Refactor internal functions and add unit tests

code/+openminds/@Collection/Collection.m

@@ -209,7 +209,7 @@ function remove(obj, instance)
             end
 
             if obj.NumNodes > 0 && isKey(obj.Nodes, instanceId)
-                try 
+                try
                     instanceType = class( obj.Nodes{instanceId} );
                 catch % < R2023a
                     instance = obj.Nodes(instanceId);

code/+openminds/fromTypeName.m

@@ -3,35 +3,35 @@
 %
 % Syntax:
 %   instance = openminds.fromTypeName(typeNameIRI, identifier)
-%   Creates an instance of the class corresponding to the specified type 
+%   Creates an instance of the class corresponding to the specified type
 %   name IRI using the provided identifier.
 %
 % Input Arguments:
-%   typeNameIRI (string) - The IRI representing the type name (must 
+%   typeNameIRI (string) - The IRI representing the type name (must
 %       be a valid OpenMINDS IRI).
 %   instanceIdentifier (string) - Optional. An identifier (@id) of the instance
 %       to create.
 %
 % Output Arguments:
-%   instance - A blank metadata instance of the class corresponding to the 
+%   instance - A blank metadata instance of the class corresponding to the
 %   given type name.
 %
 % Example:
 %  IRI = 'https://openminds.om-i.org/types/Person';
 %  openminds.fromTypeName(IRI)
-%  
-%  ans = 
-%  
+%
+%  ans =
+%
 %    Person (https://openminds.om-i.org/types/Person) with properties:
-%  
+%
 %             affiliation: [None]  (Affiliation)
 %           alternateName: [1×0 string]
 %       associatedAccount: [None]  (AccountInformation)
 %      contactInformation: [None]  (ContactInformation)
 %       digitalIdentifier: [None]  (ORCID)
 %              familyName: ""
 %               givenName: ""
-%  
+%
 %    Required Properties: givenName
 
     arguments

code/+openminds/instanceFromIRI.m

@@ -1,33 +1,33 @@
 function instance = instanceFromIRI(IRI)
 % instanceFromIRI - Create an instance from an openMINDS IRI
-% 
+%
 % Syntax:
-%   instance = openminds.instanceFromIRI(IRI) Creates an instance based on the 
+%   instance = openminds.instanceFromIRI(IRI) Creates an instance based on the
 %   provided openMINDS IRI.
-% 
+%
 % Input Arguments:
 %   IRI - A scalar string representing an openMINDS instance IRI.
-% 
+%
 % Output Arguments:
 %   instance - A metadata instance corresponding to the given IRI.
 %
 % Example:
-%   
+%
 %  IRI = "https://openminds.ebrains.eu/instances/biologicalSex/male";
 %  instance = openminds.instanceFromIRI(IRI)
-%  
-%  instance = 
-%  
+%
+%  instance =
+%
 %    BiologicalSex (https://openminds.om-i.org/types/BiologicalSex) with properties:
-%  
+%
 %                       definition: "Biological sex that produces sperm cells (spermatozoa)."
 %                      description: "A male organism typically has the capacity to produce relatively small, usually mobile gametes (reproductive cells), called sperm cells (or spermatozoa). In the process of fertilization, these sperm cells fuse with a larger, usually immobile female gamete, called egg cell (or ovum)."
 %               interlexIdentifier: "http://uri.interlex.org/base/ilx_0106489"
 %               knowledgeSpaceLink: ""
 %                             name: "male"
 %      preferredOntologyIdentifier: "http://purl.obolibrary.org/obo/PATO_0000384"
 %                          synonym: [1×0 string]
-%  
+%
 %    Required Properties: name
 
     arguments

code/+openminds/toolboxdir.m

@@ -1,7 +1,7 @@
 function folderPath = toolboxdir()
 % Root folder for the openMINDS_MATLAB toolbox
 %
-%    folderPath = openminds.toolboxdir() returns a character vector that is the 
+%    folderPath = openminds.toolboxdir() returns a character vector that is the
 %       absolute path to the root of the toolbox folder
 
