Merge branch 'master' into 597-nwb-to-table-bug

+file/fillExport.m

@@ -235,15 +235,30 @@
         propertyChecks{end+1} = sprintf(['~isempty(%1$s) ' ...
         '&& ~isa(%1$s, ''types.untyped.SoftLink'') ' ...
         '&& ~isa(%1$s, ''types.untyped.ExternalLink'')'], propertyReference);
+
+        % Properties that are required and dependent will not be exported
+        % if the property they depend on are unset (empty). Ensure such cases 
+        % are warned against if they occur.
+        if prop.required && ~prop.readonly
+            warnIfNotExportedString = sprintf('obj.warnIfPropertyAttributeNotExported(''%s'', ''%s'', fullpath)', name, depPropname);
+            warningNeededCheck = sprintf('isempty(obj.%s) && ~isempty(obj.%s)', depPropname, name);
+        end
     end
 
     if ~prop.required
         propertyChecks{end+1} = ['~isempty(obj.' name ')'];
     end
 
     if ~isempty(propertyChecks)
-        dataExportString = sprintf('if %s\n%s\nend' ...
+        dataExportString = sprintf('if %s\n%s' ...
             , strjoin(propertyChecks, ' && '), file.addSpaces(dataExportString, 4) ...
             );
+        if prop.required && ~prop.readonly
+            dataExportString = sprintf('%s\nelseif %s\n%s\nend' ...
+                , dataExportString, warningNeededCheck, file.addSpaces(warnIfNotExportedString, 4) ...
+                );
+        else
+             dataExportString = sprintf('%s\nend', dataExportString);
+        end
     end
-end
+end

+tests/+unit/nwbExportTest.m

@@ -0,0 +1,72 @@
+classdef nwbExportTest < matlab.unittest.TestCase
+
+    properties
+        NwbObject
+        OutputFolder = "out"
+    end
+
+    methods (TestClassSetup)
+        function setupClass(testCase)
+            % Get the root path of the matnwb repository
+            rootPath = misc.getMatnwbDir();
+
+            % Use a fixture to add the folder to the search path
+            testCase.applyFixture(matlab.unittest.fixtures.PathFixture(rootPath));
+
+            % Use a fixture to create a temporary working directory
+            testCase.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture);
+            generateCore('savedir', '.');
+        end
+    end
+
+    methods (TestMethodSetup)
+        function setupMethod(testCase)
+            testCase.NwbObject = testCase.initNwbFile();
+
+            if isfolder( testCase.OutputFolder )
+                rmdir(testCase.OutputFolder, "s")
+            end
+            mkdir(testCase.OutputFolder)
+        end
+    end
+
+    methods (Test)
+        function testExportDependentAttributeWithMissingParentA(testCase)
+            testCase.NwbObject.general_source_script_file_name = 'my_test_script.m';
+            nwbFilePath = fullfile(testCase.OutputFolder, 'test_part1.nwb');
+            testCase.verifyWarning(@(f, fn) nwbExport(testCase.NwbObject, nwbFilePath), 'NWB:DependentAttributeNotExported')
+
+            % Add value for dataset which attribute depends on and export again
+            testCase.NwbObject.general_source_script = 'my test';
+            nwbFilePath = fullfile(testCase.OutputFolder, 'test_part2.nwb');
+            testCase.verifyWarningFree(@(f, fn) nwbExport(testCase.NwbObject, nwbFilePath))
+        end
+
+        function testExportDependentAttributeWithMissingParentB(testCase)
+            time_series = types.core.TimeSeries( ...
+                'data', linspace(0, 0.4, 50), ...
+                'starting_time_rate', 10.0, ...
+                'description', 'a test series', ...
+                'data_unit', 'n/a' ...
+            );
+
+            testCase.NwbObject.acquisition.set('time_series', time_series);
+            nwbFilePath = fullfile(testCase.OutputFolder, 'test_part1.nwb');
+            testCase.verifyWarning(@(f, fn) nwbExport(testCase.NwbObject, nwbFilePath), 'NWB:DependentAttributeNotExported')
+
+            % Add value for dataset which attribute depends on and export again
+            time_series.starting_time = 1;
+            nwbFilePath = fullfile(testCase.OutputFolder, 'test_part2.nwb');
+            testCase.verifyWarningFree(@(f, fn) nwbExport(testCase.NwbObject, nwbFilePath))
+        end
+    end
+
+    methods (Static)
+        function nwb = initNwbFile()
+            nwb = NwbFile( ...
+                'session_description', 'test file for nwb export', ...
+                'identifier', 'export_test', ...
+                'session_start_time', datetime("now", 'TimeZone', 'local') );
+        end
+    end
+end

