Merge pull request #295 from NeurodataWithoutBorders/196-direct-objec…

…t-reference

196 direct object reference

+io/getRefData.m

@@ -6,7 +6,12 @@
 validPaths = find(~cellfun('isempty', refpaths));
 if isa(ref, 'types.untyped.RegionView')
     for i=validPaths
-        did = H5D.open(fid, refpaths{i});
+        try
+            did = H5D.open(fid, refpaths{i});
+        catch ME
+            error('MatNWB:getRefData:InvalidPath',...
+                'Reference path `%s` was invalid', refpaths{i});
+        end
         sid = H5D.get_space(did);
         %by default, we use block mode.
         regionShapes = ref(i).region;
@@ -21,8 +26,12 @@
 typesize = H5T.get_size(ref(1).type);
 ref_data = zeros([typesize size(ref)], 'uint8');
 for i=validPaths
-    ref_data(:, i) = H5R.create(fid, ref(i).path, ref(i).reftype, ...
-        refspace(i));
+    try
+        ref_data(:, i) = H5R.create(fid, ref(i).path, ref(i).reftype, refspace(i));
+    catch ME
+        error('MatNWB:getRefData:InvalidPath',...
+            'Reference path `%s` was invalid', ref(i).path);
+    end
     if H5I.is_valid(refspace(i))
         H5S.close(refspace(i));
     end

+tests/+sanity/GenerationTest.m

@@ -23,10 +23,8 @@ function roundtripTest(testCase)
             expected = NwbFile('identifier', 'TEST',...
                 'session_description', 'test nwbfile',...
                 'session_start_time', datetime());
-            expected.export('empty.nwb');
-
-            actual = nwbRead('empty.nwb');
-            tests.util.verifyContainerEqual(testCase, actual, expected);
+            nwbExport(expected, 'empty.nwb');
+            tests.util.verifyContainerEqual(testCase, nwbRead('empty.nwb'), expected);
         end
 
         function dynamicTableMethodsTest(testCase)
@@ -47,8 +45,7 @@ function dynamicTableMethodsTest(testCase)
                     'stop_time', stop_time,...
                     'randomvalues', rand_data,...
                     'stringdata', {'TRUE'},...
-                    'id', id(i),...
-                    'tablepath', '/intervals/trials');
+                    'id', id(i));
             end
             t = table(id(101:200), (101:200) .', (102:201) .',...
                 mat2cell(rand(500,1), repmat(5, 100, 1)), repmat({'TRUE'}, 100, 1),...

+tests/+system/AmendTest.m

@@ -9,7 +9,7 @@ function testAmend(testCase)
             writeContainer = testCase.getContainer(testCase.file);
             readFile = nwbRead(filename);
             readContainer = testCase.getContainer(readFile);
-            testCase.verifyContainerEqual(readContainer, writeContainer);
+            tests.util.verifyContainerEqual(testCase, readContainer, writeContainer);
         end
     end
 

+tests/+system/DynamicTableTest.m

@@ -16,8 +16,7 @@ function addContainer(~, file)
                     'stop_time', stop_time,...
                     'randomvalues', rand_data,...
                     'stringdata', {'TRUE'},...
-                    'id', id(i),...
-                    'tablepath', '/intervals/trials');
+                    'id', id(i));
             end
             t = table(id(101:200), (101:200) .', (102:201) .',...
                 mat2cell(rand(500,1), repmat(5, 100, 1)), repmat({'TRUE'}, 100, 1),...

+tests/+system/ElectricalSeriesIOTest.m

@@ -2,20 +2,14 @@
 
     methods
         function addContainer(testCase, file) %#ok<INUSL>
-            devnm = 'dev1';
-            egnm = 'tetrode1';
-            esnm = 'test_eS';
-            devBase = '/general/devices/';
-            ephysBase = '/general/extracellular_ephys/';
-            devlink = types.untyped.SoftLink([devBase devnm]);
-            eglink = types.untyped.ObjectView([ephysBase egnm]);
-            etReg = types.untyped.ObjectView([ephysBase 'electrodes']);
             dev = types.core.Device();
-            file.general_devices.set(devnm, dev);
+            file.general_devices.set('dev1', dev);
+
+            egnm = 'tetrode1';
             eg = types.core.ElectrodeGroup( ...
                 'description', 'tetrode description', ...
                 'location', 'tetrode location', ...
-                'device', devlink);
+                'device', types.untyped.SoftLink(dev));
 
             electrodes = util.createElectrodeTable();
             for i = 1:4
@@ -24,7 +18,7 @@ function addContainer(testCase, file) %#ok<INUSL>
                     'imp', 1,...
                     'location', {'CA1'},...
                     'filtering', 0,...
-                    'group', eglink, 'group_name', {egnm});
+                    'group', types.untyped.ObjectView(eg), 'group_name', {egnm});
             end
             file.general_extracellular_ephys_electrodes = electrodes;
 
