Merge branch 'development' into feature/disable-new-validators

config/schemes/ontology_submission.yml

@@ -589,10 +589,6 @@ pullLocation:
                  "DOAP:  Web page from which the project software can be downloaded" ]
   metadataMappings: [ "doap:download-page" , "dcat:accessURL" , "omv:resourceLocator" ]
   label: "Access URL"
-  enforcedValues: {
-    "https://www.w3.org/TR/rdf-schema/#ch_subclassof": "rdfs:subClassOf",
-    "http://www.sparna.fr/skos/SKOS-traduction-francais.html#broader": "skos:broader"
-  }
   display: "links"
 
 uriLookupEndpoint:
@@ -1034,9 +1030,10 @@ associatedMedia:
 
 
 # object description properties
+
 prefLabelProperty:
   extractedMetadata: true
-  description: "MOD: Property used to specify objects preferred label"
+  description: "MOD: Property used to specify objects preferred label."
   label: "Object preferred label property"
   enforcedValues: {
     "http://www.w3.org/2004/02/skos/core#prefLabel": "prefLabel",
@@ -1046,10 +1043,10 @@ prefLabelProperty:
     "http://purl.org/dc/terms/title": "title"
   }
   display: "object description properties"
-
+  
 synonymProperty:
   extractedMetadata: true
-  description: "MOD: Property used to specify objects synonyms"
+  description: "MOD: Property used to specify objects synonyms."
   label: "Object synonym property"
   enforcedValues: {
     "http://www.w3.org/2004/02/skos/core#altLabel ": "altLabel",
@@ -1058,10 +1055,9 @@ synonymProperty:
   }
   display: "object description properties"
 
-
 definitionProperty:
   extractedMetadata: true
-  description: "MOD: Property used to specify objects' definition"
+  description: "MOD: Property used to specify objects definition."
   label: "Object definition property"
   enforcedValues: {
     "http://www.w3.org/2004/02/skos/core#definition": "definition",
@@ -1071,10 +1067,9 @@ definitionProperty:
   }
   display: "object description properties"
 
-
 authorProperty:
   extractedMetadata: true
-  description: "MOD: Property used to specify object's author"
+  description: "MOD: Property used to specify object author."
   label: "Object author property"
   enforcedValues: {
     "http://purl.org/dc/elements/1.1/creator": "creator",
@@ -1088,7 +1083,7 @@ authorProperty:
 
 obsoleteProperty:
   extractedMetadata: true
-  description: "MOD: Property used to specify obsolete objects"
+  description: "MOD: Property used to specify obsolete objects."
   label: "Object obsolete property"
   enforcedValues: {
     "http://www.w3.org/2002/07/owl#owl:deprecated": "deprecated",
@@ -1101,15 +1096,14 @@ createdProperty:
   description: "MOD: Property used to specify the date of creation of a class or another object in the ontology."
   label: "Object creation date property"
   enforcedValues: {
-    "http://purl.org/dc/terms/created ": "created",
-    "http://purl.org/dc/terms/issued ": "issued",
-    "http://purl.org/dc/terms/date": "date",
-    "http://purl.org/pav/authoredOn ": "authoredOn",
-    "http://purl.org/pav/contributedOn": "contributedOn",
-    "http://purl.org/pav/createdOn": "createdOn",
-    "http://www.isibang.ac.in/ns/mod/1.1/creationDate": "creationDate",
-    "http://schema.org/dateCreated ": "dateCreated",
-    "http://www.w3.org/ns/prov#generatedAtTime": "generatedAtTime"
+    "http://purl.org/dc/terms/created ": "dcterms:created",
+    "http://purl.org/dc/terms/issued ": "dcterms:issued",
+    "http://purl.org/dc/terms/date": "dcterms:date",
+    "http://purl.org/pav/authoredOn ": "pav:authoredOn",
+    "http://purl.org/pav/contributedOn": "pav:contributedOn",
+    "http://purl.org/pav/createdOn": "pav:createdOn",
+    "http://schema.org/dateCreated": "sdo:dateCreated",
+    "http://www.w3.org/ns/prov#generatedAtTime": "prov:generatedAtTime"
   }
   display: "object description properties"
 
