Merge branch 'master' into merge-to-master-2.3.2

Gemfile

@@ -1,6 +1,6 @@
 source 'https://rubygems.org'
 
-gem 'activesupport', '~> 3.0'
+gem 'activesupport', '~> 3.1'
 # see https://github.com/ncbo/ontologies_api/issues/69
 gem 'bigdecimal', '1.4.2'
 gem 'faraday', '~> 1.9'
@@ -19,7 +19,7 @@ gem 'request_store'
 gem 'ffi'
 gem 'rack-accept', '~> 0.4'
 gem 'rack-attack', '~> 6.6.1', require: 'rack/attack'
-gem 'rack-cache', '~> 1.0'
+gem 'rack-cache', '~> 1.13.0'
 gem 'rack-cors', require: 'rack/cors'
 # GitHub dependency can be removed when https://github.com/niko/rack-post-body-to-params/pull/6 is merged and released
 gem 'rack-post-body-to-params', github: 'palexander/rack-post-body-to-params', branch: 'multipart_support'
@@ -29,6 +29,7 @@ gem 'redis-rack-cache', '~> 2.0'
 # Data access (caching)
 gem 'redis', '~> 4.8.1'
 gem 'redis-activesupport'
+gem 'redis-store', '1.9.1'
 
 # Monitoring
 gem 'cube-ruby', require: 'cube'
@@ -43,12 +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
@@ -72,4 +73,5 @@ group :test do
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
-end
+  gem 'webmock'
+end

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
@@ -239,7 +241,7 @@ 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)
@@ -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)
@@ -340,14 +339,19 @@ 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
-  activesupport (~> 3.0)
+  activesupport (~> 3.1)
   bcrypt_pbkdf (>= 1.0, < 2.0)
   bigdecimal (= 1.4.2)
   capistrano (~> 3)
@@ -375,7 +379,7 @@ DEPENDENCIES
   rack
   rack-accept (~> 0.4)
   rack-attack (~> 6.6.1)
-  rack-cache (~> 1.0)
+  rack-cache (~> 1.13.0)
   rack-cors
   rack-mini-profiler
   rack-post-body-to-params!
@@ -386,6 +390,7 @@ DEPENDENCIES
   redis (~> 4.8.1)
   redis-activesupport
   redis-rack-cache (~> 2.0)
+  redis-store (= 1.9.1)
   request_store
   shotgun!
   simplecov
@@ -396,6 +401,7 @@ DEPENDENCIES
   sparql-client!
   unicorn
   unicorn-worker-killer
+  webmock
 
 BUNDLED WITH
-   2.3.23
+   2.4.21

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|

controllers/admin_controller.rb

@@ -68,7 +68,7 @@ class AdminController < ApplicationController
       latest = ont.latest_submission(status: :any)
       error 404, "Ontology #{params["acronym"]} contains no submissions" if latest.nil?
       check_last_modified(latest)
-      latest.bring(*OntologySubmission.goo_attrs_to_load(includes_param))
+      latest.bring(*submission_include_params)
       NcboCron::Models::OntologySubmissionParser.new.queue_submission(latest, actions)
       halt 204
     end
@@ -84,7 +84,7 @@ class AdminController < ApplicationController
         latest = ont.latest_submission(status: :any)
       end
       check_last_modified(latest) if latest
-      latest.bring(*OntologySubmission.goo_attrs_to_load(includes_param)) if latest
+      latest.bring(*submission_include_params) if latest
       reply(latest || {})
     end
 

controllers/classes_controller.rb

@@ -262,13 +262,7 @@ def includes_param_check
       end
     end
 
-    def concept_schemes
-      params["concept_schemes"]&.split(',') || []
-    end
 
-    def concept_collections
-      params["concept_collections"]&.split(',') || []
-    end
 
     def request_display(attrs)
 

controllers/ontologies_controller.rb

@@ -38,25 +38,12 @@ class OntologiesController < ApplicationController
       else
         latest = ont.latest_submission(status: :any)
       end
-      check_last_modified(latest) if latest
-      # When asking to display all metadata, we are using bring_remaining which is more performant than including all metadata (remove this when the query to get metadata will be fixed)
+
       if latest
-        if includes_param.first == :all
-          # Bring what we need to display all attr of the submission
-          latest.bring_remaining
-          latest.bring({:contact=>[:name, :email],
-                      :ontology=>[:acronym, :name, :administeredBy, :group, :viewingRestriction, :doNotUpdate, :flat,
-                                  :hasDomain, :summaryOnly, :acl, :viewOf, :ontologyType],
-                      :submissionStatus=>[:code], :hasOntologyLanguage=>[:acronym], :metrics =>[:classes, :individuals, :properties]})
-        else
-          includes = OntologySubmission.goo_attrs_to_load(includes_param)
-
-          includes << {:contact=>[:name, :email]} if includes.find{|v| v.is_a?(Hash) && v.keys.first.eql?(:contact)}
-
-          latest.bring(*includes)
-        end
+        check_last_modified(latest)
+        latest.bring(*submission_include_params)
       end
-      #remove the whole previous if block and replace by it: latest.bring(*OntologySubmission.goo_attrs_to_load(includes_param)) if latest
+
       reply(latest || {})
     end
 
@@ -66,7 +53,7 @@ class OntologiesController < ApplicationController
     patch '/:acronym/latest_submission' do
       ont = Ontology.find(params["acronym"]).first
       error 422, "You must provide an existing `acronym` to patch" if ont.nil?
-      
+
       submission = ont.latest_submission(status: :any)
 
       submission.bring(*OntologySubmission.attributes)