poc

src/hdmf/backends/hdf5/h5_utils.py

@@ -110,10 +110,11 @@ def shape(self):
 
     def append(self, arg):
         # Get Builder
-        builder = self.io.manager.build(arg)
+        builder = self.io.manager.builders[arg.object_id]
 
         # Get HDF5 Reference
         ref = self.io._create_ref(builder)
+        breakpoint()
         append_data(self.dataset, ref)
 
 

src/hdmf/backends/hdf5/h5tools.py

@@ -1513,7 +1513,9 @@ def __get_ref(self, **kwargs):
         else:
             self.logger.debug("Getting reference for %s '%s'" % (container.__class__.__name__, container.name))
             builder = self.manager.build(container)
+        breakpoint()
         path = self.__get_path(builder)
+
         self.logger.debug("Getting reference at path '%s'" % path)
         if isinstance(container, RegionBuilder):
             region = container.region
@@ -1531,8 +1533,7 @@ def __get_ref(self, **kwargs):
              'default': None},
             returns='the reference', rtype=Reference)
     def _create_ref(self, **kwargs):
-        self.__get_ref(**kwargs)
-
+        return self.__get_ref(**kwargs)
 
     def __is_ref(self, dtype):
         if isinstance(dtype, DtypeSpec):

src/hdmf/build/manager.py

@@ -94,6 +94,10 @@ def __init__(self, type_map):
         self.__type_map = type_map
         self.__ref_queue = deque()  # a queue of the ReferenceBuilders that need to be added
 
+    @property
+    def builders(self):
+        return self.__builders
+
     @property
     def namespace_catalog(self):
         return self.__type_map.namespace_catalog
@@ -198,7 +202,7 @@ def prebuilt(self, **kwargs):
         ''' Save the Builder for a given AbstractContainer for future use '''
         container, builder = getargs('container', 'builder', kwargs)
         container_id = self.__conthash__(container)
-        self.__builders[container_id] = builder
+        self.__builders[container.object_id] = builder
         builder_id = self.__bldrhash__(builder)
         self.__containers[builder_id] = container
 
@@ -263,7 +267,7 @@ def get_builder(self, **kwargs):
         """Return the prebuilt builder for the given container or None if it does not exist."""
         container = getargs('container', kwargs)
         container_id = self.__conthash__(container)
-        result = self.__builders.get(container_id)
+        result = self.__builders.get(container.object_id)
         return result
 
     @docval({'name': 'builder', 'type': (DatasetBuilder, GroupBuilder),

tests/unit/test_io_hdf5_h5tools.py

@@ -2961,7 +2961,7 @@ def test_append_data(self):
     def test_append_dataset_of_references(self):
         """Test that exporting a written container with a dataset of references works."""
         bazs = []
-        num_bazs = 10
+        num_bazs = 1
         for i in range(num_bazs):
             bazs.append(Baz(name='baz%d' % i))
         array_bazs=np.array(bazs)
@@ -2976,15 +2976,19 @@ def test_append_dataset_of_references(self):
             read_bucket1 = read_io.read()
             new_baz = Baz(name='new')
             read_bucket1.add_baz(new_baz)
+            read_io.write(read_bucket1)
 
+        with HDF5IO(self.paths[0], manager=get_baz_buildmanager(), mode='a') as read_io:
+            read_bucket1 = read_io.read()
+            breakpoint()
             DoR = read_bucket1.baz_data.data
             DoR.append(new_baz)
             read_io.write(read_bucket1)
 
         with HDF5IO(self.paths[0], manager=get_baz_buildmanager(), mode='r') as read_io:
             read_bucket1 = read_io.read()
-            self.assertEqual(len(read_bucket1.baz_data.data), 11)
-            self.assertIs(read_bucket1.baz_data.data[10], read_bucket1.bazs["new"])
+            self.assertEqual(len(read_bucket1.baz_data.data), 2)
+            self.assertIs(read_bucket1.baz_data.data[1], read_bucket1.bazs["new"])
 
     def test_append_external_link_data(self):
         """Test that exporting a written container after adding a link with link_data=True creates external links."""