Add function for running nwbinspector on tutorial files during testing …

…#484

+tests/+unit/TutorialTest.m

@@ -61,12 +61,7 @@ function setupClass(testCase)
             setenv('PYTHONPATH', fileparts(mfilename('fullpath')));
 
             nwbClearGenerated()
-        end
-    end
-
-    methods (TestClassTeardown)
-        function tearDownClass(testCase) %#ok<MANU>
-            %generateCore()
+            testCase.addTeardown(@generateCore)
         end
     end
 
@@ -79,60 +74,134 @@ function setupMethod(testCase)
 
     methods (Test)
         function testTutorial(testCase, tutorialFile) %#ok<INUSD>
+            % Intentionally capturing output, in order for tests to cover
+            % code which overloads display methods for nwb types/objects.
             C = evalc( 'run(tutorialFile)' ); %#ok<NASGU>
-            testCase.testReadTutorialNwbFileWithPynwb()
+
+            testCase.readTutorialNwbFileWithPynwb()
+            %testCase.inspectTutorialFileWithNwbInspector()
         end
     end
 
     methods 
-        function testReadTutorialNwbFileWithPynwb(testCase)
+        function readTutorialNwbFileWithPynwb(testCase)
 
             % Retrieve all files generated by tutorial
-            nwbListing = dir('*.nwb');
-
-            for i = 1:numel(nwbListing)
-                nwbFilename = nwbListing(i).name;
-                if any(strcmp(nwbFilename, tests.unit.TutorialTest.SkippedFiles))
-                    continue
-                end
-
+            nwbFileNameList = testCase.listNwbFiles();
+            for nwbFilename = nwbFileNameList
                 try
                     try
-                        io = py.pynwb.NWBHDF5IO(nwbListing(i).name);
+                        io = py.pynwb.NWBHDF5IO(nwbFilename);
                         nwbObject = io.read();
                         testCase.verifyNotEmpty(nwbObject, 'The NWB file should not be empty.');
                         io.close()
-
                     catch ME
                         if strcmp(ME.identifier, 'MATLAB:undefinedVarOrClass') && ...
                                 contains(ME.message, 'py.pynwb.NWBHDF5IO')
 
                             pythonExecutable = tests.util.getPythonPath();
                             cmd = sprintf('"%s" -B -m read_nwbfile_with_pynwb %s',...
                                             pythonExecutable, nwbFilename);
-
                             status = system(cmd);
+
                             if status ~= 0
                                 error('Failed to read NWB file "%s" using pynwb', nwbFilename)
                             end
                         else
                             rethrow(ME)
                         end
                     end
-
                 catch ME
                     error(ME.message)
                     %testCase.verifyFail(sprintf('Failed to read file %s with error: %s', nwbListing(i).name, ME.message));
                 end
             end
         end
+
+        function inspectTutorialFileWithNwbInspector(testCase)
+            % Retrieve all files generated by tutorial
+            nwbFileNameList = testCase.listNwbFiles();
+            for nwbFilename = nwbFileNameList
+                results = py.list(py.nwbinspector.inspect_nwbfile(nwbfile_path=nwbFilename));
+
+                if isempty(cell(results))
+                    return
+                end
+
+                results = testCase.convertNwbInspectorResultsToStruct(results);
+                T = struct2table(results); disp(T)
+
+                for j = 1:numel(results)
+                    testCase.verifyLessThanOrEqual(results(j).importance, 0, ...
+                        sprintf('Message: %s\nLocation: %s\n File: %s\n', ...
+                        string(results(j).message), results(j).location, results(j).filepath))
+                end
+            end
+        end
+    end
+
+    methods (Access = private)
+        function nwbFileNames = listNwbFiles(testCase)
+            nwbListing = dir('*.nwb');
+            nwbFileNames = string( {nwbListing.name} );
+            nwbFileNames = setdiff(nwbFileNames, testCase.SkippedFiles);
+            assert(isrow(nwbFileNames), 'Expected output to be a row vector')
+            if ~isscalar(nwbFileNames)
+                if iscolumn(nwbFileNames)
+                    nwbFileNames = transpose(nwbFileNames);
+                end
+            end
+        end
+    end
+
+    methods (Static)
+        function resultsOut = convertNwbInspectorResultsToStruct(resultsIn)
+            CHECK_IGNORE = "check_image_series_external_file_valid";
+
+            C = cell(resultsIn);
+
+            resultsOut = struct(...
+                'importance', {}, ...
+                'severity', {}, ...
+                'location', {}, ...
+                'filepath', {}, ...
+                'check_name', {}, ...
+                'ignore', {});
+
+            for i = 1:numel(C)
+                resultsOut(i).importance = double( py.getattr(C{i}.importance, 'value') );
+                resultsOut(i).severity = double( py.getattr(C{i}.severity, 'value') );
+
+                try
+                    resultsOut(i).location =  string(C{i}.location);
+                catch
+                    resultsOut(i).location = "N/A";
+                end
+
+                resultsOut(i).message = string(C{i}.message);
+                resultsOut(i).filepath = string(C{i}.file_path);
+                resultsOut(i).check_name = string(C{i}.check_function_name);
+                resultsOut(i).ignore = any(strcmp(CHECK_IGNORE, resultsOut(i).check_name));
+
+                % Special case to ignore
+                if resultsOut(i).location == "/acquisition/ExternalVideos" && ...
+                        resultsOut(i).check_name == "check_timestamps_match_first_dimension"
+                    resultsOut(i).ignore = true;
+                end
+            end
+            resultsOut([resultsOut.ignore]) = [];
+        end
     end
 end
 
 function tutorialNames = listTutorialFiles()
 % listTutorialFiles - List names of all tutorial files (exclude skipped files)
     rootPath = getMatNwbRootDirectory();
-    L = dir(fullfile(rootPath, 'tutorials'));
+    L = cat(1, ...
+        dir(fullfile(rootPath, 'tutorials', '*.mlx')), ...
+        dir(fullfile(rootPath, 'tutorials', '*.m')) ...
+        );
+
     L( [L.isdir] ) = []; % Ignore folders
     tutorialNames = setdiff({L.name}, tests.unit.TutorialTest.SkippedTutorials);
 end

+tests/requirements.txt

@@ -1,2 +1,3 @@
 pynwb
-hdf5plugin
+hdf5plugin
+nwbinspector

nwbtest.m

@@ -46,6 +46,7 @@
         ws = pwd;
 
         nwbClearGenerated(); % Clear default files if any.
+        cleanupObj = onCleanup(@() generateCore);
         cleaner = onCleanup(@generateCore); % Regenerate core when finished
 
         pvcell = struct2pvcell(parser.Unmatched);