Merge to master: Release 2.4.3 - New metadata model (#97)

* fix json serializer nil exception (#79) if hash was missing @context key the json serializer throwed a nil exception * Merge pull request #72 from ontoportal-lirmm/feature/migrate-attrbiutes-metadata-to-scheme-file Feature: Update ontology submission model 2023 - Part 1 - Update attributes validators and metadata * Merge pull request #82 from ontoportal-lirmm/feature/embed-meterics-for-submissions Feature: embed metrics for submission model * Merge pull request #86 from ontoportal-lirmm/fix/read_restricted_based_on-nil Fix: call to read_restricted? only if instance_to_base_on not nil * Merge pull request #90 from ontoportal-lirmm/feature/add-persons-and-organization-models Feature: Update ontology submission model 2023 - Part 2 - Add person & organization models * in tests no more use the reload argument in the exist? method --------- Co-authored-by: Raimi Solorzano Niederhausen <[email protected]>
ontoportal-lirmm · Dec 5, 2023 · c20e1d3 · c20e1d3
1 parent aa5081d
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diff --git a/Gemfile b/Gemfile
@@ -34,7 +34,6 @@ 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: 'master'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
diff --git a/config/config.rb.sample b/config/config.rb.sample
@@ -15,6 +15,7 @@ LinkedData.config do |config|
   config.purl_password          = ""
   config.purl_maintainers       = ""
   config.purl_target_url_prefix = "http://bioportal.bioontology.org"
+  config.sparql_endpoint_url    = "http:://sparql_endpoint.com"
   Goo.configure do |conf|
       conf.main_languages = ['en']
   end

diff --git a/config/config.test.rb b/config/config.test.rb
@@ -31,5 +31,6 @@
   config.ontology_analytics_redis_port = REDIS_PORT.to_i
   config.search_server_url             = SOLR_TERM_SEARCH_URL.to_s
   config.property_search_server_url    = SOLR_PROP_SEARCH_URL.to_s
+  config.sparql_endpoint_url    = "http:://sparql_endpoint.com"
   #  config.enable_notifications          = false
 end
diff --git a/config/schemes/ontology_submission.yml b/config/schemes/ontology_submission.yml
diff --git a/lib/ontologies_linked_data/concerns/ontology_submissions/submission_metadata_extractor.rb b/lib/ontologies_linked_data/concerns/ontology_submissions/submission_metadata_extractor.rb
@@ -28,7 +28,12 @@ def extract_metadata(logger, user_params)
             logger.error("Error while setting default metadata: #{e}")
           end
 
-          self.save
+          if self.valid?
+            self.save
+          else
+            logger.error("Error while extracting additional metadata: #{self.errors}")
+          end
+
         end
 
         def extract_version
@@ -101,85 +106,6 @@ def extract_ontology_metadata(logger, user_params)
         # Set some metadata to default values if nothing extracted
         def set_default_metadata
 
-          self.identifier = uri.to_s if identifier.nil?
-
-          self.deprecated = status.eql?('retired') if deprecated.nil?
-
-          # Add the ontology hasDomain to the submission hasDomain metadata value
-          ontology_domain_list = []
-          ontology.bring(:hasDomain).hasDomain.each do |domain|
-            ontology_domain_list << domain.id
-          end
-
-          self.hasDomain = '' if !ontology_domain_list.empty? && hasDomain.nil?
-
-          self.hasDomain << ontology_domain_list.join(', ') unless hasDomain.nil?
-
-          # Only get the first view because the attribute is not a list
-          ontology_view = ontology.bring(:views).views.first
-          self.hasPart = ontology_view.id if hasPart.nil? && !ontology_view.nil?
-
-          # If no example identifier extracted: take the first class
-          self.exampleIdentifier = LinkedData::Models::Class.in(self).first.id if exampleIdentifier.nil?
-
-          # Metadata specific to BioPortal that have been removed:
-          #if self.hostedBy.nil?
-          #  self.hostedBy = [ RDF::URI.new("http://#{LinkedData.settings.ui_host}") ]
-          #end
-
-          # Add the search endpoint URL
-          if openSearchDescription.nil?
-            self.openSearchDescription = RDF::URI.new("#{LinkedData.settings.rest_url_prefix}search?ontologies=#{ontology.acronym}&q=")
-          end
-
-          # Search allow to search by URI too
-          if uriLookupEndpoint.nil?
-            self.uriLookupEndpoint = RDF::URI.new("#{LinkedData.settings.rest_url_prefix}search?ontologies=#{ontology.acronym}&require_exact_match=true&q=")
-          end
-
-          # Add the dataDump URL
-          if dataDump.nil?
-            self.dataDump = RDF::URI.new("#{LinkedData.settings.rest_url_prefix}ontologies/#{ontology.acronym}/download?download_format=rdf")
-          end
-
-          if csvDump.nil?
-            self.csvDump = RDF::URI.new("#{LinkedData.settings.rest_url_prefix}ontologies/#{ontology.acronym}/download?download_format=csv")
-          end
-
-          # Add the previous submission as a prior version
-          if submissionId > 1
-=begin
-          if prior_versions.nil?
-            prior_versions = []
-          else
-            prior_versions = self.hasPriorVersion.dup
-          end
-          prior_versions.push(RDF::URI.new("#{LinkedData.settings.rest_url_prefix}ontologies/#{self.ontology.acronym}/submissions/#{self.submissionId - 1}"))
-          self.hasPriorVersion = prior_versions
-=end
-            self.hasPriorVersion = RDF::URI.new("#{LinkedData.settings.rest_url_prefix}ontologies/#{ontology.acronym}/submissions/#{submissionId - 1}")
-          end
-
-          if hasOntologyLanguage.umls?
-            self.hasOntologySyntax = 'http://www.w3.org/ns/formats/Turtle'
-          elsif hasOntologyLanguage.obo?
-            self.hasOntologySyntax = 'http://purl.obolibrary.org/obo/oboformat/spec.html'
-          end
-
-          # Define default properties for prefLabel, synonyms, definition, author:
-          if hasOntologyLanguage.owl?
-            self.prefLabelProperty = Goo.vocabulary(:skos)[:prefLabel] if prefLabelProperty.nil?
-            self.synonymProperty = Goo.vocabulary(:skos)[:altLabel] if synonymProperty.nil?
-            self.definitionProperty = Goo.vocabulary(:rdfs)[:comment] if definitionProperty.nil?
-            self.authorProperty = Goo.vocabulary(:dc)[:creator] if authorProperty.nil?
-            # Add also hierarchyProperty? Could not find any use of it
-          end
-
-          # Add the sparql endpoint URL
-          if endpoint.nil? && LinkedData.settings.sparql_endpoint_url
-            self.endpoint = RDF::URI.new(LinkedData.settings.sparql_endpoint_url)
-          end
-
         end
 
         def empty_value?(value)
@@ -284,7 +210,8 @@ def extract_each_metadata(ontology_uri, attr, prop_to_extract, logger)
             value = sol[:extractedObject]
             if enforce?(attr, :uri)
               # If the attr is enforced as URI then it directly takes the URI
-              hash_results[value] = value if value.is_a?(RDF::URI)
+              uri_value = value ? RDF::URI.new(value.to_s.strip) : nil
+              hash_results[value] = uri_value if uri_value&.valid?
             elsif enforce?(attr, :date_time)
               begin
                 hash_results[value] = DateTime.iso8601(value.to_s)