Merge pull request #156 from ontoportal-lirmm/pr/fix/get-rest-mapping…

…-with-prefix-url Fix: bug in the get_rest_mapping method
ncbo · Aug 9, 2023 · e00c4e3 · e00c4e3
2 parents 0cdb8f8 + dc35d50
commit e00c4e3
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Showing 6 changed files with 121 additions and 49 deletions.
diff --git a/lib/ontologies_linked_data/mappings/mappings.rb b/lib/ontologies_linked_data/mappings/mappings.rb
@@ -380,7 +380,7 @@ def self.get_rest_mapping(mapping_id)
   GRAPH ?s2 {
     ?c2 <#{rest_predicate}> ?uuid .
   }
-FILTER(?uuid = <#{mapping_id}>)
+FILTER(?uuid = <#{LinkedData::Models::Base.replace_url_prefix_to_id(mapping_id)}>)
 FILTER(?s1 != ?s2)
 } LIMIT 1
 eos
@@ -437,7 +437,7 @@ def self.create_rest_mapping(classes,process)
       graph_insert << [c.id, RDF::URI.new(rest_predicate), backup_mapping.id]
       Goo.sparql_update_client.insert_data(graph_insert, graph: sub.id)
     end
-    mapping = LinkedData::Models::Mapping.new(classes,"REST",process)
+    mapping = LinkedData::Models::Mapping.new(classes,"REST",process, backup_mapping.id)
     return mapping
   end
 

diff --git a/lib/ontologies_linked_data/models/base.rb b/lib/ontologies_linked_data/models/base.rb
@@ -27,12 +27,10 @@ def delete(*args)
       # Override find method to make sure the id matches what is in the RDF store
       # Only do this if the setting is enabled, string comparison sucks
       def self.find(id, *options)
-        if LinkedData.settings.replace_url_prefix && id.to_s.start_with?(LinkedData.settings.rest_url_prefix)
-          id = RDF::IRI.new(id.to_s.sub(LinkedData.settings.rest_url_prefix, LinkedData.settings.id_url_prefix))
-        end
+        id = replace_url_prefix_to_id(id)
 
         # Handle `+` to ` ` conversion here because Sinatra doesn't do it for URI's
-        id = id.gsub("+", " ") unless id.start_with?("http")
+        id = id.gsub('+', ' ') unless id.start_with?('http')
 
         super(id, *options)
       end
@@ -137,8 +135,33 @@ def self.goo_aggregates_to_load(attributes = [])
         included_aggregates
       end
 
+      def self.replace_url_prefix_to_id(id)
+        if replace_url_prefix?(id)
+          id = RDF::IRI.new(id.to_s.sub(LinkedData.settings.rest_url_prefix, LinkedData.settings.id_url_prefix))
+        end
+        id
+      end
+
+      def self.replace_url_id_to_prefix(id)
+        if replace_url_id?(id)
+          id.to_s.gsub(LinkedData.settings.id_url_prefix, LinkedData.settings.rest_url_prefix)
+        else
+          id
+        end
+      end
+
+      def self.replace_url_prefix?(id)
+        LinkedData.settings.replace_url_prefix && id.to_s.start_with?(LinkedData.settings.rest_url_prefix)
+      end
+
+      def self.replace_url_id?(id)
+        LinkedData.settings.replace_url_prefix && id.to_s.start_with?(LinkedData.settings.id_url_prefix)
+      end
+
       private
 
+
+
       ##
       # Looks for an object 'owner' and looks in Thread.current[:remote_user]
       # to see if the user for this request matches the owner

diff --git a/lib/ontologies_linked_data/monkeypatches/object.rb b/lib/ontologies_linked_data/monkeypatches/object.rb
@@ -155,16 +155,10 @@ def convert_nonstandard_types(value, options, &block)
   ##
   # If the config option is set, turn http://data.bioontology.org urls into the configured REST url
   def convert_url_prefix(value)
-    if LinkedData.settings.replace_url_prefix
-      if value.is_a?(String) && value.start_with?(LinkedData.settings.id_url_prefix)
-        value = value.sub(LinkedData.settings.id_url_prefix, LinkedData.settings.rest_url_prefix)
-      end
-
-      if (value.is_a?(Array) || value.is_a?(Set)) && value.first.is_a?(String) && value.first.start_with?(LinkedData.settings.id_url_prefix)
-        value = value.map {|v| v.sub(LinkedData.settings.id_url_prefix, LinkedData.settings.rest_url_prefix)}
-      end
+    tmp = Array(value).map do |val|
+      LinkedData::Models::Base.replace_url_id_to_prefix(val)
     end
-    value
+    value.is_a?(Array) || value.is_a?(Set) ? tmp : tmp.first
   end
 
