update /refactor validation.rb

4 files changed, 134 insertions, 58 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index ae05e16..bfa9860 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -34,7 +34,7 @@ module OpenTox
       # Find Generic Opentox Algorithm via URI, and loads metadata
       # @param [String] uri Algorithm URI
       # @return [OpenTox::Algorithm::Generic] Algorithm instance, nil if alogrithm was not found
-      def self.find(uri, subjectid)
+      def self.find(uri, subjectid=nil)
         return nil unless uri
         alg = Generic.new(uri)
         alg.load_metadata( subjectid )
diff --git a/lib/rest_client_wrapper.rb b/lib/rest_client_wrapper.rb
index f59dce7..658f111 100644
--- a/lib/rest_client_wrapper.rb
+++ b/lib/rest_client_wrapper.rb
@@ -55,11 +55,12 @@ module OpenTox
       
       raise OpenTox::BadRequestError.new "uri is null" unless uri
       raise OpenTox::BadRequestError.new "not a uri: "+uri.to_s unless uri.to_s.uri?
-      raise OpenTox::BadRequestError.new "headers are no hash: "+headers.inspect unless headers==nil or headers.is_a?(Hash)
-      raise OpenTox::BadRequestError.new "nil headers for post not allowed, use {}" if rest_call=="post" and headers==nil
-      headers.each{ |k,v| headers.delete(k) if v==nil } if headers #remove keys with empty values, as this can cause problems
+      raise "headers are no hash: "+headers.inspect unless headers==nil or headers.is_a?(Hash)
       raise OpenTox::BadRequestError.new "accept should go into the headers" if payload and payload.is_a?(Hash) and payload[:accept] 
       raise OpenTox::BadRequestError.new "content_type should go into the headers" if payload and payload.is_a?(Hash) and payload[:content_type]
+      raise "__waiting_task__ must be 'nil' or '(sub)task', is "+waiting_task.class.to_s if
+        waiting_task!=nil and !(waiting_task.is_a?(Task) || waiting_task.is_a?(SubTask))
+      headers.each{ |k,v| headers.delete(k) if v==nil } if headers #remove keys with empty values, as this can cause problems
       
       # PENDING needed for NUTA, until we finally agree on how to send subjectid
       headers[:subjectid] = payload.delete(:subjectid) if uri=~/ntua/ and payload and payload.is_a?(Hash) and payload.has_key?(:subjectid) 
diff --git a/lib/task.rb b/lib/task.rb
index f635b43..9c52299 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -33,7 +33,7 @@ module OpenTox
     def self.create( title=nil, creator=nil, max_duration=DEFAULT_TASK_MAX_DURATION, description=nil )
       
       params = {:title=>title, :creator=>creator, :max_duration=>max_duration, :description=>description }
-      task_uri = RestClientWrapper.post(CONFIG[:services]["opentox-task"], params, {}, false).to_s
+      task_uri = RestClientWrapper.post(CONFIG[:services]["opentox-task"], params, {}, nil, false).to_s
       task = Task.new(task_uri.chomp)
 
       # measure current memory consumption
@@ -284,7 +284,6 @@ module OpenTox
         raise OpenTox::BadRequestError.new ex.message+" (task-uri:"+@uri+")" 
       end
     end
-
   end
 
   # Convenience class to split a (sub)task into subtasks
diff --git a/lib/validation.rb b/lib/validation.rb
index 83be91a..b1ccb7b 100644
--- a/lib/validation.rb
+++ b/lib/validation.rb
@@ -1,70 +1,146 @@
 module OpenTox
-	class Validation
+	class Crossvalidation
     include OpenTox
 
-		attr_accessor :report_uri, :qmrf_report_uri
+		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 )
+      # PENDING load crossvalidation data?
+      OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid})
+      Crossvalidation.new(uri)
+    end
 		
-		def self.create_crossvalidation(params)
-			params[:uri] = File.join(CONFIG[:services]['opentox-validation'], "crossvalidation")
+    # creates a crossvalidations, waits until it finishes, may take some time
+    # @param [Hash] params
+    # @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[:uri] = File.join(CONFIG[:services]['opentox-validation'], "crossvalidation")
       params[:num_folds] = 10 unless params[:num_folds]
-		 	params[:random_seed] = 2 unless params[:random_seed]
-		 	params[:stratified] = false unless params[:stratified]
-      uri = OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/crossvalidation"),params,{},false)
-			OpenTox::Validation.new(uri)
-		end
-
-    def create_report
-			@report_uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/report/crossvalidation"), :validation_uris => @uri).to_s
-      @report_uri
+      params[:random_seed] = 2 unless params[:random_seed]
+      params[:stratified] = false unless params[:stratified]
+      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
 
