fix: decode controlled instance files through the shared JSON-LD path

code/internal/+openminds/+internal/+mixin/HasControlledInstance.m

@@ -16,7 +16,10 @@
             instances = openminds.internal.listControlledInstances(type);
             isMatch = instances.InstanceName==string(name);
             if any(isMatch)
-                data = jsondecode(fileread(instances.Filepath(isMatch)));
+                % Shared JSON-LD decode, so the struct carries at_-form
+                % keywords; raw jsondecode would mangle @id into x_id.
+                data = openminds.internal.utility.json.decode( ...
+                    fileread(instances.Filepath(isMatch)));
                 instance = feval(type.ClassName, data);
             else
                 error(['Could not find data for instance of type "%s" ', ...

code/internal/+openminds/+internal/+resolver/InstanceResolver.m

@@ -21,8 +21,11 @@
                     'Could not find data for instance with IRI "%s"', instance.id)
             end
 
-            % Todo: use the JSON-LD deserializer once it exists
-            data = jsondecode(fileread(instances.Filepath(isMatch)));
+            % Decode through the shared JSON-LD utility, so the struct
+            % carries at_-form keywords like every other decoded document.
+            % Raw jsondecode would mangle @id into x_id.
+            data = openminds.internal.utility.json.decode( ...
+                fileread(instances.Filepath(isMatch)));
             instance.fromStruct(data);
         end
 

code/internal/+openminds/+internal/getControlledInstance.m

@@ -60,7 +60,6 @@
     end
 
     jsonStr = fileread(filePath);
-    jsonStr = strrep(jsonStr, '''', ''''''); %If character array contains ', need to replace with ''
     data = openminds.internal.utility.json.decode(jsonStr);
 end
 

tools/tests/unitTests/ControlledInstanceTest.m

@@ -20,6 +20,48 @@ function testGetControlledInstanceLocal(testCase, instanceSpecification, version
             testCase.assertTrue(contains(jsonStr.at_id, expectedIdUriPrefix));
         end
 
+        function testApostrophesInDefinitionsAreNotDoubled(testCase)
+        % Apostrophes inside JSON values survive decoding unchanged, so a
+        % definition written as 'associative array' reads back with single
+        % apostrophes. The offline and online readers must agree here, so
+        % an instance decodes the same way wherever its file came from.
+
+            term = openminds.controlledterms.DataType("associativeArray");
+
+            testCase.verifyTrue(contains(term.definition, "'associative array'"), ...
+                'The definition should contain the apostrophes as written in the file.')
+            testCase.verifyFalse(contains(term.definition, "''"), ...
+                'Apostrophes inside values must not be doubled by the reader.')
+        end
+
+        function testResolvedInstanceCarriesFileContent(testCase)
+        % Resolving a controlled instance IRI populates the instance from
+        % the library file, keeping the identifier and enriching values.
+
+            IRI = "https://openminds.om-i.org/instances/dataType/associativeArray";
+            instance = openminds.instanceFromIRI(IRI);
+
+            testCase.verifyEqual(string(instance.id), IRI)
+            testCase.verifyEqual(instance.name, "associative array")
+            testCase.verifyFalse(contains(instance.definition, "''"))
+        end
+
+        function testFromNameCarriesFileIdentifier(testCase)
+        % A controlled instance built by name through the mixin gets its
+        % identifier from the library file rather than a generated one.
+
+            instanceNames = openminds.core.data.ContentType.listInstances();
+            testCase.assumeNotEmpty(instanceNames, ...
+                'No controlled ContentType instances available locally.')
+
+            instance = openminds.core.data.ContentType.fromName(instanceNames(1));
+
+            testCase.verifyTrue(startsWith(string(instance.id), ...
+                "https://openminds.om-i.org/instances/contentTypes/"), ...
+                'The identifier should come from the library file.')
+            testCase.verifyNotEqual(string(instance.name), "")
+        end
+
         function testGetControlledInstanceRemote(testCase, instanceSpecification, versionNumber)
             jsonStr = openminds.internal.getControlledInstance(...
                 instanceSpecification{:}, versionNumber, "FileSource", "github");