Merge branch 'master' into merge-to-master-2.3.3

ontoportal-lirmm · Dec 5, 2023 · f04b433 · f04b433
2 parents 15d1d53 + 7afc661
commit f04b433
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diff --git a/Gemfile b/Gemfile
@@ -44,12 +44,12 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'development'
+gem 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'master'
 gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'master'
 gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
-gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'development'
+gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'master'
 
 group :development do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42
@@ -73,4 +73,5 @@ group :test do
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
-end
+  gem 'webmock'
+end
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 83e835de368bc9f19da800a477982e0ad770900d
+  revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
   branch: master
   specs:
     ncbo_ontology_recommender (0.0.1)
@@ -11,8 +11,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: ddb95e427950fde3ac715aec340394208c8166fe
-  branch: development
+  revision: 74ea47defc7f6260b045a6c6997bbe6a59c7bf62
+  branch: master
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -53,8 +53,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 4c89c8346766d23e09b24c8e29750bf3a91e6b53
-  branch: development
+  revision: 80a331d053ea04397a903452288c2186822c340c
+  branch: master
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -105,14 +105,15 @@ GEM
       multi_json (~> 1.0)
     addressable (2.8.5)
       public_suffix (>= 2.0.2, < 6.0)
-    airbrussh (1.4.2)
+    airbrussh (1.5.0)
       sshkit (>= 1.6.1, != 1.7.0)
     backports (3.24.1)
-    bcrypt (3.1.19)
+    base64 (0.2.0)
+    bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.0)
     bigdecimal (1.4.2)
     builder (3.2.4)
-    capistrano (3.17.3)
+    capistrano (3.18.0)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -126,13 +127,14 @@ GEM
       sshkit (~> 1.3)
     coderay (1.1.3)
     concurrent-ruby (1.2.2)
+    crack (0.4.5)
+      rexml
     cube-ruby (0.0.3)
     dante (0.2.0)
-    date (3.3.3)
+    date (3.3.4)
     declarative (0.0.20)
     docile (1.4.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
+    domain_name (0.6.20231109)
     ed25519 (1.3.0)
     faraday (1.10.3)
       faraday-em_http (~> 1.0)
@@ -157,12 +159,12 @@ GEM
     faraday-patron (1.0.0)
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
-    ffi (1.15.5)
+    ffi (1.16.3)
     get_process_mem (0.2.7)
       ffi (~> 1.0)
     google-apis-analytics_v3 (0.13.0)
       google-apis-core (>= 0.11.0, < 2.a)
-    google-apis-core (0.11.1)
+    google-apis-core (0.11.2)
       addressable (~> 2.5, >= 2.5.1)
       googleauth (>= 0.16.2, < 2.a)
       httpclient (>= 2.8.1, < 3.a)
@@ -171,42 +173,41 @@ GEM
       retriable (>= 2.0, < 4.a)
       rexml
       webrick
-    googleauth (1.7.0)
+    googleauth (1.8.1)
       faraday (>= 0.17.3, < 3.a)
       jwt (>= 1.4, < 3.0)
-      memoist (~> 0.16)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
     haml (5.2.2)
       temple (>= 0.8.0)
       tilt
+    hashdiff (1.0.1)
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
     httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.6.3)
+    json (2.7.1)
     json-schema (2.8.1)
       addressable (>= 2.4)
-    json_pure (2.6.3)
+    json_pure (2.7.1)
     jwt (2.7.1)
     kgio (2.11.4)
-    libxml-ruby (4.1.1)
-    logger (1.5.3)
+    libxml-ruby (4.1.2)
+    logger (1.6.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
       mini_mime (>= 0.1.1)
       net-imap
       net-pop
       net-smtp
-    memoist (0.16.2)
     method_source (1.0.0)
     mime-types (3.5.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.0808)
+    mime-types-data (3.2023.1003)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
@@ -215,20 +216,21 @@ GEM
     multi_json (1.15.0)
     multipart-post (2.3.0)
     net-http-persistent (2.9.4)
-    net-imap (0.3.7)
+    net-imap (0.4.7)
       date
       net-protocol
     net-pop (0.1.2)
       net-protocol
-    net-protocol (0.2.1)
+    net-protocol (0.2.2)
       timeout
     net-scp (4.0.0)
       net-ssh (>= 2.6.5, < 8.0.0)
-    net-smtp (0.3.3)
+    net-smtp (0.4.0)
       net-protocol
     net-ssh (7.2.0)
     netrc (0.11.0)
-    newrelic_rpm (9.4.2)
+    newrelic_rpm (9.6.0)
+      base64
     oj (2.18.5)
     omni_logger (0.1.4)
       logger
@@ -239,13 +241,13 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.3)
+    public_suffix (5.0.4)
     rack (1.6.13)
     rack-accept (0.4.5)
       rack (>= 0.4)
     rack-attack (6.6.1)
       rack (>= 1.0, < 3)
-    rack-cache (1.13.0)
+    rack-cache (1.14.0)
       rack (>= 0.4)
     rack-cors (1.0.6)
       rack (>= 1.6.0)
@@ -268,8 +270,8 @@ GEM
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)
       redis-store (>= 1.6, < 2)
-    redis-store (1.9.1)
-      redis (>= 4, < 5)
+    redis-store (1.9.2)
+      redis (>= 4, < 6)
     representable (3.2.0)
       declarative (< 0.1.0)
       trailblazer-option (>= 0.1.1, < 0.2.0)
@@ -291,7 +293,7 @@ GEM
     rubyzip (2.3.2)
     rufus-scheduler (2.0.24)
       tzinfo (>= 0.3.22)
-    signet (0.17.0)
+    signet (0.18.0)
       addressable (~> 2.8)
       faraday (>= 0.17.5, < 3.a)
       jwt (>= 1.5, < 3.0)
@@ -318,20 +320,17 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.21.5)
+    sshkit (1.21.6)
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     systemu (2.6.5)
-    temple (0.10.2)
-    tilt (2.2.0)
-    timeout (0.4.0)
+    temple (0.10.3)
+    tilt (2.3.0)
+    timeout (0.4.1)
     trailblazer-option (0.1.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uber (0.1.0)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.8.2)
     unicorn (6.1.0)
       kgio (~> 2.6)
       raindrops (~> 0.7)
@@ -340,10 +339,15 @@ GEM
       unicorn (>= 4, < 7)
     uuid (2.3.9)
       macaddr (~> 1.0)
+    webmock (3.19.1)
+      addressable (>= 2.8.0)
+      crack (>= 0.3.2)
+      hashdiff (>= 0.4.0, < 2.0.0)
     webrick (1.8.1)
 
