Get rid of built-in pydantic dump for CRUD and for patch. Rename dump…

… to dump_resource

CHANGELOG.md

@@ -1,3 +1,15 @@
+## 2.0.11
+
+* Rename dump to dump_resource
+* Get rid of built-in dumping for dict-like structure
+* Get rid of built-in dumping for patch
+* Some breaking changes here, but the functional was introduced recently 
+that's why the version is not increased according to semver
+  * Migration guide for pydantic-users:
+  * Pass `dump_resource=lambda d: d.model_dump()`
+  * Manually dump your models for patch
+
+
 ## 2.0.10
 
 * Update serializer with recursive cleaning and removing null values

fhirpy/base/client.py

@@ -1,5 +1,6 @@
 import warnings
 from abc import ABC, abstractmethod
+from collections.abc import Callable
 from typing import Any, TypeVar, Union
 
 from yarl import URL
@@ -14,6 +15,7 @@ class AbstractClient(ABC):
     url: str
     authorization: Union[str, None]
     extra_headers: Union[dict, None]
+    dump_resource: Callable[[Any], Any]
 
     # Deprecated
     @property  # pragma: no cover
@@ -30,10 +32,17 @@ def __init__(
         url: str,
         authorization: Union[str, None] = None,
         extra_headers: Union[dict, None] = None,
+        *,
+        dump_resource: Callable[[Any], dict] = lambda x: dict(x),
     ):
+        """
+        dump kwarg is a function that is called for all CRUD operations.
+        It's needed for custom typing model like pydantic
+        """
         self.url = url
         self.authorization = authorization
         self.extra_headers = extra_headers
+        self.dump_resource = dump_resource
 
     def __str__(self) -> str:
         return f"<{self.__class__.__name__} {self.url}>"

fhirpy/base/lib_async.py

@@ -29,12 +29,12 @@ def __init__(
         authorization: Union[str, None] = None,
         extra_headers: Union[dict, None] = None,
         aiohttp_config: Union[dict, None] = None,
-        dump: Callable[[Any], Any] = lambda x: x,
+        *,
+        dump_resource: Callable[[Any], dict] = lambda x: dict(x),
     ):
         self.aiohttp_config = aiohttp_config or {}
-        self.dump = dump
 
-        super().__init__(url, authorization, extra_headers)
+        super().__init__(url, authorization, extra_headers, dump_resource=dump_resource)
 
     async def execute(
         self,
@@ -111,7 +111,7 @@ async def save(
         # _as_dict is a private api used internally
         _as_dict: bool = False,
     ) -> Union[TResource, Any]:
-        data = serialize(self.dump(resource), drop_nulls_from_dicts=fields is None)
+        data = serialize(self.dump_resource(resource), drop_nulls_from_dicts=fields is None)
         if fields:
             if not resource.id:
                 raise TypeError("Resource `id` is required for update operation")
@@ -171,7 +171,7 @@ async def patch(
         response_data = await self._do_request(
             "patch",
             f"{resource_type}/{resource_id}",
-            data=serialize(self.dump(kwargs), drop_nulls_from_dicts=False),
+            data=serialize(kwargs, drop_nulls_from_dicts=False),
         )
 
         if custom_resource_class:
@@ -444,7 +444,7 @@ async def get_or_create(self, resource: TResource) -> tuple[TResource, bool]:
         response_data, status_code = await self.client._do_request(
             "post",
             self.resource_type,
-            serialize(self.client.dump(resource)),
+            serialize(self.client.dump_resource(resource)),
             self.params,
             returning_status=True,
         )
@@ -457,7 +457,7 @@ async def update(self, resource: TResource) -> tuple[TResource, bool]:
         response_data, status_code = await self.client._do_request(
             "put",
             self.resource_type,
-            serialize(self.client.dump(resource)),
+            serialize(self.client.dump_resource(resource)),
             self.params,
             returning_status=True,
         )
@@ -472,7 +472,7 @@ async def patch(self, _resource: Any = None, **kwargs) -> TResource:
             stacklevel=2,
         )
         data = serialize(
-            self.client.dump(_resource if _resource is not None else kwargs),
+            self.client.dump_resource(_resource) if _resource is not None else kwargs,
             drop_nulls_from_dicts=False,
         )
         response_data = await self.client._do_request(

fhirpy/base/lib_sync.py

@@ -29,12 +29,12 @@ def __init__(
         authorization: Union[str, None] = None,
         extra_headers: Union[dict, None] = None,
         requests_config: Union[dict, None] = None,
-        dump: Callable[[Any], Any] = lambda x: x,
+        *,
+        dump_resource: Callable[[Any], dict] = lambda x: dict(x),
     ):
         self.requests_config = requests_config or {}
-        self.dump = dump
 
