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Fix namespace bug for hdmf-experimental types (#779)
* Fix namespace bug for hdmf-experimental types Adds a workaround for a bug where neurodata types are incorrectly assigned the 'hdmf-experimental' namespace instead of 'hdmf-common'. If the class does not exist for 'hdmf-experimental' but does for 'hdmf-common', the namespace and typename are corrected accordingly. See hdmf-dev/hdmf#1347 for details. * Update getNeurodataTypeInfo.m * Added unittest --------- Co-authored-by: Ben Dichter <[email protected]>
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‎+io/getNeurodataTypeInfo.m‎

Lines changed: 29 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -46,7 +46,34 @@
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% Get full classname given a namespace and a neurodata type
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if hasTypeDef && hasNamespace
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typeInfo.typename = matnwb.common.composeFullClassName(...
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typeInfo.namespace, typeInfo.name);
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typeInfo.typename = char( matnwb.common.composeFullClassName(...
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typeInfo.namespace, typeInfo.name) );
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if strcmp(typeInfo.namespace, 'hdmf-experimental') && ~exist(typeInfo.typename, 'class')
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typeInfo = correctNamespaceIfShouldBeHdmfCommon(typeInfo);
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end
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end
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end
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function typeInfo = correctNamespaceIfShouldBeHdmfCommon(typeInfo)
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% correctNamespaceIfShouldBeHdmfCommon - Correct namespace if value in file is wrong.
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%
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% This function provides a workaround for a bug where the namespace of a
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% neurodata type was wrongly written to file as hdmf-experimental instead
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% of hdmf-common.
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%
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% If the namespace of a type is hdmf-experimental, and the corresponding type
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% class does not exist in MATLAB, but the equivalent hdmf_common class exists,
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% the namespace is changed from hdmf-experimental to hdmf-common.
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%
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% The bug is described in this issue:
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% https://github.com/hdmf-dev/hdmf/issues/1347
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if strcmp(typeInfo.namespace, 'hdmf-experimental') && ~exist(typeInfo.typename, 'class')
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correctedTypename = replace(typeInfo.typename, 'hdmf_experimental', 'hdmf_common');
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if exist(correctedTypename, 'class') == 8
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typeInfo.typename = correctedTypename;
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typeInfo.namespace = 'hdmf-common';
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end
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end
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end

