Merge branch 'master' into update-readme-2024

+file/fillValidators.m

@@ -14,6 +14,8 @@
             else
                 continue
             end
+        elseif isa(prop, 'file.Link')
+            validationBody = fillLinkValidation(nm, prop, namespacereg);
         else
             if startsWith(class(prop), 'file.')
                 validationBody = fillUnitValidation(nm, prop, namespacereg);
@@ -173,6 +175,31 @@
     end
 end
 
+function validationStr = fillLinkValidation(name, prop, namespacereg)
+    fullName = namespacereg.getFullClassName(prop.type);
+
+    % Create a validation function body that 1) checks (validates) the
+    % target if the input is a SoftLink type, otherwise 2) checks (validates) 
+    % if the expected (target) type is provided. If the validation passes
+    % and the value is not empty, it is wrapped in a SoftLink.
+
+    validationStr = sprintf([ ...
+        'if isa(val, ''types.untyped.SoftLink'')\n', ...
+        '    if isprop(val, ''target'')\n', ...
+        '        types.util.checkDtype(''%s'', ''%s'', val.target);\n', ...
+        '    end\n', ...
+        'else\n', ...
+        '    %s\n', ...
+        '    if ~isempty(val)\n', ...
+        '        val = types.untyped.SoftLink(val);\n', ...
+        '    end\n', ...
+        'end' ...
+        ], ...
+        name, fullName, ...
+        fillDtypeValidation(name, fullName) ...
+    );
+end
+
 function fdvstr = fillDimensionValidation(type, shape)
     if strcmp(type, 'any')
         fdvstr = '';

+tests/+unit/linkTest.m

@@ -88,3 +88,25 @@ function testExternalResolution(testCase)
 % for links, deref() should return its own link.
 tests.util.verifyContainerEqual(testCase, metaExternalLink.deref().deref(), expected);
 end
+
+function testDirectTypeAssignmentToSoftLinkProperty(testCase)
+    device = types.core.Device('description', 'test_device');
+    electrodeGroup = types.core.ElectrodeGroup(...
+        'description', 'test_group', ...
+        'device', device);
+
+    testCase.verifyClass(electrodeGroup.device, 'types.untyped.SoftLink')
+    testCase.verifyClass(electrodeGroup.device.target, 'types.core.Device')
+end
+
+function testWrongTypeInSoftLinkAssignment(testCase)
+
+    function createElectrodeGroupWithWrongDeviceType()
+        not_a_device = types.core.OpticalChannel('description', 'test_channel');
+        electrodeGroup = types.core.ElectrodeGroup(...
+            'description', 'test_group', ...
+            'device', not_a_device); %#ok<NASGU>
+    end
+    testCase.verifyError(@createElectrodeGroupWithWrongDeviceType, ...
+        'NWB:TypeCorrection:InvalidConversion')
+end

+types/+core/ClusterWaveforms.m

@@ -53,7 +53,16 @@
     %% VALIDATORS
 
     function val = validate_clustering_interface(obj, val)
-        val = types.util.checkDtype('clustering_interface', 'types.core.Clustering', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('clustering_interface', 'types.core.Clustering', val.target);
+            end
+        else
+            val = types.util.checkDtype('clustering_interface', 'types.core.Clustering', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_waveform_filtering(obj, val)
         val = types.util.checkDtype('waveform_filtering', 'char', val);

+types/+core/CorrectedImageStack.m

@@ -50,7 +50,16 @@
         val = types.util.checkDtype('corrected', 'types.core.ImageSeries', val);
     end
     function val = validate_original(obj, val)
-        val = types.util.checkDtype('original', 'types.core.ImageSeries', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('original', 'types.core.ImageSeries', val.target);
+            end
+        else
+            val = types.util.checkDtype('original', 'types.core.ImageSeries', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_xy_translation(obj, val)
         val = types.util.checkDtype('xy_translation', 'types.core.TimeSeries', val);

