Replace error with warning for unmapped instance folders (#82)

* Update getSchemaName.m

Remove concatenation of structs. Structs might have different fields, and the concatenation would fail. Only need name and potentially label, so explicitly get these instead of relying on struct concatenation

* Warn once for unmapped instance folders

Replace a hard error for unimplemented instance folder names with a warning that is emitted only once per unique folder name. Introduces a containers.Map (hasWarned) to track which folder names have already triggered the warning and uses the identifier 'OPENMINDS:InstanceLibrary:createInstanceTable:MissingTypeMapping'. This avoids aborting execution for unmapped folders while preventing repeated duplicate warnings.

* Update getModelVersion.m

* Temporarily skip latest model version assertion in MetaTypeTest

* debug uriJoin

* debug urijoin

* debug

* Remove debug code, more targeted version pin in getControlledInstances

* Update getControlledInstance.m

* Update testReadTheDocLinks.m

Replace UBERONParcellation with BiologicalSex. UBERONParcellation has been removed in latest

Author: ehennestad

code/internal/+openminds/+internal/+vocab/getSchemaName.m

@@ -24,14 +24,12 @@
     end
 
     C = struct2cell(typesVocab);
-    S = [C{:}];
-
-    allNames = {S.name};
 
+    allNames = cellfun(@(c) string(c.name), C);
     isMatch = strcmpi(allNames, nameAlias);
 
     if ~any(isMatch)
-        allLabels = {S.label};
+        allLabels = cellfun(@(c) string(c.label), C);
         isMatch = strcmpi(allLabels, nameAlias);
     end
 

code/internal/+openminds/+internal/@InstanceLibrary/InstanceLibrary.m

@@ -148,6 +148,9 @@ function postSetLibraryVersion(obj)
 
             numInstances = numel(filePaths);
             [types, modules, subGroups] = deal(repmat("", numInstances, 1));
+
+            hasWarned = containers.Map();
+
             for i = 1:numInstances
 
                 thisFolderSplit = split(folderNames(i), filesep);
@@ -179,7 +182,13 @@ function postSetLibraryVersion(obj)
                     modules(i) = "core";
                     subGroups(i) = missing;
                 else
-                    error('The instance folder with name "%s" is not implemented. Please report', thisFolderSplit(1))
+                    
+                    if ~isKey(hasWarned, thisFolderSplit(1))
+                        warning('OPENMINDS:InstanceLibrary:createInstanceTable:MissingTypeMapping', ...
+                           ['The instance folder with name "%s" is not ', ...
+                           'mapped to an openMINDS type. Please report'], thisFolderSplit(1))
+                        hasWarned(thisFolderSplit(1)) = true;
+                    end
                 end
             end
 

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

@@ -13,6 +13,13 @@
     if ismissing(versionNumber)
         versionNumber = openminds.getModelVersion("VersionNumber");
     end
+
+    % Todo: remove. Pin latest version to v4.0 as instances from v5.0 are not 
+    % supported yet.
+    if versionNumber == "latest"
+        versionNumber = openminds.internal.utility.VersionNumber("4.0");
+        versionNumber.Format = "vX.Y";
+    end
     versionNumber = string(versionNumber);
 
     % Make type name lowercase unless it is an abbreviated typename like

tools/tests/unitTests/testReadTheDocLinks.m

@@ -31,18 +31,18 @@ function testInvalidDocumentationUrl(testCase)
                 'MATLAB:webservices:HTTP404StatusCodeError')
         end
 
-        function testSchemaDocLinkUBERONParcellation(testCase)
+        function testSchemaDocLinkBiologicalSex(testCase)
             import openminds.internal.utility.getSchemaDocLink
 
             url = getSchemaDocLink(...
-                "openminds.controlledterms.UBERONParcellation", ...
+                "openminds.controlledterms.BiologicalSex", ...
                 "Raw URL");
 
             try
                 webread(url);
             catch ME
                 errorMessage = sprintf([...
-                    'Failed to read documentation for UBERONParcellation with error:\n', ...
+                    'Failed to read documentation for BiologicalSex with error:\n', ...
                     '%s'], ME.message);
                 testCase.verifyFail(errorMessage)
             end