_gather_columns agnostic search

CHANGELOG.md

@@ -1,5 +1,10 @@
 # HDMF Changelog
 
+## HDMF 3.11.1 (Upcoming)
+
+### Minor Improvements
+- Updated `__gather_columns` to ignore the order of bases when generating columns from the super class. @mavaylon1 [#991](https://github.com/hdmf-dev/hdmf/pull/991)
+
 ## HDMF 3.11.0 (October 30, 2023)
 
 ### Enhancements

src/hdmf/common/table.py

@@ -278,11 +278,17 @@ def __gather_columns(cls, name, bases, classdict):
             msg = "'__columns__' must be of type tuple, found %s" % type(cls.__columns__)
             raise TypeError(msg)
 
-        if (len(bases) and 'DynamicTable' in globals() and issubclass(bases[-1], Container)
-                and bases[-1].__columns__ is not cls.__columns__):
-            new_columns = list(cls.__columns__)
-            new_columns[0:0] = bases[-1].__columns__  # prepend superclass columns to new_columns
-            cls.__columns__ = tuple(new_columns)
+        if len(bases) and 'DynamicTable' in globals():
+            for item in bases[::-1]: # look for __columns__ in the base classes, closest first
+                if issubclass(item, Container):
+                    try:
+                        if item.__columns__ is not cls.__columns__:
+                            new_columns = list(cls.__columns__)
+                            new_columns[0:0] = item.__columns__  # prepend superclass columns to new_columns
+                            cls.__columns__ = tuple(new_columns)
+                            break
+                    except AttributeError:   # raises error when "__columns__" is not an attr of item
+                        continue
 
     @docval({'name': 'name', 'type': str, 'doc': 'the name of this table'},  # noqa: C901
             {'name': 'description', 'type': str, 'doc': 'a description of what is in this table'},

src/hdmf/utils.py

@@ -837,6 +837,10 @@ class ExtenderMeta(ABCMeta):
 
     @classmethod
     def pre_init(cls, func):
+        """
+        A decorator that sets a '__preinit' attribute on the target function and
+        then returns the function as a classmethod.
+        """
         setattr(func, cls.__preinit, True)
         return classmethod(func)
 

tests/unit/common/test_table.py

@@ -15,7 +15,8 @@
 from hdmf.utils import StrDataset
 from hdmf.data_utils import DataChunkIterator
 
-from tests.unit.helpers.utils import get_temp_filepath
+from tests.unit.helpers.utils import (get_temp_filepath, FooExtendDynamicTable0,
+                                      FooExtendDynamicTable1, FooExtendDynamicTable2)
 
 try:
     import linkml_runtime  # noqa: F401
@@ -2676,3 +2677,19 @@ def test_list_prev_data_inc_precision_2steps(self):
         index.add_vector(list(range(65536 - 255)))
         self.assertEqual(index.data[0], 255)  # make sure the 255 is upgraded
         self.assertEqual(type(index.data[0]), np.uint32)
+
+
+class TestDynamicTableSubclassColumns(TestCase):
+    def setUp(self):
+        self.foo1 = FooExtendDynamicTable0()
+        self.foo2 = FooExtendDynamicTable1()
+        self.foo3 = FooExtendDynamicTable2()
+
+    def test_columns(self):
+        self.assertEqual(self.foo1.__columns__,
+                        ({'name': 'col1', 'description': '...'}, {'name': 'col2', 'description': '...'}))
+        self.assertEqual(self.foo2.__columns__,
+                        ({'name': 'col1', 'description': '...'}, {'name': 'col2', 'description': '...'},
+                         {'name': 'col3', 'description': '...'}, {'name': 'col4', 'description': '...'})
+)
+        self.assertEqual(self.foo2.__columns__, self.foo3.__columns__)

tests/unit/helpers/utils.py

@@ -3,7 +3,8 @@
 from copy import copy, deepcopy
 
 from hdmf.build import BuildManager, ObjectMapper, TypeMap
-from hdmf.container import Container, HERDManager, Data
+from hdmf.common.table import DynamicTable
+from hdmf.container import Container, HERDManager, Data, MultiContainerInterface
 from hdmf.spec import (
     AttributeSpec,
     DatasetSpec,
@@ -653,3 +654,50 @@ class CustomSpecNamespace(SpecNamespace):
     @classmethod
     def types_key(cls):
         return cls.__types_key
+
+class FooExtendDynamicTable0(DynamicTable):
+    """
+    Within PyNWB, PlaneSegmentation extends DynamicTable and sets __columns__. This class is a helper
+    class for testing and is directly meant to test __gather_columns, i.e., class generation, downstream.
+    """
+    __columns__ = (
+        {'name': 'col1', 'description': '...'},
+        {'name': 'col2', 'description': '...'},
+    )
+
+    def __init__(self, **kwargs):
+        kwargs['name'] = 'foo0'
+        kwargs['description'] = '...'
+        super().__init__(**kwargs)
+
+
+class FooExtendDynamicTable1(FooExtendDynamicTable0):
+    """
+    In extensions, users can create new classes that inherit from classes that inherit from DynamicTable.
+    This is a helper class for testing and is directly meant to test __gather_columns, i.e.,
+    class generation, downstream.
+    """
+    __columns__ = (
+        {'name': 'col3', 'description': '...'},
+        {'name': 'col4', 'description': '...'},
+    )
+
+    def __init__(self, **kwargs):
+        kwargs['name'] = 'foo1'
+        kwargs['description'] = '...'
+        super().__init__(**kwargs)
+
+
+class FooExtendDynamicTable2(FooExtendDynamicTable1, MultiContainerInterface):
+    __clsconf__ = {
+        'add': '...',
+        'get': '...',
+        'create': '...',
+        'type': Container,
+        'attr': '...'
+    }
+
+    def __init__(self, **kwargs):
+        kwargs['name'] = 'foo2'
+        kwargs['description'] = '...'
+        super().__init__(**kwargs)