Merge branch 'develop'

Gemfile

@@ -6,16 +6,16 @@ gem 'bcrypt', '~> 3.0'
 gem 'cube-ruby', require: 'cube'
 gem 'faraday', '~> 1.9'
 gem 'ffi'
-gem 'libxml-ruby', '~> 2.0'
+gem 'libxml-ruby'
 gem 'minitest'
 gem 'multi_json', '~> 1.0'
-gem 'oj', '~> 2.0'
+gem 'oj', '~> 3.0'
 gem 'omni_logger'
 gem 'pony'
-gem 'rack', '~> 1.0'
+gem 'rack'
 gem 'rake', '~> 10.0'
 gem 'rest-client'
-gem 'rsolr', '~> 1.0'
+gem 'rsolr'
 gem 'rubyzip', '~> 1.0'
 gem 'thin'
 

Gemfile.lock

@@ -36,18 +36,18 @@ GEM
       public_suffix (>= 2.0.2, < 6.0)
     ansi (1.5.0)
     ast (2.4.2)
-    bcrypt (3.1.18)
+    bcrypt (3.1.19)
     builder (3.2.4)
     coderay (1.1.3)
     concurrent-ruby (1.2.2)
-    connection_pool (2.4.0)
+    connection_pool (2.4.1)
     cube-ruby (0.0.3)
     daemons (1.4.1)
     date (3.3.3)
     docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
-    email_spec (2.2.1)
+    email_spec (2.2.2)
       htmlentities (~> 4.3.3)
       launchy (~> 2.1)
       mail (~> 2.7)
@@ -85,9 +85,10 @@ GEM
       concurrent-ruby (~> 1.0)
     json (2.6.3)
     json_pure (2.6.3)
+    language_server-protocol (3.17.0.3)
     launchy (2.5.2)
       addressable (~> 2.8)
-    libxml-ruby (2.9.0)
+    libxml-ruby (4.1.1)
     logger (1.5.3)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
@@ -110,7 +111,7 @@ GEM
     multi_json (1.15.0)
     multipart-post (2.3.0)
     net-http-persistent (2.9.4)
-    net-imap (0.3.4)
+    net-imap (0.3.7)
       date
       net-protocol
     net-pop (0.1.2)
@@ -120,21 +121,23 @@ GEM
     net-smtp (0.3.3)
       net-protocol
     netrc (0.11.0)
-    oj (2.18.5)
+    oj (3.15.0)
     omni_logger (0.1.4)
       logger
     parallel (1.23.0)
-    parser (3.2.2.1)
+    parser (3.2.2.3)
       ast (~> 2.4.1)
+      racc
     pony (1.13.1)
       mail (>= 2.0)
     powerbar (2.0.1)
       hashie (>= 1.1.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.1)
-    rack (1.6.13)
+    public_suffix (5.0.3)
+    racc (1.7.1)
+    rack (2.2.7)
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
     rainbow (3.1.1)
@@ -145,26 +148,28 @@ GEM
       redis-client (>= 0.9.0)
     redis-client (0.14.1)
       connection_pool
-    regexp_parser (2.8.0)
+    regexp_parser (2.8.1)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.2.5)
-    rsolr (1.1.2)
+    rexml (3.2.6)
+    rsolr (2.5.0)
       builder (>= 2.1.2)
-    rubocop (1.50.2)
+      faraday (>= 0.9, < 3, != 2.0.0)
+    rubocop (1.55.0)
       json (~> 2.3)
+      language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.0.0)
+      parser (>= 3.2.2.3)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.28.0, < 2.0)
+      rubocop-ast (>= 1.28.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.28.1)
+    rubocop-ast (1.29.0)
       parser (>= 3.2.1.0)
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
@@ -186,7 +191,7 @@ GEM
       eventmachine (~> 1.0, >= 1.0.4)
       rack (>= 1, < 3)
     thread_safe (0.3.6)
-    timeout (0.3.2)
+    timeout (0.4.0)
     tzinfo (0.3.62)
     unf (0.1.4)
       unf_ext
@@ -209,19 +214,19 @@ DEPENDENCIES
   faraday (~> 1.9)
   ffi
   goo!
-  libxml-ruby (~> 2.0)
+  libxml-ruby
   minitest
   minitest-reporters (>= 0.5.0)
   multi_json (~> 1.0)
-  oj (~> 2.0)
+  oj (~> 3.0)
   omni_logger
   pony
   pry
-  rack (~> 1.0)
+  rack
   rack-test (~> 0.6)
   rake (~> 10.0)
   rest-client
-  rsolr (~> 1.0)
+  rsolr
   rubocop
   rubyzip (~> 1.0)
   simplecov

lib/ontologies_linked_data/models/ontology_submission.rb

@@ -918,7 +918,7 @@ def process_submission(logger, options={})
         # Wrap the whole process so we can email results
         begin
           process_rdf = false
-          generate_labels = true
+          generate_labels = false
           index_search = false
           index_properties = false
           index_commit = false
@@ -929,6 +929,7 @@ def process_submission(logger, options={})
 
           if options.empty?
             process_rdf = true
+            generate_labels = true
             index_search = true
             index_properties = true
             index_commit = true
@@ -938,10 +939,14 @@ def process_submission(logger, options={})
             archive = false
           else
             process_rdf = options[:process_rdf] == true ? true : false
-            generate_labels = options[:generate_labels] == false ? false : true
+
+            if options.has_key?(:generate_labels)
+              generate_labels = options[:generate_labels] == false ? false : true
+            else
+              generate_labels = process_rdf
+            end
             index_search = options[:index_search] == true ? true : false
             index_properties = options[:index_properties] == true ? true : false
-            index_commit = options[:index_commit] == true ? true : false
             run_metrics = options[:run_metrics] == true ? true : false
 
             if !process_rdf || options[:reasoning] == false

run-unit-tests.sh

@@ -2,18 +2,16 @@
 # sample script to run unit tests with docker
 
 #DC='docker-compose --profile 4store'
-DC='docker-compose'
+DC='docker compose'
 
 # unit test expects config file even though all settings are set via env vars.
-[ -f config/config.rb ] || cp config/config.rb.sample config/config.rb
+[ -f config/config.rb ] || cp config/config.test.rb config/config.rb
 
 # generate solr configsets for solr container
 test/solr/generate_ncbo_configsets.sh
 
 # build docker containers
-#$DC up --build -d
-#$DC run --rm ruby wait-for-it solr-ut:8983 -- bundle exec rake test TESTOPTS='-v' TEST='./test/models/test_mappings.rb'
 $DC run --rm ruby bundle exec rake test TESTOPTS='-v'
 # run unit test with AG backend
 #$DC run --rm ruby-agraph bundle exec rake test TESTOPTS='-v'
-#$DC down
+$DC stop