+types/+core/ImageSeries.m

@@ -175,6 +175,8 @@
         end
         if ~isempty(obj.external_file) && ~isa(obj.external_file, 'types.untyped.SoftLink') && ~isa(obj.external_file, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/external_file/starting_frame'], obj.external_file_starting_frame, 'forceArray');
+        elseif isempty(obj.external_file) && ~isempty(obj.external_file_starting_frame)
+            obj.warnIfPropertyAttributeNotExported('external_file_starting_frame', 'external_file', fullpath)
         end
         if ~isempty(obj.format)
             if startsWith(class(obj.format), 'types.untyped.')

+types/+core/ImagingPlane.m

@@ -388,6 +388,8 @@
         end
         if ~isempty(obj.grid_spacing) && ~isa(obj.grid_spacing, 'types.untyped.SoftLink') && ~isa(obj.grid_spacing, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/grid_spacing/unit'], obj.grid_spacing_unit);
+        elseif isempty(obj.grid_spacing) && ~isempty(obj.grid_spacing_unit)
+            obj.warnIfPropertyAttributeNotExported('grid_spacing_unit', 'grid_spacing', fullpath)
         end
         if ~isempty(obj.imaging_rate)
             if startsWith(class(obj.imaging_rate), 'types.untyped.')
@@ -429,6 +431,8 @@
         end
         if ~isempty(obj.origin_coords) && ~isa(obj.origin_coords, 'types.untyped.SoftLink') && ~isa(obj.origin_coords, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/origin_coords/unit'], obj.origin_coords_unit);
+        elseif isempty(obj.origin_coords) && ~isempty(obj.origin_coords_unit)
+            obj.warnIfPropertyAttributeNotExported('origin_coords_unit', 'origin_coords', fullpath)
         end
         if ~isempty(obj.reference_frame)
             if startsWith(class(obj.reference_frame), 'types.untyped.')