+types/+core/DecompositionSeries.m

@@ -118,7 +118,16 @@
         val = types.util.checkDtype('source_channels', 'types.hdmf_common.DynamicTableRegion', val);
     end
     function val = validate_source_timeseries(obj, val)
-        val = types.util.checkDtype('source_timeseries', 'types.core.TimeSeries', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('source_timeseries', 'types.core.TimeSeries', val.target);
+            end
+        else
+            val = types.util.checkDtype('source_timeseries', 'types.core.TimeSeries', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     %% EXPORT
     function refs = export(obj, fid, fullpath, refs)

+types/+core/ElectrodeGroup.m

@@ -68,7 +68,16 @@
         types.util.checkDims(valsz, validshapes);
     end
     function val = validate_device(obj, val)
-        val = types.util.checkDtype('device', 'types.core.Device', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('device', 'types.core.Device', val.target);
+            end
+        else
+            val = types.util.checkDtype('device', 'types.core.Device', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_location(obj, val)
         val = types.util.checkDtype('location', 'char', val);

+types/+core/EventDetection.m

@@ -78,7 +78,16 @@
         types.util.checkDims(valsz, validshapes);
     end
     function val = validate_source_electricalseries(obj, val)
-        val = types.util.checkDtype('source_electricalseries', 'types.core.ElectricalSeries', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('source_electricalseries', 'types.core.ElectricalSeries', val.target);
+            end
+        else
+            val = types.util.checkDtype('source_electricalseries', 'types.core.ElectricalSeries', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_source_idx(obj, val)
         val = types.util.checkDtype('source_idx', 'int32', val);

+types/+core/ImageMaskSeries.m

@@ -32,7 +32,16 @@
     %% VALIDATORS
 
     function val = validate_masked_imageseries(obj, val)
-        val = types.util.checkDtype('masked_imageseries', 'types.core.ImageSeries', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('masked_imageseries', 'types.core.ImageSeries', val.target);
+            end
+        else
+            val = types.util.checkDtype('masked_imageseries', 'types.core.ImageSeries', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     %% EXPORT
     function refs = export(obj, fid, fullpath, refs)

+types/+core/ImageSeries.m

@@ -76,7 +76,16 @@
         types.util.checkDims(valsz, validshapes);
     end
     function val = validate_device(obj, val)
-        val = types.util.checkDtype('device', 'types.core.Device', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('device', 'types.core.Device', val.target);
+            end
+        else
+            val = types.util.checkDtype('device', 'types.core.Device', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_dimension(obj, val)
         val = types.util.checkDtype('dimension', 'int32', val);

+types/+core/ImagingPlane.m

@@ -137,7 +137,16 @@
         types.util.checkDims(valsz, validshapes);
     end
     function val = validate_device(obj, val)
-        val = types.util.checkDtype('device', 'types.core.Device', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('device', 'types.core.Device', val.target);
+            end
+        else
+            val = types.util.checkDtype('device', 'types.core.Device', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_excitation_lambda(obj, val)
         val = types.util.checkDtype('excitation_lambda', 'single', val);

+types/+core/IndexSeries.m

@@ -128,10 +128,28 @@
         end
     end
     function val = validate_indexed_images(obj, val)
-        val = types.util.checkDtype('indexed_images', 'types.core.Images', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('indexed_images', 'types.core.Images', val.target);
+            end
+        else
+            val = types.util.checkDtype('indexed_images', 'types.core.Images', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_indexed_timeseries(obj, val)
-        val = types.util.checkDtype('indexed_timeseries', 'types.core.ImageSeries', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('indexed_timeseries', 'types.core.ImageSeries', val.target);
+            end
+        else
+            val = types.util.checkDtype('indexed_timeseries', 'types.core.ImageSeries', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     %% EXPORT
     function refs = export(obj, fid, fullpath, refs)

