Nested Links are saved as embedded documents instead of references

[iamgoeldhruv]

Describe the bug
When using Link fields inside nested documents, Beanie saves them as embedded documents instead of storing them as references. Only the top-level Link is stored correctly as a reference.

To Reproduce

from beanie import Document, Link

class FilterItem(Document):
    name: str
    param1: object
    param2: object
    operator: str

    class Settings:
        name = "filter_items"

class Operation(Document):
    class Settings:
        name = "operations"
        is_root = True

class FilterOperation(Operation):
    filter: Link[FilterItem]

    class Settings(Operation.Settings):
        name = "filter_operation"
        is_root = False

class FilterGroupOperation(Operation):
    operator: Literal["and", "or", "anyOf"]
    operands: list[Link[Operation]]

    class Settings(Operation.Settings):
        name = "filter_group_operation"
        is_root = False

class FilterGroup(Document):
    operation: Link[Operation]

    class Settings:
        name = "filter_groups"

_ = Operation.model_rebuild()
_ = FilterOperation.model_rebuild()
_ = FilterGroupOperation.model_rebuild()

# Example creation
item = await FilterItem(name="f1", param1=1, param2=2, operator="eq").insert()
op = await FilterOperation(filter=item).insert()
group = await FilterGroupOperation(operator="and", operands=[op]).insert()
fg = await FilterGroup(operation=group).insert()

Expected behavior
It should insert various nested operations as link but its embedding entire document there

[gelvetica]

+1

[ADR-007]

I'm using this hack for now:

@lru_cache
def is_link_field(field: FieldInfo, field_name: str) -> bool:
    # detect_link is actually, a static method, so it is safe to pass any
    # value instead of "self"
    return Initializer.detect_link(None, field, field_name) is not None  # type: ignore[arg-type]


def Encoder__iter_model_items(  # noqa: N802
    self: Encoder, obj: pydantic.BaseModel
) -> Iterable[tuple[str, Any]]:
    # Override of the Encoder__iter_model_items method with minimal changes
    # to serialize nested links as Ref objects instead of Document objects.
    # The same logic is currently implemented to the first-level fields only.
    exclude, keep_nulls = self.exclude, self.keep_nulls
    get_model_field = get_model_fields(obj).get
    is_nested = not isinstance(obj, Document)
    for key, value in obj.__iter__():
        field_info = get_model_field(key)
        if field_info is not None:
            key = field_info.alias or key  # noqa: PLW2901
            if (
                is_nested
                and isinstance(value, Document)
                and is_link_field(field_info, key)
            ):
                value = value.to_ref()  # noqa: PLW2901

        if key not in exclude and (value is not None or keep_nulls):
            yield key, value


def patch_beanie_encode_nested_links() -> None:
    """Patch beanie.odm.utils.encoder.Encoder.__iter_model_items to encode nested links.

    Without this fix nested links are saved as Document objects instead of Ref objects.
    Issue link: https://github.com/BeanieODM/beanie/issues/1235
    """
    Encoder._iter_model_items = Encoder__iter_model_items  # type: ignore[method-assign] # noqa: SLF001

A proper solution may take some effort and may require a custom base class (e.g., DocumentNestedModel), as the Document-based solution relies on the Document._link_fields field, which is populated during model initialization.