checkpoint

src/hdmf/backends/hdf5/h5_utils.py

@@ -147,7 +147,6 @@ def __next__(self):
         return self._get_ref(super().__next__())
 
     def append(self, arg):
-        breakpoint()
         append_data(self.dataset, arg)
 
 

src/hdmf/backends/hdf5/h5tools.py

@@ -1117,7 +1117,6 @@ def write_dataset(self, **kwargs):  # noqa: C901
         data = builder.data
         dataio = None
         options = dict()  # dict with additional
-        breakpoint()
         if isinstance(data, H5DataIO):
             options['io_settings'] = data.io_settings
             dataio = data

src/hdmf/backends/io.py

@@ -96,7 +96,6 @@ def write(self, **kwargs):
 
         """Write a container to the IO source."""
         f_builder = self.__manager.build(container, source=self.__source, root=True)
-        breakpoint()
         self.write_builder(f_builder, **kwargs)
 
     @docval({'name': 'src_io', 'type': 'hdmf.backends.io.HDMFIO',

src/hdmf/build/objectmapper.py

@@ -11,6 +11,8 @@
                      ConstructError)
 from .manager import Proxy, BuildManager
 from .warnings import MissingRequiredBuildWarning, DtypeConversionWarning, IncorrectQuantityBuildWarning
+from hdmf.backends.hdf5.h5_utils import H5DataIO
+
 from ..container import AbstractContainer, Data, DataRegion
 from ..term_set import TermSetWrapper
 from ..data_utils import DataIO, AbstractDataChunkIterator
@@ -771,7 +773,6 @@ def build(self, **kwargs):
         # TODO: Check the BuildManager as refinements should probably be resolved rather than be passed in via spec_ext
         all_attrs = list({a.name: a for a in all_attrs[::-1]}.values())
         self.__add_attributes(builder, all_attrs, container, manager, source, export)
-        # breakpoint()
         return builder
 
     def __check_dset_spec(self, orig, ext):
@@ -821,7 +822,8 @@ def __set_dataset_to_refs(self, builder, dtype, shape, container, build_manager)
                           % (builder.__class__.__name__, builder.name))
 
         def _filler():
-            builder.data = self.__get_ref_builder(builder, dtype, shape, container, build_manager)
+            data = self.__get_ref_builder(builder, dtype, shape, container, build_manager)
+            builder.data = data
 
         return _filler
 
@@ -890,6 +892,8 @@ def __get_ref_builder(self, builder, dtype, shape, container, build_manager):
                 for d in container.data:
                     target_builder = self.__get_target_builder(d, build_manager, builder)
                     bldr_data.append(ReferenceBuilder(target_builder))
+                if isinstance(container.data, H5DataIO):
+                    bldr_data = H5DataIO(bldr_data, **container.data.get_io_params())
             else:
                 self.logger.debug("Setting %s '%s' data to reference builder"
                                   % (builder.__class__.__name__, builder.name))

tests/unit/test_io_hdf5_h5tools.py

@@ -2964,27 +2964,20 @@ def test_append_dataset_of_references(self):
         num_bazs = 10
         for i in range(num_bazs):
             bazs.append(Baz(name='baz%d' % i))
-        wrapped_bazs = H5DataIO(bazs)
+        array_bazs=np.array(bazs)
+        wrapped_bazs = H5DataIO(array_bazs, maxshape=(None,))
         baz_data = BazData(name='baz_data1', data=wrapped_bazs)
         bucket = BazBucket(name='bucket1', bazs=bazs.copy(), baz_data=baz_data)
-        breakpoint()
 
         with HDF5IO(self.paths[0], manager=get_baz_buildmanager(), mode='w') as write_io:
             write_io.write(bucket)
 
         with HDF5IO(self.paths[0], manager=get_baz_buildmanager(), mode='a') as read_io:
             read_bucket1 = read_io.read()
-            new_baz = Baz(name='baz000')
-            breakpoint()
             DoR = read_bucket1.baz_data.data
-            DoR.append(new_baz)
-            breakpoint()
-
-            #
-            # read_container = reader.read()
-            # new_baz = Baz(name='baz0')
-            # DoR = read_bucket1.baz_data.data
-            # DoR.append(new_baz)
+            ref = read_bucket1.baz_data.data.dataset[0]
+            DoR.append(ref)
+            self.assertEqual(len(read_bucket1.baz_data.data), 11)
 
     def test_append_external_link_data(self):
         """Test that exporting a written container after adding a link with link_data=True creates external links."""