+types/+core/ImagingRetinotopy.m

@@ -785,12 +785,18 @@
         end
         if ~isempty(obj.axis_1_phase_map) && ~isa(obj.axis_1_phase_map, 'types.untyped.SoftLink') && ~isa(obj.axis_1_phase_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_1_phase_map/dimension'], obj.axis_1_phase_map_dimension, 'forceArray');
+        elseif isempty(obj.axis_1_phase_map) && ~isempty(obj.axis_1_phase_map_dimension)
+            obj.warnIfPropertyAttributeNotExported('axis_1_phase_map_dimension', 'axis_1_phase_map', fullpath)
         end
         if ~isempty(obj.axis_1_phase_map) && ~isa(obj.axis_1_phase_map, 'types.untyped.SoftLink') && ~isa(obj.axis_1_phase_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_1_phase_map/field_of_view'], obj.axis_1_phase_map_field_of_view, 'forceArray');
+        elseif isempty(obj.axis_1_phase_map) && ~isempty(obj.axis_1_phase_map_field_of_view)
+            obj.warnIfPropertyAttributeNotExported('axis_1_phase_map_field_of_view', 'axis_1_phase_map', fullpath)
         end
         if ~isempty(obj.axis_1_phase_map) && ~isa(obj.axis_1_phase_map, 'types.untyped.SoftLink') && ~isa(obj.axis_1_phase_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_1_phase_map/unit'], obj.axis_1_phase_map_unit);
+        elseif isempty(obj.axis_1_phase_map) && ~isempty(obj.axis_1_phase_map_unit)
+            obj.warnIfPropertyAttributeNotExported('axis_1_phase_map_unit', 'axis_1_phase_map', fullpath)
         end
         if ~isempty(obj.axis_1_power_map)
             if startsWith(class(obj.axis_1_power_map), 'types.untyped.')
@@ -801,12 +807,18 @@
         end
         if ~isempty(obj.axis_1_power_map) && ~isa(obj.axis_1_power_map, 'types.untyped.SoftLink') && ~isa(obj.axis_1_power_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_1_power_map/dimension'], obj.axis_1_power_map_dimension, 'forceArray');
+        elseif isempty(obj.axis_1_power_map) && ~isempty(obj.axis_1_power_map_dimension)
+            obj.warnIfPropertyAttributeNotExported('axis_1_power_map_dimension', 'axis_1_power_map', fullpath)
         end
         if ~isempty(obj.axis_1_power_map) && ~isa(obj.axis_1_power_map, 'types.untyped.SoftLink') && ~isa(obj.axis_1_power_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_1_power_map/field_of_view'], obj.axis_1_power_map_field_of_view, 'forceArray');
+        elseif isempty(obj.axis_1_power_map) && ~isempty(obj.axis_1_power_map_field_of_view)
+            obj.warnIfPropertyAttributeNotExported('axis_1_power_map_field_of_view', 'axis_1_power_map', fullpath)
         end
         if ~isempty(obj.axis_1_power_map) && ~isa(obj.axis_1_power_map, 'types.untyped.SoftLink') && ~isa(obj.axis_1_power_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_1_power_map/unit'], obj.axis_1_power_map_unit);
+        elseif isempty(obj.axis_1_power_map) && ~isempty(obj.axis_1_power_map_unit)
+            obj.warnIfPropertyAttributeNotExported('axis_1_power_map_unit', 'axis_1_power_map', fullpath)
         end
         if startsWith(class(obj.axis_2_phase_map), 'types.untyped.')
             refs = obj.axis_2_phase_map.export(fid, [fullpath '/axis_2_phase_map'], refs);
@@ -815,12 +827,18 @@
         end
         if ~isempty(obj.axis_2_phase_map) && ~isa(obj.axis_2_phase_map, 'types.untyped.SoftLink') && ~isa(obj.axis_2_phase_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_2_phase_map/dimension'], obj.axis_2_phase_map_dimension, 'forceArray');
+        elseif isempty(obj.axis_2_phase_map) && ~isempty(obj.axis_2_phase_map_dimension)
+            obj.warnIfPropertyAttributeNotExported('axis_2_phase_map_dimension', 'axis_2_phase_map', fullpath)
         end
         if ~isempty(obj.axis_2_phase_map) && ~isa(obj.axis_2_phase_map, 'types.untyped.SoftLink') && ~isa(obj.axis_2_phase_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_2_phase_map/field_of_view'], obj.axis_2_phase_map_field_of_view, 'forceArray');
+        elseif isempty(obj.axis_2_phase_map) && ~isempty(obj.axis_2_phase_map_field_of_view)
+            obj.warnIfPropertyAttributeNotExported('axis_2_phase_map_field_of_view', 'axis_2_phase_map', fullpath)
         end
