Merge pull request #148 from ontoportal-lirmm/development

Merge to master: Release 2.5.2

Gemfile

@@ -5,11 +5,11 @@ gem 'addressable', '~> 2.8'
 gem 'bcrypt', '~> 3.0'
 gem 'cube-ruby', require: 'cube'
 gem 'faraday', '~> 1.9'
-gem 'ffi'
+gem 'ffi', '~> 1.16.3'
 gem 'libxml-ruby', '~> 2.0'
 gem 'minitest'
 gem 'multi_json', '~> 1.0'
-gem 'oj', '~> 2.0'
+gem 'oj'
 gem 'omni_logger'
 gem 'pony'
 gem 'rack', '~> 1.0'
@@ -42,4 +42,3 @@ end
 # NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
-

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: 8f0a9a5bddba03d9d660a363c4e6618da479db9f
+  revision: a95245b8c964431505ca6315907440996c59a00d
   branch: development
   specs:
     goo (0.0.2)
@@ -18,7 +18,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/sparql-client.git
-  revision: c96da3ad479724a31ccd6217ab9939dddfaca40e
+  revision: 59251e59346c9a69a67c88552ba55a1244eec602
   branch: development
   specs:
     sparql-client (3.2.2)
@@ -34,16 +34,16 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.8.6)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     ansi (1.5.0)
     ast (2.4.2)
     base64 (0.2.0)
     bcrypt (3.1.20)
-    bigdecimal (3.1.7)
-    builder (3.2.4)
+    bigdecimal (3.1.8)
+    builder (3.3.0)
     coderay (1.1.3)
-    concurrent-ruby (1.2.3)
+    concurrent-ruby (1.3.3)
     connection_pool (2.4.1)
     crack (1.0.0)
       bigdecimal
@@ -86,15 +86,15 @@ GEM
     hashie (5.0.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.5)
+    http-cookie (1.0.6)
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
     json (2.7.2)
     json-ld (3.0.2)
       multi_json (~> 1.12)
       rdf (>= 2.2.8, < 4.0)
-    jwt (2.8.1)
+    jwt (2.8.2)
       base64
     language_server-protocol (3.17.0.3)
     launchy (2.5.2)
@@ -112,7 +112,7 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0305)
+    mime-types-data (3.2024.0604)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-reporters (0.14.24)
@@ -121,10 +121,10 @@ GEM
       minitest (>= 2.12, < 5.0)
       powerbar
     multi_json (1.15.0)
-    multipart-post (2.4.0)
+    multipart-post (2.4.1)
     net-http-persistent (4.0.2)
       connection_pool (~> 2.2)
-    net-imap (0.4.10)
+    net-imap (0.4.14)
       date
       net-protocol
     net-pop (0.1.2)
@@ -134,11 +134,12 @@ GEM
     net-smtp (0.5.0)
       net-protocol
     netrc (0.11.0)
-    oj (2.18.5)
+    oj (3.16.4)
+      bigdecimal (>= 3.0)
     omni_logger (0.1.4)
       logger
-    parallel (1.24.0)
-    parser (3.3.1.0)
+    parallel (1.25.1)
+    parser (3.3.3.0)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
@@ -148,8 +149,8 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.5)
-    racc (1.7.3)
+    public_suffix (5.1.1)
+    racc (1.8.0)
     rack (1.6.13)
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
@@ -172,20 +173,21 @@ GEM
       rexml (~> 3.2)
     redis (5.2.0)
       redis-client (>= 0.22.0)
-    redis-client (0.22.1)
+    redis-client (0.22.2)
       connection_pool
-    regexp_parser (2.9.0)
-    request_store (1.6.0)
+    regexp_parser (2.9.2)
+    request_store (1.7.0)
       rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.2.6)
+    rexml (3.3.1)
+      strscan
     rsolr (1.1.2)
       builder (>= 2.1.2)
-    rubocop (1.63.4)
+    rubocop (1.64.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -210,6 +212,7 @@ GEM
       simplecov (~> 0.19)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.4)
+    strscan (3.1.0)
     systemu (2.6.5)
     test-unit-minitest (0.9.1)
       minitest (~> 4.7)
@@ -223,14 +226,13 @@ GEM
     unicode-display_width (2.5.0)
     uuid (2.3.9)
       macaddr (~> 1.0)
-    webmock (3.23.0)
+    webmock (3.23.1)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
 
