EMDB().get_entry() fails for EMD-6483 due to BaseMapFile abstract class instantiation in mask parsing

[shuuul]

Hi, thanks for maintaining this package.

I ran into an issue when calling EMDB().get_entry("EMD-6483"). The API request itself succeeds, but the Python wrapper fails while parsing the returned entry metadata.

Minimal reproduction

from emdb.client import EMDB

entry = EMDB().get_entry("EMD-6483")

Observed error

Traceback (most recent call last):
  File ".../site-packages/emdb/client.py", line 40, in get_entry
    return EMDBEntry.from_api(data, client=self)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File ".../site-packages/emdb/models/entry.py", line 118, in from_api
    mask_file = MaskFile.from_api(m)
                ^^^^^^^^^^^^^^^^^^^^
  File ".../site-packages/emdb/models/files.py", line 222, in from_api
    map_file=BaseMapFile.from_api(data.get("mask_details", {})) if data.get("mask_details") else None,
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File ".../site-packages/emdb/models/files.py", line 108, in from_api
    return cls(
           ^^^^
TypeError: Can't instantiate abstract class BaseMapFile without an implementation for abstract method 'source_path'

During handling of the above exception, another exception occurred:

emdb.exceptions.EMDBAPIError: EMDB API Error: Failed to retrieve entry EMD-6483: Can't instantiate abstract class BaseMapFile without an implementation for abstract method 'source_path'

Environment

Python: 3.12
Package: emdb-api-wrapper / emdb

I observed this through a downstream dependency (cryopy.database.get_contour_level), but the minimal reproduction above fails directly with this package.

Expected behavior

EMDB().get_entry("EMD-6483") should return an EMDBEntry object successfully.

The raw EMDB API response for this entry appears to contain a valid contour level:

/map/contour_list/contour[0]/level = 0.03
/map/contour_list/contour[0]/primary = True

So the entry metadata is accessible from the API, but the wrapper fails during object construction.

Possible cause

The failure seems to happen while parsing mask metadata:

# emdb/models/files.py
map_file = (
    BaseMapFile.from_api(data.get("mask_details", {}))
    if data.get("mask_details")
    else None
)

BaseMapFile is an abstract class because it has an abstract source_path property, so calling BaseMapFile.from_api(...) eventually attempts to instantiate an abstract class.

Maybe mask_details should be parsed into a concrete map-file class, or MaskFile.map_file should use a non-abstract concrete model for mask map details.

Why this matters

This breaks downstream workflows that only need fields such as primary_map.contour_list, because get_entry() parses the full entry and fails on unrelated mask metadata before the caller can access the contour level.

Thanks!