add the serialize_defaults if attributes to load set to :all and some…

… refactor
ncbo · May 6, 2024 · 37f74d3 · 37f74d3
1 parent 5391eb6
commit 37f74d3
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Showing 7 changed files with 85 additions and 41 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
+.bundle/
 *.swp
 *.gemtags
 .bundle

diff --git a/lib/ontologies_linked_data/config/config.rb b/lib/ontologies_linked_data/config/config.rb
@@ -94,15 +94,13 @@ def config(&block)
     yield @settings, overide_connect_goo if block_given?
 
     # Check to make sure url prefix has trailing slash
-    @settings.rest_url_prefix = @settings.rest_url_prefix + '/' unless @settings.rest_url_prefix[-1].eql?('/')
+    @settings.rest_url_prefix = "#{@settings.rest_url_prefix}/" unless @settings.rest_url_prefix[-1].eql?('/')
 
     puts "(LD) >> Using rdf store #{@settings.goo_host}:#{@settings.goo_port}#{@settings.goo_path_query}"
     puts "(LD) >> Using term search server at #{@settings.search_server_url}"
     puts "(LD) >> Using property search server at #{@settings.property_search_server_url}"
-    puts '(LD) >> Using HTTP Redis instance at '+
-            "#{@settings.http_redis_host}:#{@settings.http_redis_port}"
-    puts '(LD) >> Using Goo Redis instance at '+
-            "#{@settings.goo_redis_host}:#{@settings.goo_redis_port}"
+    puts "(LD) >> Using HTTP Redis instance at #{@settings.http_redis_host}:#{@settings.http_redis_port}"
+    puts "(LD) >> Using Goo Redis instance at #{@settings.goo_redis_host}:#{@settings.goo_redis_port}"
 
     connect_goo unless overide_connect_goo
   end
@@ -132,15 +130,14 @@ def connect_goo
                                port: @settings.goo_redis_port)
 
         if @settings.enable_monitoring
-          puts "(LD) >> Enable SPARQL monitoring with cube #{@settings.cube_host}:"+
-                    "#{@settings.cube_port}"
+          puts "(LD) >> Enable SPARQL monitoring with cube #{@settings.cube_host}:#{@settings.cube_port}"
           conf.enable_cube do |opts|
             opts[:host] = @settings.cube_host
             opts[:port] = @settings.cube_port
           end
         end
       end
-    rescue Exception => e
+    rescue StandardError => e
       abort("EXITING: Cannot connect to triplestore and/or search server:\n  #{e}\n#{e.backtrace.join("\n")}")
     end
   end
@@ -153,23 +150,48 @@ def goo_namespaces
       conf.add_namespace(:omv, RDF::Vocabulary.new("http://omv.ontoware.org/2005/05/ontology#"))
       conf.add_namespace(:skos, RDF::Vocabulary.new("http://www.w3.org/2004/02/skos/core#"))
       conf.add_namespace(:owl, RDF::Vocabulary.new("http://www.w3.org/2002/07/owl#"))
+      conf.add_namespace(:rdf, RDF::Vocabulary.new("http://www.w3.org/1999/02/22-rdf-syntax-ns#"))
       conf.add_namespace(:rdfs, RDF::Vocabulary.new("http://www.w3.org/2000/01/rdf-schema#"))
-      conf.add_namespace(:metadata,
-                         RDF::Vocabulary.new("http://data.bioontology.org/metadata/"),
-                         default = true)
-      conf.add_namespace(:metadata_def,
-                         RDF::Vocabulary.new("http://data.bioontology.org/metadata/def/"))
+      conf.add_namespace(:metadata, RDF::Vocabulary.new("http://data.bioontology.org/metadata/"), default = true)
+      conf.add_namespace(:metadata_def, RDF::Vocabulary.new("http://data.bioontology.org/metadata/def/"))
       conf.add_namespace(:dc, RDF::Vocabulary.new("http://purl.org/dc/elements/1.1/"))
       conf.add_namespace(:xsd, RDF::Vocabulary.new("http://www.w3.org/2001/XMLSchema#"))
-      conf.add_namespace(:oboinowl_gen,
-                         RDF::Vocabulary.new("http://www.geneontology.org/formats/oboInOwl#"))
+      conf.add_namespace(:oboinowl_gen, RDF::Vocabulary.new("http://www.geneontology.org/formats/oboInOwl#"))
       conf.add_namespace(:obo_purl, RDF::Vocabulary.new("http://purl.obolibrary.org/obo/"))
-      conf.add_namespace(:umls,
-                         RDF::Vocabulary.new("http://bioportal.bioontology.org/ontologies/umls/"))
-      conf.id_prefix = "http://data.bioontology.org/"
+      conf.add_namespace(:umls, RDF::Vocabulary.new("http://bioportal.bioontology.org/ontologies/umls/"))
+      conf.add_namespace(:door, RDF::Vocabulary.new("http://kannel.open.ac.uk/ontology#"))
+      conf.add_namespace(:dct, RDF::Vocabulary.new("http://purl.org/dc/terms/"))
+
+      conf.add_namespace(:void, RDF::Vocabulary.new("http://rdfs.org/ns/void#"))
+      conf.add_namespace(:foaf, RDF::Vocabulary.new("http://xmlns.com/foaf/0.1/"))
+      conf.add_namespace(:vann, RDF::Vocabulary.new("http://purl.org/vocab/vann/"))
+      conf.add_namespace(:adms, RDF::Vocabulary.new("http://www.w3.org/ns/adms#"))
+      conf.add_namespace(:voaf, RDF::Vocabulary.new("http://purl.org/vocommons/voaf#"))
+      conf.add_namespace(:dcat, RDF::Vocabulary.new("http://www.w3.org/ns/dcat#"))
+      conf.add_namespace(:mod, RDF::Vocabulary.new("http://www.isibang.ac.in/ns/mod#"))
+      conf.add_namespace(:prov, RDF::Vocabulary.new("http://www.w3.org/ns/prov#"))
+      conf.add_namespace(:cc, RDF::Vocabulary.new("http://creativecommons.org/ns#"))
+      conf.add_namespace(:schema, RDF::Vocabulary.new("http://schema.org/"))
+      conf.add_namespace(:doap, RDF::Vocabulary.new("http://usefulinc.com/ns/doap#"))
+      conf.add_namespace(:bibo, RDF::Vocabulary.new("http://purl.org/ontology/bibo/"))
+      conf.add_namespace(:wdrs, RDF::Vocabulary.new("http://www.w3.org/2007/05/powder-s#"))
+      conf.add_namespace(:cito, RDF::Vocabulary.new("http://purl.org/spar/cito/"))
+      conf.add_namespace(:pav, RDF::Vocabulary.new("http://purl.org/pav/"))
+      conf.add_namespace(:oboInOwl, RDF::Vocabulary.new("http://www.geneontology.org/formats/oboInOwl#"))
+      conf.add_namespace(:idot, RDF::Vocabulary.new("http://identifiers.org/idot/"))
+      conf.add_namespace(:sd, RDF::Vocabulary.new("http://www.w3.org/ns/sparql-service-description#"))
+      conf.add_namespace(:org, RDF::Vocabulary.new("http://www.w3.org/ns/org#"))
+      conf.add_namespace(:cclicense, RDF::Vocabulary.new("http://creativecommons.org/licenses/"))
+      conf.add_namespace(:nkos, RDF::Vocabulary.new("http://w3id.org/nkos#"))
+      conf.add_namespace(:skosxl, RDF::Vocabulary.new("http://www.w3.org/2008/05/skos-xl#"))
+      conf.add_namespace(:dcterms, RDF::Vocabulary.new("http://purl.org/dc/terms/"))
+      conf.add_namespace(:uneskos, RDF::Vocabulary.new("http://purl.org/umu/uneskos#"))
+
+
+      conf.id_prefix = 'http://data.bioontology.org/'
       conf.pluralize_models(true)
     end
   end
-  self.goo_namespaces
+  goo_namespaces
 
