From 7872eb38241fd462f57ee6712674105b2b605322 Mon Sep 17 00:00:00 2001 From: Syphax bouazzouni Date: Thu, 27 Jun 2024 01:26:42 +0200 Subject: [PATCH 1/2] Merge to master: Release 2.4.0 - Fix mappings slices and parsing issues 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 <61744974+Bilelkihal@users.noreply.github.com> --- Gemfile | 4 +- Gemfile.lock | 53 ++++++++++--------- .../controllers/test_properties_controller.rb | 8 +-- 3 files changed, 34 insertions(+), 31 deletions(-) diff --git a/Gemfile b/Gemfile index bd445a1e..adaeb43a 100644 --- 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 \ No newline at end of file +end diff --git a/Gemfile.lock b/Gemfile.lock index dc2272a6..023fd1b4 100644 --- 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 @@ -198,14 +198,15 @@ 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) @@ -213,6 +214,9 @@ GEM 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) @@ -252,7 +256,7 @@ 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) @@ -260,10 +264,9 @@ GEM 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 index 38f8708f..96879083 100644 --- 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| From 77926d5d1e5f3b95aa7e2d4ac8f47605d0ec3d0b Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Thu, 27 Jun 2024 02:47:42 +0200 Subject: [PATCH 2/2] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 17 +++-------------- 1 file changed, 3 insertions(+), 14 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 023fd1b4..5eaf798e 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -40,7 +40,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/ncbo_cron.git - revision: 6bb53a13f514a60513afe25e37c5c69475140452 + revision: fabd04ef4fa37989d526fc6a7aa1e98830008dae branch: master specs: ncbo_cron (0.0.1) @@ -114,7 +114,6 @@ GEM base64 (0.2.0) bcrypt (3.1.20) bcrypt_pbkdf (1.1.1) - bcrypt_pbkdf (1.1.1-x86_64-darwin) bigdecimal (1.4.2) builder (3.3.0) capistrano (3.19.0) @@ -165,7 +164,7 @@ GEM faraday-patron (1.0.0) faraday-rack (1.0.0) faraday-retry (1.0.3) - ffi (1.16.3) + ffi (1.17.0-x86_64-linux-gnu) gapic-common (0.21.1) faraday (>= 1.9, < 3.a) faraday-retry (>= 1.0, < 3.a) @@ -198,8 +197,6 @@ 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 (1.6.0) google-protobuf (>= 3.18, < 5.a) @@ -214,12 +211,6 @@ GEM 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) grpc (1.64.0-x86_64-linux) google-protobuf (~> 3.25) googleapis-common-protos-types (~> 1.0) @@ -414,8 +405,6 @@ GEM hashdiff (>= 0.4.0, < 2.0.0) PLATFORMS - ruby - x86_64-darwin-23 x86_64-linux DEPENDENCIES @@ -473,4 +462,4 @@ DEPENDENCIES webmock (~> 3.19.1) BUNDLED WITH - 2.4.22 + 2.3.23