 PLATFORMS
-  x86_64-darwin-23
-  x86_64-linux
+  ruby
 
 DEPENDENCIES
   activesupport (~> 4)
@@ -239,15 +241,15 @@ DEPENDENCIES
   cube-ruby
   email_spec
   faraday (~> 1.9)
-  ffi
+  ffi (~> 1.16.3)
   goo!
   json-ld (~> 3.0.2)
   jwt
   libxml-ruby (~> 2.0)
   minitest
   minitest-reporters (>= 0.5.0)
   multi_json (~> 1.0)
-  oj (~> 2.0)
+  oj
   omni_logger
   parallel (~> 1.24)
   pony
@@ -268,4 +270,4 @@ DEPENDENCIES
   webmock
 
 BUNDLED WITH
-   2.4.22
+   2.1.4

lib/ontologies_linked_data/concerns/ontology_submissions/submission_validators.rb

@@ -46,31 +46,6 @@ def deprecated?(inst = self)
       module Validators
         include ValidatorsHelpers
 
-        def enforce_agent_type(values, type, attr)
-          Array(values).each do |aff|
-            error = ["is_#{type}", "`#{attr}` must contain only agents of type #{type.capitalize}"]
-
-            return error unless aff.is_a?(LinkedData::Models::Agent)
-
-            aff.bring(:agentType) if aff.bring?(:agentType)
-            return error unless aff.agentType&.eql?(type)
-          end
-          []
-        end
-
-        def is_organization(inst, attr)
-          inst.bring(attr) if inst.bring?(attr)
-          affiliations = inst.send(attr)
-
-          enforce_agent_type(affiliations, 'organization', attr)
-        end
-
-        def is_person(inst, attr)
-          inst.bring(attr) if inst.bring?(attr)
-          persons = inst.send(attr)
-          enforce_agent_type(persons, 'person', attr)
-        end
-
         def lexvo_language(inst, attr)
           values = Array(attr_value(inst, attr))
 
@@ -290,7 +265,7 @@ def uri_lookup_default(sub)
         end
 
         def data_dump_default(sub)
-          RDF::URI.new("#{LinkedData.settings.rest_url_prefix}ontologies/#{sub.ontology.acronym}/download?download_format=rdf")
+          RDF::URI.new("#{LinkedData.settings.rest_url_prefix}ontologies/#{sub.ontology.acronym}/download")
         end
 
         def csv_dump_default(sub)
@@ -316,4 +291,3 @@ def default_hierarchy_property(sub)
     end
   end
 end
-

lib/ontologies_linked_data/models/class.rb

@@ -284,7 +284,7 @@ def index_doc(to_set=nil)
             if cur_val.is_a?(Hash) # Multi language
               if multi_language_fields.include?(att)
                 doc[att] = cur_val.values.flatten # index all values of each language
-                cur_val.each { |lang, values| doc["#{att}_#{lang}".to_sym] = values } # index values per language
+                cur_val.each { |lang, values| doc["#{att}_#{lang.to_s.gsub('@', '')}".to_sym] = values } # index values per language
               else
                 doc[att] = cur_val.values.flatten.first
               end

lib/ontologies_linked_data/models/ontology.rb

@@ -77,6 +77,7 @@ class OntologyAnalyticsError < StandardError; end
               LinkedData::Hypermedia::Link.new("download", lambda {|s| "ontologies/#{s.acronym}/download"}, self.type_uri),
               LinkedData::Hypermedia::Link.new("views", lambda {|s| "ontologies/#{s.acronym}/views"}, self.type_uri),
               LinkedData::Hypermedia::Link.new("analytics", lambda {|s| "ontologies/#{s.acronym}/analytics"}, "#{Goo.namespaces[:metadata].to_s}Analytics"),
+              LinkedData::Hypermedia::Link.new("agents", lambda {|s| "ontologies/#{s.acronym}/agents"}, LinkedData::Models::Agent.uri_type),
               LinkedData::Hypermedia::Link.new("ui", lambda {|s| "http://#{LinkedData.settings.ui_host}/ontologies/#{s.acronym}"}, self.uri_type)
 