 end
diff --git a/lib/ontologies_linked_data/models/base.rb b/lib/ontologies_linked_data/models/base.rb
@@ -42,17 +42,17 @@ def self.goo_attrs_to_load(attributes = [], level = 0)
         raise ArgumentError, "`attributes` should be an array" unless attributes.is_a?(Array)
 
         # Get attributes, either provided, all, or default
-        if !attributes.empty?
-          if attributes.first == :all
-            default_attrs = self.attributes
-          else
-            default_attrs = attributes
-          end
-        elsif self.hypermedia_settings[:serialize_default].empty?
-          default_attrs = self.attributes
-        else
-          default_attrs = self.hypermedia_settings[:serialize_default].dup
-        end
+        default_attrs = if !attributes.empty?
+                          if attributes.first == :all
+                            (self.attributes + self.hypermedia_settings[:serialize_default]).uniq
+                          else
+                            attributes
+                          end
+                        elsif self.hypermedia_settings[:serialize_default].empty?
+                          self.attributes
+                        else
+                          self.hypermedia_settings[:serialize_default].dup
+                        end
 
         embed_attrs = {}
         extra_attrs = []

diff --git a/lib/ontologies_linked_data/models/ontology_submission.rb b/lib/ontologies_linked_data/models/ontology_submission.rb
@@ -91,6 +91,13 @@ def synchronize(&block)
         @mutex.synchronize(&block)
       end
 
+      def URI=(value)
+        self.uri  = value
+      end
+      def URI
+        self.uri
+      end
+
       def self.ontology_link(m)
         ontology_link = ""
 

diff --git a/lib/ontologies_linked_data/monkeypatches/object.rb b/lib/ontologies_linked_data/monkeypatches/object.rb
@@ -54,7 +54,7 @@ def to_flex_hash(options = {}, &block)
     # Add methods
     methods = methods - do_not_serialize_nested(options)
     methods.each do |method|
-      hash[method] = self.send(method.to_s) if self.respond_to?(method) rescue next
+      populate_attribute(hash, method) if self.respond_to?(method) rescue next
     end
 