‎+tests/+unit/+io/GetNeurodataTypeInfoTest.m‎

Lines changed: 141 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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classdef GetNeurodataTypeInfoTest < matlab.unittest.TestCase
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% GetNeurodataTypeInfoTest - Unit tests for io.getNeurodataTypeInfo function.
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properties (TestParameter)
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HDMFCommonType = {'DynamicTable', 'VectorData', 'VectorIndex'}
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end
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methods (Test)
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function testEmptyInput(testCase)
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% Test that empty input returns empty typeInfo
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typeInfo = io.getNeurodataTypeInfo([]);
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testCase.verifyEqual(typeInfo.namespace, '');
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testCase.verifyEqual(typeInfo.name, '');
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testCase.verifyEqual(typeInfo.typename, '');
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end
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function testValidNeurodataType(testCase)
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% Test with valid neurodata type and namespace
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attributeInfo = struct(...
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'Name', {'neurodata_type', 'namespace'}, ...
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'Value', {'DynamicTable', 'hdmf-common'});
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typeInfo = io.getNeurodataTypeInfo(attributeInfo);
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testCase.verifyEqual(typeInfo.namespace, 'hdmf-common');
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testCase.verifyEqual(typeInfo.name, 'DynamicTable');
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testCase.verifyEqual(typeInfo.typename, 'types.hdmf_common.DynamicTable');
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end
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function testOnlyNeurodataType(testCase)
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% Test with only neurodata_type attribute (no namespace)
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attributeInfo = struct(...
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'Name', {'neurodata_type'}, ...
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'Value', {'DynamicTable'});
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typeInfo = io.getNeurodataTypeInfo(attributeInfo);
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testCase.verifyEqual(typeInfo.namespace, '');
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testCase.verifyEqual(typeInfo.name, 'DynamicTable');
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testCase.verifyEqual(typeInfo.typename, '');
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end
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function testOnlyNamespace(testCase)
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% Test with only namespace attribute (no neurodata_type)
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attributeInfo = struct(...
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'Name', {'namespace'}, ...
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'Value', {'hdmf-common'});
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typeInfo = io.getNeurodataTypeInfo(attributeInfo);
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testCase.verifyEqual(typeInfo.namespace, 'hdmf-common');
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testCase.verifyEqual(typeInfo.name, '');
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testCase.verifyEqual(typeInfo.typename, '');
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end
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function testHdmfExperimentalFallbackToHdmfCommon(testCase, HDMFCommonType)
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% Test fallback correction for VectorData with incorrect
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% hdmf-experimental namespace (should be hdmf-common)
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attributeInfo = struct(...
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'Name', {'neurodata_type', 'namespace'}, ...
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'Value', {HDMFCommonType, 'hdmf-experimental'});
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typeInfo = io.getNeurodataTypeInfo(attributeInfo);
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% Should be corrected to hdmf-common
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testCase.verifyEqual(typeInfo.namespace, 'hdmf-common');
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testCase.verifyEqual(typeInfo.name, HDMFCommonType);
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testCase.verifyEqual(typeInfo.typename, sprintf('types.hdmf_common.%s', HDMFCommonType));
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end
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function testCellStringValueHandling(testCase)
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% Test that cell string values are handled correctly
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attributeInfo = struct(...
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'Name', {'neurodata_type', 'namespace'}, ...
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'Value', {{'DynamicTable'}, {'hdmf-common'}});
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typeInfo = io.getNeurodataTypeInfo(attributeInfo);
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testCase.verifyEqual(typeInfo.namespace, 'hdmf-common');
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testCase.verifyEqual(typeInfo.name, 'DynamicTable');
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testCase.verifyEqual(typeInfo.typename, 'types.hdmf_common.DynamicTable');
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end
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function testNoFallbackForValidHdmfExperimentalType(testCase)
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% Test that valid hdmf-experimental types are not incorrectly
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% changed to hdmf-common
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%
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% Note: This test verifies that if a type genuinely belongs to
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% hdmf-experimental and exists there, it should not be changed.
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% EnumData is an example type that exists only in
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% hdmf-experimental.
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% First, check if types.hdmf_experimental exists and has types
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if exist('types.hdmf_experimental.EnumData', 'class') == 8
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attributeInfo = struct(...
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'Name', {'neurodata_type', 'namespace'}, ...
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'Value', {'EnumData', 'hdmf-experimental'});
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typeInfo = io.getNeurodataTypeInfo(attributeInfo);
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% Should remain hdmf-experimental since the class exists there
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testCase.verifyEqual(typeInfo.namespace, 'hdmf-experimental');
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testCase.verifyEqual(typeInfo.typename, 'types.hdmf_experimental.EnumData');
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else
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% If hdmf-experimental types don't exist, skip this test
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testCase.assumeTrue(false, ...
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'Skipping test: types.hdmf_experimental.EnumData class not found');
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end
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end
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function testNoFallbackForNonExistentType(testCase)
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% Test that non-existent types in hdmf-experimental that also
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% don't exist in hdmf-common remain unchanged (the typename
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% will still point to hdmf-experimental since no fallback exists)
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attributeInfo = struct(...
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'Name', {'neurodata_type', 'namespace'}, ...
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'Value', {'NonExistentType', 'hdmf-experimental'});
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typeInfo = io.getNeurodataTypeInfo(attributeInfo);
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% Should remain hdmf-experimental since there's no hdmf-common fallback
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testCase.verifyEqual(typeInfo.namespace, 'hdmf-experimental');
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testCase.verifyEqual(typeInfo.name, 'NonExistentType');
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testCase.verifyEqual(typeInfo.typename, 'types.hdmf_experimental.NonExistentType');
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end
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function testCoreNamespaceUnchanged(testCase)
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% Test that core namespace types are not affected by fallback logic
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attributeInfo = struct(...
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'Name', {'neurodata_type', 'namespace'}, ...
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'Value', {'NWBFile', 'core'});
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typeInfo = io.getNeurodataTypeInfo(attributeInfo);
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testCase.verifyEqual(typeInfo.namespace, 'core');
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testCase.verifyEqual(typeInfo.name, 'NWBFile');
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testCase.verifyEqual(typeInfo.typename, 'types.core.NWBFile');
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end
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end
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end

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