     folderPath = fileparts(fileparts(mfilename('fullpath')));

code/+openminds/version.m

@@ -5,16 +5,16 @@
 %   versionStr = openminds.version() returns the version string of the currently active
 %       version of the openMINDS metadata model
 %
-%   openminds.version(versionSpec) changes the currently active version of the 
+%   openminds.version(versionSpec) changes the currently active version of the
 %       openMINDS metadata model to the provided version
 %
-% Input Arguments: 
-%   version (numeric or string) - 
-%    The version number to set for the openMINDS metadata model. If this 
+% Input Arguments:
+%   version (numeric or string) -
+%    The version number to set for the openMINDS metadata model. If this
 %    argument is missing, the current version will be retrieved.
 %
-% Output Arguments: 
-%   versionStr - A string representing the current or newly set version 
+% Output Arguments:
+%   versionStr - A string representing the current or newly set version
 %   of the openMINDS metadata model.
 
     arguments

code/internal/+openminds/+abstract/Schema.m

@@ -99,51 +99,6 @@
         end
     end
 
-    methods (Access = public, Hidden)
-
-        function tf = isPropertyWithLinkedType(obj, propertyName)
-            % Return true if property value is a linked type.
-            propertyNamesWithLinkedType = fieldnames(obj.LINKED_PROPERTIES);
-            tf = any( strcmp(propertyNamesWithLinkedType, propertyName) );
-        end
-
-        function linkedTypesForProperty = getLinkedTypesForProperty(obj, propertyName)
-            % Return linked types that are allowed for given property.
-            if obj.isPropertyWithLinkedType(propertyName)
-                linkedTypesForProperty = obj.LINKED_PROPERTIES.(propertyName);
-            else
-                error('Property %s does not have linked types', propertyName);
-            end
-        end
-
-        function tf = isLinkedTypeOfProperty(obj, type)
-        %isLinkedTypeOfProperty ???
-            tf = false;
-
-            propertyNames = fieldnames( obj.LINKED_PROPERTIES );
-
-            for i = 1:numel(propertyNames)
-                types = obj.LINKED_PROPERTIES.(propertyNames{i});
-
-                for j = 1:numel(types)
-                    thisType = types{j};
-
-                    tf = strcmp(thisType, type);
-                    if tf; return; end
-
-                    thisTypeSplit = strsplit(thisType, '/');
-                    tf = strcmp(thisTypeSplit{end}, type);
-                    if tf; return; end
-                end
-            end
-        end
-
-        function propertyName = linkedTypeOfProperty(obj, type)
-            % Get property name which can be linked to given type
-            propertyName = obj.linkedTypeOfPropertyStatic(type, obj.LINKED_PROPERTIES);
-        end
-    end
-
     methods (Hidden) % Todo: remove?
         function str = char(obj)
             str = obj.getDisplayLabel();
@@ -172,11 +127,11 @@
                     propName = subs(1).subs;
                     className = class(obj.(propName));
 
-                    % Get the actual instance from a linkset subclass.
+                    % Get the actual instance from a MixedTypeSet subclass.
                     if contains(className, 'openminds.internal.mixedtype')
                         try
-                            % Place the openMINDS instance object in a linkset
-                            % wrapper class
+                            % Place the openMINDS instance object in a
+                            % MixedTypeSet wrapper class
                             classFcn = str2func(className);
                             value = classFcn(value);
                         catch MECause
@@ -440,7 +395,7 @@
                 % if strcmp(s(1).type, '.') && strcmp(s(2).type, '()')
                 %     %linkedTypeValues = builtin('subsref', obj, s(1:2));
                 %     linkedTypeValues = obj.subsref(s(1:2));
-                % 
+                %
                 % elseif strcmp(s(1).type, '.')
                 %     linkedTypeValues = builtin('subsref', obj, s(1));
                 % end
@@ -569,7 +524,7 @@ function assignInstanceId(obj, id)
         end
     end
 
