clean up

src/hdmf/backends/hdf5/h5_utils.py

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

src/hdmf/backends/hdf5/h5tools.py

@@ -1513,7 +1513,6 @@ 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)

src/hdmf/build/manager.py

@@ -92,11 +92,7 @@ def __init__(self, type_map):
         self.__containers = dict()
         self.__active_builders = set()
         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
+        self.__ref_queue = deque()  # a queue of the ReferenceBuilders that need to be addedq
 
     @property
     def namespace_catalog(self):
@@ -202,7 +198,7 @@ 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.object_id] = builder
+        self.__builders[container_id] = builder
         builder_id = self.__bldrhash__(builder)
         self.__containers[builder_id] = container
 
@@ -267,7 +263,7 @@ 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.object_id)
+        result = self.__builders.get(container_id)
         return result
 
     @docval({'name': 'builder', 'type': (DatasetBuilder, GroupBuilder),

src/hdmf/build/objectmapper.py

@@ -11,7 +11,8 @@
                      ConstructError)
 from .manager import Proxy, BuildManager
 
-from .warnings import MissingRequiredBuildWarning, DtypeConversionWarning, IncorrectQuantityBuildWarning
+from .warnings import (MissingRequiredBuildWarning, DtypeConversionWarning, IncorrectQuantityBuildWarning,
+                       IncorrectDatasetShapeBuildWarning)
 from hdmf.backends.hdf5.h5_utils import H5DataIO
 
 from ..container import AbstractContainer, Data, DataRegion

tests/unit/test_io_hdf5_h5tools.py

@@ -2972,18 +2972,16 @@ def test_append_dataset_of_references(self):
         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()
+        with HDF5IO(self.paths[0], manager=get_baz_buildmanager(), mode='a') as append_io:
+            read_bucket1 = append_io.read()
             new_baz = Baz(name='new')
             read_bucket1.add_baz(new_baz)
-            read_io.write(read_bucket1)
+            append_io.write(read_bucket1)
 
-        with HDF5IO(self.paths[0], manager=get_baz_buildmanager(), mode='a') as read_io:
-            read_bucket1 = read_io.read()
-            breakpoint()
+        with HDF5IO(self.paths[0], manager=get_baz_buildmanager(), mode='a') as ref_io:
+            read_bucket1 = ref_io.read()
             DoR = read_bucket1.baz_data.data
-            DoR.append(new_baz)
-            read_io.write(read_bucket1)
+            DoR.append(read_bucket1.bazs['new'])
 
         with HDF5IO(self.paths[0], manager=get_baz_buildmanager(), mode='r') as read_io:
             read_bucket1 = read_io.read()