Merge branch 'master' into development

ontoportal-lirmm · Dec 5, 2023 · 9dd8d03 · 9dd8d03
2 parents a199eff + c20e1d3
commit 9dd8d03
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Showing 5 changed files with 97 additions and 103 deletions.
diff --git a/Gemfile b/Gemfile
@@ -36,7 +36,6 @@ end
 group :development do
   gem 'rubocop', require: false
 end
-
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
+gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'master'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: 5979402d5138850fb9bdb34edfa350e9af1b5d22
-  branch: development
+  revision: 74ea47defc7f6260b045a6c6997bbe6a59c7bf62
+  branch: master
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -36,7 +36,7 @@ GEM
       public_suffix (>= 2.0.2, < 6.0)
     ansi (1.5.0)
     ast (2.4.2)
-    bcrypt (3.1.19)
+    bcrypt (3.1.20)
     builder (3.2.4)
     coderay (1.1.3)
     concurrent-ruby (1.2.2)
@@ -47,8 +47,7 @@ GEM
     daemons (1.4.1)
     date (3.3.4)
     docile (1.4.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
+    domain_name (0.6.20231109)
     email_spec (2.2.2)
       htmlentities (~> 4.3.3)
       launchy (~> 2.1)
@@ -86,8 +85,8 @@ GEM
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.6.3)
-    json_pure (2.6.3)
+    json (2.7.1)
+    json_pure (2.7.1)
     jwt (2.7.1)
     language_server-protocol (3.17.0.3)
     launchy (2.5.2)
@@ -115,7 +114,7 @@ GEM
     multi_json (1.15.0)
     multipart-post (2.3.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.4)
+    net-imap (0.4.7)
       date
       net-protocol
     net-pop (0.1.2)
@@ -139,7 +138,7 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.3)
+    public_suffix (5.0.4)
     racc (1.7.3)
     rack (1.6.13)
     rack-test (0.8.3)
@@ -152,7 +151,7 @@ GEM
       redis-client (>= 0.17.0)
     redis-client (0.18.0)
       connection_pool
-    regexp_parser (2.8.2)
+    regexp_parser (2.8.3)
     request_store (1.5.1)
       rack (>= 1.4)
     rest-client (2.1.0)
@@ -163,15 +162,15 @@ GEM
     rexml (3.2.6)
     rsolr (1.1.2)
       builder (>= 2.1.2)
-    rubocop (1.57.2)
+    rubocop (1.58.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.2.2.4)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.28.1, < 2.0)
+      rubocop-ast (>= 1.30.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
     rubocop-ast (1.30.0)
@@ -198,9 +197,6 @@ GEM
     thread_safe (0.3.6)
     timeout (0.4.1)
     tzinfo (0.3.62)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.9)
     unicode-display_width (2.5.0)
     uuid (2.3.9)
       macaddr (~> 1.0)

diff --git a/lib/ontologies_linked_data/models/ontology.rb b/lib/ontologies_linked_data/models/ontology.rb
@@ -50,7 +50,7 @@ class OntologyAnalyticsError < StandardError; end
 
       attribute :acl, enforce: [:list, :user]
 
-      attribute :viewOf, enforce: [:ontology]
+      attribute :viewOf, enforce: [:ontology], onUpdate: :update_submissions_has_part
       attribute :views, :inverse => { on: :ontology, attribute: :viewOf }
       attribute :ontologyType, enforce: [:ontology_type], default: lambda { |record| LinkedData::Models::OntologyType.find("ONTOLOGY").include(:code).first }
 

diff --git a/lib/ontologies_linked_data/serializers/json.rb b/lib/ontologies_linked_data/serializers/json.rb
@@ -19,7 +19,7 @@ def self.serialize(obj, options = {})
           end
 
           # Add the type
-          hash["@type"] = type(current_cls, hashed_obj) if  hash["@id"]
+          hash["@type"] = type(current_cls, hashed_obj) if hash["@id"]
 
           # Generate links
           # NOTE: If this logic changes, also change in xml.rb
@@ -39,8 +39,8 @@ def self.serialize(obj, options = {})
             end
           elsif (hashed_obj.instance_of?(LinkedData::Models::ExternalClass) || hashed_obj.instance_of?(LinkedData::Models::InterportalClass)) && !current_cls.embedded?
             # Add context for ExternalClass
-            context_hash = {"@vocab" => Goo.vocabulary.to_s, "prefLabel" => "http://data.bioontology.org/metadata/skosprefLabel"}
-            context = {"@context" => context_hash}
+            context_hash = { "@vocab" => Goo.vocabulary.to_s, "prefLabel" => "http://data.bioontology.org/metadata/skosprefLabel" }
+            context = { "@context" => context_hash }
             hash.merge!(context)
           end
           hash['@context']['@language'] = result_lang if hash['@context']
@@ -103,17 +103,17 @@ def self.generate_context(object, serialized_attrs = [], options = {})
 
           if linked_model && linked_model.ancestors.include?(Goo::Base::Resource) && !embedded?(object, attr)
             # linked object
-            predicate = {"@id" => linked_model.type_uri.to_s, "@type" => "@id"}
+            predicate = { "@id" => linked_model.type_uri.to_s, "@type" => "@id" }
           else
             # use the original predicate property if set
-            predicate_attr =  current_cls.model_settings[:attributes][attr][:property] || attr
+            predicate_attr = current_cls.model_settings[:attributes][attr][:property] || attr
             # predicate with custom namespace
             # if the namespace can be resolved by the namespaces added in Goo then it will be resolved.
             predicate = "#{Goo.vocabulary(current_cls.model_settings[:attributes][attr][:namespace])&.to_s}#{predicate_attr}"
           end
           hash[attr] = predicate unless predicate.nil?
         end
-        context = {"@context" => hash}
+        context = { "@context" => hash }
         CONTEXTS[object.hash] = context
         context = remove_unused_attrs(context, serialized_attrs) unless options[:params] && options[:params]["full_context"].eql?("true")
         context
@@ -126,12 +126,12 @@ def self.generate_links_context(object)
         links.each do |link|
           links_context[link.type] = link.type_uri.to_s
         end
-        return {"@context" => links_context}
+        return { "@context" => links_context }
       end
 
       def self.remove_unused_attrs(context, serialized_attrs = [])
-        new_context = context["@context"].reject {|k,v| !serialized_attrs.include?(k) && !k.to_s.start_with?("@")}
-        {"@context" => new_context}
+        new_context = context["@context"].reject { |k, v| !serialized_attrs.include?(k) && !k.to_s.start_with?("@") }
+        { "@context" => new_context }
       end
 
       def self.embedded?(object, attribute)
@@ -148,20 +148,19 @@ def self.generate_context?(options)
         params = options[:params]
         params.nil? ||
           (params["no_context"].nil? ||
-                     !params["no_context"].eql?("true")) &&
-          (params["display_context"].nil? ||
-                    !params["display_context"].eql?("false"))
+            !params["no_context"].eql?("true")) &&
+            (params["display_context"].nil? ||
+              !params["display_context"].eql?("false"))
       end
 
       def self.generate_links?(options)
         params = options[:params]
         params.nil? ||
           (params["no_links"].nil? ||
-                     !params["no_links"].eql?("true")) &&
-          (params["display_links"].nil? ||
-                    !params["display_links"].eql?("false"))
+            !params["no_links"].eql?("true")) &&
+            (params["display_links"].nil? ||
+              !params["display_links"].eql?("false"))
       end
     end
   end
-end
-
+end