Deepcopy on throws on certain Dataset

[erikogabrielsson]

Describe the bug
Doing a deepcopy() on a Dataset after an update() with another Dataset containing a Sequence throws AttributeError: 'DataElement' object has no attribute 'VR'.
I'm using 2.4.1 (not sure why version info says otherwise).

Expected behavior
Using 2.3.1 I get a copy of the Dataset including the elements from the update-with Dataset.
With the steps to reproduce:

(0048, 0105)  Optical Path Sequence  1 item(s) ---- 
   (0048, 0106) Optical Path Identifier             SH: '0'
   ---------

Steps To Reproduce

from copy import deepcopy
from pydicom import Dataset, Sequence
optical_path_dataset = Dataset()
optical_path_item = Dataset()
optical_path_item.OpticalPathIdentifier = "0"
optical_path_dataset.OpticalPathSequence = Sequence([optical_path_item])
# Does not throw
deepcopy(optical_path_dataset)

# Also does not throw
dataset = Dataset()
dataset.update(deepcopy(optical_path_dataset))
deepcopy(dataset)

# Throws
dataset = Dataset()
dataset.update(optical_path_dataset)
deepcopy(dataset)

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[3], line 18
     16 dataset = Dataset()
     17 dataset.update(optical_path_dataset)
---> 18 deepcopy(dataset)

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\copy.py:153](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/copy.py:153), in deepcopy(x, memo, _nil)
    151 copier = getattr(x, "__deepcopy__", None)
    152 if copier is not None:
--> 153     y = copier(memo)
    154 else:
    155     reductor = dispatch_table.get(cls)

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\site-packages\pydicom\dataset.py:477](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/site-packages/pydicom/dataset.py:477), in Dataset.__deepcopy__(self, memo)
    475     memo[id(self)] = copied   # add the new class to the memo
    476 # Insert a deepcopy of all instance attributes
--> 477 copied.__dict__.update(copy.deepcopy(self.__dict__, memo))
    478 # Manually update the weakref to be correct
    479 for elem in copied:  # DICOM elements

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\copy.py:146](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/copy.py:146), in deepcopy(x, memo, _nil)
    144 copier = _deepcopy_dispatch.get(cls)
    145 if copier is not None:
--> 146     y = copier(x, memo)
    147 else:
    148     if issubclass(cls, type):

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\copy.py:231](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/copy.py:231), in _deepcopy_dict(x, memo, deepcopy)
    229 memo[id(x)] = y
    230 for key, value in x.items():
--> 231     y[deepcopy(key, memo)] = deepcopy(value, memo)
    232 return y

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\copy.py:146](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/copy.py:146), in deepcopy(x, memo, _nil)
    144 copier = _deepcopy_dispatch.get(cls)
    145 if copier is not None:
--> 146     y = copier(x, memo)
    147 else:
    148     if issubclass(cls, type):

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\copy.py:231](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/copy.py:231), in _deepcopy_dict(x, memo, deepcopy)
    229 memo[id(x)] = y
    230 for key, value in x.items():
--> 231     y[deepcopy(key, memo)] = deepcopy(value, memo)
    232 return y

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\copy.py:172](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/copy.py:172), in deepcopy(x, memo, _nil)
    170                 y = x
    171             else:
--> 172                 y = _reconstruct(x, memo, *rv)
    174 # If is its own copy, don't memoize.
    175 if y is not x:

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\copy.py:271](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/copy.py:271), in _reconstruct(x, memo, func, args, state, listiter, dictiter, deepcopy)
    269 if state is not None:
    270     if deep:
--> 271         state = deepcopy(state, memo)
    272     if hasattr(y, '__setstate__'):
    273         y.__setstate__(state)

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\copy.py:146](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/copy.py:146), in deepcopy(x, memo, _nil)
    144 copier = _deepcopy_dispatch.get(cls)
    145 if copier is not None:
--> 146     y = copier(x, memo)
    147 else:
    148     if issubclass(cls, type):

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\copy.py:231](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/copy.py:231), in _deepcopy_dict(x, memo, deepcopy)
    229 memo[id(x)] = y
    230 for key, value in x.items():
--> 231     y[deepcopy(key, memo)] = deepcopy(value, memo)
    232 return y

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\copy.py:153](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/copy.py:153), in deepcopy(x, memo, _nil)
    151 copier = getattr(x, "__deepcopy__", None)
    152 if copier is not None:
--> 153     y = copier(memo)
    154 else:
    155     reductor = dispatch_table.get(cls)

File [c:\Users\er-gac\.pyenv\pyenv-win\versions\3.11.2\Lib\site-packages\pydicom\dataset.py:480](file:///C:/Users/er-gac/.pyenv/pyenv-win/versions/3.11.2/Lib/site-packages/pydicom/dataset.py:480), in Dataset.__deepcopy__(self, memo)
    478 # Manually update the weakref to be correct
    479 for elem in copied:  # DICOM elements
--> 480     if elem.VR == VR_.SQ:
    481         elem.value.parent_dataset = copied  # setter does weakref
    482 return copied

AttributeError: 'DataElement' object has no attribute 'VR'

Your environment

module	version
platform	Windows-10-10.0.19045-SP0
Python	3.11.2 (tags/v3.11.2:878ead1, Feb 7 2023, 16:38:35) [MSC v.1934 64 bit (AMD64)]
pydicom	2.4.0
gdcm	module not found
jpeg_ls	module not found
numpy	1.24.0
PIL	9.4.0
pylibjpeg	module not found
openjpeg	module not found
libjpeg	module not found

[darcymason]

Thanks for the issue and detailed explanation/report.

I'm using 2.4.1 (not sure why version info says otherwise).

I see that too now in a local venv ... I'll look into that as well.

[darcymason]

I've confirmed the issue, will try to work on it when I get a chance.

[erikogabrielsson]

Thanks for the fix @scaramallion!