add validation, some debug messages, small adjustments

1 files changed, 356 insertions, 0 deletions

diff --git a/lib/validation.rb b/lib/validation.rb
new file mode 100644
index 0000000..47f74d7
--- /dev/null
+++ b/lib/validation.rb
@@ -0,0 +1,356 @@
+require "yaml"
+
+module OldOpenTox
+  attr_accessor :metadata, :uri
+  
+  def initialize(uri=nil)
+    @metadata = {}
+    self.uri = uri if uri
+  end
+
+  # loads metadata via yaml
+  def load_metadata( subjectid=nil )
+    yaml = OpenTox::RestClientWrapper.get(uri,nil,{:subjectid => subjectid, :accept => "application/x-yaml"})
+    #puts uri
+    #puts yaml
+    @metadata = YAML.load(yaml)
+  end
+end
+
+module OpenTox
+  
+  class Validation
+    include OldOpenTox
+    
+    # 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 += (filter_string.length==0 ? "?" : "&")
+        v = v.to_s.gsub(/;/, "%3b") if v.to_s =~ /;/
+        filter_string += k.to_s+"="+v.to_s
+      end
+      (OpenTox::RestClientWrapper.get($validation[:uri]+filter_string).split("\n"))
+    end
+    
+    # creates a training test split validation, waits until it finishes, may take some time
+    # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,split_ratio(0.67),random_seed(1))
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::Validation]
+    def self.create_training_test_split( params, subjectid=nil, waiting_task=nil )
+      params[:subjectid] = subjectid if subjectid
+      uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"training_test_split"),
+        params,{:content_type => "text/uri-list"},waiting_task )
+      Validation.new(OpenTox.wait_for_task(uri))
+    end
+    
+    # creates a training test validation, waits until it finishes, may take some time
+    # @param [Hash] params (required:algorithm_uri,training_dataset_uri,prediction_feature,test_dataset_uri,optional:algorithm_params)
+    # @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_validation( params, subjectid=nil, waiting_task=nil )
+      params[:subjectid] = subjectid if subjectid
+      uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"training_test_validation"),
+        params,{:content_type => "text/uri-list"},waiting_task )
+      Validation.new(OpenTox.wait_for_task(uri))
+    end
+    
+    # creates a bootstrapping validation, waits until it finishes, may take some time
+    # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,random_seed(1))
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::Validation]
+    def self.create_bootstrapping_validation( params, subjectid=nil, waiting_task=nil )
+      params[:subjectid] = subjectid if subjectid
+      uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"bootstrapping"),
+        params,{:content_type => "text/uri-list"},waiting_task )
+      Validation.new(OpenTox.wait_for_task(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
+    
+    # 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]]
+    # -> 99 inactive compounds have been predicted as active 
+    def confusion_matrix
+      raise "no classification statistics, probably a regression valdiation" unless @metadata[OT.classificationStatistics]
+      matrix =  @metadata[OT.classificationStatistics][OT.confusionMatrix][OT.confusionMatrixCell]
+      values = matrix.collect{|cell| cell[OT.confusionMatrixPredicted]}.uniq
+      table = [[nil]+values]
+      values.each do |c|
+        table << [c]
+        values.each do |r|
+          matrix.each do |cell|
+            if cell[OT.confusionMatrixPredicted]==c and cell[OT.confusionMatrixActual]==r
+              table[-1] << cell[OT.confusionMatrixValue].to_f
+              break
+            end
+          end
+        end
+      end
+      table
+    end
+    
+    # returns probability-distribution for a given prediction
+    # it takes all predictions into account that have a confidence value that is >= confidence and that have the same predicted value
+    # (minimum 12 predictions with the hightest confidence are selected (even if the confidence is lower than the given param)
+    # 
+    # @param [Float] confidence value (between 0 and 1)
+    # @param [String] predicted value
+    # @param [String,optional] subjectid
+    # @return [Hash] see 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
+    #
+    # 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,
+        {:subjectid => subjectid, :accept => "application/x-yaml"}))
+    end
+  end
+  
+  class Crossvalidation
+    include OldOpenTox
+
+    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 += (filter_string.length==0 ? "?" : "&")
+        v = v.to_s.gsub(/;/, "%3b") if v.to_s =~ /;/
+        filter_string += k.to_s+"="+v.to_s
+      end
+      (OpenTox::RestClientWrapper.get(File.join($validation[:uri],"crossvalidation")+filter_string).split("\n"))
+    end
+		
+    # creates a crossvalidations, waits until it finishes, may take some time
+    # @param [Hash] params (required:algorithm_uri,dataset_uri,prediction_feature, optional:algorithm_params,num_folds(10),random_seed(1),stratified(false))
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::Crossvalidation]
