Merge to master: Release 2.4.0 - Fix mappings slices and parsing issu…

…es of resources with no owl:Ontology (#81) * Feature: mappings statistics slices support (#78) * restrict mapping statistics ontologies to the ontologies of the current slice * add a test for the mappings slices support * add test for mappings statistics slices support * update owl wrapper version to v1.4.3 --------- Co-authored-by: Bilel Kihal <[email protected]>
ontoportal-lirmm · Jun 26, 2024 · 7872eb3 · 7872eb3
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diff --git a/Gemfile b/Gemfile
@@ -6,7 +6,7 @@ gem 'bigdecimal', '1.4.2'
 gem 'faraday', '~> 1.9'
 gem 'json-schema', '~> 2.0'
 gem 'multi_json', '~> 1.0'
-gem 'oj', '~> 2.0'
+gem 'oj'
 gem 'parseconfig'
 gem 'rack'
 gem 'rake', '~> 10.0'
@@ -77,4 +77,4 @@ group :test do
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
   gem 'webmock', '~> 3.19.1'
-end
+end
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -40,7 +40,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
-  revision: 5a6af32adc867ff0741d81b7a7162c3f34f45ade
+  revision: 6bb53a13f514a60513afe25e37c5c69475140452
   branch: master
   specs:
     ncbo_cron (0.0.1)
@@ -57,7 +57,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 0855adfce5365c6ef7a494e3d3ad9af2611974d9
+  revision: a5b56a68e6dc8ecfc9db708d44350342dac38ce6
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -106,8 +106,8 @@ GEM
     activesupport (3.2.22.5)
       i18n (~> 0.6, >= 0.6.4)
       multi_json (~> 1.0)
-    addressable (2.8.6)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     airbrussh (1.5.2)
       sshkit (>= 1.6.1, != 1.7.0)
     backports (3.25.0)
@@ -116,8 +116,8 @@ GEM
     bcrypt_pbkdf (1.1.1)
     bcrypt_pbkdf (1.1.1-x86_64-darwin)
     bigdecimal (1.4.2)
-    builder (3.2.4)
-    capistrano (3.18.1)
+    builder (3.3.0)
+    capistrano (3.19.0)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -130,7 +130,7 @@ GEM
       capistrano (~> 3.1)
       sshkit (~> 1.3)
     coderay (1.1.3)
-    concurrent-ruby (1.2.3)
+    concurrent-ruby (1.3.3)
     connection_pool (2.4.1)
     crack (1.0.0)
       bigdecimal
@@ -198,21 +198,25 @@ GEM
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
+    google-protobuf (3.25.3)
     google-protobuf (3.25.3-x86_64-darwin)
     google-protobuf (3.25.3-x86_64-linux)
-    googleapis-common-protos (1.5.0)
-      google-protobuf (~> 3.18)
+    googleapis-common-protos (1.6.0)
+      google-protobuf (>= 3.18, < 5.a)
       googleapis-common-protos-types (~> 1.7)
       grpc (~> 1.41)
-    googleapis-common-protos-types (1.14.0)
-      google-protobuf (~> 3.18)
+    googleapis-common-protos-types (1.15.0)
+      google-protobuf (>= 3.18, < 5.a)
     googleauth (1.11.0)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.1)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
+    grpc (1.64.0)
+      google-protobuf (~> 3.25)
+      googleapis-common-protos-types (~> 1.0)
     grpc (1.64.0-x86_64-darwin)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
@@ -225,7 +229,7 @@ GEM
     hashdiff (1.1.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.5)
+    http-cookie (1.0.6)
       domain_name (~> 0.5)
     httpclient (2.8.3)
     i18n (0.9.5)
@@ -236,7 +240,7 @@ GEM
       rdf (>= 2.2.8, < 4.0)
     json-schema (2.8.1)
       addressable (>= 2.4)
-    jwt (2.8.1)
+    jwt (2.8.2)
       base64
     kgio (2.11.4)
     libxml-ruby (5.0.3)
@@ -252,18 +256,17 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0507)
+    mime-types-data (3.2024.0604)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
     multipart-post (2.4.1)
-    mutex_m (0.2.0)
     net-http-persistent (4.0.2)
       connection_pool (~> 2.2)
-    net-imap (0.4.11)
+    net-imap (0.4.14)
       date
       net-protocol
     net-pop (0.1.2)
@@ -278,19 +281,19 @@ GEM
       net-protocol
     net-ssh (7.2.3)
     netrc (0.11.0)
-    newrelic_rpm (9.9.0)
-    oj (2.18.5)
+    newrelic_rpm (9.11.0)
+    oj (3.16.1)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
-    parallel (1.24.0)
+    parallel (1.25.1)
     parseconfig (1.1.2)
     pony (1.13.1)
       mail (>= 2.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.5)
+    public_suffix (5.1.1)
     rack (1.6.13)
     rack-accept (0.4.5)
       rack (>= 0.4)
@@ -346,8 +349,8 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
-    rexml (3.2.8)
-      strscan (>= 3.0.9)
+    rexml (3.3.1)
+      strscan
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -383,9 +386,8 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.22.2)
+    sshkit (1.23.0)
       base64
-      mutex_m
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
       net-ssh (>= 2.8.0)
@@ -412,6 +414,7 @@ GEM
       hashdiff (>= 0.4.0, < 2.0.0)
 
 PLATFORMS
+  ruby
   x86_64-darwin-23
   x86_64-linux
 
@@ -438,7 +441,7 @@ DEPENDENCIES
   ncbo_cron!
   ncbo_ontology_recommender!
   newrelic_rpm
-  oj (~> 2.0)
+  oj
   ontologies_linked_data!
   parallel
   parseconfig

diff --git a/test/controllers/test_properties_controller.rb b/test/controllers/test_properties_controller.rb
@@ -35,12 +35,12 @@ def test_properties
     get "/ontologies/#{@@acronyms.first}/properties"
     assert last_response.ok?
     results = MultiJson.load(last_response.body)
-    assert_includes [85, 56], results.length # depending if owlapi imports SKOS
+    assert_equal 81, results.length
 
     get "/ontologies/#{@@acronyms.last}/properties"
     assert last_response.ok?
     results = MultiJson.load(last_response.body)
-    assert_includes [35] , results.length # depending if owlapi imports SKOS
+    assert_equal 35, results.length
   end
 
   def test_single_property
@@ -59,7 +59,7 @@ def test_property_roots
     get "/ontologies/#{@@acronyms.first}/properties/roots"
     assert last_response.ok?
     pr = MultiJson.load(last_response.body)
-    assert_includes [62, 52], pr.length #depending if owlapi import SKOS
+    assert_equal 58, pr.length
 
     # count object properties
     opr = pr.select { |p| p["@type"] == "http://www.w3.org/2002/07/owl#ObjectProperty" }
@@ -108,7 +108,7 @@ def test_property_tree
     get "/ontologies/#{@@acronyms.first}/properties/http%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23topConceptOf/tree"
     assert last_response.ok?
     pr = MultiJson.load(last_response.body)
-    assert_equal 62, pr.length
+    assert_equal 58, pr.length
     num_found = 0
 
     pr.each do |p|