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Added getTypeObjects method (#745)
* Added getTypeObjects method * Fix behavior of getTypeObjects when search for subtypes - Added properly formatted examples in docstring - Refactor code and fix bugs for getting type including subtypes * Update searchTest.m Added tests for new getTypeObject methods and a test comparing its behavior to searchFor * Properly format method docstring for readthedocs * Update NwbFile.m Remove unused function Changed order of local functions * Update NwbFile.m Co-authored-by: Ben Dichter <[email protected]> * Fixed method to also resolve types from specific namespaces * Fix failing test --------- Co-authored-by: Ben Dichter <[email protected]>
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‎+tests/+unit/searchTest.m‎

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@@ -24,5 +24,88 @@ function testSearch(testCase)
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% use includeSubClasses keyword
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testCase.assertLength(nwb.searchFor('types.core.TimeSeries', 'includeSubClasses'), 2);
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end
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function testSearchWithoutTypeNamespace(testCase)
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nwb = NwbFile();
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nwb.acquisition.set('ts1', types.core.TimeSeries());
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nwb.acquisition.set('ts2', types.core.BehavioralTimeSeries());
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testCase.assertLength(nwb.searchFor('TimeSeries'), 2);
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end
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function testGetType(testCase)
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% Test that getTypeObjects method does exact type match,
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% contrary to searchFor
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nwb = NwbFile();
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nwb.acquisition.set('ts1', types.core.TimeSeries());
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nwb.acquisition.set('ts2', types.core.BehavioralTimeSeries());
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testCase.assertLength(nwb.getTypeObjects('TimeSeries'), 1);
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end
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function testGetTypeWithSubclasses(testCase)
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% Test that getTypeObjects method does exact type match and
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% includes subclasses
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nwb = NwbFile();
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nwb.acquisition.set('ts1', types.core.TimeSeries());
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nwb.acquisition.set('ts2', types.core.PatchClampSeries());
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nwb.acquisition.set('ts3', types.core.BehavioralTimeSeries());
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testCase.verifyLength(...
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nwb.getTypeObjects('TimeSeries', 'IncludeSubTypes', true), 2);
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end
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function testGetTypeVsSearchFor(testCase)
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% Test that getTypeObjects method does exact type match,
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% contrary to searchFor
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nwb = NwbFile();
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nwb.acquisition.set('im1', types.core.Images());
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nwb.acquisition.set('im2', types.core.ImageSeries());
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nwb.acquisition.set('im3', types.core.OpticalSeries());
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% GetTypeObjects should only match objects of "Images" type
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testCase.verifyLength(...
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nwb.getTypeObjects('Images'), 1);
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% searchFor should find both objects of "Images" and "ImageSeries" type
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testCase.verifyLength(...
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nwb.searchFor('Images'), 2);
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% GetTypeObjects with subclasses should only match objects of "Images" type
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testCase.verifyLength(...
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nwb.getTypeObjects('Images', 'IncludeSubTypes', true), 1);
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% searchFor with subclasses will also match OpticalSeries as it
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% is a subclass of ImageSeries.
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testCase.verifyLength(...
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nwb.searchFor('Images', 'includeSubClasses'), 3);
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end
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function testSameNameDifferentNamespace(testCase)
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schemaRootDirectory = fullfile(misc.getMatnwbDir(), '+tests', 'test-schema');
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import tests.fixtures.ExtensionGenerationFixture
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F = testCase.getSharedTestFixtures();
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isMatch = arrayfun(@(x) isa(x, 'tests.fixtures.GenerateCoreFixture'), F);
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F = F(isMatch);
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typesOutputFolder = F.TypesOutputFolder;
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namespaceFilePath = fullfile( ...
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schemaRootDirectory, 'dupliNameSchema', 'dn.namespace.yaml');
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testCase.applyFixture( ...
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ExtensionGenerationFixture(namespaceFilePath, typesOutputFolder) )
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nwb = NwbFile();
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nwb.acquisition.set('im1', types.core.Images());
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nwb.acquisition.set('im2', types.dn.Images());
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testCase.verifyLength( nwb.getTypeObjects('Images'), 2 );
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testCase.verifyLength( nwb.getTypeObjects('types.core.Images'), 1 );
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testCase.verifyLength( nwb.getTypeObjects('types.dn.Images'), 1 );
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end
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end
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end

‎+tests/test-schema/dupliNameSchema/dn.dupliname.yaml‎

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@@ -0,0 +1,13 @@
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groups:
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- neurodata_type_def: Images
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neurodata_type_inc: NWBDataInterface
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default_name: Images
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doc: A type with same name as Images in core namespace
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attributes:
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- name: description
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dtype: text
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doc: A description
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datasets:
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- neurodata_type_inc: BaseImage
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doc: Images stored in this collection.
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quantity: '+'

‎+tests/test-schema/dupliNameSchema/dn.namespace.yaml‎

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namespaces:
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- full_name: Duplicate Type Names Schema Test
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name: dn
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schema:
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- namespace: core
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- source: dn.dupliname.yaml
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version: 1.0.0
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‎NwbFile.m‎