         if ~isempty(obj.axis_2_phase_map) && ~isa(obj.axis_2_phase_map, 'types.untyped.SoftLink') && ~isa(obj.axis_2_phase_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_2_phase_map/unit'], obj.axis_2_phase_map_unit);
+        elseif isempty(obj.axis_2_phase_map) && ~isempty(obj.axis_2_phase_map_unit)
+            obj.warnIfPropertyAttributeNotExported('axis_2_phase_map_unit', 'axis_2_phase_map', fullpath)
         end
         if ~isempty(obj.axis_2_power_map)
             if startsWith(class(obj.axis_2_power_map), 'types.untyped.')
@@ -831,12 +849,18 @@
         end
         if ~isempty(obj.axis_2_power_map) && ~isa(obj.axis_2_power_map, 'types.untyped.SoftLink') && ~isa(obj.axis_2_power_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_2_power_map/dimension'], obj.axis_2_power_map_dimension, 'forceArray');
+        elseif isempty(obj.axis_2_power_map) && ~isempty(obj.axis_2_power_map_dimension)
+            obj.warnIfPropertyAttributeNotExported('axis_2_power_map_dimension', 'axis_2_power_map', fullpath)
         end
         if ~isempty(obj.axis_2_power_map) && ~isa(obj.axis_2_power_map, 'types.untyped.SoftLink') && ~isa(obj.axis_2_power_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_2_power_map/field_of_view'], obj.axis_2_power_map_field_of_view, 'forceArray');
+        elseif isempty(obj.axis_2_power_map) && ~isempty(obj.axis_2_power_map_field_of_view)
+            obj.warnIfPropertyAttributeNotExported('axis_2_power_map_field_of_view', 'axis_2_power_map', fullpath)
         end
         if ~isempty(obj.axis_2_power_map) && ~isa(obj.axis_2_power_map, 'types.untyped.SoftLink') && ~isa(obj.axis_2_power_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/axis_2_power_map/unit'], obj.axis_2_power_map_unit);
+        elseif isempty(obj.axis_2_power_map) && ~isempty(obj.axis_2_power_map_unit)
+            obj.warnIfPropertyAttributeNotExported('axis_2_power_map_unit', 'axis_2_power_map', fullpath)
         end
         if startsWith(class(obj.axis_descriptions), 'types.untyped.')
             refs = obj.axis_descriptions.export(fid, [fullpath '/axis_descriptions'], refs);
@@ -852,18 +876,28 @@
         end
         if ~isempty(obj.focal_depth_image) && ~isa(obj.focal_depth_image, 'types.untyped.SoftLink') && ~isa(obj.focal_depth_image, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/focal_depth_image/bits_per_pixel'], obj.focal_depth_image_bits_per_pixel);
+        elseif isempty(obj.focal_depth_image) && ~isempty(obj.focal_depth_image_bits_per_pixel)
+            obj.warnIfPropertyAttributeNotExported('focal_depth_image_bits_per_pixel', 'focal_depth_image', fullpath)
         end
         if ~isempty(obj.focal_depth_image) && ~isa(obj.focal_depth_image, 'types.untyped.SoftLink') && ~isa(obj.focal_depth_image, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/focal_depth_image/dimension'], obj.focal_depth_image_dimension, 'forceArray');
+        elseif isempty(obj.focal_depth_image) && ~isempty(obj.focal_depth_image_dimension)
+            obj.warnIfPropertyAttributeNotExported('focal_depth_image_dimension', 'focal_depth_image', fullpath)
         end
         if ~isempty(obj.focal_depth_image) && ~isa(obj.focal_depth_image, 'types.untyped.SoftLink') && ~isa(obj.focal_depth_image, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/focal_depth_image/field_of_view'], obj.focal_depth_image_field_of_view, 'forceArray');
+        elseif isempty(obj.focal_depth_image) && ~isempty(obj.focal_depth_image_field_of_view)
+            obj.warnIfPropertyAttributeNotExported('focal_depth_image_field_of_view', 'focal_depth_image', fullpath)
         end
         if ~isempty(obj.focal_depth_image) && ~isa(obj.focal_depth_image, 'types.untyped.SoftLink') && ~isa(obj.focal_depth_image, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/focal_depth_image/focal_depth'], obj.focal_depth_image_focal_depth);
+        elseif isempty(obj.focal_depth_image) && ~isempty(obj.focal_depth_image_focal_depth)
+            obj.warnIfPropertyAttributeNotExported('focal_depth_image_focal_depth', 'focal_depth_image', fullpath)
         end