@@ -35,9 +29,9 @@ function addContainer(testCase, file) %#ok<INUSL>
                 'electrodes', ...
                 types.hdmf_common.DynamicTableRegion(...
                 'data', [0;2],...
-                'table', etReg,...
+                'table', types.untyped.ObjectView(electrodes),...
                 'description', 'the first and third electrodes'));
-            file.acquisition.set(esnm, es);
+            file.acquisition.set('test_eS', es);
         end
 
         function c = getContainer(testCase, file) %#ok<INUSL>

+tests/+system/ElectrodeGroupIOTest.m

@@ -7,7 +7,7 @@ function addContainer(testCase, file) %#ok<INUSL>
             eg = types.core.ElectrodeGroup( ...
                 'description', 'a test ElectrodeGroup', ...
                 'location', 'a nonexistent place', ...
-                'device', types.untyped.SoftLink('/general/devices/dev1'));
+                'device', types.untyped.SoftLink(dev));
             file.general_extracellular_ephys.set('elec1', eg);
         end
 

+tests/+system/ImagingPlaneIOTest.m

@@ -8,7 +8,7 @@ function addContainer(testCase, file) %#ok<INUSL>
             ip = types.core.ImagingPlane( ...
                 'description', 'a fake ImagingPlane', ...
                 'optchan1', oc, ...
-                'device', types.untyped.SoftLink('/general/devices/imaging_device_1'), ...
+                'device', types.untyped.SoftLink(dev), ...
                 'excitation_lambda', 6.28, ...
                 'imaging_rate', 2.718, ...
                 'indicator', 'GFP', ...

+tests/+system/NwbTestInterface.m

@@ -31,79 +31,7 @@ function setupMethod(testCase)
         function n = className(testCase)
             classSplit = strsplit(class(testCase), '.');
             n = classSplit{end};
-        end
-
-        function verifyContainerEqual(testCase, actual, expected)
-            testCase.verifyEqual(class(actual), class(expected));
-            props = properties(actual);
-            for i = 1:numel(props)
-                prop = props{i};
-                if strcmp(prop, 'file_create_date')
-                    continue;
-                end
-                actualVal = actual.(prop);
-                expectedVal = expected.(prop);
-                failmsg = ['Values for property ''' prop ''' are not equal'];
-                if startsWith(class(actualVal), 'types.')...
-                        && ~startsWith(class(actualVal), 'types.untyped')
-                    verifyContainerEqual(testCase, actualVal, expectedVal);
-                elseif isa(actualVal, 'types.untyped.Set')
-                    verifySetEqual(testCase, actualVal, expectedVal, failmsg);
-                elseif isdatetime(actualVal)
-                    testCase.verifyEqual(char(actualVal), char(expectedVal), failmsg);
-                else
-                    if isa(actualVal, 'types.untyped.DataStub')
-                        actualTrue = actualVal.load();
-                    else
-                        actualTrue = actualVal;
-                    end
-
-                    if isvector(expectedVal) && isvector(actualTrue) && numel(expectedVal) == numel(actualTrue)
-                        actualTrue = reshape(actualTrue, size(expectedVal));
-                    end
-
-                    if isinteger(actualTrue) && isinteger(expectedVal)
-                        actualSize = class(actualTrue);
-                        actualSize = str2double(actualSize(4:end));
-                        expectedSize = class(expectedVal);
-                        expectedSize = str2double(expectedSize(4:end));
-                        testCase.verifyGreaterThanOrEqual(actualSize, expectedSize, failmsg);
-                        testCase.verifyEqual(double(actualTrue), double(expectedVal), failmsg);
-                        continue;
-                    end
-                    testCase.verifyEqual(actualTrue, expectedVal, failmsg);
-                end
-            end
-        end
-
-        function verifySetEqual(testCase, actual, expected, failmsg)
-            testCase.verifyEqual(class(actual), class(expected));
-            ak = actual.keys();
-            ek = expected.keys();
-            verifyTrue(testCase, isempty(setxor(ak, ek)), failmsg);
-            for i=1:numel(ak)
-                key = ak{i};
-                verifyContainerEqual(testCase, actual.get(key), ...
-                    expected.get(key));
-            end
-        end
-
-        function verifyUntypedEqual(testCase, actual, expected)
-            testCase.verifyEqual(class(actual), class(expected));
-            props = properties(actual);
-            for i = 1:numel(props)
-                prop = props{i};
-                val1 = actual.(prop);
-                val2 = expected.(prop);
-                if isa(val1, 'types.core.NWBContainer') || isa(val1, 'types.core.NWBData')
-                    verifyContainerEqual(testCase, val1, val2);
-                else
-                    testCase.verifyEqual(val1, val2, ...
-                        ['Values for property ''' prop ''' are not equal']);
-                end
-            end
-        end
-
+        end    
     end
 