       # Access control
@@ -304,17 +305,18 @@ def property_roots(sub=nil, extra_include=[])
         LinkedData::Models::OntologyProperty.sort_properties(all_roots)
       end
 
-      def property(prop_id, sub=nil)
+      def property(prop_id, sub=nil, display_all_attributes: false)
         p = nil
         sub ||= latest_submission(status: [:rdf])
         self.bring(:acronym) if self.bring?(:acronym)
         raise ParsedSubmissionError, "The properties of ontology #{self.acronym} cannot be retrieved because it has not been successfully parsed" unless sub
         prop_classes = [LinkedData::Models::ObjectProperty, LinkedData::Models::DatatypeProperty, LinkedData::Models::AnnotationProperty]
 
         prop_classes.each do |c|
-          p = c.find(prop_id).in(sub).include(:label, :definition, :parents).first
+          p = c.find(prop_id).in(sub).include(:label, :definition, :parents,:domain, :range).first
 
           unless p.nil?
+            p.bring(:unmapped) if display_all_attributes
             p.load_has_children
             parents = p.parents.nil? ? [] : p.parents.dup
             c.in(sub).models(parents).include(:label, :definition).all()

lib/ontologies_linked_data/models/ontology_submission.rb

@@ -37,7 +37,7 @@ class OntologySubmission < LinkedData::Models::Base
       attribute :classType, type: :uri
       attribute :hierarchyProperty, type: :uri, default: ->(s) { default_hierarchy_property(s) }
       attribute :obsoleteProperty, type: :uri, default: ->(s) { Goo.vocabulary(:owl)[:deprecated] }
-      attribute :obsoleteParent, type: :uri, default: ->(s) { RDF::URI.new("http://www.geneontology.org/formats/oboInOwl#ObsoleteClass") }
+      attribute :obsoleteParent, type: :uri
       attribute :createdProperty, type: :uri, default: ->(s) { Goo.vocabulary(:dc)[:created] }
       attribute :modifiedProperty, type: :uri, default: ->(s) { Goo.vocabulary(:dc)[:modified] }
 
@@ -81,12 +81,12 @@ class OntologySubmission < LinkedData::Models::Base
 
       # Person and organizations metadata
       attribute :contact, type: %i[contact list], enforce: [:existence]
-      attribute :hasCreator, namespace: :omv, type: %i[list Agent], enforce: [:is_person]
-      attribute :hasContributor, namespace: :omv, type: %i[list Agent], enforce: [:is_person]
+      attribute :hasCreator, namespace: :omv, type: %i[list Agent]
+      attribute :hasContributor, namespace: :omv, type: %i[list Agent]
       attribute :curatedBy, namespace: :pav, type: %i[list Agent]
       attribute :publisher, namespace: :dct, type: %i[list Agent]
-      attribute :fundedBy, namespace: :foaf, type: %i[list Agent], enforce: [:is_organization]
-      attribute :endorsedBy, namespace: :omv, type: %i[list Agent], enforce: [:is_organization]
+      attribute :fundedBy, namespace: :foaf, type: %i[list Agent]
+      attribute :endorsedBy, namespace: :omv, type: %i[list Agent]
       attribute :translator, namespace: :schema, type: %i[list Agent]
 
       # Community metadata

lib/ontologies_linked_data/models/properties/annotation_property.rb

@@ -18,11 +18,12 @@ class AnnotationProperty < LinkedData::Models::OntologyProperty
       attribute :children, namespace: :rdfs, inverse: { on: :annotation_property, :attribute => :parents }
       attribute :ancestors, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_ancestors
       attribute :descendants, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_descendants
-      # attribute :domain
-      # attribute :range
+      attribute :domain, namespace: :rdfs
+      attribute :range, namespace: :rdfs
 
