diff options
Diffstat (limited to 'report/validation_access.rb')
| -rwxr-xr-x | report/validation_access.rb | 60 |
1 files changed, 51 insertions, 9 deletions
diff --git a/report/validation_access.rb b/report/validation_access.rb index 2cb0c6f..aaa7bdc 100755 --- a/report/validation_access.rb +++ b/report/validation_access.rb @@ -7,6 +7,8 @@ require "lib/validation_db.rb" # class Reports::ValidationDB + @@tmp_resources = [] + def same_service?(uri) self_uri = URI.parse($url_provider.url) val_uri = URI.parse(uri) @@ -132,27 +134,67 @@ class Reports::ValidationDB validation.send("#{p.to_s}=".to_sym, cv.send(p.to_s)) end end + + def training_feature_dataset_uri(validation, subjectid) + m = OpenTox::Model::Generic.find(validation.model_uri, subjectid) + if m + f = m.metadata[OT.featureDataset] + return f.chomp if f + end + raise "no feature dataset found" + end + def test_feature_dataset_uri(validation, subjectid) + m = OpenTox::Model::Generic.find(validation.model_uri, subjectid) + feat_gen = nil + m.metadata[OT.parameters].each do |h| + if h[DC.title] and h[DC.title]=~/feature_generation/ and h[OT.paramValue] + feat_gen = h[OT.paramValue] + break + end + end if m and m.metadata[OT.parameters] + raise "no feature creation alg found" unless feat_gen + feat_gen = File.join(feat_gen,"match") if feat_gen=~/fminer/ + uri = OpenTox::RestClientWrapper.post(feat_gen,{:subjectid => subjectid, + :feature_dataset_uri=>training_feature_dataset_uri(validation,subjectid), + :dataset_uri=>validation.test_dataset_uri}) + @@tmp_resources << uri + uri + end + + def delete_tmp_resources(subjectid) + @@tmp_resources.each do |uri| + OpenTox::RestClientWrapper.delete uri,{:subjectid=>subjectid} + end + @@tmp_resources = [] + end + def get_predictions(validation, filter_params, subjectid, task) # we need compound info, cannot reuse stored prediction data data = Lib::PredictionData.create( validation.feature_type, validation.test_dataset_uri, validation.test_target_dataset_uri, validation.prediction_feature, validation.prediction_dataset_uri, - validation.predicted_variable, validation.predicted_confidence, subjectid, task ) + validation.predicted_variable, validation.predicted_confidence, subjectid, OpenTox::SubTask.create(task, 0, 80 ) ) data = Lib::PredictionData.filter_data( data.data, data.compounds, filter_params[:min_confidence], filter_params[:min_num_predictions], filter_params[:max_num_predictions] ) if filter_params!=nil + task.progress(100) if task Lib::OTPredictions.new( data.data, data.compounds ) end def get_accept_values( validation, subjectid=nil ) # PENDING So far, one has to load the whole dataset to get the accept_value from ambit - test_target_dataset = validation.test_target_dataset_uri - test_target_dataset = validation.test_dataset_uri unless test_target_dataset - d = Lib::DatasetCache.find( test_target_dataset, subjectid ) - raise "cannot get test target dataset for accept values, dataset: "+test_target_dataset.to_s unless d - accept_values = d.accept_values(validation.prediction_feature) - raise "cannot get accept values from dataset "+test_target_dataset.to_s+" for feature "+ - validation.prediction_feature+":\n"+d.features[validation.prediction_feature].to_yaml unless accept_values!=nil - accept_values + test_target_datasets = validation.test_target_dataset_uri + test_target_datasets = validation.test_dataset_uri unless test_target_datasets + res = nil + test_target_datasets.split(";").each do |test_target_dataset| + d = Lib::DatasetCache.find( test_target_dataset, subjectid ) + raise "cannot get test target dataset for accept values, dataset: "+test_target_dataset.to_s unless d + accept_values = d.accept_values(validation.prediction_feature) + raise "cannot get accept values from dataset "+test_target_dataset.to_s+" for feature "+ + validation.prediction_feature+":\n"+d.features[validation.prediction_feature].to_yaml unless accept_values!=nil + raise "different accept values" if res && res!=accept_values + res = accept_values + end + res end def feature_type( validation, subjectid=nil ) |