Merge branch 'schema_2.2.1'

Author: Lawrence

+file/Dataset.m

@@ -75,6 +75,10 @@
                 end
             end
 
+            if source.isKey('required')
+                obj.required = strcmp(source('required'), 'true');
+            end
+            
             obj.isConstrainedSet = ~isempty(obj.type) && ~obj.scalar;
 
             boundsKey = 'dims';

+file/fillClass.m

@@ -54,9 +54,15 @@
     depnm = namespace.getFullClassName(parentName);
 end
 
+if isa(processed, 'file.Group')
+    classTag = 'types.untyped.GroupClass';
+else
+    classTag = 'types.untyped.DatasetClass';
+end
+
 %% return classfile string
 classDef = [...
-    'classdef ' name ' < ' depnm newline... %header, dependencies
+    'classdef ' name ' < ' depnm ' & ' classTag newline... %header, dependencies
     '% ' upper(name) ' ' class.doc]; %name, docstr
 propgroups = {...
     @()file.fillProps(classprops, readonly, 'SetAccess=protected')...

+file/fillExport.m

@@ -18,15 +18,15 @@
     bodystr = [bodystr {'fullpath = '''';'}];
 end
 
-for i=1:length(propnames)
+for i = 1:length(propnames)
     pnm = propnames{i};
     pathProps = traverseRaw(pnm, raw);
     prop = pathProps{end};
     elideProps = pathProps(1:end-1);
 
     %Construct elisions
     elisions = cell(length(elideProps),1);
-    for j=1:length(elideProps)
+    for j = 1:length(elideProps)
         elisions{j} = elideProps{j}.name;
     end
 

+tests/+system/DynamicTableTest.m

@@ -1,20 +1,20 @@
 classdef DynamicTableTest < tests.system.RoundTripTest & tests.system.AmendTest
     methods
         function addContainer(~, file)
-            start_time = types.core.VectorData(...
+            start_time = types.hdmf_common.VectorData(...
                 'description', 'start_time',...
                 'data', 1:100);
-            stop_time = types.core.VectorData(...
+            stop_time = types.hdmf_common.VectorData(...
                 'description', 'stop_time',...
                 'data', 2:200);
             colnames = {'start_time', 'stop_time', 'randomvalues'};
-            id = types.core.ElementIdentifiers(...
+            id = types.hdmf_common.ElementIdentifiers(...
                 'data', 1:100);
 
-            randcol = types.core.VectorData(...
+            randcol = types.hdmf_common.VectorData(...
                 'description', 'random data to be indexed into',...
                 'data', rand(500,1));
-            randidx = types.core.VectorIndex(...
+            randidx = types.hdmf_common.VectorIndex(...
                 'target', types.untyped.ObjectView('/intervals/trials/randomvalues'),...
                 'data', 5:5:500 - 1);
 
@@ -37,7 +37,7 @@ function appendContainer(testCase, file)
             container.data = rand(500, 1); % new random values.
             file.intervals_trials.colnames{end+1} = 'newcolumn';
             file.intervals_trials.vectordata.set('newcolumn',...
-                types.core.VectorData(...
+                types.hdmf_common.VectorData(...
                 'description', 'newly added column',...
                 'data', 100:-1:1));
         end

+tests/+system/ElectricalSeriesIOTest.m

@@ -17,24 +17,24 @@ function addContainer(testCase, file) %#ok<INUSL>
                 'location', 'tetrode location', ...
                 'device', devlink);
 
