test_dataset_uri") + post_command.attributes << OpenTox::PostAttribute.new("test_target_dataset_uri",false,nil,"Specify if target endpoint values are not available in test dataset.") + post_command.attributes << OpenTox::PostAttribute.new("prediction_feature") + post_command.attributes << OpenTox::PostAttribute.new("algorithm_params",false,nil,"Params used for model building, separate with ';', example: param1=v1;param2=v2") content_type "text/html" - OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_params + OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_command else content_type "text/uri-list" uri_list @@ -331,19 +365,21 @@ get '/training_test_validation' do end post '/bootstrapping' do + LOGGER.info "performing bootstrapping validation "+params.inspect + 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 task = OpenTox::Task.create( "Perform bootstrapping validation", url_for("/bootstrapping", :full) ) do |task| #, params - LOGGER.info "performing bootstrapping validation "+params.inspect - raise OpenTox::BadRequestError.new "dataset_uri missing" unless params[:dataset_uri] - raise OpenTox::BadRequestError.new "algorithm_uri missing" unless params[:algorithm_uri] - raise OpenTox::BadRequestError.new "prediction_feature missing" unless params[:prediction_feature] - params.merge!( Validation::Util.bootstrapping( params[:dataset_uri], params[:prediction_feature], @subjectid, params[:random_seed], OpenTox::SubTask.create(task,0,33)) ) + LOGGER.info "params after bootstrapping: "+params.inspect v = Validation::Validation.create :validation_type => "bootstrapping", :test_target_dataset_uri => params[:dataset_uri], :prediction_feature => params[:prediction_feature], - :algorithm_uri => params[:algorithm_uri] + :algorithm_uri => params[:algorithm_uri], + :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.validation_uri @@ -357,7 +393,7 @@ get '/bootstrapping' do #uri_list = Validation::Validation.all( :validation_type => "bootstrapping" ).collect{ |v| v.validation_uri }.join("\n")+"\n" #params[:validation_type] = "bootstrapping" #uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" - uri_list = Validation::Validation.find(:validation_type => "bootstrapping").collect{|v| v.validation_uri}.join("\n") + "\n" + uri_list = Validation::Validation.find(:validation_type => "bootstrapping").sort.collect{|v| v.validation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = @@ -366,13 +402,14 @@ get '/bootstrapping' do description = "A list of all bootstrapping-validations.\n"+ "To perform a bootstrapping-validation use the POST method." - post_params = [[:algorithm_uri, - :dataset_uri, - :prediction_feature, - [:algorithm_params, ""], - [:random_seed, 1]]] + post_command = OpenTox::PostCommand.new request.url,"Perform bootstrapping-validation" + post_command.attributes << OpenTox::PostAttribute.new("algorithm_uri") + post_command.attributes << OpenTox::PostAttribute.new("dataset_uri") + post_command.attributes << OpenTox::PostAttribute.new("prediction_feature") + post_command.attributes << OpenTox::PostAttribute.new("algorithm_params",false,nil,"Params used for model building, separate with ';', example: param1=v1;param2=v2") + post_command.attributes << OpenTox::PostAttribute.new("random_seed",false,"1","An equal random seed value ensures the excact same random dataset split.") content_type "text/html" - OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_params + OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_command else content_type "text/uri-list" uri_list @@ -380,13 +417,11 @@ get '/bootstrapping' do end post '/training_test_split' do - + LOGGER.info "creating training test split "+params.inspect + 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 task = OpenTox::Task.create( "Perform training test split validation", url_for("/training_test_split", :full) ) do |task| #, params - LOGGER.info "creating training test split "+params.inspect - raise OpenTox::BadRequestError.new "dataset_uri missing" unless params[:dataset_uri] - raise OpenTox::BadRequestError.new "algorithm_uri missing" unless params[:algorithm_uri] - raise OpenTox::BadRequestError.new "prediction_feature missing" unless params[:prediction_feature] - params.merge!( Validation::Util.train_test_dataset_split(params[:dataset_uri], params[:prediction_feature], @subjectid, params[:split_ratio], params[:random_seed], OpenTox::SubTask.create(task,0,33))) v = Validation::Validation.create :validation_type => "training_test_split", @@ -409,7 +444,7 @@ get '/training_test_split' do #uri_list = Validation::Validation.all( :validation_type => "training_test_split" ).collect{ |v| v.validation_uri }.join("\n")+"\n" #params[:validation_type] = "training_test_split" #uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n" - uri_list = Validation::Validation.find(:validation_type => "training_test_split").collect{|v| v.validation_uri}.join("\n") + "\n" + uri_list = Validation::Validation.find(:validation_type => "training_test_split").sort.collect{|v| v.validation_uri}.join("\n") + "\n" if request.env['HTTP_ACCEPT'] =~ /text\/html/ related_links = @@ -418,14 +453,15 @@ get '/training_test_split' do description = "A list of all training-test-split-validations.