-    methods (Access = protected)
+    methods (Access = protected) % Methods related to object display
         function displayLabel = getDisplayLabel(obj)
             %schemaShortName = obj.getSchemaShortName(class(obj));
 
@@ -615,35 +570,6 @@ function assignInstanceId(obj, id)
             shortSchemaName = getSchemaName(fullSchemaName);
         end
     end
-
-    methods (Static, Hidden)
-
-        function propertyName = linkedTypeOfPropertyStatic(type, linkedTypeProperties)
-            propertyName = "";
-            propertyNamesWithLinkedType = fieldnames( linkedTypeProperties );
-
-            for i = 1:numel(propertyNamesWithLinkedType)
-                types = linkedTypeProperties.(propertyNamesWithLinkedType{i});
-
-                for j = 1:numel(types)
-                    thisType = types{j};
-
-                    tf = strcmp(thisType, type);
-                    if tf
-                        propertyName = propertyNamesWithLinkedType{i};
-                        return
-                    end
-
-                    thisTypeSplit = strsplit(thisType, '/');
-                    tf = strcmp(thisTypeSplit{end}, type);
-                    if tf
-                        propertyName = propertyNamesWithLinkedType{i};
-                        return
-                    end
-                end
-            end
-        end
-    end
 end
 
 function x = row(x)

code/internal/+openminds/+base/TypesEnumerationBase.m

@@ -69,25 +69,25 @@
         % fromClassName - Get a Type enum from a class name
         %
         % Syntax:
-        %   typeEnum = openminds.enum.Types.fromClassName(className) Converts 
+        %   typeEnum = openminds.enum.Types.fromClassName(className) Converts
         %   the provided class name(s) into the appropriate enumeration value (s).
         %
         % Input Arguments:
         %   className - A string array representing the class name(s) to be
         %              converted.
         %
         % Output Arguments:
-        %   typeEnum - The corresponding enumeration value(s) from 
+        %   typeEnum - The corresponding enumeration value(s) from
         %              openminds.enum.Types.
         %
         % Example:
         %
         %  openminds.enum.Types.fromClassName("openminds.core.Person")
-        %  
-        %  ans = 
-        % 
+        %
+        %  ans =
+        %
         %    Types enumeration
-        % 
+        %
         %       Person
 
             arguments
@@ -107,26 +107,26 @@
         % fromAtType - Convert an @type string to its corresponding enumeration.
         %
         % Syntax:
-        %   typeEnum = openminds.enum.Types.fromAtType(typeName) Converts the 
+        %   typeEnum = openminds.enum.Types.fromAtType(typeName) Converts the
         %   provided @type string into the appropriate enumeration value.
         %
         % Input Arguments:
         %   typeName - A string array representing the @type to be converted.
-        %              The @type URI is expected to match Base URI for the 
+        %              The @type URI is expected to match Base URI for the
         %              currently active openMINDS version
         %
         % Output Arguments:
-        %   typeEnum - The corresponding enumeration value(s) from 
+        %   typeEnum - The corresponding enumeration value(s) from
         %              openminds.enum.Types.
         %
         % Example:
         %
         %  openminds.enum.Types.fromAtType("https://openminds.om-i.org/types/Person")
-        %  
-        %  ans = 
-        % 
+        %
+        %  ans =
+        %
         %    Types enumeration
-        % 
+        %
         %       Person
 
             arguments

code/internal/+openminds/+constant/BaseURI.m

@@ -3,8 +3,8 @@
 %
 %   baseURI = openminds.constant.BaseURI(version) returns the base URI as a
 %   string that corresponds to the base resource identifier for the specified
-%   OpenMINDS model version. This function dynamically selects the URI based on 
-%   the version input. If no version is specified, the version number of the 
+%   OpenMINDS model version. This function dynamically selects the URI based on
+%   the version input. If no version is specified, the version number of the
 %   currently active openMINDS model is selected.
 %
 %   Input: