Updates to support conversion from metadata downloaded from KG

code/+openminds/@Collection/Collection.m

@@ -55,6 +55,10 @@
     properties (SetAccess = protected, Hidden)
         TypeMap (1,1) dictionary
     end
+
+    properties
+        LinkResolver
+    end
 
     methods % Constructor
         function obj = Collection(instance, options)
@@ -93,6 +97,7 @@
             arguments
                 options.Name (1,1) string = ""
                 options.Description (1,1) string = ""
+                options.LinkResolver (1,:) = []
             end
 
             % Initialize nodes
@@ -130,6 +135,16 @@
         function len = length(obj)
             len = numEntries(obj.Nodes);
         end
+
+        function tf = isKey(obj, identifier)
+            tf = false;
+
+            if isConfigured(obj.Nodes)
+                if isKey(obj.Nodes, identifier)
+                    tf = true;
+                end
+            end
+        end
 
         function add(obj, instance, options)
         %add Add single or multiple instances to a collection.

code/+openminds/@Collection/loadInstances.m

@@ -121,7 +121,7 @@
                 else
                     % Check if instance is a controlled instance
                     if startsWith(instanceId, "https://openminds.ebrains.eu/instances/")
-                        resolvedInstances{j} = om.instance.getControlledInstance(instanceId);
+                        resolvedInstances{j} = openminds.instanceFromIRI(instanceId);
                     end
                 end
             end

code/+openminds/fromIdentifier.m

@@ -0,0 +1,5 @@
+function instance = fromIdentifier(atId)
+    [type, name] = openminds.utility.parseAtID(atId);
+    enumType = openminds.enum.Types(type);
+    instance = feval(enumType.ClassName, name);
+end

code/+openminds/fromTypeName.m

@@ -0,0 +1,8 @@
+function instance = fromTypeName( typeNameURI, identifier )
+    arguments
+        typeNameURI
+        identifier = ''
+    end
+    enumType = openminds.enum.Types.fromAtType(typeNameURI);
+    instance = feval(enumType.ClassName, 'id', identifier);
+end

code/+openminds/getModelVersion.m

@@ -1,25 +1,35 @@
 function versionNum = getModelVersion(outputType)
 
+    % Todo: save version number in prefs/singleton?
+
     arguments
         % outputType - char or VersionNumber. char is default to keep
         % backwards compatibility. Todo: Deprecate char option
         outputType (1,1) string ...
             {mustBeMember(outputType, ["char", "VersionNumber"])} = "char"
     end
 
-    typeFolder = fullfile(openminds.internal.rootpath, 'types/');
-    pathSplit = strsplit(path, pathsep);
-
-    matchedIdx = find(contains(pathSplit, typeFolder));
+    persistent lastTic cachedVersionNumber
+    if isempty(lastTic); lastTic = uint64(0); end
 
-    if numel(matchedIdx) > 1
-        warning('Multiple openMINDS model versions are present on the search path.');
+    if toc(lastTic) > 1
+        typeFolder = fullfile(openminds.internal.rootpath, 'types/');
+        pathSplit = strsplit(path, pathsep);
+
+        matchedIdx = find(contains(pathSplit, typeFolder));
+
+        if numel(matchedIdx) > 1
+            warning('Multiple openMINDS model versions are present on the search path.');
+        end
+
+        versionName = strrep(pathSplit{matchedIdx(1)}, typeFolder, '');
+        cachedVersionNumber = openminds.internal.utility.VersionNumber(versionName);
+        cachedVersionNumber.Format = "vX.Y";
+        lastTic = tic();
     end
+    versionNum = cachedVersionNumber;
 
-    versionNum = strrep(pathSplit{matchedIdx(1)}, typeFolder, '');
-
-    if outputType == "VersionNumber"
-        versionNum = openminds.internal.utility.VersionNumber(versionNum);
-        versionNum.Format = "vX.Y";
+    if outputType == "char"
+        versionNum = char(versionNum);
     end
 end

code/+openminds/instanceFromIRI.m

@@ -0,0 +1,5 @@
+function instance = instanceFromIRI(iri)
+    [type, ~] = openminds.utility.parseAtID(iri);
+    typeEnum = openminds.enum.Types(type);
+    instance = feval(typeEnum.ClassName, iri);
+end

code/+openminds/version.m

@@ -0,0 +1,12 @@
+function versionStr = version(version)
+    arguments
+        version (1,1) openminds.internal.utility.VersionNumber ...
+            {openminds.mustBeValidVersion(version)} = missing
+    end
+    if ismissing(version)
+        versionStr = string(openminds.getModelVersion());
+    else
+        openminds.selectOpenMindsVersion(version)
+        versionStr = string(version);
+    end
+end