-            ettable = types.core.DynamicTable(...
+            ettable = types.hdmf_common.DynamicTable(...
                 'colnames', {'x', 'y', 'z', 'imp', 'location', 'filtering', 'group', 'group_name'},...
-                'id', types.core.ElementIdentifiers('data', 1:4),...
-                'x', types.core.VectorData('data', ones(4,1),...
+                'id', types.hdmf_common.ElementIdentifiers('data', 1:4),...
+                'x', types.hdmf_common.VectorData('data', ones(4,1),...
                     'description', 'the x coordinate of the channel location'),...
-                'y', types.core.VectorData('data', repmat(2, 4, 1),...
+                'y', types.hdmf_common.VectorData('data', repmat(2, 4, 1),...
                     'description', 'the y coordinate of the channel location'),...
-                'z', types.core.VectorData('data', repmat(3, 4, 1),...
+                'z', types.hdmf_common.VectorData('data', repmat(3, 4, 1),...
                     'description', 'the z coordinate of the channel location'),...
-                'imp', types.core.VectorData('data', ones(4,1),...
+                'imp', types.hdmf_common.VectorData('data', ones(4,1),...
                     'description', 'the impedance of the channel'),...
-                'location', types.core.VectorData('data', repmat({'CA1'},4,1),...
+                'location', types.hdmf_common.VectorData('data', repmat({'CA1'},4,1),...
                     'description', 'the location of channel within the subject e.g. brain region'),...
-                'filtering', types.core.VectorData('data', repmat({'none'},4,1),...
+                'filtering', types.hdmf_common.VectorData('data', repmat({'none'},4,1),...
                     'description', 'description of hardware filtering'),...
-                'group', types.core.VectorData('data', repmat(eglink,4,1),...
+                'group', types.hdmf_common.VectorData('data', repmat(eglink,4,1),...
                     'description', 'a reference to the ElectrodeGroup this electrodes is a part of'),...
-                'group_name', types.core.VectorData('data', repmat({egnm},4,1),...
+                'group_name', types.hdmf_common.VectorData('data', repmat({egnm},4,1),...
                     'description', 'name of the ElectrodeGroup this electrode is a part of'),...
                 'description', 'electrodes'...
                 );
@@ -45,7 +45,7 @@ function addContainer(testCase, file) %#ok<INUSL>
                 'data', [0:9;10:19], ...
                 'timestamps', (0:9) .', ...
                 'electrodes', ...
-                types.core.DynamicTableRegion(...
+                types.hdmf_common.DynamicTableRegion(...
                 'data', [0;2],...
                 'table', etReg,...
                 'description', 'the first and third electrodes'));

+tests/+system/ImagingPlaneIOTest.m

@@ -12,7 +12,8 @@ function addContainer(testCase, file) %#ok<INUSL>
                 'excitation_lambda', 6.28, ...
                 'imaging_rate', 2.718, ...
                 'indicator', 'GFP', ...
-                'location', 'somewhere in the brain');
+                'location', 'somewhere in the brain',...
+                'grid_spacing', []);
             file.general_devices.set('imaging_device_1', dev);
             file.general_optophysiology.set('imgpln1', ip);
         end

+tests/+system/NwbTestInterface.m

@@ -16,8 +16,11 @@ function setupClass(testCase)
     methods (TestMethodSetup)
         function setupMethod(testCase)
             testCase.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture);
-            generateCore(fullfile(testCase.root, ...
-                'nwb-schema', 'core', 'nwb.namespace.yaml'));
+            schemaPath = fullfile(testCase.root, 'nwb-schema');
+            
+            generateCore(...
+                fullfile(schemaPath, 'hdmf-common-schema', 'common', 'namespace.yaml'),...
+                fullfile(schemaPath, 'core', 'nwb.namespace.yaml'));
             testCase.file = NwbFile( ...
                 'session_description', 'a test NWB File', ...
                 'identifier', 'TEST123', ...
@@ -45,7 +48,8 @@ function verifyContainerEqual(testCase, actual, expected)
                 val1 = actual.(prop);
                 val2 = expected.(prop);
                 failmsg = ['Values for property ''' prop ''' are not equal'];
-                if startsWith(class(val1), 'types.core.')
+                if startsWith(class(val1), 'types.')...
+                        && ~startsWith(class(val1), 'types.untyped')
                     verifyContainerEqual(testCase, val1, val2);
                 elseif isa(val1, 'types.untyped.Set')
                     verifySetEqual(testCase, val1, val2, failmsg);

+tests/+system/PyNWBIOTest.py

@@ -6,10 +6,11 @@
 import numpy.testing as npt
 import h5py
 
-from pynwb import NWBContainer, get_manager, NWBFile, NWBData, TimeSeries
+from pynwb import get_manager, NWBFile, TimeSeries
 from pynwb.ecephys import ElectricalSeries, Clustering
 from pynwb.ophys import OpticalChannel, TwoPhotonSeries
 from hdmf.backends.hdf5 import HDF5IO
+from hdmf.container import Container, Data
 