+    def self.create( params, subjectid=nil, waiting_task=nil )
+      params[:subjectid] = subjectid if subjectid
+      uri = OpenTox::RestClientWrapper.post( File.join($validation[:uri],"crossvalidation"),
+        params,{:content_type => "text/uri-list"},waiting_task )
+      Crossvalidation.new(OpenTox.wait_for_task(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,nil,{:subjectid => subjectid, :accept => "application/x-yaml"}))
+    end
+    
+    # returns a Validation object containing the statistics of the crossavlidation
+    def statistics( subjectid=nil )
+      Validation.from_cv_statistics( @uri, subjectid )
+    end
+    
+    # documentation see OpenTox::Validation.probabilities
+    def probabilities( confidence, prediction, subjectid=nil )
+      YAML.load(OpenTox::RestClientWrapper.get(@uri+"/statistics/probabilities?prediction="+prediction.to_s+"&confidence="+confidence.to_s,nil,
+        {:subjectid => subjectid, :accept => "application/x-yaml"}))
+    end
+    
+  end
+  
+  class ValidationReport
+    include OldOpenTox
+    
+    # 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,nil,{: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($validation[:uri],
+        "/report/validation?validation="+validation_uri),nil,{:subjectid => subjectid}).chomp.split("\n")
+      uris.size==0 ? nil : ValidationReport.new(uris[-1])
+    end
+    
+    # creates a validation report via validation
+    # @param [String] validation uri 
+    # @param [Hash] params addiditonal possible 
+    #               (min_confidence, params={}, min_num_predictions, max_num_predictions)
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::ValidationReport]
+    def self.create( validation_uri, params={}, subjectid=nil, waiting_task=nil )
+      params = {} if params==nil
+      raise OpenTox::BadRequestError.new "params is no hash" unless params.is_a?(Hash)
+      params[:validation_uris] = validation_uri
+      params[:subjectid] = subjectid
+      uri = RestClientWrapper.post(File.join($validation[:uri],"/report/validation"),
+        params, {}, waiting_task )
+      ValidationReport.new(OpenTox.wait_for_task(uri))
+    end
+    
+  end
+
+  class CrossvalidationReport
+    include OldOpenTox
+    
+    # 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,nil,{: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($validation[:uri],
+        "/report/crossvalidation?crossvalidation="+crossvalidation_uri),nil,{:subjectid => subjectid}).chomp.split("\n")
+      uris.size==0 ? nil : CrossvalidationReport.new(uris[-1])
+    end
+    
+    # creates a crossvalidation report via crossvalidation
+    # @param [String] crossvalidation uri 
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::CrossvalidationReport]
+    def self.create( crossvalidation_uri, subjectid=nil, waiting_task=nil )
+      uri = RestClientWrapper.post(File.join($validation[:uri],"/report/crossvalidation"),
+        { :validation_uris => crossvalidation_uri, :subjectid => subjectid }, {}, waiting_task )
+      CrossvalidationReport.new(OpenTox.wait_for_task(uri))
+    end
+  end
+  
+  
+  class AlgorithmComparisonReport
+    include OldOpenTox
+    
+    # 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,nil,{: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($validation[:uri],
+        "/report/algorithm_comparison?crossvalidation="+crossvalidation_uri),nil,{:subjectid => subjectid}).chomp.split("\n")
+      uris.size==0 ? nil : AlgorithmComparisonReport.new(uris[-1])
+    end
+    
+    # creates a algorithm comparison report via crossvalidation uris
+    # @param [Hash] crossvalidation uri_hash, see example 
+    # @param [Hash] params addiditonal possible 
+    #               (ttest_significance, ttest_attributes, min_confidence, min_num_predictions, max_num_predictions)
+    # @param [String,optional] subjectid
+    # @param [OpenTox::Task,optional] waiting_task (can be a OpenTox::Subtask as well), progress is updated accordingly
+    # @return [OpenTox::AlgorithmComparisonReport]
+    # example for hash:
+    # { :lazar-bbrc => [ http://host/validation/crossvalidation/x1, http://host/validation/crossvalidation/x2 ],
+    #   :lazar-last => [ http://host/validation/crossvalidation/xy, http://host/validation/crossvalidation/xy ] }
+    def self.create( crossvalidation_uri_hash, params={}, subjectid=nil, waiting_task=nil )
+      identifier = []
+      validation_uris = []
+      crossvalidation_uri_hash.each do |id, uris|
+        uris.each do |uri|
+          identifier << id
+          validation_uris << uri
+        end
+      end
+      params = {} if params==nil
+      raise OpenTox::BadRequestError.new "params is no hash" unless params.is_a?(Hash)
+      params[:validation_uris] = validation_uris.join(",")
+      params[:identifier] = identifier.join(",")
+      params[:subjectid] = subjectid
+      uri = RestClientWrapper.post(File.join($validation[:uri],"/report/algorithm_comparison"),
+        params, {}, waiting_task )
+      AlgorithmComparisonReport.new(OpenTox.wait_for_task(uri))
+    end
+  end  
+  
+end
+