 PLATFORMS
   x86_64-darwin-21
+  x86_64-darwin-23
   x86_64-linux
 
 DEPENDENCIES
@@ -397,6 +401,7 @@ DEPENDENCIES
   sparql-client!
   unicorn
   unicorn-worker-killer
+  webmock
 
 BUNDLED WITH
-   2.3.23
+   2.4.21
diff --git a/app.rb b/app.rb
@@ -29,6 +29,7 @@
 require_relative 'lib/rack/cube_reporter'
 require_relative 'lib/rack/param_translator'
 require_relative 'lib/rack/slice_detection'
+require_relative 'lib/rack/request_lang'
 
 # Logging setup
 require_relative "config/logging"
@@ -146,6 +147,7 @@
 use Rack::ParamTranslator
 
 use RequestStore::Middleware
+use Rack::RequestLang
 
 use LinkedData::Security::Authorization
 use LinkedData::Security::AccessDenied

diff --git a/config/environments/test.rb b/config/environments/test.rb
@@ -55,6 +55,24 @@
       "apikey" => "1cfae05f-9e67-486f-820b-b393dec5764b"
     }
   }
+  config.oauth_providers = {
+    github: {
+      check: :access_token,
+      link: 'https://api.github.com/user'
+    },
+    keycloak: {
+      check: :jwt_token,
+      cert: 'KEYCLOAK_SECRET_KEY'
+    },
+    orcid: {
+      check: :access_token,
+      link: 'https://pub.orcid.org/v3.0/me'
+    },
+    google: {
+      check: :access_token,
+      link: 'https://www.googleapis.com/oauth2/v3/userinfo'
+    }
+  }
 end
 
 Annotator.config do |config|

diff --git a/config/solr/property_search/enumsconfig.xml b/config/solr/property_search/enumsconfig.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" ?>
+<enumsConfig>
+  <enum name="ontologyType">
+    <value>ONTOLOGY</value>
+    <value>VALUE_SET_COLLECTION</value>
+  </enum>
+  <enum name="propertyType">
+    <value>ANNOTATION</value>
+    <value>DATATYPE</value>
+    <value>OBJECT</value>
+  </enum>
+</enumsConfig>