Merge pull request #231 from ncbo/develop

Develop to Master merge.  Resolve missing metrics issue

Author: alexskr

Gemfile.lock

@@ -37,7 +37,6 @@ GEM
       public_suffix (>= 2.0.2, < 7.0)
     ansi (1.5.0)
     ast (2.4.2)
-    base64 (0.2.0)
     bcrypt (3.1.20)
     bigdecimal (3.1.8)
     builder (3.3.0)
@@ -48,35 +47,37 @@ GEM
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     daemons (1.4.1)
-    date (3.4.0)
+    date (3.4.1)
     docile (1.4.1)
     domain_name (0.6.20240107)
     email_spec (2.3.0)
       htmlentities (~> 4.3.3)
       launchy (>= 2.1, < 4.0)
       mail (~> 2.7)
     eventmachine (1.2.7)
-    faraday (2.8.1)
-      base64
-      faraday-net_http (>= 2.0, < 3.1)
-      ruby2_keywords (>= 0.0.4)
-    faraday-net_http (3.0.2)
+    faraday (2.12.2)
+      faraday-net_http (>= 2.0, < 3.5)
+      json
+      logger
+    faraday-net_http (3.4.0)
+      net-http (>= 0.5.0)
     ffi (1.17.0)
+    ffi (1.17.0-arm64-darwin)
     hashie (5.0.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.7)
+    http-cookie (1.0.8)
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.8.2)
+    json (2.9.0)
     json_pure (2.8.1)
     language_server-protocol (3.17.0.3)
     launchy (3.0.1)
       addressable (~> 2.8)
       childprocess (~> 5.0)
     libxml-ruby (5.0.3)
-    logger (1.6.1)
+    logger (1.6.2)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -88,7 +89,7 @@ GEM
     mime-types (3.6.0)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.1105)
+    mime-types-data (3.2024.1203)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-reporters (0.14.24)
@@ -97,6 +98,8 @@ GEM
       minitest (>= 2.12, < 5.0)
       powerbar
     multi_json (1.15.0)
+    net-http (0.6.0)
+      uri
     net-http-persistent (2.9.4)
     net-imap (0.4.18)
       date
@@ -125,7 +128,7 @@ GEM
     pry (0.15.0)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.1.1)
+    public_suffix (6.0.1)
     racc (1.8.1)
     rack (2.2.10)
     rack-test (0.8.3)
@@ -136,9 +139,9 @@ GEM
       addressable (>= 2.2)
     redis (5.3.0)
       redis-client (>= 0.22.0)
-    redis-client (0.22.2)
+    redis-client (0.23.0)
       connection_pool
-    regexp_parser (2.9.2)
+    regexp_parser (2.9.3)
     request_store (1.7.0)
       rack (>= 1.4)
     rest-client (2.1.0)
@@ -150,20 +153,19 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.68.0)
+    rubocop (1.69.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 2.4, < 3.0)
-      rubocop-ast (>= 1.32.2, < 2.0)
+      regexp_parser (>= 2.9.3, < 3.0)
+      rubocop-ast (>= 1.36.2, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.36.1)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.36.2)
       parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
-    ruby2_keywords (0.0.5)
     rubyzip (1.3.0)
     simplecov (0.22.0)
       docile (~> 1.1)
@@ -182,7 +184,10 @@ GEM
     thread_safe (0.3.6)
     timeout (0.4.2)
     tzinfo (0.3.62)
-    unicode-display_width (2.6.0)
+    unicode-display_width (3.1.2)
+      unicode-emoji (~> 4.0, >= 4.0.4)
+    unicode-emoji (4.0.4)
+    uri (1.0.2)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
@@ -222,4 +227,4 @@ DEPENDENCIES
   thin
 
 BUNDLED WITH
-   2.4.22
+   2.5.11

lib/ontologies_linked_data/services/submission_process/submission_processor.rb

@@ -56,6 +56,8 @@ def process_submission(logger, options = {})
               @submission.index_properties(logger, commit: index_commit)
             end
 
+            @submission.generate_diff(logger) if diff
+
             if run_metrics
               unless parsed
                 raise StandardError, "Metrics cannot be generated on the submission
@@ -64,7 +66,6 @@ def process_submission(logger, options = {})
               end
               @submission.generate_metrics(logger)
             end
-            @submission.generate_diff(logger) if diff
           end
 
           @submission.save