-    def create_qmrf_report
-      @qmrf_report_uri = RestClientWrapper.post(File.join(CONFIG[:services]["opentox-validation"],"/reach_report/qmrf"), :model_uri => @uri).to_s
-      @qmrf_report_uri
+    # 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 [OpenTox::CrossvalidationReport]
+    def find_or_create_report( subjectid=nil, waiting_task=nil )
+      @report = CrossvalidationReport.find_for_crossvalidation(self, subjectid) unless @report
+      @report = CrossvalidationReport.create(self, subjectid, waiting_task) unless @report
+      @report
     end
 
-    def summary(type)
-      v = YAML.load RestClientWrappper.get(File.join(@uri, 'statistics'),:accept => "application/x-yaml").to_s
-
-      case type
-      when "classification"
-        tp=0; tn=0; fp=0; fn=0; n=0
-        v[:classification_statistics][:confusion_matrix][:confusion_matrix_cell].each do |cell|
-          if cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "true"
-            tp = cell[:confusion_matrix_value]
-            n += tp
-          elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "false"
-            tn = cell[:confusion_matrix_value]
-            n += tn
-          elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "true"
-            fn = cell[:confusion_matrix_value]
-            n += fn
-          elsif cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "false"
-            fp = cell[:confusion_matrix_value]
-            n += fp
+    # PENDING: creates summary as used for ToxCreate
+    def summary
+      v = YAML.load RestClientWrapper.get(File.join(@uri, 'statistics'),:accept => "application/x-yaml").to_s
+      if v[OT.classificationStatistics]
+        res = {
+          :nr_predictions => v[OT.numInstances] - v[OT.numUnpredicted],
+          :correct_predictions => v[OT.classificationStatistics][OT.percentCorrect],
+          :weighted_area_under_roc => v[OT.classificationStatistics][OT.weightedAreaUnderRoc],
+        }
+        v[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.falsePositiveRate]
+            break
           end
         end
+        res
+      elsif v[OT.regressionStatistics]
         {
-          :nr_predictions => n,
-          :true_positives => tp,
-          :false_positives => fp,
-          :true_negatives => tn,
-          :false_negatives => fn,
-          :correct_predictions => 100*(tp+tn).to_f/n,
-          :weighted_area_under_roc => v[:classification_statistics][:weighted_area_under_roc].to_f,
-          :sensitivity => tp.to_f/(tp+fn),
-          :specificity => tn.to_f/(tn+fp),
-        }
-      when "regression"
-        {
-          :nr_predictions => v[:num_instances] - v[:num_unpredicted],
-          :r_square => v[:regression_statistics][:r_square],
-          :root_mean_squared_error => v[:regression_statistics][:root_mean_squared_error],
-          :mean_absolute_error => v[:regression_statistics][:mean_absolute_error],
+          :nr_predictions => v[OT.numInstances] - v[OT.numUnpredicted],
+          :r_square => v[OT.regressionStatistics][OT.rSquare],
+          :root_mean_squared_error => v[OT.regressionStatistics][OT.rootMeanSquaredError],
+          :mean_absolute_error => v[OT.regressionStatistics][OT.meanAbsoluteError],
         }
       end
     end
+  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 )
+      # PENDING load report data?
+      OpenTox::RestClientWrapper.get(uri,{:subjectid => subjectid})
+      CrossvalidationReport.new(uri)
+    end
+    
+    # finds CrossvalidationReport for a particular crossvalidation
+    # @param [OpenTox::Crossvalidation] 
+    # @param [String,optional] subjectid
+    # @return [OpenTox::CrossvalidationReport] nil if no report found
+    def self.find_for_crossvalidation( crossvalidation, 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 [OpenTox::Crossvalidation] 
+    # @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, 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 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 [OpenTox::Crossvalidation] 
+    # @param [String,optional] subjectid
+    # @return [OpenTox::QMRFReport] nil if no report found
+    def self.find_for_model( model, 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 [OpenTox::Model] 
+    # @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, 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