Merge branch 'develop'

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: fd7d45cb862c5c2c1833b64a5c8c14154384edc2
+  revision: 562826ba21f7da641159071531375776a1414207
   branch: master
   specs:
     goo (0.0.2)
@@ -32,8 +32,8 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.8.0)
-      public_suffix (>= 2.0.2, < 5.0)
+    addressable (2.8.1)
+      public_suffix (>= 2.0.2, < 6.0)
     ansi (1.5.0)
     ast (2.4.2)
     bcrypt (3.1.18)
@@ -50,7 +50,7 @@ GEM
       launchy (~> 2.1)
       mail (~> 2.7)
     eventmachine (1.2.7)
-    faraday (1.10.0)
+    faraday (1.10.1)
       faraday-em_http (~> 1.0)
       faraday-em_synchrony (~> 1.0)
       faraday-excon (~> 1.1)
@@ -110,7 +110,7 @@ GEM
     omni_logger (0.1.4)
       logger
     parallel (1.22.1)
-    parser (3.1.2.0)
+    parser (3.1.2.1)
       ast (~> 2.4.1)
     pony (1.13.1)
       mail (>= 2.0)
@@ -119,7 +119,7 @@ GEM
     pry (0.14.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (4.0.7)
+    public_suffix (5.0.0)
     rack (1.6.13)
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
@@ -137,17 +137,17 @@ GEM
     rexml (3.2.5)
     rsolr (1.1.2)
       builder (>= 2.1.2)
-    rubocop (1.31.2)
+    rubocop (1.35.0)
       json (~> 2.3)
       parallel (~> 1.10)
-      parser (>= 3.1.0.0)
+      parser (>= 3.1.2.1)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.18.0, < 2.0)
+      rubocop-ast (>= 1.20.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 3.0)
-    rubocop-ast (1.19.1)
+    rubocop-ast (1.21.0)
       parser (>= 3.1.1.0)
     ruby-progressbar (1.11.0)
     ruby2_keywords (0.0.5)
@@ -169,7 +169,7 @@ GEM
       eventmachine (~> 1.0, >= 1.0.4)
       rack (>= 1, < 3)
     thread_safe (0.3.6)
-    tzinfo (0.3.60)
+    tzinfo (0.3.61)
     unf (0.1.4)
       unf_ext
     unf_ext (0.0.8.2)
@@ -178,8 +178,6 @@ GEM
       macaddr (~> 1.0)
 
 PLATFORMS
-  x86_64-darwin-18
-  x86_64-darwin-21
   x86_64-linux
 
 DEPENDENCIES
@@ -213,4 +211,4 @@ DEPENDENCIES
   thin
 
 BUNDLED WITH
-   2.3.14
+   2.3.15

lib/ontologies_linked_data/metrics/metrics.rb

@@ -33,10 +33,12 @@ def self.metrics_for_submission(submission, logger)
         metrics.properties = prop_count
         logger.info("properties finished")
         logger.flush
+
         # re-generate metrics file
-        submission.generate_metrics_file(cls_metrics[:classes], indiv_count, prop_count)
+        submission.generate_metrics_file2(cls_metrics[:classes], indiv_count, prop_count, cls_metrics[:maxDepth])
         logger.info("generation of metrics file finished")
         logger.flush
+
       rescue Exception => e
         logger.error(e.message)
         logger.error(e)
@@ -46,35 +48,51 @@ def self.metrics_for_submission(submission, logger)
       metrics
     end
 
+    def self.max_depth_fn(submission, logger, is_flat, rdfsSC)
+      max_depth = 0
+      mx_from_file = submission.metrics_from_file(logger)
+      if (mx_from_file && mx_from_file.length == 2 && mx_from_file[0].length >= 4)
+      then
+        max_depth = mx_from_file[1][3].to_i
+      else
+        logger.info("Unable to find metrics providing max_depth in file for submission #{submission.id.to_s}.  Using ruby calculation of max_depth.")  
+        roots = submission.roots
+
+        unless is_flat
+          depths = []
+          roots.each do |root|
+            ok = true
+            n=1
+            while ok
+              ok = hierarchy_depth?(submission.id.to_s,root.id.to_s,n,rdfsSC)
+              if ok
+                n += 1
+              end
+              if n > 40
+                #safe guard
+                ok = false
+              end
+            end
+            n -= 1
+            depths << n
+          end
+          max_depth = depths.max
+        end
+      end
+      max_depth
+    end
+
     def self.class_metrics(submission, logger)
       t00 = Time.now
       submission.ontology.bring(:flat) if submission.ontology.bring?(:flat)
 
       is_flat = submission.ontology.flat
-      roots = submission.roots
-
-      max_depth = 0
+      rdfsSC = nil
       unless is_flat
-        depths = []
-        rdfsSC = Goo.namespaces[:rdfs][:subClassOf]
-        roots.each do |root|
-          ok = true
-          n=1
-          while ok
-            ok = hierarchy_depth?(submission.id.to_s,root.id.to_s,n,rdfsSC)
-            if ok
-              n += 1
-            end
-            if n > 40
-              #safe guard
-              ok = false
-            end
-          end
-          n -= 1
-          depths << n
-        end
-        max_depth = depths.max
+          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

lib/ontologies_linked_data/models/ontology_submission.rb

@@ -414,6 +414,13 @@ def generate_metrics_file(class_count, indiv_count, prop_count)
         end
       end
 
+      def 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 generate_umls_metrics_file(tr_file_path=nil)
         tr_file_path ||= self.triples_file_path
         class_count = 0

lib/ontologies_linked_data/parser/owlapi.rb

@@ -13,7 +13,7 @@ class RDFFileNotGeneratedException < Parser::ParserException
 
     class OWLAPICommand
       def initialize(input_file, output_repo, opts = {})
-        @owlapi_wrapper_jar_path = LinkedData.bindir + "/owlapi-wrapper-1.3.8.jar"
+        @owlapi_wrapper_jar_path = LinkedData.bindir + "/owlapi-wrapper-1.4.0.jar"
         @input_file = input_file
         @output_repo = output_repo
         @master_file = opts[:master_file]

test/models/test_ontology_submission.rb

@@ -956,7 +956,7 @@ def test_submission_metrics
     assert_equal 0, metrics.classesWithMoreThan25Children
     assert_equal 18, metrics.maxChildCount
     assert_equal 3, metrics.averageChildCount
-    assert_equal 3, metrics.maxDepth
+    assert_equal 4, metrics.maxDepth
 
     submission_parse("BROTEST-METRICS", "BRO testing metrics",
                      "./test/data/ontology_files/BRO_v3.2.owl", 33,
@@ -1006,12 +1006,13 @@ def test_submission_metrics
     assert_equal 63, metrics.properties
     assert_equal 124, metrics.individuals
     assert_equal 0, metrics.classesWithOneChild
+    assert_equal 7, metrics.maxDepth
     #cause it has not the subproperty added
     assert_equal 474, metrics.classesWithNoDefinition
     assert_equal 0, metrics.classesWithMoreThan25Children
     assert_equal 0, metrics.maxChildCount
     assert_equal 0, metrics.averageChildCount
-    assert_equal 0, metrics.maxDepth
+
 
     #test UMLS metrics
     acronym = 'UMLS-TST'