Merge branch 'main' into 635-customizable-chunking

Author: bendichter

+io/+spec/validateEmbeddedSpecifications.m

@@ -30,7 +30,13 @@ function checkMissingNamespaces(expectedNamespaceNames, embeddedNamespaceNames)
     missingNamespaces = setdiff(expectedNamespaceNames, embeddedNamespaceNames);
     if ~isempty(missingNamespaces)
         missingNamespacesStr = strjoin("  " + string(missingNamespaces), newline);
-        warning('NWB:validators:MissingEmbeddedNamespace', 'Namespace is missing:\n%s', missingNamespacesStr)
+        warning('NWB:validators:MissingEmbeddedNamespace', ...
+            ['The following namespace specifications are not embedded in ' ...
+             'the file:\n%s\n' ...
+             'To facilitate reading and validating the file across systems, it is ' ...
+             'recommended to embed the specifications for these namespaces. ' ...
+             'Please generate the missing extensions (using generateCore or ' ...
+             'generateExtension) and then re-export the file.'], missingNamespacesStr)
     end
 end
 

+io/mapData2H5.m

@@ -13,7 +13,14 @@
         || all(cellfun('isclass', data, 'string')) ...
         , 'NWB:MapData:NonCellStr', ['Cell arrays must be cell arrays of character vectors. ' ...
         'Cell arrays of other types are not supported.']);
+elseif isstring(data)
+    if isscalar(data)
+        data = char(data);
+    else
+        data = cellstr(data);
+    end
 end
+
 tid = io.getBaseType(class(data));
 
 % max size is always unlimited

+tests/+unit/dynamicTableTest.m

@@ -103,7 +103,7 @@ function testToTableForTableImportedFromFile(testCase)
 
             nwbExport(nwb, fileName)
 
-            nwbIn = nwbRead(fileName);
+            nwbIn = nwbRead(fileName, "ignorecache");
 
             T = nwbIn.acquisition.get('DynamicTable').toTable();
             testCase.verifyClass(T, 'table')

+tests/+unit/nwbExportTest.m

@@ -169,9 +169,9 @@ function testEmbeddedSpecs(testCase)
             nwbFilePath = testCase.getRandomFilename();
             nwbExport(nwb, nwbFilePath);
 
-            % Verify that no namespaces were embedded in file
+            % Verify that core and hdmf-common were embedded in "empty" file
             embeddedNamespaces = io.spec.listEmbeddedSpecNamespaces(nwbFilePath);
-            testCase.verifyEmpty(embeddedNamespaces)
+            testCase.verifyEqual(sort(embeddedNamespaces), {'core', 'hdmf-common'})
 
             ts = tests.factory.TimeSeriesWithTimestamps();
             nwb.acquisition.set('test', ts);
@@ -249,5 +249,42 @@ function testWarnIfMissingNamespaceSpecification(testCase)
                 @() nwbExport(nwb, nwbFilePath), ...
                 'NWB:validators:MissingEmbeddedNamespace')
         end
+
+        function testExportFileWithStringDataType(testCase)
+            nwb = tests.factory.NWBFile();
+
+            generalExperimenter = ["John Doe", "Jane Doe"];
+            generalExperimentDescription = "Test with string data types";
+            nwb.general_experimenter = generalExperimenter;
+            nwb.general_experiment_description = generalExperimentDescription;
+
+            ts = tests.factory.TimeSeriesWithTimestamps();
+            ts.comments = "String comment";
+            ts.data_unit = "test";
+
+            nwb.acquisition.set("TimeSeries", ts);
+            nwbFilename = testCase.getRandomFilename();
+            nwbExport(nwb, nwbFilename);
+
+            nwbIn = nwbRead(nwbFilename, 'ignorecache');
+
+            testCase.assertEqual( ...
+                string( nwbIn.general_experimenter.load())', ...
+                generalExperimenter)
+
+            testCase.assertEqual( ...
+                string(nwbIn.general_experiment_description)', ...
+                generalExperimentDescription)
+
+            tsIn = nwbIn.acquisition.get("TimeSeries");
+                     
+            testCase.assertEqual( ...
+                string(tsIn.comments), ...
+                ts.comments)
+
+            testCase.assertEqual( ...
+                string(tsIn.data_unit), ...
+                ts.data_unit)
+        end
     end
 end

NwbFile.m

@@ -123,6 +123,7 @@ function export(obj, filename, mode)
             arguments
                 obj (1,1) NwbFile
                 options.IncludeParentTypes (1,1) logical = false
+                options.IncludeNwbFile (1,1) logical = false
             end
 
             objectMap = searchProperties(containers.Map, obj, '', '');
@@ -136,6 +137,14 @@ function export(obj, filename, mode)
 
             nwbTypeNames = objectClassNames(keep & ~ignore);
 
+            if options.IncludeNwbFile
+                % Include class name for NWBFile superclass
+                allSuperclasses = string(superclasses(obj));
+                nwbTypeNames = [...
+                    allSuperclasses(endsWith(allSuperclasses, 'NWBFile')), ...
+                    nwbTypeNames];
+            end
+
             if options.IncludeParentTypes
                 includedNwbTypesWithParents = string.empty;
                 for i = 1:numel(nwbTypeNames)
@@ -152,12 +161,20 @@ function export(obj, filename, mode)
         function embedSpecifications(obj, output_file_id)
             jsonSpecs = schemes.exportJson();
 
+            if isempty(jsonSpecs)
+                % Call generateCore to create cached namespaces
+                generateCore(obj.nwb_version)
+                jsonSpecs = schemes.exportJson();
+            end
+
             % Resolve the name of all types and parent types that are
             % included in this file. This will be used to filter the specs
             % to embed, so that only specs with used neurodata types are
             % embedded.
-            includedNeurodataTypes = obj.listNwbTypes("IncludeParentTypes", true);
-            
+            includedNeurodataTypes = obj.listNwbTypes(...
+                "IncludeParentTypes", true, ...
+                "IncludeNwbFile", true);
+
             % Get the namespace names
             namespaceNames = getNamespacesForDataTypes(includedNeurodataTypes);
 

nwbClearGenerated.m

@@ -35,7 +35,9 @@
     moduleNames = setdiff({listing.name}, {'+untyped', '+util', '.', '..'});
     generatedPaths = fullfile(typesPath, moduleNames);
     for i=1:length(generatedPaths)
-        rmdir(generatedPaths{i}, 's');
+        if isfolder(generatedPaths{i})
+            rmdir(generatedPaths{i}, 's');
+        end
     end
 
     if options.ClearCache