-        super().__init__(url, authorization, extra_headers)
+        super().__init__(url, authorization, extra_headers, dump_resource=dump_resource)
 
     def execute(
         self,
@@ -111,7 +111,7 @@ def save(
         # _as_dict is a private api used internally
         _as_dict: bool = False,
     ) -> Union[TResource, Any]:
-        data = serialize(self.dump(resource), drop_nulls_from_dicts=fields is None)
+        data = serialize(self.dump_resource(resource), drop_nulls_from_dicts=fields is None)
         if fields:
             if not resource.id:
                 raise TypeError("Resource `id` is required for update operation")
@@ -167,7 +167,7 @@ def patch(
         response_data = self._do_request(
             "patch",
             f"{resource_type}/{resource_id}",
-            data=serialize(self.dump(kwargs), drop_nulls_from_dicts=False),
+            data=serialize(kwargs, drop_nulls_from_dicts=False),
         )
 
         if custom_resource_class:
@@ -442,7 +442,7 @@ def get_or_create(self, resource: TResource) -> tuple[TResource, int]:
         response_data, status_code = self.client._do_request(
             "post",
             self.resource_type,
-            serialize(self.client.dump(resource)),
+            serialize(self.client.dump_resource(resource)),
             self.params,
             returning_status=True,
         )
@@ -455,7 +455,7 @@ def update(self, resource: TResource) -> tuple[TResource, int]:
         response_data, status_code = self.client._do_request(
             "put",
             self.resource_type,
-            serialize(self.client.dump(resource)),
+            serialize(self.client.dump_resource(resource)),
             self.params,
             returning_status=True,
         )
@@ -472,7 +472,7 @@ def patch(self, _resource: Any = None, **kwargs) -> TResource:
             )
 
         data = serialize(
-            self.client.dump(_resource if _resource is not None else kwargs),
+            self.client.dump_resource(_resource) if _resource is not None else kwargs,
             drop_nulls_from_dicts=False,
         )
         response_data = self.client._do_request("patch", self.resource_type, data, self.params)

fhirpy/base/resource.py

@@ -1,5 +1,4 @@
 from abc import ABC, abstractmethod
-from collections.abc import Iterable, Sequence
 from typing import Any, Generic, Union
 
 from fhirpy.base.client import TClient
@@ -265,10 +264,6 @@ def convert_fn(item):
         if isinstance(item, BaseReference):
             return serialize(item), True
 
-        if _is_serializable_dict_like(item):
-            # Handle dict-serializable structures like pydantic Model
-            return dict(item), False
-
         return item, False
 
     converted_values = convert_values(dict(resource), convert_fn)
@@ -277,25 +272,3 @@ def convert_fn(item):
         converted_values = remove_nulls_from_dicts(converted_values)
 
     return clean_empty_values(converted_values)
-
-
-def _is_serializable_dict_like(item):
-    """
-    >>> _is_serializable_dict_like({})
-    True
-    >>> _is_serializable_dict_like([])
-    False
-    >>> _is_serializable_dict_like(())
-    False
-    >>> _is_serializable_dict_like(set())
-    False
-    >>> _is_serializable_dict_like("string")
-    False
-    >>> _is_serializable_dict_like(42)
-    False
-    >>> _is_serializable_dict_like(True)
-    False
-    >>> _is_serializable_dict_like(None)
-    False
-    """
-    return isinstance(item, Iterable) and not isinstance(item, (Sequence, set))

fhirpy/base/resource_protocol.py

@@ -1,14 +1,10 @@
-from collections.abc import Iterator
 from typing import Any, Protocol, TypeVar, Union, get_args, get_type_hints
 
 
 class ResourceProtocol(Protocol):
     resourceType: Any  # noqa: N815
     id: Union[str, None]
 
-    def __iter__(self) -> Iterator:
-        ...
-
 
 TResource = TypeVar("TResource", bound=ResourceProtocol)
 TReference = TypeVar("TReference")

tests/test_lib_async.py

@@ -13,6 +13,7 @@
 
 from .config import FHIR_SERVER_AUTHORIZATION, FHIR_SERVER_URL
 from .types import HumanName, Identifier, Patient, Reference
+from .utils import dump_resource
 
 
 class TestLibAsyncCase:
@@ -33,7 +34,9 @@ async def _clear_db(self):
 
