use owlapi_wrapper for max_depth calculation

add back changes in PR#182 that were overwritten by PR#143
ncbo · Apr 25, 2024 · da1642e · da1642e
1 parent cf3ff84
commit da1642e
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Showing 2 changed files with 16 additions and 12 deletions.
diff --git a/lib/ontologies_linked_data/metrics/metrics.rb b/lib/ontologies_linked_data/metrics/metrics.rb
@@ -83,12 +83,7 @@ def self.max_depth_fn(submission, logger, is_flat, rdfsSC)
       end
       max_depth
     end
-    def self.generate_metrics_file2(class_count, indiv_count, prop_count, max_depth)
-      CSV.open(self.metrics_path, "wb") do |csv|
-        csv << ["Class Count", "Individual Count", "Property Count", "Max Depth"]
-        csv << [class_count, indiv_count, prop_count, max_depth]
-      end
-    end
+
     def self.class_metrics(submission, logger)
       t00 = Time.now
       submission.ontology.bring(:flat) if submission.ontology.bring?(:flat)
@@ -99,7 +94,7 @@ def self.class_metrics(submission, logger)
           rdfsSC = Goo.namespaces[:rdfs][:subClassOf]
       end
       max_depth = max_depth_fn(submission, logger, is_flat, rdfsSC) 
-      
+
       cls_metrics = {}
       cls_metrics[:classes] = 0
       cls_metrics[:averageChildCount] = 0

diff --git a/...gies_linked_data/services/submission_process/operations/submission_mertrics_calculator.rb b/...gies_linked_data/services/submission_process/operations/submission_mertrics_calculator.rb
@@ -10,14 +10,23 @@ def generate_umls_metrics_file(tr_file_path=nil)
         class_count = 0
         indiv_count = 0
         prop_count = 0
+        max_depth = 0
 
         File.foreach(tr_file_path) do |line|
           class_count += 1 if line =~ /owl:Class/
           indiv_count += 1 if line =~ /owl:NamedIndividual/
           prop_count += 1 if line =~ /owl:ObjectProperty/
           prop_count += 1 if line =~ /owl:DatatypeProperty/
         end
-        generate_metrics_file(class_count, indiv_count, prop_count)
+
+        # Get max depth from the metrics.csv file which is already generated
+        # by owlapi_wrapper when new submission of UMLS ontology is created.
+        # Ruby code/sparql for calculating max_depth fails for large UMLS
+        # ontologies with AllegroGraph backend
+        metrics_from_owlapi = @submission.metrics_from_file
+        max_depth = metrics_from_owlapi[1][3] unless metrics_from_owlapi.empty?
+
+        generate_metrics_file(class_count, indiv_count, prop_count, max_depth)
       end
 
       private
@@ -78,7 +87,7 @@ def metrics_for_submission(logger)
           logger.info('properties finished')
           logger.flush
           # re-generate metrics file
-          generate_metrics_file(cls_metrics[:classes], indiv_count, prop_count)
+          generate_metrics_file(cls_metrics[:classes], indiv_count, prop_count, cls_metrics[:maxDepth])
           logger.info('generation of metrics file finished')
           logger.flush
         rescue StandardError => e
@@ -90,10 +99,10 @@ def metrics_for_submission(logger)
         metrics
       end
 
-      def generate_metrics_file(class_count, indiv_count, prop_count)
+      def generate_metrics_file(class_count, indiv_count, prop_count, max_depth)
         CSV.open(@submission.metrics_path, 'wb') do |csv|
-          csv << ['Class Count', 'Individual Count', 'Property Count']
-          csv << [class_count, indiv_count, prop_count]
+          csv << ['Class Count', 'Individual Count', 'Property Count', 'Max Depth']
+          csv << [class_count, indiv_count, prop_count, max_depth]
         end
       end