     # Get rid of everything except the 'only'
@@ -245,7 +245,7 @@ def populate_attributes(hash, all = false, only = [], options = {})
 
       attributes.each do |attribute|
         next unless self.respond_to?(attribute)
-        hash[attribute] = self.send(attribute)
+        populate_attribute(hash, attribute)
       end
     elsif !only.empty?
       # Only get stuff we need
@@ -257,13 +257,22 @@ def populate_attributes(hash, all = false, only = [], options = {})
     hash
   end
 
+  def populate_attribute(hash, attribute)
+    if self.method(attribute).parameters.eql?([[:rest, :args]])
+      hash[attribute] = self.send(attribute, include_languages: true)
+    else
+      # a serialized method
+      hash[attribute] = self.send(attribute)
+    end
+  end
+
   def populate_hash_from_list(hash, attributes)
     attributes.each do |attribute|
       attribute = attribute.to_sym
 
       next unless self.respond_to?(attribute)
       begin
-        hash[attribute] = self.send(attribute)
+        populate_attribute(hash, attribute)
       rescue Goo::Base::AttributeNotLoaded
         next
       rescue ArgumentError
@@ -338,6 +347,8 @@ def embed_goo_objects_just_values(hash, attribute, value, options, &block)
   end
 
   def add_goo_values(goo_object, embedded_values, attributes_to_embed, options, &block)
+    return if goo_object.nil?
+
     if attributes_to_embed.length > 1
       embedded_values_hash = {}
       attributes_to_embed.each do |a|

diff --git a/lib/ontologies_linked_data/security/access_control.rb b/lib/ontologies_linked_data/security/access_control.rb
@@ -57,12 +57,12 @@ def access_for_all?
     def read_restricted_based_on?(based_on)
       if based_on.is_a?(Proc)
         instance_to_base_on = based_on.call(self)
-        restricted = instance_to_base_on.read_restricted?
+        restricted = instance_to_base_on ? instance_to_base_on.read_restricted?  : false
       elsif based_on.is_a?(LinkedData::Models::Base)
         restricted = based_on.read_restricted?
       elsif based_on.is_a?(Symbol)
         instance_to_base_on = based_on.send(based_on)
-        restricted = instance_to_base_on.read_restricted?
+        restricted =  instance_to_base_on ? instance_to_base_on.read_restricted?  : false
       else
         restricted = false
       end

diff --git a/lib/ontologies_linked_data/utils/triples.rb b/lib/ontologies_linked_data/utils/triples.rb
@@ -20,23 +20,26 @@ def self.rdf_for_custom_properties(ont_sub)
         triples << triple(Goo.vocabulary(:rdfs)[:comment], subPropertyOf, Goo.vocabulary(:skos)[:definition])
 
 
+        # Add subPropertyOf triples for custom properties
         unless ont_sub.prefLabelProperty.nil?
-          unless ont_sub.prefLabelProperty == Goo.vocabulary(:rdfs)[:label]
-            triples << triple(ont_sub.prefLabelProperty, subPropertyOf, Goo.vocabulary(:metadata_def)[:prefLabel])
+          unless ont_sub.prefLabelProperty == Goo.vocabulary(:rdfs)[:label] || ont_sub.prefLabelProperty == Goo.vocabulary(:metadata_def)[:prefLabel]
+              triples << triple(ont_sub.prefLabelProperty, subPropertyOf, Goo.vocabulary(:metadata_def)[:prefLabel])
           end
         end
         unless ont_sub.definitionProperty.nil?
-          unless ont_sub.definitionProperty == Goo.vocabulary(:rdfs)[:label]
-            triples << triple(ont_sub.definitionProperty, subPropertyOf, Goo.vocabulary(:skos)[:definition])
+          unless ont_sub.definitionProperty == Goo.vocabulary(:rdfs)[:label] || ont_sub.definitionProperty == Goo.vocabulary(:skos)[:definition]
+              triples << triple(ont_sub.definitionProperty, subPropertyOf, Goo.vocabulary(:skos)[:definition])
           end
         end
         unless ont_sub.synonymProperty.nil?
-          unless ont_sub.synonymProperty == Goo.vocabulary(:rdfs)[:label]
+          unless ont_sub.synonymProperty == Goo.vocabulary(:rdfs)[:label] || ont_sub.synonymProperty == Goo.vocabulary(:skos)[:altLabel]
             triples << triple(ont_sub.synonymProperty, subPropertyOf, Goo.vocabulary(:skos)[:altLabel])
           end
         end
         unless ont_sub.authorProperty.nil?
-          triples << triple(ont_sub.authorProperty, subPropertyOf, Goo.vocabulary(:dc)[:creator])
+          unless ont_sub.authorProperty == Goo.vocabulary(:dc)[:creator]
+            triples << triple(ont_sub.authorProperty, subPropertyOf, Goo.vocabulary(:dc)[:creator])
+          end
         end
 
         if ont_sub.hasOntologyLanguage.obo? || ont_sub.hasOntologyLanguage.owl?