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

@@ -62,10 +62,21 @@
                     obj.deserializeFromName(varargin{1});
                 end
             elseif nargin == 1 && isstruct( varargin{1} ) && isfield(varargin{1}, 'at_id')
-                obj.deserializeFromName(varargin{1}.at_id);
+                numInstances = numel(varargin{1});
+                if numInstances > 1
+                    obj(numInstances) = feval(class(obj));
+                end
+                for i = 1:numel(varargin{1})
+                    obj(i).deserializeFromName(varargin{1}(i).at_id);
+                end
             else
+                [varargin, id] = obj.removeArg('id', varargin{:});
+                if ~isempty(id)
+                    obj.id = id; % Assign provided id
+                else
+                    obj.id = obj.generateInstanceId();
+                end
                 obj.assignPVPairs(varargin{:})
-                obj.id = obj.generateInstanceId();
             end
         end
     end
@@ -87,13 +98,18 @@
 
             import openminds.internal.getControlledInstance
             import openminds.internal.utility.getSchemaName
-
+            instanceName = char(instanceName);
             schemaName = getSchemaName(class(obj));
 
-            if openminds.utility.isSemanticInstanceName(instanceName)
-                 [~, instanceName] = openminds.utility.parseAtID(instanceName);
+            if openminds.utility.isIRI(instanceName)
+                if openminds.utility.isSemanticInstanceName(instanceName)
+                     [~, instanceName] = openminds.utility.parseAtID(instanceName);
+                else
+                    obj.id = instanceName;
+                    return
+                end
             end
-
+            
             [instanceName, instanceNameOrig] = deal(instanceName);
             if ~any(strcmp(obj.CONTROLLED_INSTANCES, instanceName))
                 % Try to make a valid name
@@ -112,7 +128,8 @@
                     return
                 end
             else
-                error('No matching instances were found for name "%s"', instanceName)
+                warning('No matching instances were found for name "%s"', instanceName)
+                return
                 % error('Deserialization from user instance is not implemented yet')
             end
             propNames = {'at_id', 'name', 'definition', 'description', 'interlexIdentifier', 'knowledgeSpaceLink', 'preferredOntologyIdentifier', 'synonym'};

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

@@ -1,5 +1,6 @@
 classdef Schema < handle & openminds.internal.extern.uiw.mixin.AssignPVPairs & ...
-                  openminds.internal.mixin.CustomInstanceDisplay & openminds.internal.mixin.StructAdapter
+                  openminds.internal.mixin.CustomInstanceDisplay & ...
+                  openminds.internal.mixin.StructAdapter
 % Schema Abstract base class shared by all concrete Schema classes
 
 % Todo:
@@ -29,7 +30,7 @@
         LINKED_PROPERTIES struct %todo: name and classname, not openminds uri
         EMBEDDED_PROPERTIES struct
     end
-
+    
     events % Todo: Remove??
         InstanceChanged
         PropertyWithLinkedInstanceChanged
@@ -428,17 +429,27 @@
                     varargout = cell(1, numOutputs);
                     [varargout{:}] = builtin('subsref', obj, subs);
                 else
-                    builtin('subsref', obj, subs)
+                    obj = builtin('subsref', obj, subs);
                 end
             end
         end
 
         function n = numArgumentsFromSubscript(obj, s, indexingContext)
             if (obj(1).isSubsForLinkedProperty(s) || obj(1).isSubsForEmbeddedProperty(s)) && numel(s) > 1
+
+                % 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
+
                 linkedTypeValues = builtin('subsref', obj, s(1));
-%                 if openminds.utility.isMixedInstance(linkedTypeValues)
-%                     linkedTypeValues = {linkedTypeValues.Instance};
-%                 end
+
+                if openminds.utility.isMixedInstance(linkedTypeValues)
+                    linkedTypeValues = {linkedTypeValues.Instance};
+                end
 
                 if strcmp( s(2).type, '()' ) && iscell(linkedTypeValues)
                     s(2).type = '{}';
@@ -535,10 +546,14 @@
             if isa(values, 'cell')
                 instanceType = cellfun(@(c) class(c), values, 'uni', false);
             else
-                instanceType = class(values);
+                instanceType = string(class(values));
             end
             if numel( unique(instanceType) ) == 1
-                outValues = [values{:}];
+                if iscell(values)
+                    outValues = [values{:}];
+                else
+                    outValues = values;
+                end
             else
                 outValues = feval(mixedTypeClassName, values);
             end

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

@@ -95,6 +95,15 @@
                     % resolved externally in order to put a real instance in place.
                     obj(i).Instance = struct;
                     obj(i).Instance.id = instance{i}.at_id;
+                elseif isstruct(instance{i}) && isfield(instance{i}, 'x_id')
+                    % Variation of before
+                    obj(i).Instance = struct;
+                    obj(i).Instance.id = instance{i}.x_id;
+                elseif isstruct(instance{i}) && isfield(instance{i}, 'at_type')
+                    % Embedded type as structure
+                    obj(i).Instance = openminds.fromTypeName(instance{i}.at_type);
+                    obj(i).Instance = obj(i).Instance.fromStruct(instance{i});
+
                 elseif isa(instance{i}, class(obj))
                     obj(i) = instance{i};
                 else
@@ -226,7 +235,7 @@
         function displayScalarObject(obj)
             % This should not happen...
             disp(obj.Instance)
-            warning('Displaying scalar mixed type object')
+            warning('Displaying scalar mixed type object. This is a non-critical bug.')
         end
 
