Improve ObjectMapper and fix related issues (#463)

CHANGELOG.md

@@ -1,19 +1,27 @@
 # HDMF Changelog
 
-## HDMF 2.3.0 (Upcoming)
+## HDMF 3.0.0 (Upcoming)
+
+### Breaking changes
+- Drop support for Python 3.5. @ajtritt (#459)
+- Remove `hdmf.get_region_slicer` function. @ajtritt (#442)
+- Remove unused or refactored internal builder functions `GroupBuilder.add_group`, `GroupBuilder.add_dataset`,
+  `GroupBuilder.add_link`, `GroupBuilder.set_builder`, `BaseBuilder.deep_update`, `GroupBuilder.deep_update`,
+  `DatasetBuilder.deep_update`. Make `BaseBuilder` not instantiable and refactor builder code. @rly (#452)
+- Remove `hdmf.build.map.py`. Classes formerly in this file should be imported from `hdmf.build` instead. @rly (#463)
+- Replace `MissingRequiredWarning` with `MissingRequiredBuildWarning`. @rly (#463)
 
 ### New features
-- Drop support for Python 3.5. Add testing for Python 3.9. @ajtritt (#459)
 - Add methods for automatic creation of `MultiContainerInterface` classes. @bendichter (#420, #425)
 - Add ability to specify a custom class for new columns to a `DynamicTable` that are not `VectorData`,
   `DynamicTableRegion`, or `VocabData` using `DynamicTable.__columns__` or `DynamicTable.add_column(...)`. @rly (#436)  
 - Add support for creating and specifying multi-index columns in a `DynamicTable` using `add_column(...)`.
   @bendichter, @rly (#430)
 - Add capability to add a row to a column after IO. @bendichter (#426)
-- Add functionality for storing external resource references @ajtritt (#442)
+- Add functionality for storing external resource references. @ajtritt (#442)
 - Add method `hdmf.utils.get_docval_macro` to get a tuple of the current values for a docval_macro, e.g., 'array_data'  
   and 'scalar_data'. @rly (#446)
-- Add SimpleMultiContainer, a data_type for storing a Container and Data objects together. @ajtritt (#449)
+- Add `SimpleMultiContainer`, a data_type for storing a `Container` and `Data` objects together. @ajtritt (#449)
 - Support `pathlib.Path` paths in `HDMFIO.__init__`, `HDF5IO.__init__`, and `HDF5IO.load_namespaces`. @dsleiter (#439)
 - Use hdmf-common-schema 1.2.1. See https://hdmf-common-schema.readthedocs.io/en/latest/format_release_notes.html for details.
 - Block usage of h5py 3+. h5py>=2.9, <3 is supported. @rly (#461)
@@ -22,9 +30,7 @@
 ### Internal improvements
 - Refactor `HDF5IO.write_dataset` to be more readable. @rly (#428)
 - Fix bug in slicing tables with DynamicTableRegions. @ajtritt (#449)
-- Remove unused or refactored internal builder functions `GroupBuilder.add_group`, `GroupBuilder.add_dataset`,
-  `GroupBuilder.add_link`, `GroupBuilder.set_builder`, `BaseBuilder.deep_update`, `GroupBuilder.deep_update`,
-  `DatasetBuilder.deep_update`. Make `BaseBuilder` not instantiable and refactor builder code. @rly (#452)
+- Add testing for Python 3.9. @ajtritt (#459)
 
 ### Bug fixes
 - Fix development package dependency issues. @rly (#431)

src/hdmf/build/__init__.py

@@ -10,5 +10,6 @@
 from .manager import BuildManager
 from .manager import TypeMap
 
-from .warnings import MissingRequiredWarning, OrphanContainerWarning, DtypeConversionWarning
-from .errors import BuildError, OrphanContainerBuildError, ReferenceTargetNotBuiltError
+from .warnings import BuildWarning, MissingRequiredBuildWarning, DtypeConversionWarning, IncorrectQuantityBuildWarning
+from .errors import (BuildError, OrphanContainerBuildError, ReferenceTargetNotBuiltError, ContainerConfigurationError,
+                     ConstructError)

src/hdmf/build/errors.py

@@ -4,6 +4,7 @@
 
 
 class BuildError(Exception):
+    """Error raised when building a container into a builder."""
 
     @docval({'name': 'builder', 'type': Builder, 'doc': 'the builder that cannot be built'},
             {'name': 'reason', 'type': str, 'doc': 'the reason for the error'})
@@ -36,3 +37,12 @@ def __init__(self, **kwargs):
         reason = ("Could not find already-built Builder for %s '%s' in BuildManager"
                   % (self.__container.__class__.__name__, self.__container.name))
         super().__init__(builder=builder, reason=reason)
+
+
+class ContainerConfigurationError(Exception):
+    """Error raised when the container class is improperly configured."""
+    pass
+
+
+class ConstructError(Exception):
+    """Error raised when constructing a container from a builder."""

src/hdmf/build/manager.py

@@ -347,17 +347,22 @@ def get_builder_dt(self, **kwargs):
         builder = getargs('builder', kwargs)
         return self.__type_map.get_builder_dt(builder)
 
-    @docval({'name': 'builder', 'type': (GroupBuilder, DatasetBuilder), 'doc': 'the builder to check'},
-            {'name': 'parent_data_type', 'type': (str, type), 'doc': 'the potential parent data_type'},
+    @docval({'name': 'builder', 'type': (GroupBuilder, DatasetBuilder, AbstractContainer),
+             'doc': 'the builder or container to check'},
+            {'name': 'parent_data_type', 'type': str,
+             'doc': 'the potential parent data_type that refers to a data_type'},
             returns="True if data_type of *builder* is a sub-data_type of *parent_data_type*, False otherwise",
             rtype=bool)
     def is_sub_data_type(self, **kwargs):
         '''
         Return whether or not data_type of *builder* is a sub-data_type of *parent_data_type*
         '''
         builder, parent_dt = getargs('builder', 'parent_data_type', kwargs)
-        dt = self.get_builder_dt(builder)
-        ns = self.get_builder_ns(builder)
+        if isinstance(builder, (GroupBuilder, DatasetBuilder)):
+            ns = self.get_builder_ns(builder)
+            dt = self.get_builder_dt(builder)
+        else:  # builder is an AbstractContainer
+            ns, dt = self.type_map.get_container_ns_dt(builder)
         return self.namespace_catalog.is_sub_data_type(ns, dt, parent_dt)