diff options
Diffstat (limited to 'lib/validation.rb')
| -rw-r--r-- | lib/validation.rb | 74 |
1 files changed, 72 insertions, 2 deletions
diff --git a/lib/validation.rb b/lib/validation.rb index a47a554..d58d36e 100644 --- a/lib/validation.rb +++ b/lib/validation.rb @@ -12,6 +12,40 @@ module OpenTox val end + # returns a filtered list of validation uris + # @param [Hash,optional] params, validation-params to filter the uris (could be model, training_dataset, ..) + # @return [Array] + def self.list( params={} ) + filter_string = "" + params.each do |k,v| + filter_string = "?" if filter_string.length==0 + filter_string += k.to_s+"="+v + end + (OpenTox::RestClientWrapper.get(CONFIG[:services]["opentox-validation"]+filter_string).split("\n")) + end + + # creates a training test split validation, waits until it finishes, may take some time + # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,split_ratio(0.67),random_seed(1)) + # @param [String,optional] subjectid + # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly + # @return [OpenTox::Validation] + def self.create_training_test_split( params, subjectid=nil, waiting_task=nil ) + params[:subjectid] = subjectid if subjectid + uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"training_test_split"), + params,{:content_type => "text/uri-list"},waiting_task ) + Validation.new(uri) + end + + # looks for report for this validation, creates a report if no report is found + # @param [String,optional] subjectid + # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly + # @return [String] report uri + def find_or_create_report( subjectid=nil, waiting_task=nil ) + @report = ValidationReport.find_for_validation(@uri, subjectid) unless @report + @report = ValidationReport.create(@uri, subjectid, waiting_task) unless @report + @report.uri + end + # creates a validation object from crossvaldiation statistics, raise error if not found # (as crossvaldiation statistics are returned as an average valdidation over all folds) # @param [String] crossvalidation uri @@ -42,7 +76,7 @@ module OpenTox res[:true_negatives] = s[OT.numTrueNegatives] res[:false_negatives] = s[OT.numFalseNegatives] res[:sensitivity] = s[OT.truePositiveRate] - res[:specificity] = s[OT.falsePositiveRate] + res[:specificity] = s[OT.trueNegativeRate] break end end @@ -72,6 +106,18 @@ module OpenTox cv.load_metadata( subjectid ) cv end + + # returns a filtered list of crossvalidation uris + # @param [Hash,optional] params, crossvalidation-params to filter the uris (could be algorithm, dataset, ..) + # @return [Array] + def self.list( params={} ) + filter_string = "" + params.each do |k,v| + filter_string = "?" if filter_string.length==0 + filter_string += k.to_s+"="+v + end + (OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],"crossvalidation")+filter_string).split("\n")) + end # creates a crossvalidations, waits until it finishes, may take some time # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,num_folds(10),random_seed(1),stratified(false)) @@ -110,6 +156,17 @@ module OpenTox class ValidationReport include OpenTox + # finds ValidationReport via uri, raises error if not found + # @param [String] uri + # @param [String,optional] subjectid + # @return [OpenTox::ValidationReport] + def self.find( uri, subjectid=nil ) + OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid}) + rep = ValidationReport.new(uri) + rep.load_metadata( subjectid ) + rep + end + # finds ValidationReport for a particular validation # @param [String] crossvalidation uri # @param [String,optional] subjectid @@ -120,6 +177,17 @@ module OpenTox uris.size==0 ? nil : ValidationReport.new(uris[-1]) end + # creates a validation report via validation + # @param [String] validation uri + # @param [String,optional] subjectid + # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly + # @return [OpenTox::ValidationReport] + def self.create( validation_uri, subjectid=nil, waiting_task=nil ) + uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/report/validation"), + { :validation_uris => validation_uri, :subjectid => subjectid }, {}, waiting_task ) + ValidationReport.new(uri) + end + end class CrossvalidationReport @@ -132,7 +200,9 @@ module OpenTox def self.find( uri, subjectid=nil ) # PENDING load report data? OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid}) - CrossvalidationReport.new(uri) + rep = CrossvalidationReport.new(uri) + rep.load_metadata( subjectid ) + rep end # finds CrossvalidationReport for a particular crossvalidation |