Merge to master: Release 2.6.3 - Security fixes, XML diff parsing and portal configuration model

Gemfile.lock

@@ -42,20 +42,22 @@ GEM
     bcrypt (3.1.20)
     bigdecimal (3.1.8)
     builder (3.3.0)
+    childprocess (5.1.0)
+      logger (~> 1.5)
     coderay (1.1.3)
-    concurrent-ruby (1.3.3)
+    concurrent-ruby (1.3.4)
     connection_pool (2.4.1)
     crack (1.0.0)
       bigdecimal
       rexml
     cube-ruby (0.0.3)
     daemons (1.4.1)
     date (3.3.4)
-    docile (1.4.0)
+    docile (1.4.1)
     domain_name (0.6.20240107)
-    email_spec (2.2.2)
+    email_spec (2.3.0)
       htmlentities (~> 4.3.3)
-      launchy (~> 2.1)
+      launchy (>= 2.1, < 4.0)
       mail (~> 2.7)
     eventmachine (1.2.7)
     faraday (1.10.3)
@@ -76,32 +78,33 @@ GEM
     faraday-httpclient (1.0.1)
     faraday-multipart (1.0.4)
       multipart-post (~> 2)
-    faraday-net_http (1.0.1)
+    faraday-net_http (1.0.2)
     faraday-net_http_persistent (1.2.0)
     faraday-patron (1.0.0)
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
     ffi (1.16.3)
-    hashdiff (1.1.0)
+    hashdiff (1.1.1)
     hashie (5.0.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.6)
+    http-cookie (1.0.7)
       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 (2.8.2)
+    jwt (2.9.0)
       base64
     language_server-protocol (3.17.0.3)
-    launchy (2.5.2)
+    launchy (3.0.1)
       addressable (~> 2.8)
+      childprocess (~> 5.0)
     libxml-ruby (2.9.0)
     link_header (0.0.8)
-    logger (1.6.0)
+    logger (1.6.1)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -112,7 +115,7 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0604)
+    mime-types-data (3.2024.0903)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-reporters (0.14.24)
@@ -122,9 +125,9 @@ GEM
       powerbar
     multi_json (1.15.0)
     multipart-post (2.4.1)
-    net-http-persistent (4.0.2)
+    net-http-persistent (4.0.4)
       connection_pool (~> 2.2)
-    net-imap (0.4.14)
+    net-imap (0.4.16)
       date
       net-protocol
     net-pop (0.1.2)
@@ -134,12 +137,14 @@ GEM
     net-smtp (0.5.0)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.4)
+    oj (3.16.6)
       bigdecimal (>= 3.0)
+      ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
-    parallel (1.25.1)
-    parser (3.3.3.0)
+    ostruct (0.6.0)
+    parallel (1.26.3)
+    parser (3.3.5.0)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
@@ -150,7 +155,7 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.1.1)
-    racc (1.8.0)
+    racc (1.8.1)
     rack (1.6.13)
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
@@ -171,7 +176,7 @@ GEM
     rdf-xsd (3.2.1)
       rdf (~> 3.2)
       rexml (~> 3.2)
-    redis (5.2.0)
+    redis (5.3.0)
       redis-client (>= 0.22.0)
     redis-client (0.22.2)
       connection_pool
@@ -183,22 +188,20 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.3.1)
-      strscan
+    rexml (3.3.7)
     rsolr (1.1.2)
       builder (>= 2.1.2)
-    rubocop (1.64.1)
+    rubocop (1.66.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 1.8, < 3.0)
-      rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.31.1, < 2.0)
+      regexp_parser (>= 2.4, < 3.0)
+      rubocop-ast (>= 1.32.2, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.31.3)
+    rubocop-ast (1.32.3)
       parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
@@ -210,9 +213,8 @@ GEM
     simplecov-cobertura (2.1.0)
       rexml
       simplecov (~> 0.19)
-    simplecov-html (0.12.3)
+    simplecov-html (0.13.1)
     simplecov_json_formatter (0.1.4)
-    strscan (3.1.0)
     systemu (2.6.5)
     test-unit-minitest (0.9.1)
       minitest (~> 4.7)
@@ -223,7 +225,7 @@ GEM
     thread_safe (0.3.6)
     timeout (0.4.1)
     tzinfo (0.3.62)
-    unicode-display_width (2.5.0)
+    unicode-display_width (2.6.0)
     uuid (2.3.9)
       macaddr (~> 1.0)
     webmock (3.23.1)

