From 4daf449b001f4e44fbb337ebc29ceef29ce6ac64 Mon Sep 17 00:00:00 2001 From: rautenberg Date: Mon, 1 Jul 2013 09:25:44 +0200 Subject: add subjectids, changes in yard doc --- lib/validation.rb | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) (limited to 'lib/validation.rb') diff --git a/lib/validation.rb b/lib/validation.rb index cb73ce6..76e723e 100644 --- a/lib/validation.rb +++ b/lib/validation.rb @@ -44,7 +44,7 @@ module OpenTox v = v.to_s.gsub(/;/, "%3b") if v.to_s =~ /;/ filter_string += k.to_s+"="+v.to_s end - (OpenTox::RestClientWrapper.get($validation[:uri]+filter_string).split("\n")) + (OpenTox::RestClientWrapper.get($validation[:uri]+filter_string,nil,{:subjectid => subjectid}).split("\n")) end # creates a training test split validation, waits until it finishes, may take some time @@ -55,7 +55,7 @@ module OpenTox def self.create_training_test_split( params, subjectid=nil, waiting_task=nil ) params[:subjectid] = subjectid if subjectid uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"training_test_split"), - params,{:content_type => "text/uri-list"},waiting_task ) + params,{:content_type => "text/uri-list", :subjectid => subjectid},waiting_task ) Validation.new(wait_for_task(uri)) end @@ -67,7 +67,7 @@ module OpenTox def self.create_training_test_validation( params, subjectid=nil, waiting_task=nil ) params[:subjectid] = subjectid if subjectid uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"training_test_validation"), - params,{:content_type => "text/uri-list"},waiting_task ) + params,{:content_type => "text/uri-list", :subjectid => subjectid},waiting_task ) Validation.new(wait_for_task(uri)) end @@ -79,7 +79,7 @@ module OpenTox def self.create_bootstrapping_validation( params, subjectid=nil, waiting_task=nil ) params[:subjectid] = subjectid if subjectid uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"bootstrapping"), - params,{:content_type => "text/uri-list"},waiting_task ) + params,{:content_type => "text/uri-list", :subjectid => subjectid},waiting_task ) Validation.new(wait_for_task(uri)) end @@ -103,8 +103,8 @@ module OpenTox end # returns confusion matrix as array, predicted values are in rows - # example: - # [[nil,"active","moderate","inactive"],["active",1,3,99],["moderate",4,2,8],["inactive",3,8,6]] + # @example + # [[nil,"active","moderate","inactive"],["active",1,3,99],["moderate",4,2,8],["inactive",3,8,6]] # -> 99 inactive compounds have been predicted as active def confusion_matrix raise "no classification statistics, probably a regression valdiation" unless @metadata[RDF::OT.classificationStatistics] @@ -133,17 +133,17 @@ module OpenTox # @param prediction [String] predicted value # @param subjectid [String,optional] # @return [Hash] see example - # - # Example 1: + # @example + # Example 1: # validation.probabilities(0.3,"active") # -> { :min_confidence=>0.32, :num_predictions=>20, :probs=>{"active"=>0.7, "moderate"=>0.25 "inactive"=>0.05 } } - # there have been 20 "active" predictions with confidence >= 0.3, 70 percent of them beeing correct + # there have been 20 "active" predictions with confidence >= 0.3, 70 percent of them beeing correct # - # Example 2: - # validation.probabilities(0.8,"active") - # -> { :min_confidence=>0.45, :num_predictions=>12, :probs=>{"active"=>0.9, "moderate"=>0.1 "inactive"=>0 } } - # the given confidence value was to high (i.e. <12 predictions with confidence value >= 0.8) - # the top 12 "active" predictions have a min_confidence of 0.45, 90 percent of them beeing correct + # Example 2: + # validation.probabilities(0.8,"active") + # -> { :min_confidence=>0.45, :num_predictions=>12, :probs=>{"active"=>0.9, "moderate"=>0.1 "inactive"=>0 } } + # the given confidence value was to high (i.e. <12 predictions with confidence value >= 0.8) + # the top 12 "active" predictions have a min_confidence of 0.45, 90 percent of them beeing correct # def probabilities( confidence, prediction, subjectid=nil ) YAML.load(OpenTox::RestClientWrapper.get(@uri+"/probabilities?prediction="+prediction.to_s+"&confidence="+confidence.to_s,nil, @@ -187,7 +187,7 @@ module OpenTox def self.create( params, subjectid=nil, waiting_task=nil ) params[:subjectid] = subjectid if subjectid uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"crossvalidation"), - params,{:content_type => "text/uri-list"},waiting_task ) + params,{:content_type => "text/uri-list", :subjectid => subjectid},waiting_task ) uri = wait_for_task(uri) Crossvalidation.new(uri) end @@ -258,7 +258,7 @@ module OpenTox params[:validation_uris] = validation_uri params[:subjectid] = subjectid uri = RestClientWrapper.post(File.join($validation[:uri],"/report/validation"), - params, {}, waiting_task ) + params, {:subjectid => subjectid}, waiting_task ) uri = wait_for_task(uri) ValidationReport.new(uri) end @@ -351,7 +351,7 @@ module OpenTox params[:validation_uris] = validation_uris.join(",") params[:identifier] = identifier.join(",") params[:subjectid] = subjectid - uri = RestClientWrapper.post(File.join($validation[:uri],"/report/algorithm_comparison"), params, {}, waiting_task ) + uri = RestClientWrapper.post(File.join($validation[:uri],"/report/algorithm_comparison"), params, {:subjectid => subjectid}, waiting_task ) uri = wait_for_task(uri) AlgorithmComparisonReport.new(uri) end -- cgit v1.2.3