     methods(Abstract)

+tests/+system/PhotonSeriesIOTest.m

@@ -9,15 +9,15 @@ function addContainer(testCase, file) %#ok<INUSL>
             ip = types.core.ImagingPlane( ...
                 'description', 'a fake ImagingPlane', ...
                 'optchan1', oc, ...
-                'device', types.untyped.SoftLink('/general/devices/dev1'), ...
+                'device', types.untyped.SoftLink(dev), ...
                 'excitation_lambda', 6.28, ...
                 'imaging_rate', 2.718, ...
                 'indicator', 'GFP', ...
                 'location', 'somewhere in the brain');
 
             tps = types.core.TwoPhotonSeries( ...
                 'data', ones(3,3,3), ...
-                'imaging_plane', types.untyped.SoftLink('/general/optophysiology/imgpln1'), ...
+                'imaging_plane', types.untyped.SoftLink(ip), ...
                 'data_unit', 'image_unit', ...
                 'format', 'raw', ...
                 'field_of_view', [2, 2, 5] .', ...
@@ -37,18 +37,18 @@ function addContainer(testCase, file) %#ok<INUSL>
 
         function appendContainer(~, file)
             oldImagingPlane = file.general_optophysiology.get('imgpln1');
-            file.general_optophysiology.set('imgpln2',...
-                types.core.ImagingPlane(...
+            newImagingPlane = types.core.ImagingPlane(...
                 'description', 'a different imaging plane',...
                 'device', oldImagingPlane.device,...
                 'optchan1', oldImagingPlane.opticalchannel.get('optchan1'),...
                 'excitation_lambda', 1,...
                 'imaging_rate', 2,...
                 'indicator', 'ASL',...
-                'location', 'somewhere else in the brain'));
+                'location', 'somewhere else in the brain');
+            file.general_optophysiology.set('imgpln2', newImagingPlane);
 
             hTwoPhotonSeries = file.acquisition.get('test_2ps');
-            hTwoPhotonSeries.imaging_plane.path = '/general/optophysiology/imgpln2';
+            hTwoPhotonSeries.imaging_plane = types.untyped.SoftLink(newImagingPlane);
             hTwoPhotonSeries.data = hTwoPhotonSeries.data + rand();
         end
     end

+tests/+system/PyNWBIOTest.m

@@ -1,51 +1,54 @@
 classdef PyNWBIOTest < tests.system.RoundTripTest
-  % Assumes PyNWB and unittest2 has been installed on the system.
-  %
-  % To install PyNWB, execute:
-  % $ pip install pynwb
-  %
-  % To install unittest2, execute:
-  % $ pip install unittest2
-  methods(Test)
-    function testOutToPyNWB(testCase)
-      filename = ['MatNWB.' testCase.className() '.testOutToPyNWB.nwb'];
-      nwbExport(testCase.file, filename);
-      [status, cmdout] = testCase.runPyTest('testInFromMatNWB');
-      if status
-        testCase.verifyFail(cmdout);
-      end
+    % Assumes PyNWB and unittest2 has been installed on the system.
+    %
+    % To install PyNWB, execute:
+    % $ pip install pynwb
+    %
+    % To install unittest2, execute:
+    % $ pip install unittest2
+    methods(Test)
+        function testOutToPyNWB(testCase)
+            filename = ['MatNWB.' testCase.className() '.testOutToPyNWB.nwb'];
+            nwbExport(testCase.file, filename);
+            [status, cmdout] = testCase.runPyTest('testInFromMatNWB');
+            if status
+                testCase.verifyFail(cmdout);
+            end
+        end
+
+        function testInFromPyNWB(testCase)
+            [status, cmdout] = testCase.runPyTest('testOutToMatNWB');
+            if status
+                testCase.assertFail(cmdout);
+            end
+            filename = ['PyNWB.' testCase.className() '.testOutToMatNWB.nwb'];
+            pyfile = nwbRead(filename);
+            pycontainer = testCase.getContainer(pyfile);
+            matcontainer = testCase.getContainer(testCase.file);
+            nwbExport(testCase.file, 'temp.nwb'); % hack to fill out ObjectView container paths.
+            % ignore file_create_date because nwbExport will actually
+            % mutate the property every export.
+            tests.util.verifyContainerEqual(testCase, pycontainer, matcontainer, {'file_create_date'});
+        end
     end
 
