diff options
Diffstat (limited to 'lib/validation.rb')
| -rw-r--r-- | lib/validation.rb | 313 |
1 files changed, 0 insertions, 313 deletions
diff --git a/lib/validation.rb b/lib/validation.rb deleted file mode 100644 index d7a337c..0000000 --- a/lib/validation.rb +++ /dev/null @@ -1,313 +0,0 @@ -module OpenTox - class Validation - include OpenTox - - # find validation, raises error if not found - # @param [String] uri - # @param [String,optional] subjectid - # @return [OpenTox::Validation] - def self.find( uri, subjectid=nil ) - val = Validation.new(uri) - val.load_metadata( subjectid ) - 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 - # @param [String,optional] subjectid - # @return [OpenTox::Validation] - def self.from_cv_statistics( crossvalidation_uri, subjectid=nil ) - find( File.join(crossvalidation_uri, 'statistics'),subjectid ) - end - - # loads metadata via yaml from validation object - # fields (like for example the validated model) can be acces via validation.metadata[OT.model] - def load_metadata( subjectid=nil ) - @metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid, :accept => "application/x-yaml"})) - end - - # PENDING: creates summary as used for ToxCreate - def summary - if @metadata[OT.classificationStatistics] - res = { - :nr_predictions => @metadata[OT.numInstances].to_i - @metadata[OT.numUnpredicted].to_i, - :correct_predictions => @metadata[OT.classificationStatistics][OT.percentCorrect], - :weighted_area_under_roc => @metadata[OT.classificationStatistics][OT.weightedAreaUnderRoc], - } - @metadata[OT.classificationStatistics][OT.classValueStatistics].each do |s| - if s[OT.classValue].to_s=="true" - res[:true_positives] = s[OT.numTruePositives] - res[:false_positives] = s[OT.numFalsePositives] - res[:true_negatives] = s[OT.numTrueNegatives] - res[:false_negatives] = s[OT.numFalseNegatives] - res[:sensitivity] = s[OT.truePositiveRate] - res[:specificity] = s[OT.trueNegativeRate] - break - end - end - res - elsif @metadata[OT.regressionStatistics] - { - :nr_predictions => @metadata[OT.numInstances].to_i - @metadata[OT.numUnpredicted].to_i, - :r_square => @metadata[OT.regressionStatistics][OT.rSquare], - :root_mean_squared_error => @metadata[OT.regressionStatistics][OT.rootMeanSquaredError], - :mean_absolute_error => @metadata[OT.regressionStatistics][OT.meanAbsoluteError], - } - end - end - end - - class Crossvalidation - include OpenTox - - attr_reader :report - - # find crossvalidation, raises error if not found - # @param [String] uri - # @param [String,optional] subjectid - # @return [OpenTox::Crossvalidation] - def self.find( uri, subjectid=nil ) - cv = Crossvalidation.new(uri) - 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)) - # @param [String,optional] subjectid - # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly - # @return [OpenTox::Crossvalidation] - def self.create( params, subjectid=nil, waiting_task=nil ) - params[:subjectid] = subjectid if subjectid - uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-validation"],"crossvalidation"), - params,{:content_type => "text/uri-list"},waiting_task ) - Crossvalidation.new(uri) - end - - # looks for report for this crossvalidation, 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 = CrossvalidationReport.find_for_crossvalidation(@uri, subjectid) unless @report - @report = CrossvalidationReport.create(@uri, subjectid, waiting_task) unless @report - @report.uri - end - - # loads metadata via yaml from crossvalidation object - # fields (like for example the validations) can be acces via validation.metadata[OT.validation] - def load_metadata( subjectid=nil ) - @metadata = YAML.load(OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid, :accept => "application/x-yaml"})) - end - - # PENDING: creates summary as used for ToxCreate - def summary( subjectid=nil ) - Validation.from_cv_statistics( @uri, subjectid ).summary - end - end - - 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 - # @return [OpenTox::ValidationReport] nil if no report found - def self.find_for_validation( validation_uri, subjectid=nil ) - uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"], - "/report/validation?validation="+validation_uri), {:subjectid => subjectid}).chomp.split("\n") - 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 - include OpenTox - - # finds CrossvalidationReport via uri, raises error if not found - # @param [String] uri - # @param [String,optional] subjectid - # @return [OpenTox::CrossvalidationReport] - def self.find( uri, subjectid=nil ) - OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid}) - rep = CrossvalidationReport.new(uri) - rep.load_metadata( subjectid ) - rep - end - - # finds CrossvalidationReport for a particular crossvalidation - # @param [String] crossvalidation uri - # @param [String,optional] subjectid - # @return [OpenTox::CrossvalidationReport] nil if no report found - def self.find_for_crossvalidation( crossvalidation_uri, subjectid=nil ) - uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"], - "/report/crossvalidation?crossvalidation="+crossvalidation_uri), {:subjectid => subjectid}).chomp.split("\n") - uris.size==0 ? nil : CrossvalidationReport.new(uris[-1]) - end - - # creates a crossvalidation report via crossvalidation - # @param [String] crossvalidation uri - # @param [String,optional] subjectid - # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly - # @return [OpenTox::CrossvalidationReport] - def self.create( crossvalidation_uri, subjectid=nil, waiting_task=nil ) - uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/report/crossvalidation"), - { :validation_uris => crossvalidation_uri, :subjectid => subjectid }, {}, waiting_task ) - CrossvalidationReport.new(uri) - end - end - - - class AlgorithmComparisonReport - include OpenTox - - # finds AlgorithmComparisonReport via uri, raises error if not found - # @param [String] uri - # @param [String,optional] subjectid - # @return [OpenTox::CrossvalidationReport] - def self.find( uri, subjectid=nil ) - OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid}) - rep = AlgorithmComparisonReport.new(uri) - rep.load_metadata( subjectid ) - rep - end - - # finds AlgorithmComparisonReport for a particular crossvalidation - # @param [String] crossvalidation uri - # @param [String,optional] subjectid - # @return [OpenTox::AlgorithmComparisonReport] nil if no report found - def self.find_for_crossvalidation( crossvalidation_uri, subjectid=nil ) - uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"], - "/report/algorithm_comparison?crossvalidation="+crossvalidation_uri), {:subjectid => subjectid}).chomp.split("\n") - uris.size==0 ? nil : AlgorithmComparisonReport.new(uris[-1]) - end - - # creates a crossvalidation report via crossvalidation - # @param [Hash] crossvalidation uri_hash, see example - # @param [String,optional] subjectid - # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly - # @return [OpenTox::AlgorithmComparisonReport] - # example for hash: - # { :lazar-bbrc => [ http://host/validation/crossvalidation/x1, http://host/validation/crossvalidation/x2 ], - # :lazar-last => [ http://host/validation/crossvalidation/xy, http://host/validation/crossvalidation/xy ] } - def self.create( crossvalidation_uri_hash, subjectid=nil, waiting_task=nil ) - identifier = [] - validation_uris = [] - crossvalidation_uri_hash.each do |id, uris| - uris.each do |uri| - identifier << id - validation_uris << uri - end - end - uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/report/algorithm_comparison"), - { :validation_uris => validation_uris.join(","), :identifier => identifier.join(","), :subjectid => subjectid }, {}, waiting_task ) - AlgorithmComparisonReport.new(uri) - end - end - - class QMRFReport - include OpenTox - - # finds QMRFReport, raises Error if not found - # @param [String] uri - # @param [String,optional] subjectid - # @return [OpenTox::QMRFReport] - def self.find( uri, subjectid=nil ) - # PENDING load crossvalidation data? - OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid}) - QMRFReport.new(uri) - end - - # finds QMRF report for a particular model - # @param [String] model_uri - # @param [String,optional] subjectid - # @return [OpenTox::QMRFReport] nil if no report found - def self.find_for_model( model_uri, subjectid=nil ) - uris = RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"], - "/reach_report/qmrf?model="+model_uri), {:subjectid => subjectid}).chomp.split("\n") - uris.size==0 ? nil : QMRFReport.new(uris[-1]) - end - - # creates a qmrf report via model - # @param [String] model_uri - # @param [String,optional] subjectid - # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly - # @return [OpenTox::QMRFReport] - def self.create( model_uri, subjectid=nil, waiting_task=nil ) - uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/reach_report/qmrf"), - { :model_uri => model_uri, :subjectid => subjectid }, {}, waiting_task ) - QMRFReport.new(uri) - end - end - -end - |