     @classmethod
     def setup_class(cls):
-        cls.client = AsyncFHIRClient(cls.URL, authorization=FHIR_SERVER_AUTHORIZATION)
+        cls.client = AsyncFHIRClient(
+            cls.URL, authorization=FHIR_SERVER_AUTHORIZATION, dump_resource=dump_resource
+        )
 
     async def create_resource(self, resource_type, **kwargs):
         return await self.client.resource(
@@ -204,7 +207,7 @@ async def test_client_patch_specifying_reference(self):
 
         patched_patient = await self.client.patch(
             f"{patient.resourceType}/{patient.id}",
-            identifier=new_identifier,
+            identifier=[x.model_dump(exclude_none=True) for x in new_identifier],
             managingOrganization=None,
         )
 
@@ -220,7 +223,9 @@ async def test_client_patch_specifying_resource_type_str_and_id(self):
         new_identifier = [*patient.identifier, Identifier(system="url", value="value")]
 
         patched_patient = await self.client.patch(
-            patient.resourceType, patient.id, identifier=new_identifier
+            patient.resourceType,
+            patient.id,
+            identifier=[x.model_dump(exclude_none=True) for x in new_identifier],
         )
 
         assert isinstance(patched_patient, dict)
@@ -231,7 +236,11 @@ async def test_client_patch_specifying_resource_type_type_and_id(self):
         patient = await self.create_patient_model()
         new_identifier = [*patient.identifier, Identifier(system="url", value="value")]
 
-        patched_patient = await self.client.patch(Patient, patient.id, identifier=new_identifier)
+        patched_patient = await self.client.patch(
+            Patient,
+            patient.id,
+            identifier=[x.model_dump(exclude_none=True) for x in new_identifier],
+        )
 
         assert isinstance(patched_patient, Patient)
         assert len(patched_patient.identifier) == 2  # noqa: PLR2004
@@ -241,7 +250,9 @@ async def test_client_patch_specifying_resource(self):
         patient = await self.create_patient_model()
         new_identifier = [*patient.identifier, Identifier(system="url", value="value")]
 
-        patched_patient = await self.client.patch(patient, identifier=new_identifier)
+        patched_patient = await self.client.patch(
+            patient, identifier=[x.model_dump(exclude_none=True) for x in new_identifier]
+        )
 
         assert isinstance(patched_patient, Patient)
         assert len(patched_patient.identifier) == 2  # noqa: PLR2004
@@ -1228,8 +1239,11 @@ async def test_typed_patch(self):
             .search(name=name)
             .patch(
                 identifier=[
-                    Identifier(system="url", value="value"),
-                    Identifier(**self.identifier[0]),
+                    x.model_dump(exclude_none=True)
+                    for x in [
+                        Identifier(system="url", value="value"),
+                        Identifier(**self.identifier[0]),
+                    ]
                 ],
             )
         )

tests/test_lib_base.py

@@ -3,14 +3,20 @@
 import pytest
 
 from fhirpy import AsyncFHIRClient, SyncFHIRClient
-from fhirpy.base.resource import serialize
 from fhirpy.base.utils import AttrDict, SearchList, parse_pagination_url, set_by_path
 from fhirpy.lib import BaseFHIRReference
 
 from .types import HumanName, Identifier, Patient
+from .utils import dump_resource
 
 
-@pytest.mark.parametrize("client", [SyncFHIRClient("mock"), AsyncFHIRClient("mock")])
+@pytest.mark.parametrize(
+    "client",
+    [
+        SyncFHIRClient("mock", dump_resource=dump_resource),
+        AsyncFHIRClient("mock", dump_resource=dump_resource),
+    ],
+)
 class TestLibBase:
     def test_to_reference_for_reference(self, client: Union[SyncFHIRClient, AsyncFHIRClient]):
         reference = client.reference("Patient", "p1")
@@ -272,24 +278,6 @@ def test_pluggable_type_model_resource_instantiation(
         assert isinstance(patient.name[0], HumanName)
         assert patient.name[0].text == "Name"
 
-    def test_pluggable_type_model_serialize_with_dict_null_values(
-        self, client: Union[SyncFHIRClient, AsyncFHIRClient]
-    ):
-        patient = client.resource(
-            Patient,
-            **{
-                "resourceType": "Patient",
-                "identifier": [{"system": "url", "value": "value"}],
-                "name": [{"text": "Name"}],
-                "managingOrganization": None,
-            },
-        )
-        assert serialize(patient) == {
-            "resourceType": "Patient",
-            "identifier": [{"system": "url", "value": "value"}],
-            "name": [{"text": "Name"}],
-        }
-
     def test_resource_resource_type_setter(self, client: Union[SyncFHIRClient, AsyncFHIRClient]):
         patient = client.resource("Patient", id="p1")
         patient.resourceType = "Patient"