@@ -1118,21 +1112,26 @@ modifiedProperty:
   description: "MOD: Property used to specify the date of modification of a class or another object in the ontology."
   label: "Object modification date property"
   enforcedValues: {
-                    "http://purl.org/dc/terms" ,
-                    "http://schema.org" ,
-                    "http://purl.org/pav" ,
-                    "https://omv2.sourceforge.net"
+    "http://purl.org/dc/terms/modified ": "dc:modified",
+    "http://purl.org/dc/terms/issued ": "dcterms:issued",
+    "http://purl.org/dc/terms/date": "dcterms:date",
+    "http://purl.org/pav/authoredOn ": "pav:authoredOn",
+    "http://purl.org/pav/contributedOn": "pav:contributedOn",
+    "http://purl.org/pav/lastUpdateOn": "pav:lastUpdateOn",
+    "http://schema.org/dateModified": "sdo:dateModified"
   }
   display: "object description properties"
-
+  
 hierarchyProperty:
   extractedMetadata: true
-  description: "MOD: A property that is used to specify the hierarchy"
+  description: "MOD: A property that is used to specify the hierarchy."
   label: "Hierarchy property"
   enforcedValues: {
-    "https://www.w3.org/TR/rdf-schema/#ch_subclassof": "rdfs:subClassOf",
-    "http://www.sparna.fr/skos/SKOS-traduction-francais.html#broader": "skos:broader"
+    "http://www.w3.org/2000/01/rdf-schema#subClassOf": "rdfs:subClassOf",
+    "http://www.w3.org/2004/02/skos/core#broader": "skos:broader"
   }
   display: "object description properties"
 
 
+
+

lib/ontologies_linked_data/concerns/mappings/mapping_creator.rb

@@ -198,7 +198,7 @@ def generate_class_urns(classes)
         def find_submission_by_ontology_id(ontology_id)
           return nil if ontology_id.nil?
 
-          o = LinkedData::Models::Ontology.where(submissions: { URI: ontology_id })
+          o = LinkedData::Models::Ontology.where(submissions: { URI: RDF::URI.new(ontology_id) })
                                           .include(submissions: %i[submissionId submissionStatus URI])
                                           .first
           o.nil? ? nil : o.latest_submission

lib/ontologies_linked_data/concerns/ontology_submissions/submission_metadata_extractor.rb

@@ -55,7 +55,7 @@ def extract_ontology_iri
                              RDF::URI.new('http://www.w3.org/1999/02/22-rdf-syntax-ns#type'),
                              RDF::URI.new('http://www.w3.org/2002/07/owl#Ontology')])
           sol = query.each_solution.first || {}
-          sol[:uri]&.to_s
+          RDF::URI.new(sol[:uri]) if sol[:uri]
         end
 
         private

lib/ontologies_linked_data/models/ontology_submission.rb

@@ -45,7 +45,7 @@ class OntologySubmission < LinkedData::Models::Base
 
       # Ontology metadata
       # General metadata
-      attribute :URI, namespace: :omv, enforce: %i[existence distinct_of_identifier]
+      attribute :URI, namespace: :omv,  type: :uri, enforce: %i[existence distinct_of_identifier]
       attribute :versionIRI, namespace: :owl, type: :uri, enforce: [:distinct_of_URI]
       attribute :version, namespace: :omv
       attribute :status, namespace: :omv, enforce: %i[existence], default: ->(x) { 'production' }
@@ -1672,7 +1672,7 @@ def uri
       end
 
       def uri=(uri)
-        self.URI = uri
+        self.URI = RDF::URI.new(uri)
       end
 
       def roots_sorted(extra_include = nil, concept_schemes: [])

test/mappings/test_mappings_bulk_load.rb

@@ -221,7 +221,7 @@ def mapping_load(mapping_hash, ontology_id)
     LinkedData::Mappings.create_mapping_counts(Logger.new(TestLogFile.new))
     ct = LinkedData::Models::MappingCount.where.all.length
     assert ct > 2
-    o = LinkedData::Models::Ontology.where(submissions: { URI: ontology_id })
+    o = LinkedData::Models::Ontology.where(submissions: { URI: RDF::URI.new(ontology_id) })
                                     .include(submissions: %i[submissionId submissionStatus])
                                     .first
     latest_sub = o.nil? ? nil : o.latest_submission

test/models/test_ontology_submission_validators.rb

@@ -10,6 +10,7 @@ def test_enforce_symmetric_ontologies
   end
 
   def test_lexvo_language_validator
+
     submissions = sorted_submissions_init(1)
 
     sub = submissions.first
@@ -31,6 +32,7 @@ def test_lexvo_language_validator
   # Regroup all validity test related to a submission retired status (deprecated, valid date)
   def test_submission_retired_validity
     skip 'complex validators disabled'
+
     sorted_submissions = sorted_submissions_init
 
     latest = sorted_submissions.first
@@ -121,6 +123,7 @@ def test_has_prior_version_callback
 
   def test_update_submissions_has_part
     skip 'complex validators disabled'
+
     ont_count, ont_acronyms, ontologies =
       create_ontologies_and_submissions(ont_count: 3, submission_count: 1,
                                         process_submission: false, acronym: 'NCBO-545')
@@ -193,7 +196,8 @@ def sorted_submissions_init(submission_count = 3)
   end
 
   def ontologies_properties_callbacks(attr, inverse_attr = nil)
-    inverse_attr = attr unless inverse_attr
+    skip('skip new callbacks tests until reimplemented')
+    inverse_attr = attr unless  inverse_attr
     ont_count, ont_acronyms, ontologies =
       create_ontologies_and_submissions(ont_count: 3, submission_count: 1,
                                         process_submission: false, acronym: 'NCBO-545')