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Original file line numberDiff line numberDiff line change
@@ -119,6 +119,69 @@ function export(obj, filename, mode)
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typename,...
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varargin{:});
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end
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function nwbObjects = getTypeObjects(obj, typeName, options)
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% GETTYPEOBJECTS - Retrieve NWB objects of a specified type.
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%
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% Syntax:
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% nwbObjects = GETTYPEOBJECTS(obj, typeName) Retrieves NWB
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% objects of the specified type from the NwbFile object.
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%
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% nwbObjects = GETTYPEOBJECTS(obj, typeName, Name, Value) Retrieves NWB
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% objects of the specified type from the NwbFile object using provided
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% name-value pairs controlling options.
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%
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% Input Arguments:
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% - obj (NwbFile) -
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% The NwbFile object from which to retrieve NWB objects.
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%
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% - typeName (1,1) string -
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% The name of the type to search for. Can include namespace, but
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% does not have to, i.e types.core.TimeSeries and TimeSeries are
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% supported.
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%
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% - options (name-value pairs) -
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% Optional name-value pairs. Available options:
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%
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% - IncludeSubTypes logical -
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% Optional: set to true to include subclasses in the search.
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% Default is false.
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%
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% Output Arguments:
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% - nwbObjects (cell) -
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% A cell array of NWB objects of the specified type.
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%
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% Usage:
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% Example 1 - Get all ElectricalSeries objects from NwbFile::
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%
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% evalc('run("ecephys.mlx")');
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% nwb.getTypeObjects('ElectricalSeries')
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%
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% Example 2 - Get all ElectricalSeries and subtype objects from NwbFile::
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%
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% evalc('run("ecephys.mlx")')
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% nwb.getTypeObjects('ElectricalSeries', 'IncludeSubTypes', true)
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arguments
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obj
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typeName (1,1) string
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options.IncludeSubTypes (1,1) logical = false
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end
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flags = {};
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if options.IncludeSubTypes
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flags{end+1} = 'includeSubClasses';
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end
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objectMap = searchProperties(...
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containers.Map,...
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obj,...
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'',...
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char(typeName),...
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flags{:}, 'exactTypeMatch');
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% Filter to return exact types.
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nwbObjects = objectMap.values;
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end
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function nwbTypeNames = listNwbTypes(obj, options)
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% listNwbTypes - List all unique NWB (neurodata) types in file
@@ -255,23 +318,7 @@ function resolveReferences(obj, fid, references)
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end
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end
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function tf = metaHasType(mc, typeSuffix)
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assert(isa(mc, 'meta.class'));
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tf = false;
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if contains(mc.Name, typeSuffix, 'IgnoreCase', true)
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tf = true;
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return;
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end
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for i = 1:length(mc.SuperclassList)
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sc = mc.SuperclassList(i);
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if metaHasType(sc, typeSuffix)
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tf = true;
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return;
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end
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end
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end
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% Local functions
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function pathToObjectMap = searchProperties(...
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pathToObjectMap,...
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obj,...
@@ -282,6 +329,7 @@ function resolveReferences(obj, fid, references)
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'NWB:NwbFile:SearchProperties:InvalidVariableArguments',...
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'Optional keywords for searchFor must be char arrays.');
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shouldSearchSuperClasses = any(strcmpi(varargin, 'includeSubClasses'));
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exactTypeMatch = any(strcmpi(varargin, 'exactTypeMatch'));
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if isa(obj, 'types.untyped.MetaClass')
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propertyNames = properties(obj);
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'Invalid object type passed %s', class(obj));
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end
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searchTypename = @(obj, typename) contains(class(obj), typename, 'IgnoreCase', true);
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searchTypename = @(obj, typename) isMatchedType(class(obj), typename, 'ExactMatch', exactTypeMatch);
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if shouldSearchSuperClasses
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searchTypename = @(obj, typename) metaHasType(metaclass(obj), typename);
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searchTypename = @(obj, typename) metaHasType(metaclass(obj), typename, 'ExactMatch', exactTypeMatch);
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end
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for i = 1:length(propertyNames)
@@ -319,6 +367,56 @@ function resolveReferences(obj, fid, references)
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end
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end
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function tf = metaHasType(mc, typeSuffix, options)
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arguments
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mc meta.class
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typeSuffix (1,1) string
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options.ExactMatch (1,1) logical = false
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end
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tf = false;
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if isMatchedType(mc.Name, typeSuffix, 'ExactMatch', options.ExactMatch)
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tf = true;
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return;
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end
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for i = 1:length(mc.SuperclassList)
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sc = mc.SuperclassList(i);
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if metaHasType(sc, typeSuffix, 'ExactMatch', options.ExactMatch)
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tf = true;
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return;
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end
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end
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end
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function tf = isMatchedType(typeNameA, typeNameB, options)
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arguments
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typeNameA (1,1) string
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typeNameB (1,1) string
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options.ExactMatch (1,1) logical = false
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end
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if options.ExactMatch
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if contains(typeNameB, '.')
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% If namespace is provided, need to match on namespace and type.
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tf = strcmpi(typeNameA, typeNameB);
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else
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tf = strcmpi(...
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extractTypeNameWithoutNamespace(typeNameA), ...
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extractTypeNameWithoutNamespace(typeNameB));
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end
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else
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tf = contains(typeNameA, typeNameB, 'IgnoreCase', true);
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end
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end
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function typeName = extractTypeNameWithoutNamespace(typeName)
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if contains(typeName, '.')
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splitName = split(typeName, '.');
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typeName = splitName{end};
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end
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end
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function namespaceNames = getNamespacesForDataTypes(nwbTypeNames)
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% getNamespacesOfTypes - Get namespace names for a list of nwb types
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arguments

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