Enhance node addition logic in Collection class

Added 'AbortIfNodeExists' option to node addition methods and improved handling of controlled term instances based on preferences. Subnodes are now added before the main node, and code comments were updated to reflect new functionality.

Author: ehennestad

code/+openminds/@Collection/Collection.m

@@ -36,6 +36,7 @@
 
 %   Todo: Validation.
 %   - Linked subject states should have same subject
+%   - Add method to update links for specified instances
 
 % Need mechanism to check if embedded nodes are added to the collection
 
@@ -190,12 +191,15 @@ function add(obj, instance, options)
             end
             arguments
                 options.AddSubNodesOnly = false;
+                options.AbortIfNodeExists = true;
             end
 
             for i = 1:numel(instance)
                 thisInstance = instance{i};
                 for j = 1:numel(thisInstance) % If thisInstance is an array
-                    obj.addNode(thisInstance(j), "AddSubNodesOnly", options.AddSubNodesOnly);
+                    obj.addNode(thisInstance(j), ...
+                        "AddSubNodesOnly", options.AddSubNodesOnly, ...
+                        "AbortIfNodeExists", options.AbortIfNodeExists);
                 end
             end
         end
@@ -498,9 +502,13 @@ function load(obj, loadPath, options)
                 instance.id = obj.getBlankNodeIdentifier();
             end
 
-            % Do not add openminds controlled term instances
-            if startsWith(instance.id, "https://openminds.ebrains.eu/instances/")
-                return
+            % Do not add openminds controlled term instances if disabled in
+            % preferences
+            if startsWith(instance.id, "https://openminds.ebrains.eu/instances/") ...
+                || startsWith(instance.id, "https://openminds.om-i.org/instances/")
+                if ~openminds.getpref('AddControlledInstanceToCollection')
+                    return
+                end
             end
 
             if obj.NumNodes > 0
@@ -511,6 +519,10 @@ function load(obj, loadPath, options)
                     end
                 end
             end
+
+            % Add subnodes first
+            obj.addSubNodes(instance)
+
 
             if ~options.AddSubNodesOnly
                 obj.Nodes(instance.id) = {instance};
@@ -530,7 +542,6 @@ function load(obj, loadPath, options)
                 end
             end
 
-            obj.addSubNodes(instance)
             if ~nargout
                 clear wasAdded
             end

code/+openminds/getpref.m

@@ -20,6 +20,7 @@
                 [ ...
                     "PropertyDisplayMode", ...
                     "DocLinkTarget", ...
+                    "AddControlledInstanceToCollection", ...
                     "" ...
                 ])...
             } = ""

code/internal/+openminds/+utility/Preferences.m

@@ -10,12 +10,16 @@
 %                                       - "help" : MATLAB docstrings
 %                                       - "online" : Online ReadTheDocs
 %                                       documentation
+%       AddControlledInstanceToCollection (logical): Whether to add
+%                                       openMINDS controlled instances to a
+%                                       collection
 
     properties (SetObservable)
         PropertyDisplayMode (1,1) string ...
             {mustBeMember(PropertyDisplayMode, ["all", "non-empty"])} = "all"
         DocLinkTarget (1,1) string ...
             {mustBeMember(DocLinkTarget, ["help", "online"])} = "online"
+        AddControlledInstanceToCollection (1,1) logical = true
     end
 
     properties (Constant, Access = private)