diff options
Diffstat (limited to 'report/validation_access.rb')
| -rwxr-xr-x[-rw-r--r--] | report/validation_access.rb | 309 |
1 files changed, 57 insertions, 252 deletions
diff --git a/report/validation_access.rb b/report/validation_access.rb index 7d318af..53ecc46 100644..100755 --- a/report/validation_access.rb +++ b/report/validation_access.rb @@ -1,65 +1,31 @@ require "lib/validation_db.rb" -# = Reports::ValidationAccess +# = Reports::ValidationDB # -# service that connects (mainly) to the validation-service +# connects directly to the validation db, overwirte with restclient calls +# if reports/reach reports are seperated from validation someday # -class Reports::ValidationAccess - - # initialize Reports::Validation object with data from Lib:Validation object - # - def init_validation(validation, uri) - raise "not implemented" - end - - # sets cv-attributes in Reports::Validation object - # - def init_cv(validation) - raise "not implemented" - end - - # yields predictions (Lib::OTPredictions) if available - # - def get_predictions(validation) - raise "not implemented" - end - - # replaces crossvalidations uris with corresponding validation uris, in-/output: array - # - def resolve_cv_uris(validation_uris) - raise "not implemented" - end +class Reports::ValidationDB - # get domain/class values of prediction feature - # - def get_prediction_feature_values(validation) - raise "not implemented" - end - - # is validation classification? - # - def classification?(validation) - raise "not implemented" - end - - def predicted_variable(validation) - raise "not implemented" - end - -end - -class Reports::ValidationDB < Reports::ValidationAccess - - def initialize - @model_store = {} - end - - def resolve_cv_uris(validation_uris) + def resolve_cv_uris(validation_uris, subjectid=nil) res = [] validation_uris.each do |u| if u.to_s =~ /.*\/crossvalidation\/[0-9]+/ cv_id = u.split("/")[-1].to_i - res += Lib::Validation.find( :all, :conditions => { :crossvalidation_id => cv_id } ).collect{|v| v.validation_uri.to_s} + cv = nil + + raise OpenTox::NotAuthorizedError.new "Not authorized: GET "+u.to_s if + AA_SERVER and !OpenTox::Authorization.authorized?(u,"GET",subjectid) +# begin +# #cv = Lib::Crossvalidation.find( cv_id ) +# rescue => ex +# raise "could not access crossvalidation with id "+validation_id.to_s+", error-msg: "+ex.message +# end + cv = Lib::Crossvalidation.get( cv_id ) + raise OpenTox::NotFoundError.new "crossvalidation with id "+cv_id.to_s+" not found" unless cv + raise OpenTox::BadRequestError.new("crossvalidation with id '"+cv_id.to_s+"' not finished") unless cv.finished + #res += Lib::Validation.find( :all, :conditions => { :crossvalidation_id => cv_id } ).collect{|v| v.validation_uri.to_s} + res += Lib::Validation.all( :crossvalidation_id => cv_id ).collect{|v| v.validation_uri.to_s } else res += [u.to_s] end @@ -67,20 +33,18 @@ class Reports::ValidationDB < Reports::ValidationAccess res end + def init_validation(validation, uri, subjectid=nil) - def init_validation(validation, uri) - - raise Reports::BadRequest.new "not a validation uri: "+uri.to_s unless uri =~ /.*\/[0-9]+/ + raise OpenTox::BadRequestError.new "not a validation uri: "+uri.to_s unless uri =~ /.*\/[0-9]+/ validation_id = uri.split("/")[-1] - raise Reports::BadRequest.new "invalid validation id "+validation_id.to_s unless validation_id!=nil and + raise OpenTox::BadRequestError.new "invalid validation id "+validation_id.to_s unless validation_id!=nil and (validation_id.to_i > 0 || validation_id.to_s=="0" ) v = nil - begin - v = Lib::Validation.find(validation_id) - rescue => ex - raise "could not access validation with id "+validation_id.to_s+", error-msg: "+ex.message - end - raise Reports::BadRequest.new "no validation found with id "+validation_id.to_s unless v #+" and uri "+uri.to_s unless v + raise OpenTox::NotAuthorizedError.new "Not authorized: GET "+uri.to_s if + AA_SERVER and !OpenTox::Authorization.authorized?(uri,"GET",subjectid) + v = Lib::Validation.get(validation_id) + raise OpenTox::NotFoundError.new "validation with id "+validation_id.to_s+" not found" unless v + raise OpenTox::BadRequestError.new "validation with id "+validation_id.to_s+" is not finished yet" unless v.finished (Lib::VAL_PROPS + Lib::VAL_CV_PROPS).each do |p| validation.send("#{p.to_s}=".to_sym, v.send(p)) @@ -95,207 +59,48 @@ class Reports::ValidationDB < Reports::ValidationAccess def init_cv(validation) - cv = Lib::Crossvalidation.find(validation.crossvalidation_id) - raise Reports::BadRequest.new "no crossvalidation found with id "+validation.crossvalidation_id.to_s unless cv + #cv = Lib::Crossvalidation.find(validation.crossvalidation_id) + cv = Lib::Crossvalidation.get(validation.crossvalidation_id) + raise OpenTox::BadRequestError.new "no crossvalidation found with id "+validation.crossvalidation_id.to_s unless cv Lib::CROSS_VAL_PROPS.each do |p| validation.send("#{p.to_s}=".to_sym, cv[p]) end end - def get_predictions(validation) - Lib::OTPredictions.new( validation.classification?, validation.test_dataset_uri, validation.test_target_dataset_uri, - validation.prediction_feature, validation.prediction_dataset_uri, validation.predicted_variable) - end - - def get_prediction_feature_values( validation ) - OpenTox::Feature.domain( validation.prediction_feature ) + def get_predictions(validation, subjectid=nil, task=nil) + Lib::OTPredictions.new( validation.feature_type, validation.test_dataset_uri, + validation.test_target_dataset_uri, validation.prediction_feature, validation.prediction_dataset_uri, + validation.predicted_variable, subjectid, task) end - def classification?( validation ) - get_model(validation).classification? + def get_class_domain( validation ) + OpenTox::Feature.new( validation.prediction_feature ).domain end - def predicted_variable(validation) - get_model(validation).predictedVariables + def feature_type( validation, subjectid=nil ) + OpenTox::Model::Generic.new(validation.model_uri).feature_type(subjectid) + #get_model(validation).classification? end - private - def get_model(validation) + def predicted_variable(validation, subjectid=nil) raise "cannot derive model depended props for merged validations" if Lib::MergeObjects.merged?(validation) - model = @model_store[validation.model_uri] - unless model - model = OpenTox::Model::PredictionModel.find(validation.model_uri) - raise "model not found '"+validation.model_uri+"'" unless validation.model_uri && model - @model_store[validation.model_uri] = model - end - return model - end - + model = OpenTox::Model::Generic.find(validation.model_uri, subjectid) + raise OpenTox::NotFoundError.new "model not found '"+validation.model_uri+"'" unless model + model.metadata[OT.predictedVariables] + #get_model(validation).predictedVariables + end + +# private +# def get_model(validation) +# raise "cannot derive model depended props for merged validations" if Lib::MergeObjects.merged?(validation) +# model = @model_store[validation.model_uri] +# unless model +# model = OpenTox::Model::PredictionModel.find(validation.model_uri) +# raise "model not found '"+validation.model_uri+"'" unless validation.model_uri && model +# @model_store[validation.model_uri] = model +# end +# return model +# end end - -# -# OUTDATED, please update before use -# -class Reports::ValidationWebservice < Reports::ValidationAccess - - def resolve_cv_uris(validation_uris) - res = [] - validation_uris.each do |u| - if u.to_s =~ /.*\/crossvalidation\/.