         if ~isempty(obj.focal_depth_image) && ~isa(obj.focal_depth_image, 'types.untyped.SoftLink') && ~isa(obj.focal_depth_image, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/focal_depth_image/format'], obj.focal_depth_image_format);
+        elseif isempty(obj.focal_depth_image) && ~isempty(obj.focal_depth_image_format)
+            obj.warnIfPropertyAttributeNotExported('focal_depth_image_format', 'focal_depth_image', fullpath)
         end
         if ~isempty(obj.sign_map)
             if startsWith(class(obj.sign_map), 'types.untyped.')
@@ -874,9 +908,13 @@
         end
         if ~isempty(obj.sign_map) && ~isa(obj.sign_map, 'types.untyped.SoftLink') && ~isa(obj.sign_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/sign_map/dimension'], obj.sign_map_dimension, 'forceArray');
+        elseif isempty(obj.sign_map) && ~isempty(obj.sign_map_dimension)
+            obj.warnIfPropertyAttributeNotExported('sign_map_dimension', 'sign_map', fullpath)
         end
         if ~isempty(obj.sign_map) && ~isa(obj.sign_map, 'types.untyped.SoftLink') && ~isa(obj.sign_map, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/sign_map/field_of_view'], obj.sign_map_field_of_view, 'forceArray');
+        elseif isempty(obj.sign_map) && ~isempty(obj.sign_map_field_of_view)
+            obj.warnIfPropertyAttributeNotExported('sign_map_field_of_view', 'sign_map', fullpath)
         end
         if startsWith(class(obj.vasculature_image), 'types.untyped.')
             refs = obj.vasculature_image.export(fid, [fullpath '/vasculature_image'], refs);
@@ -885,15 +923,23 @@
         end
         if ~isempty(obj.vasculature_image) && ~isa(obj.vasculature_image, 'types.untyped.SoftLink') && ~isa(obj.vasculature_image, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/vasculature_image/bits_per_pixel'], obj.vasculature_image_bits_per_pixel);
+        elseif isempty(obj.vasculature_image) && ~isempty(obj.vasculature_image_bits_per_pixel)
+            obj.warnIfPropertyAttributeNotExported('vasculature_image_bits_per_pixel', 'vasculature_image', fullpath)
         end
         if ~isempty(obj.vasculature_image) && ~isa(obj.vasculature_image, 'types.untyped.SoftLink') && ~isa(obj.vasculature_image, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/vasculature_image/dimension'], obj.vasculature_image_dimension, 'forceArray');
+        elseif isempty(obj.vasculature_image) && ~isempty(obj.vasculature_image_dimension)
+            obj.warnIfPropertyAttributeNotExported('vasculature_image_dimension', 'vasculature_image', fullpath)
         end
         if ~isempty(obj.vasculature_image) && ~isa(obj.vasculature_image, 'types.untyped.SoftLink') && ~isa(obj.vasculature_image, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/vasculature_image/field_of_view'], obj.vasculature_image_field_of_view, 'forceArray');
+        elseif isempty(obj.vasculature_image) && ~isempty(obj.vasculature_image_field_of_view)
+            obj.warnIfPropertyAttributeNotExported('vasculature_image_field_of_view', 'vasculature_image', fullpath)
         end
         if ~isempty(obj.vasculature_image) && ~isa(obj.vasculature_image, 'types.untyped.SoftLink') && ~isa(obj.vasculature_image, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/vasculature_image/format'], obj.vasculature_image_format);
+        elseif isempty(obj.vasculature_image) && ~isempty(obj.vasculature_image_format)
+            obj.warnIfPropertyAttributeNotExported('vasculature_image_format', 'vasculature_image', fullpath)
         end
     end
 end

+types/+core/NWBFile.m

@@ -1010,6 +1010,8 @@
         end
         if ~isempty(obj.general_source_script) && ~isa(obj.general_source_script, 'types.untyped.SoftLink') && ~isa(obj.general_source_script, 'types.untyped.ExternalLink')
             io.writeAttribute(fid, [fullpath '/general/source_script/file_name'], obj.general_source_script_file_name);
+        elseif isempty(obj.general_source_script) && ~isempty(obj.general_source_script_file_name)
+            obj.warnIfPropertyAttributeNotExported('general_source_script_file_name', 'general_source_script', fullpath)
         end
         io.writeGroup(fid, [fullpath '/general']);
         if ~isempty(obj.general_stimulus)