config/config.rb.sample

@@ -92,6 +92,38 @@ begin
         link: 'https://www.googleapis.com/oauth2/v3/userinfo'
       }
     }
+
+    config.ui_name                       = 'Bioportal'
+    config.title                         = 'NCBO BioPortal'
+    config.description                   = "The world's most comprehensive repository of biomedical ontologies"
+    config.color                         = '#234979'
+    config.logo                          = ''
+    config.fundedBy                      = [
+        {
+          img_src: 'https://identity.stanford.edu/wp-content/uploads/sites/3/2020/07/block-s-right.png',
+          url: 'https://www.stanford.edu',
+
+        },
+        {
+          img_src: 'https://ontoportal.org/images/logo.png',
+          url: 'https://ontoportal.org/',
+        }
+    ]
+    config.federated_portals = {
+          'agroportal' => {
+            api: 'http://data.agroportal.lirmm.fr',
+            ui: 'http://agroportal.lirmm.fr',
+            apikey: '1cfae05f-9e67-486f-820b-b393dec5764b',
+            color: '#1e2251'
+          },
+          'bioportal' => {
+                  api: 'http://data.bioontology.org',
+                  ui: 'http://bioportal.bioontology.org',
+                  apikey: '4a5011ea-75fa-4be6-8e89-f45c8c84844e',
+                  color: '#234979'
+           },
+
+    }
   end
 rescue NameError => e
   binding.pry

config/schemes/ontology_submission.yml

@@ -196,7 +196,8 @@ naturalLanguage:
     "http://lexvo.org/id/iso639-1/nl": "Dutch",
     "http://lexvo.org/id/iso639-1/fi": "Finnish",
     "http://lexvo.org/id/iso639-1/el": "Greek",
-    "http://lexvo.org/id/iso639-1/ja": "Japanese"
+    "http://lexvo.org/id/iso639-1/ja": "Japanese",
+    "http://lexvo.org/id/iso639-1/pt-br": "Brazilian"
   }
   metadataMappings: [ "omv:naturalLanguage", "dc:language", "dcterms:language", "doap:language", "schema:inLanguage" ]
 
@@ -289,7 +290,7 @@ copyrightHolder:
   description: [ 
     "SCHEMA: The party holding the legal copyright to the CreativeWork.",
     "DCTERMS: A person or organization owning or managing rights over the resource." ]
-  extractedMetadata: false
+  extractedMetadata: true
 
 ### Description
 
@@ -503,7 +504,7 @@ hasCreator:
     "DOAP: Maintainer of a project, a project leader.",
     "SCHEMA:author: The author of this content or rating.",
     "SCHEMA:creator: The creator/author of this CreativeWork." ]
-  extractedMetadata: false
+  extractedMetadata: true
   metadataMappings: [ "omv:hasCreator", "dc:creator", "dcterms:creator", "foaf:maker", "prov:wasAttributedTo", "doap:maintainer", "pav:authoredBy", "pav:createdBy", "schema:author", "schema:creator" ]
 
 #Contributor
@@ -517,7 +518,7 @@ hasContributor:
     "OMV: Contributors to the creation of the ontology.",
     "PAV: The resource was contributed to by the given agent.",
     "DOAP: Project contributor" ]
-  extractedMetadata: false
+  extractedMetadata: true
   metadataMappings: [ "omv:hasContributor", "dc:contributor", "dcterms:contributor", "doap:helper", "schema:contributor", "pav:contributedBy" ]
 
 #Curator
@@ -528,7 +529,7 @@ curatedBy:
   description: [ 
     "PAV: Specifies an agent specialist responsible for shaping the expression in an appropriate format. Often the primary agent responsible for ensuring the quality of the representation.", 
     "MOD: An ontology that is evaluated by an agent." ]
-  extractedMetadata: false
+  extractedMetadata: true
   metadataMappings: [ "mod:evaluatedBy", "pav:curatedBy" ]
 
 #Translator
@@ -538,7 +539,7 @@ translator:
   helpText: "Organization or person who adapts a creative work to different languages."
   description: [ 
     "SCHEMA: Organization or person who adapts a creative work to different languages, regional differences and technical requirements of a target market, or that translates during some event." ]
-  extractedMetadata: false
+  extractedMetadata: true
   metadataMappings: [ "schema:translator" ]
 