-      serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren # some of these attributes are used in Search (not shown out of context)
+      serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren,:domain, :range # some of these attributes are used in Search (not shown out of context)
       aggregates childrenCount: [:count, :children]
+      serialize_methods :properties
       # this command allows the children to be serialized in the output
       embed :children
 

lib/ontologies_linked_data/models/properties/datatype_property.rb

@@ -18,11 +18,12 @@ class DatatypeProperty < LinkedData::Models::OntologyProperty
       attribute :children, namespace: :rdfs, inverse: { on: :datatype_property, :attribute => :parents }
       attribute :ancestors, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_ancestors
       attribute :descendants, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_descendants
-      # attribute :domain
-      # attribute :range
+      attribute :domain, namespace: :rdfs
+      attribute :range, namespace: :rdfs
 
-      serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren # some of these attributes are used in Search (not shown out of context)
+      serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren, :domain, :range # some of these attributes are used in Search (not shown out of context)
       aggregates childrenCount: [:count, :children]
+      serialize_methods :properties
       # this command allows the children to be serialized in the output
       embed :children
 

lib/ontologies_linked_data/models/properties/object_property.rb

@@ -18,11 +18,12 @@ class ObjectProperty < LinkedData::Models::OntologyProperty
       attribute :children, namespace: :rdfs, inverse: { on: :object_property, :attribute => :parents }
       attribute :ancestors, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_ancestors
       attribute :descendants, namespace: :rdfs, property: :subPropertyOf, handler: :retrieve_descendants
-      # attribute :domain
-      # attribute :range
+      attribute :domain, namespace: :rdfs
+      attribute :range, namespace: :rdfs
 
-      serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren # some of these attributes are used in Search (not shown out of context)
+      serialize_default :label, :labelGenerated, :definition, :matchType, :ontologyType, :propertyType, :parents, :children, :hasChildren, :domain, :range # some of these attributes are used in Search (not shown out of context)
       aggregates childrenCount: [:count, :children]
+      serialize_methods :properties
       # this command allows the children to be serialized in the output
       embed :children
 

lib/ontologies_linked_data/models/properties/ontology_property.rb

@@ -32,7 +32,9 @@ def self.index_schema(schema_generator)
         index_schema(schema_generator)
       end
 
-
+      def properties
+        self.unmapped
+      end
 
       def retrieve_ancestors
         retrieve_ancestors_descendants(:ancestors)

lib/ontologies_linked_data/utils/notifications.rb

@@ -10,9 +10,9 @@ def self.new_note(note)
         note.relatedOntology.each { |o| o.bring(:name) if o.bring?(:name); o.bring(:subscriptions) if o.bring?(:subscriptions) }
         ontologies = note.relatedOntology.map { |o| o.name }.join(", ")
         # Fix the note URL when using replace_url_prefix (in another VM than NCBO)
-
         note_hash = note.id.to_s.split('/').last
-        note_url = "http://#{LinkedData.settings.ui_host}/notes/#{note_hash}"
+        note_url = "http://#{LinkedData.settings.ui_host}/ontologies/#{note.relatedOntology.first.acronym}?p=notes&noteid=#{note_hash}"
+
 
         subject = "[#{LinkedData.settings.ui_name} Notes] [#{ontologies}] #{note.subject}"
         body = NEW_NOTE.gsub("%username%", note.creator.username)
@@ -201,8 +201,8 @@ def self.obofoundry_sync(missing_onts, obsolete_onts)
 EOS
 
       REST_PASSWORD = <<~HTML
-        Someone has requested a password reset for user %username% . If this was 
-        you, please click on the link below to reset your password. Otherwise, please 
+        Someone has requested a password reset for user %username% . If this was
+        you, please click on the link below to reset your password. Otherwise, please
         ignore this email.<br/><br/>
 
         <a href="%password_url%">%password_url%</a><br/><br/>