+types/+core/IntracellularElectrode.m

@@ -119,7 +119,16 @@
         types.util.checkDims(valsz, validshapes);
     end
     function val = validate_device(obj, val)
-        val = types.util.checkDtype('device', 'types.core.Device', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('device', 'types.core.Device', val.target);
+            end
+        else
+            val = types.util.checkDtype('device', 'types.core.Device', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_filtering(obj, val)
         val = types.util.checkDtype('filtering', 'char', val);

+types/+core/OnePhotonSeries.m

@@ -104,7 +104,16 @@
         types.util.checkDims(valsz, validshapes);
     end
     function val = validate_imaging_plane(obj, val)
-        val = types.util.checkDtype('imaging_plane', 'types.core.ImagingPlane', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('imaging_plane', 'types.core.ImagingPlane', val.target);
+            end
+        else
+            val = types.util.checkDtype('imaging_plane', 'types.core.ImagingPlane', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_intensity(obj, val)
         val = types.util.checkDtype('intensity', 'single', val);

+types/+core/OptogeneticSeries.m

@@ -62,7 +62,16 @@
         end
     end
     function val = validate_site(obj, val)
-        val = types.util.checkDtype('site', 'types.core.OptogeneticStimulusSite', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('site', 'types.core.OptogeneticStimulusSite', val.target);
+            end
+        else
+            val = types.util.checkDtype('site', 'types.core.OptogeneticStimulusSite', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     %% EXPORT
     function refs = export(obj, fid, fullpath, refs)

+types/+core/OptogeneticStimulusSite.m

@@ -71,7 +71,16 @@
         types.util.checkDims(valsz, validshapes);
     end
     function val = validate_device(obj, val)
-        val = types.util.checkDtype('device', 'types.core.Device', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('device', 'types.core.Device', val.target);
+            end
+        else
+            val = types.util.checkDtype('device', 'types.core.Device', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_excitation_lambda(obj, val)
         val = types.util.checkDtype('excitation_lambda', 'single', val);

+types/+core/PatchClampSeries.m

@@ -90,7 +90,16 @@
         types.util.checkDims(valsz, validshapes);
     end
     function val = validate_electrode(obj, val)
-        val = types.util.checkDtype('electrode', 'types.core.IntracellularElectrode', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('electrode', 'types.core.IntracellularElectrode', val.target);
+            end
+        else
+            val = types.util.checkDtype('electrode', 'types.core.IntracellularElectrode', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_gain(obj, val)
         val = types.util.checkDtype('gain', 'single', val);

+types/+core/PlaneSegmentation.m

@@ -74,7 +74,16 @@
         val = types.util.checkDtype('image_mask', 'types.hdmf_common.VectorData', val);
     end
     function val = validate_imaging_plane(obj, val)
-        val = types.util.checkDtype('imaging_plane', 'types.core.ImagingPlane', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('imaging_plane', 'types.core.ImagingPlane', val.target);
+            end
+        else
+            val = types.util.checkDtype('imaging_plane', 'types.core.ImagingPlane', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_pixel_mask(obj, val)
         val = types.util.checkDtype('pixel_mask', 'types.hdmf_common.VectorData', val);

+types/+core/TwoPhotonSeries.m

@@ -68,7 +68,16 @@
         types.util.checkDims(valsz, validshapes);
     end
     function val = validate_imaging_plane(obj, val)
-        val = types.util.checkDtype('imaging_plane', 'types.core.ImagingPlane', val);
+        if isa(val, 'types.untyped.SoftLink')
+            if isprop(val, 'target')
+                types.util.checkDtype('imaging_plane', 'types.core.ImagingPlane', val.target);
+            end
+        else
+            val = types.util.checkDtype('imaging_plane', 'types.core.ImagingPlane', val);
+            if ~isempty(val)
+                val = types.untyped.SoftLink(val);
+            end
+        end
     end
     function val = validate_pmt_gain(obj, val)
         val = types.util.checkDtype('pmt_gain', 'single', val);