\n"+ "To perform a training-test-split-validation use the POST method." - post_params = [[:algorithm_uri, - :dataset_uri, - :prediction_feature, - [:algorithm_params, ""], - [:random_seed, 1], - [:split_ratio, 0.66]]] + post_command = OpenTox::PostCommand.new request.url,"Perform training-test-split-validation" + post_command.attributes << OpenTox::PostAttribute.new("algorithm_uri") + post_command.attributes << OpenTox::PostAttribute.new("dataset_uri") + post_command.attributes << OpenTox::PostAttribute.new("prediction_feature") + post_command.attributes << OpenTox::PostAttribute.new("algorithm_params",false,nil,"Params used for model building, separate with ';', example: param1=v1;param2=v2") + post_command.attributes << OpenTox::PostAttribute.new("random_seed",false,"1","An equal random seed value ensures the excact same random dataset split.") + post_command.attributes << OpenTox::PostAttribute.new("split_ratio",false,"0.66","A split ratio of 0.66 implies that two thirds of the compounds are used for training.") content_type "text/html" - OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_params + OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_command else content_type "text/uri-list" uri_list @@ -436,18 +472,44 @@ post '/cleanup/?' do LOGGER.info "validation cleanup, starting..." content_type "text/uri-list" deleted = [] - #Validation::Validation.find( :all, :conditions => { :prediction_dataset_uri => nil } ).each do |val| - Validation::Validation.all( :finished => false ).each do |val| - LOGGER.debug "delete val with id:"+val.id.to_s+", finished is false" - deleted << val.validation_uri - #Validation::Validation.delete(val.id) - val.subjectid = @subjectid - val.delete_validation + Validation::Validation.all.collect.delete_if{|val| val.finished}.each do |val| + if OpenTox::Authorization.authorized?(val.validation_uri,"DELETE",@subjectid) + LOGGER.debug "delete val with id:"+val.id.to_s+", finished is false" + deleted << val.validation_uri + val.subjectid = @subjectid + val.delete_validation + sleep 1 if AA_SERVER + end end LOGGER.info "validation cleanup, deleted "+deleted.size.to_s+" validations" deleted.join("\n")+"\n" end +post '/cleanup_datasets/?' do + LOGGER.info "dataset cleanup, starting..." + content_type "text/uri-list" + used_datasets = Set.new + Validation::Crossvalidation.all.each do |cv| + used_datasets << cv.dataset_uri + end + Validation::Validation.all.each do |val| + used_datasets << val.training_dataset_uri + used_datasets << val.test_target_dataset_uri + used_datasets << val.test_dataset_uri + used_datasets << val.prediction_dataset_uri + end + deleted = [] + OpenTox::Dataset.all.each do |d| + if !used_datasets.include?(d.uri) and OpenTox::Authorization.authorized?(d.uri,"DELETE",@subjectid) + deleted << d.uri + d.delete(@subjectid) + sleep 1 if AA_SERVER + end + end + LOGGER.info "dataset cleanup, deleted "+deleted.size.to_s+" datasets" + deleted.join("\n")+"\n" +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] @@ -465,21 +527,22 @@ post '/validate_datasets' do params[:validation_type] = "validate_datasets" if params[:model_uri] + raise OpenTox::BadRequestError.new "please specify 'model_uri' or set either 'classification' or 'regression' flag" if params[:classification] or params[:regression] v = Validation::Validation.create params v.subjectid = @subjectid v.compute_validation_stats_with_model(nil,false,task) else raise OpenTox::BadRequestError.new "please specify 'model_uri' or 'prediction_feature'" unless params[:prediction_feature] - raise OpenTox::BadRequestError.new "please specify 'model_uri' or 'predicted_feature'" unless params[:predicted_feature] + raise OpenTox::BadRequestError.new "please specify 'model_uri' or 'predicted_variable'" unless params[:predicted_variable] raise OpenTox::BadRequestError.new "please specify 'model_uri' or set either 'classification' or 'regression' flag" unless params[:classification] or params[:regression] - - predicted_feature = params.delete("predicted_feature") + predicted_variable = params.delete("predicted_variable") + predicted_confidence = params.delete("predicted_confidence") feature_type = "classification" if params.delete("classification")!=nil feature_type = "regression" if params.delete("regression")!=nil v = Validation::Validation.create params v.subjectid = @subjectid - v.compute_validation_stats(feature_type,predicted_feature,nil,nil,false,task) + v.compute_validation_stats(feature_type,predicted_variable,predicted_confidence,nil,nil,false,task) end v.validation_uri end |