         function displayNonScalarObject(obj)

code/internal/+openminds/+internal/+utility/+json/encode.m

@@ -2,7 +2,8 @@
 
     str = jsonencode(s, 'PrettyPrint', true);
     % Todo: Use regexp to make sure we only replace json key names
-    str = strrep(str, '"x_', '"_');
+    %str = strrep(str, '"x_', '"_');
+    str = strrep(str, '"x_', '"@');
     str = strrep(str, '"at_', '"@');
     str = strrep(str, '[]', 'null');
 

code/internal/+openminds/+internal/+utility/+string/type2class.m

@@ -1,9 +1,12 @@
 function className = type2class(openmindsType)
 
     typeSplit = strsplit(openmindsType, '/');
-
-    modelName = lower( typeSplit{end-1} );
     schemaName = typeSplit{end};
-
-    className = sprintf('openminds.%s.%s', modelName, schemaName);
+
+    if startsWith(openmindsType, "https://openminds.om-i.org/types")
+        className = openminds.enum.Types(schemaName).ClassName;
+    else
+        modelName = lower( typeSplit{end-1} );
+        className = sprintf('openminds.%s.%s', modelName, schemaName);
+    end
 end

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

@@ -0,0 +1,46 @@
+function isValid = isIRI(value)
+% isIRI Validates an Internationalized Resource Identifier (IRI)
+%   isValid = isIRI(value) returns true if the input string 'value'
+%   has the basic structure of an IRI as defined in RFC 3987 section 2.1,
+%   and false otherwise.
+%
+%   This function uses a regular expression to check for:
+%     - A scheme, which must start with a letter and can include letters,
+%       digits, plus (+), hyphen (-), and period (.)
+%     - An optional authority preceded by "//" (which should not include
+%       the delimiters ?, or #)
+%     - A path (which is any sequence of characters except '?' and '#')
+%     - An optional query (preceded by '?')
+%     - An optional fragment (preceded by '#')
+%
+%   Note: This validator provides a basic check and does not fully enforce
+%   all details of RFC 3987 (for example, the precise allowed Unicode
+%   ranges in each component).
+%
+%   Example:
+%       validIRI = 'http://例え.テスト/path?query#fragment';
+%       isValid = openminds.utility.isIRI(validIRI);
+%
+%   Author: ChatGPT o3-mini-high
+
+    % Regular expression pattern for a simplified IRI structure:
+    %   - (?<scheme>[A-Za-z][A-Za-z0-9+\-.]*):  --> scheme followed by ':'
+    %   - (?://(?<authority>[^/?#]*))?           --> optional "//" and authority
+    %   - (?<path>[^?#]*)                        --> path (no '?' or '#')
+    %   - (?:\?(?<query>[^#]*))?                  --> optional query starting with '?'
+    %   - (?:#(?<fragment>.*))?                   --> optional fragment starting with '#'
+    %
+    % Note: Double backslashes (\\) are used in MATLAB string literals.
+    pattern = ['^(?<scheme>[A-Za-z][A-Za-z0-9+\\-.]*):', ...
+               '(?://(?<authority>[^/?#]*))?', ...
+               '(?<path>[^?#]*)', ...
+               '(?:\\?(?<query>[^#]*))?', ...
+               '(?:#(?<fragment>.*))?$', ...
+              ];
+
+    % Use regexp with the 'names' option to capture components
+    tokens = regexp(value, pattern, 'names');
+
+    % The IRI is considered valid if the regex returns non-empty tokens.
+    isValid = ~isempty(tokens);
+end

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

@@ -25,10 +25,15 @@
 %
 %   See also: matlab.net.URI, openminds.constant.BaseURI
 
+    tf = false;
+    if ~startsWith(name, "http")
+        return
+    end
+
     URI = matlab.net.URI(name);
 
-    isValidUrl = sprintf("%s://%s", URI.Scheme, URI.Host) == ...
-        openminds.constant.BaseURI;
+    isValidUrl = sprintf("%s://%s", URI.Scheme, URI.Host) == openminds.constant.BaseURI("latest") ...
+        || sprintf("%s://%s", URI.Scheme, URI.Host) == openminds.constant.BaseURI(3);
 
     URIPath = URI.Path;
     URIPath(URIPath=="")=[];

code/types/latest/+openminds/+controlledterms/ActionStatusType.m

@@ -47,4 +47,10 @@
             obj@openminds.abstract.ControlledTerm(varargin{:})
         end
     end
+
+    methods (Static)
+        function instances = listInstances()
+            instances = openminds.controlledterms.ActionStatusType.CONTROLLED_INSTANCES';
+        end
+    end
 end

code/types/latest/+openminds/+controlledterms/AgeCategory.m

@@ -50,4 +50,10 @@
             obj@openminds.abstract.ControlledTerm(varargin{:})
         end
     end
+
+    methods (Static)
+        function instances = listInstances()
+            instances = openminds.controlledterms.AgeCategory.CONTROLLED_INSTANCES';
+        end
+    end
 end