   ##

diff --git a/lib/ontologies_linked_data/serializers/json.rb b/lib/ontologies_linked_data/serializers/json.rb
@@ -11,8 +11,8 @@ def self.serialize(obj, options = {})
 
           # Add the id to json-ld attribute
           if current_cls.ancestors.include?(LinkedData::Hypermedia::Resource) && !current_cls.embedded? && hashed_obj.respond_to?(:id)
-            prefixed_id = LinkedData.settings.replace_url_prefix ? hashed_obj.id.to_s.gsub(LinkedData.settings.id_url_prefix, LinkedData.settings.rest_url_prefix) : hashed_obj.id.to_s
-            hash["@id"] = prefixed_id
+            prefixed_id = LinkedData::Models::Base.replace_url_id_to_prefix(hashed_obj.id)
+            hash["@id"] = prefixed_id.to_s
           end
           # Add the type
           hash["@type"] = current_cls.type_uri.to_s if hash["@id"] && current_cls.respond_to?(:type_uri)

diff --git a/lib/ontologies_linked_data/serializers/xml.rb b/lib/ontologies_linked_data/serializers/xml.rb
@@ -9,8 +9,8 @@ def self.serialize(obj, options)
             current_cls = hashed_obj.respond_to?(:klass) ? hashed_obj.klass : hashed_obj.class
             # Add the id and type
             if current_cls.ancestors.include?(LinkedData::Hypermedia::Resource) && !current_cls.embedded?
-              prefixed_id = LinkedData.settings.replace_url_prefix ? hashed_obj.id.to_s.gsub(LinkedData.settings.id_url_prefix, LinkedData.settings.rest_url_prefix) : hashed_obj.id.to_s
-              hash["id"] = prefixed_id
+              prefixed_id = LinkedData::Models::Base.replace_url_id_to_prefix(hashed_obj.id)
+              hash["id"] = prefixed_id.to_s
               hash["type"] = current_cls.type_uri.to_s
             end
 

diff --git a/test/models/test_mappings.rb b/test/models/test_mappings.rb
@@ -226,40 +226,20 @@ def test_mappings_two_ontologies
   end
 
   def test_mappings_rest
-    mapping_term_a = ["http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Image_Algorithm",
-      "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Image",
-      "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Integration_and_Interoperability_Tools" ]
-    submissions_a = [
-"http://data.bioontology.org/ontologies/MAPPING_TEST1/submissions/latest",
-"http://data.bioontology.org/ontologies/MAPPING_TEST1/submissions/latest",
-"http://data.bioontology.org/ontologies/MAPPING_TEST1/submissions/latest" ]
-    mapping_term_b = ["http://purl.org/incf/ontology/Computational_Neurosciences/cno_alpha.owl#cno_0000202",
-      "http://purl.org/incf/ontology/Computational_Neurosciences/cno_alpha.owl#cno_0000203",
-      "http://purl.org/incf/ontology/Computational_Neurosciences/cno_alpha.owl#cno_0000205" ]
-    submissions_b = [
-"http://data.bioontology.org/ontologies/MAPPING_TEST2/submissions/latest",
-"http://data.bioontology.org/ontologies/MAPPING_TEST2/submissions/latest",
-"http://data.bioontology.org/ontologies/MAPPING_TEST2/submissions/latest" ]
-    relations = [ "http://www.w3.org/2004/02/skos/core#exactMatch",
-                  "http://www.w3.org/2004/02/skos/core#closeMatch",
-                  "http://www.w3.org/2004/02/skos/core#relatedMatch" ]
-    user = LinkedData::Models::User.where.include(:username).all[0]
-    assert user != nil
+    mapping_term_a, mapping_term_b, submissions_a, submissions_b, relations, user = rest_mapping_data
+
     mappings_created = []
 