 class PyNWBIOTest(unittest.TestCase):
     def setUp(self):
@@ -62,10 +63,10 @@ def assertContainerEqual(self, container1, container2):           # noqa: C901
                 f2 = getattr(container2, nwbfield)
                 if isinstance(f1, (tuple, list, np.ndarray)):
                     if len(f1) > 0:
-                        if isinstance(f1[0], NWBContainer):
+                        if isinstance(f1[0], Container):
                             for sub1, sub2 in zip(f1, f2):
                                 self.assertContainerEqual(sub1, sub2)
-                        elif isinstance(f1[0], NWBData):
+                        elif isinstance(f1[0], Data):
                             for sub1, sub2 in zip(f1, f2):
                                 self.assertDataEqual(sub1, sub2)
                         continue
@@ -78,21 +79,21 @@ def assertContainerEqual(self, container1, container2):           # noqa: C901
                                     self.assertAlmostEqual(v1, v2, places=6)
                         else:
                             self.assertTrue(np.array_equal(f1, f2))
-                elif isinstance(f1, dict) and len(f1) and isinstance(next(iter(f1.values())), NWBContainer):
+                elif isinstance(f1, dict) and len(f1) and isinstance(next(iter(f1.values())), Container):
                     f1_keys = set(f1.keys())
                     f2_keys = set(f2.keys())
                     self.assertSetEqual(f1_keys, f2_keys)
                     for k in f1_keys:
                         with self.subTest(module_name=k):
                             self.assertContainerEqual(f1[k], f2[k])
-                elif isinstance(f1, NWBContainer):
+                elif isinstance(f1, Container) or isinstance(f1, Container):
                     self.assertContainerEqual(f1, f2)
-                elif isinstance(f1, NWBData) or isinstance(f2, NWBData):
-                    if isinstance(f1, NWBData) and isinstance(f2, NWBData):
+                elif isinstance(f1, Data) or isinstance(f2, Data):
+                    if isinstance(f1, Data) and isinstance(f2, Data):
                         self.assertDataEqual(f1, f2)
-                    elif isinstance(f1, NWBData):
+                    elif isinstance(f1, Data):
                         self.assertTrue(np.array_equal(f1.data, f2))
-                    elif isinstance(f2, NWBData):
+                    elif isinstance(f2, Data):
                         self.assertTrue(np.array_equal(f1.data, f2))
                 else:
                     if isinstance(f1, (float, np.float32, np.float16, h5py.Dataset)):

+tests/+system/UnitTimesIOTest.m

@@ -2,17 +2,17 @@
     methods
         function addContainer(~, file)
             vdata = rand(10,1);
-            vd = types.core.VectorData('data', vdata, 'description', 'descr');
+            vd = types.hdmf_common.VectorData('data', vdata, 'description', 'descr');
 
             spike_loc = '/units/spike_times';
             vd_ref = [...
                 types.untyped.RegionView(spike_loc, 1),...
                 types.untyped.RegionView(spike_loc, 2:5),...
                 types.untyped.RegionView(spike_loc, 9:10)...
                 ];
-            vi = types.core.VectorIndex('data', vd_ref,...
+            vi = types.hdmf_common.VectorIndex('data', vd_ref,...
                 'target', types.untyped.ObjectView(spike_loc));
-            ei = types.core.ElementIdentifiers('data', 1:3);
+            ei = types.hdmf_common.ElementIdentifiers('data', 1:3);
             file.units = types.core.Units(...
                 'colnames', {'spike_times'},...
                 'description', 'test Units',...

+tests/+system/smokeTest.m

@@ -35,10 +35,10 @@ function testSmokeInstantiateCore(testCase)
 function testSmokeReadWrite(testCase)
 epochs = types.core.TimeIntervals(...
     'colnames', {'id' 'start_time' 'stop_time'} .',...
-    'id', types.core.ElementIdentifiers('data', 1),...
+    'id', types.hdmf_common.ElementIdentifiers('data', 1),...
     'description', 'test TimeIntervals',...
-    'start_time', types.core.VectorData('data', 0, 'description', 'start time'),...
-    'stop_time', types.core.VectorData('data', 1, 'description', 'stop time'));
+    'start_time', types.hdmf_common.VectorData('data', 0, 'description', 'start time'),...
+    'stop_time', types.hdmf_common.VectorData('data', 1, 'description', 'stop time'));
 file = NwbFile('identifier', 'st', 'session_description', 'smokeTest', ...
     'session_start_time', datetime, 'intervals_epochs', epochs,...
     'timestamps_reference_time', datetime);