*/ - uri = u.to_s+"/validations" - begin - vali_uri_list = RestClientWrapper.get uri - rescue => ex - raise Reports::BadRequest.new "cannot get validations for cv at '"+uri.to_s+"', error msg: "+ex.message - end - res += vali_uri_list.split("\n") - else - res += [u.to_s] - end - end - res - end - - - def init_validation(validation, uri) - - begin - data = YAML.load(RestClient.get uri) - rescue => ex - raise Reports::BadRequest.new "cannot get validation at '"+uri.to_s+"', error msg: "+ex.message - end - - Lib::VAL_PROPS.each do |p| - validation.send("#{p}=".to_sym, data[p]) - end - - #model = OpenTox::Model::LazarClassificationModel.new(v[:model_uri]) - #raise "cannot access model '"+v[:model_uri].to_s+"'" unless model - #validation.prediction_feature = model.get_prediction_feature - - {Lib::VAL_CV_PROP => Lib::VAL_CV_PROPS, - Lib::VAL_CLASS_PROP => Lib::VAL_CLASS_PROPS_EXTENDED}.each do |subset_name,subset_props| - subset = data[subset_name] - subset_props.each{ |prop| validation.send("#{prop}=".to_sym, subset[prop]) } if subset - end - end - - def init_cv(validation) - - raise "cv-uri not set" unless validation.crossvalidation_uri - - begin - data = YAML.load(RestClient.get validation.crossvalidation_uri) - rescue => ex - raise Reports::BadRequest.new "cannot get crossvalidation at '"+validation.crossvalidation_uri.to_s+"', error msg: "+ex.message - end - - Lib::CROSS_VAL_PROPS.each do |p| - validation.send("#{p.to_s}=".to_sym, data[p]) - end - end - - def get_predictions(validation) - Lib::Predictions.new( validation.prediction_feature, validation.test_dataset_uri, validation.prediction_dataset_uri) - end -end - -# = Reports::OTMockLayer -# -# OUTDATED, please update before use -# -# does not connect to other services, provides randomly generated data -# -class Reports::ValidationMockLayer < Reports::ValidationAccess - - NUM_DATASETS = 1 - NUM_ALGS = 4 - NUM_FOLDS = 5 - NUM_PREDICTIONS = 30 - ALGS = ["naive-bayes", "c4.5", "svm", "knn", "lazar", "id3"] - DATASETS = ["hamster", "mouse" , "rat", "dog", "cat", "horse", "bug", "ant", "butterfly", "rabbit", "donkey", "monkey", "dragonfly", "frog", "dragon", "dinosaur"] - FOLDS = [1,2,3,4,5,6,7,8,9,10] - - def initialize - - super - @algs = [] - @datasets = [] - @folds = [] - sum = NUM_DATASETS*NUM_ALGS*NUM_FOLDS - (0..sum-1).each do |i| - @folds[i] = FOLDS[i%NUM_FOLDS] - @algs[i] = ALGS[(i/NUM_FOLDS)%NUM_ALGS] - @datasets[i] = DATASETS[((i/NUM_FOLDS)/NUM_ALGS)%NUM_DATASETS] - end - @count = 0 - end - - def resolve_cv_uris(validation_uris) - res = [] - validation_uris.each do |u| - if u.to_s =~ /.*crossvalidation.*/ - res += ["validation_x"]*NUM_FOLDS - else - res += [u.to_s] - end - end - res - end - - def init_validation(validation, uri) - - validation.model_uri = @algs[@count] - validation.test_dataset_uri = @datasets[@count] - validation.prediction_dataset_uri = "bla" - - cv_id = @count/NUM_FOLDS - validation.crossvalidation_id = cv_id - validation.crossvalidation_fold = @folds[@count] - - validation.auc = 0.5 + cv_id*0.02 + rand/3.0 - validation.acc = 0.5 + cv_id*0.02 + rand/3.0 - validation.tp = 1 - validation.fp = 1 - validation.tn = 1 - validation.fn = 1 - - validation.algorithm_uri = @algs[@count] - validation.training_dataset_uri = @datasets[@count] - validation.test_dataset_uri = @datasets[@count] - - validation.prediction_feature = "classification" - - @count += 1 - end - - def init_cv(validation) - - raise "cv-id not set" unless validation.crossvalidation_id - - validation.num_folds = NUM_FOLDS - validation.algorithm_uri = @algs[validation.crossvalidation_id.to_i * NUM_FOLDS] - validation.dataset_uri = @datasets[validation.crossvalidation_id.to_i * NUM_FOLDS] - validation.stratified = true - validation.random_seed = 1 - #validation.CV_dataset_name = @datasets[validation.crossvalidation_id.to_i * NUM_FOLDS] - end - - def get_predictions(validation) - - p = Array.new - c = Array.new - conf = Array.new - u = Array.new - (0..NUM_PREDICTIONS).each do |i| - p.push rand(2) - c.push rand(2) - conf.push rand - u.push("compound no"+(i+1).to_s) - end - Lib::MockPredictions.new( p, c, conf, u ) - end - - end |