 #Publisher
@@ -550,7 +551,7 @@ publisher:
     "DCTERMS: An entity responsible for making the resource available.",
     "SCHEMA: The publisher of creative work.",
     "ADMS: The name of the agency that issued the identifier." ]
-  extractedMetadata: false
+  extractedMetadata: true
   metadataMappings: [ "dc:publisher", "dcterms:publisher", "schema:publisher", "adms:schemaAgency" ]
 
 #Funded or sponsored by
@@ -562,7 +563,7 @@ fundedBy:
     "MOD: An ontology that is sponsored by and developed under a project.",
     "FOAF: An organization funding a project or person.",
     "SCHEMA: The organization on whose behalf the creator was working." ]
-  extractedMetadata: false
+  extractedMetadata: true
   metadataMappings: [ "foaf:fundedBy", "mod:sponsoredBy", "schema:sourceOrganization" ]
 
 #Endorsed by
@@ -573,7 +574,7 @@ endorsedBy:
   description: [ 
     "MOD: An ontology endorsed by an agent.",
     "OMV: The parties that have expressed support or approval to this ontology." ]
-  extractedMetadata: false
+  extractedMetadata: true
   metadataMappings: [ "omv:endorsedBy", "mod:endorsedBy" ]
 
 ### Community
@@ -1429,7 +1430,7 @@ exampleIdentifier:
   description: [ 
     "VOID: Example resource of dataset.",
     "IDOT: An example identifier used by one item (or record) from a dataset." ]
-  extractedMetadata: false
+  extractedMetadata: true
   metadataMappings: [ "void:exampleResource", "idot:exampleIdentifier" ]
 
 #Key classes
@@ -1441,7 +1442,7 @@ keyClasses:
     "OMV: Representative classes in the ontology.",
     "FOAF: The primary topic of some page or document.",
     "SCHEMA: Indicates the primary entity described in some page or other CreativeWork." ]
-  extractedMetadata: false
+  extractedMetadata: true
   metadataMappings: [ "foaf:primaryTopic", "schema:mainEntity", "omv:keyClasses"]
 
 #Metadata vocabulary used
@@ -1454,7 +1455,7 @@ metadataVoc:
     "SCHEMA: Indicates (by URL or string) a particular version of a schema used in some CreativeWork.",
     "ADMS: A schema according to which the Asset Repository can provide data about its content, e.g. ADMS.",
     "MOD: A vocabulary(ies) that is used and/or referred to create the current ontology." ]
-  extractedMetadata: false
+  extractedMetadata: true
   enforcedValues: {
       "http://w3id.org/nkos/nkostype#classification_schema": "Classification scheme",
       "http://www.w3.org/2000/01/rdf-schema#": "RDF Schema (RDFS)",

lib/ontologies_linked_data/config/config.rb

@@ -42,9 +42,16 @@ def config(&block)
     # ###
 
     @settings.ui_name                       ||= 'Bioportal'
+    @settings.title                         ||= ''
+    @settings.description                   ||= ''
+    @settings.color                         ||= ''
+    @settings.logo                          ||= ''
+    @settings.fundedBy                      ||= {}
+    @settings.federated_portals             ||= {}
+
     @settings.ui_host                       ||= 'bioportal.bioontology.org'
-    @settings.replace_url_prefix             ||= false
-    @settings.id_url_prefix                  ||= DEFAULT_PREFIX
+    @settings.replace_url_prefix            ||= false
+    @settings.id_url_prefix                 ||= DEFAULT_PREFIX
     @settings.queries_debug                 ||= false
     @settings.enable_monitoring             ||= false
     @settings.cube_host                     ||= 'localhost'

lib/ontologies_linked_data/models/base.rb

@@ -46,7 +46,7 @@ def self.goo_attrs_to_load(attributes = [], level = 0)
                           if attributes.first == :all
                             (self.attributes + self.hypermedia_settings[:serialize_default]).uniq
                           else
-                            attributes
+                            attributes - self.hypermedia_settings[:serialize_never]
                           end
                         elsif self.hypermedia_settings[:serialize_default].empty?
                           self.attributes

lib/ontologies_linked_data/models/category.rb

@@ -6,10 +6,10 @@ class Category < LinkedData::Models::Base
       attribute :name, enforce: [:existence]
       attribute :description
       attribute :created, enforce: [:date_time], default: lambda { |record| DateTime.now }
-      attribute :parentCategory, enforce: [:category]
+      attribute :parentCategory, enforce: [:category, :list]
       attribute :ontologies, inverse: { on: :ontology, attribute: :hasDomain }
 
       cache_timeout 86400
     end
   end
-end
+end