-    function testInFromPyNWB(testCase)
-      [status, cmdout] = testCase.runPyTest('testOutToMatNWB');
-      if status
-        testCase.assertFail(cmdout);
-      end
-      filename = ['PyNWB.' testCase.className() '.testOutToMatNWB.nwb'];
-      pyfile = nwbRead(filename);
-      pycontainer = testCase.getContainer(pyfile);
-      matcontainer = testCase.getContainer(testCase.file);
-      testCase.verifyContainerEqual(pycontainer, matcontainer);
+    methods
+        function [status, cmdout] = runPyTest(testCase, testName)
+            setenv('PYTHONPATH', fileparts(mfilename('fullpath')));
+
+            envPath = fullfile('+tests', 'env.mat');
+            if 2 == exist(envPath, 'file')
+                Env = load(envPath, '-mat', 'pythonDir');
+
+                pythonPath = fullfile(Env.pythonDir, 'python');
+            else
+                pythonPath = 'python';
+            end
+
+            cmd = sprintf('"%s" -B -m unittest %s.%s.%s',...
+                pythonPath,...
+                'PyNWBIOTest', testCase.className(), testName);
+            [status, cmdout] = system(cmd);
+        end
     end
-  end
-
-  methods
-    function [status, cmdout] = runPyTest(testCase, testName)
-      setenv('PYTHONPATH', fileparts(mfilename('fullpath')));
-
-      envPath = fullfile('+tests', 'env.mat');
-      if 2 == exist(envPath, 'file')
-          Env = load(envPath, '-mat', 'pythonDir');
-
-          pythonPath = fullfile(Env.pythonDir, 'python');
-      else
-          pythonPath = 'python';
-      end
-
-      cmd = sprintf('"%s" -B -m unittest %s.%s.%s',...
-          pythonPath,...
-          'PyNWBIOTest', testCase.className(), testName);
-      [status, cmdout] = system(cmd);
-    end
-  end
 end

+tests/+system/RoundTripTest.m

@@ -6,7 +6,7 @@ function testRoundTrip(testCase)
             writeContainer = testCase.getContainer(testCase.file);
             readFile = nwbRead(filename);
             readContainer = testCase.getContainer(readFile);
-            testCase.verifyContainerEqual(readContainer, writeContainer);
+            tests.util.verifyContainerEqual(testCase, readContainer, writeContainer);
         end
     end
 end

+tests/+system/UnitTimesIOTest.m

@@ -3,7 +3,7 @@
         function addContainer(~, file)
             vdata = rand(10,1);
             file.units = types.core.Units('description', 'test Units', 'colnames', {'spike_times'});
-            file.units.addRow('spike_times', vdata(1), 'tablepath', '/units');
+            file.units.addRow('spike_times', vdata(1));
             file.units.addRow('spike_times', vdata(2:5));
             file.units.addRow('spike_times', vdata(6:end));
         end

+tests/+unit/anonTest.m

@@ -23,7 +23,7 @@ function testAnonDataset(testCase)
     'session_description', 'anonymous class schema testing',...
     'session_start_time', datetime());
 nwbExpected.acquisition.set('ag', ag);
-nwbExpected.export('testanon.nwb');
+nwbExport(nwbExpected, 'testanon.nwb');
 
 tests.util.verifyContainerEqual(testCase, nwbRead('testanon.nwb'), nwbExpected);
 end

+tests/+unit/dataStubTest.m

@@ -81,7 +81,7 @@ function testObjectCopy(testCase)
     'identifier', 'DATASTUB',...
     'session_description', 'test datastub object copy',...
     'session_start_time', datetime());
-rc = types.rrs.RefContainer('data', rand(100, 100));
+rc = types.rrs.RefContainer('data', types.rrs.RefData('data', rand(100, 100)));
 rcPath = '/acquisition/rc';
 rcDataPath = [rcPath '/data'];
 rcRef = types.cs.CompoundRefData('data', table(...