     3.times do |i|
-      process = LinkedData::Models::MappingProcess.new
-      process.name = "proc#{i}"
-      process.relation = RDF::URI.new(relations[i])
-      process.creator= user
-      process.save
-      classes = []
-      classes << LinkedData::Mappings.read_only_class(
-                    mapping_term_a[i], submissions_a[i])
-      classes << LinkedData::Mappings.read_only_class(
-                    mapping_term_b[i], submissions_b[i])
-      mappings_created << LinkedData::Mappings.create_rest_mapping(classes, process)
+      classes = get_mapping_classes(term_a:mapping_term_a[i], term_b: mapping_term_b[i],
+                                    submissions_a: submissions_a[i], submissions_b: submissions_b[i])
+
+      mappings_created << create_rest_mapping(relation: RDF::URI.new(relations[i]),
+                                              user: user,
+                                              classes: classes,
+                                              name: "proc#{i}")
     end
+
     ont_id = submissions_a.first.split("/")[0..-3].join("/")
     latest_sub = LinkedData::Models::Ontology.find(RDF::URI.new(ont_id)).first.latest_submission
     LinkedData::Mappings.create_mapping_counts(Logger.new(TestLogFile.new))
@@ -308,4 +288,79 @@ def test_mappings_rest
     end
     assert_equal 3, rest_mapping_count
   end
+
+  def test_get_rest_mapping
+    mapping_term_a, mapping_term_b, submissions_a, submissions_b, relations, user = rest_mapping_data
+
+    classes = get_mapping_classes(term_a:mapping_term_a[0], term_b: mapping_term_b[0],
+                                  submissions_a: submissions_a[0], submissions_b: submissions_b[0])
+
+    mappings_created = []
+    mappings_created << create_rest_mapping(relation: RDF::URI.new(relations[0]),
+                                            user: user,
+                                            classes: classes,
+                                            name: "proc#{0}")
+
+    assert_equal 1, mappings_created.size
+    created_mapping_id = mappings_created.first.id
+
+    refute_nil LinkedData::Mappings.get_rest_mapping(created_mapping_id)
+
+    old_replace = LinkedData.settings.replace_url_prefix
+    LinkedData.settings.replace_url_prefix = true
+
+    old_rest_url = LinkedData.settings.rest_url_prefix
+    LinkedData.settings.rest_url_prefix = 'data.test.org'
+
+    refute_nil LinkedData::Mappings.get_rest_mapping(LinkedData::Models::Base.replace_url_id_to_prefix(created_mapping_id))
+
+    LinkedData.settings.rest_url_prefix = old_rest_url
+    LinkedData.settings.replace_url_prefix = old_replace
+  end
+
+  private
+
+  def get_mapping_classes(term_a:, term_b:, submissions_a:, submissions_b:)
+    classes = []
+    classes << LinkedData::Mappings.read_only_class(
+      term_a, submissions_a)
+    classes << LinkedData::Mappings.read_only_class(
+      term_b, submissions_b)
+    classes
+  end
+
+  def rest_mapping_data
+    mapping_term_a = ["http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Image_Algorithm",
+                      "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Image",
+                      "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Integration_and_Interoperability_Tools" ]
+    submissions_a = [
+      "http://data.bioontology.org/ontologies/MAPPING_TEST1/submissions/latest",
+      "http://data.bioontology.org/ontologies/MAPPING_TEST1/submissions/latest",
+      "http://data.bioontology.org/ontologies/MAPPING_TEST1/submissions/latest" ]
+    mapping_term_b = ["http://purl.org/incf/ontology/Computational_Neurosciences/cno_alpha.owl#cno_0000202",
+                      "http://purl.org/incf/ontology/Computational_Neurosciences/cno_alpha.owl#cno_0000203",
+                      "http://purl.org/incf/ontology/Computational_Neurosciences/cno_alpha.owl#cno_0000205" ]
+    submissions_b = [
+      "http://data.bioontology.org/ontologies/MAPPING_TEST2/submissions/latest",
+      "http://data.bioontology.org/ontologies/MAPPING_TEST2/submissions/latest",
+      "http://data.bioontology.org/ontologies/MAPPING_TEST2/submissions/latest" ]
+    relations = [ "http://www.w3.org/2004/02/skos/core#exactMatch",
+                  "http://www.w3.org/2004/02/skos/core#closeMatch",
+                  "http://www.w3.org/2004/02/skos/core#relatedMatch" ]
+
+    user = LinkedData::Models::User.where.include(:username).all[0]
+    assert user != nil
+
+    [mapping_term_a, mapping_term_b, submissions_a, submissions_b, relations, user]
+  end
+
+  def create_rest_mapping(relation:, user:, name:, classes:)
+    process = LinkedData::Models::MappingProcess.new
+    process.name = name
+    process.relation = relation
+    process.creator= user
+    process.save
+
+    LinkedData::Mappings.create_rest_mapping(classes, process)
+  end
 end