Update serializer

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 2.0.9
+
+* Update serializer with removing empty dicts/lists and transforming empty dicts into nulls in lists
+
 ## 2.0.8
 
 * Add experimental pluggable client-level dump function

fhirpy/__init__.py

@@ -1,7 +1,7 @@
 from .lib import AsyncFHIRClient, SyncFHIRClient
 
 __title__ = "fhir-py"
-__version__ = "2.0.8"
+__version__ = "2.0.9"
 __author__ = "beda.software"
 __license__ = "None"
 __copyright__ = "Copyright 2024 beda.software"

fhirpy/base/lib_async.py

@@ -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_dict_null_values=fields is None)
+        data = serialize(self.dump(resource), remove_nulls=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_dict_null_values=False),
+            data=serialize(self.dump(kwargs), remove_nulls=False),
         )
 
         if custom_resource_class:
@@ -473,7 +473,7 @@ async def patch(self, _resource: Any = None, **kwargs) -> TResource:
         )
         data = serialize(
             self.client.dump(_resource if _resource is not None else kwargs),
-            drop_dict_null_values=False,
+            remove_nulls=False,
         )
         response_data = await self.client._do_request(
             "PATCH", self.resource_type, data, self.params

fhirpy/base/lib_sync.py

@@ -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_dict_null_values=fields is None)
+        data = serialize(self.dump(resource), remove_nulls=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_dict_null_values=False),
+            data=serialize(self.dump(kwargs), remove_nulls=False),
         )
 
         if custom_resource_class:
@@ -473,7 +473,7 @@ def patch(self, _resource: Any = None, **kwargs) -> TResource:
 
         data = serialize(
             self.client.dump(_resource if _resource is not None else kwargs),
-            drop_dict_null_values=False,
+            remove_nulls=False,
         )
         response_data = self.client._do_request("patch", self.resource_type, data, self.params)
         return self._dict_to_resource(response_data)

fhirpy/base/resource.py

@@ -251,9 +251,12 @@ def is_local(self):
         pass
 
 
-def serialize(resource: Any, drop_dict_null_values=True) -> dict:
-    # TODO: make serialization pluggable
-    # TODO: add empty dict/array cleanup
+def serialize(resource: Any, remove_nulls=True) -> dict:
+    """
+    * empty dicts/lists are always removed
+    * nulls are removed only for dicts if `remove_nulls` is set
+    * in lists empty dicts are transformed into nulls because nulls are used for alignment
+    """
 
     def convert_fn(item):
         if isinstance(item, BaseResource):
@@ -264,17 +267,40 @@ def convert_fn(item):
 
         if _is_serializable_dict_like(item):
             # Handle dict-serializable structures like pydantic Model
-            if drop_dict_null_values:
-                return _remove_dict_null_values(dict(item)), False
-            return dict(item), False
+            item = _remove_dict_empty_values(dict(item))
+
+            if remove_nulls:
+                return _remove_nulls(item), False
+            return item, False
+
+        if isinstance(item, list):
+            return _transform_list_empty_values_to_null(item), False
 
         return item, False
 
     return convert_values(dict(resource), convert_fn)
 
 
-def _remove_dict_null_values(d: dict):
-    return {key: value for key, value in d.items() if value is not None}
+def _remove_dict_empty_values(d: dict):
+    return {key: value for key, value in d.items() if not _is_empty(value)}
+
+
+def _transform_list_empty_values_to_null(d: list):
+    return [None if _is_empty(value) else value for value in d]
+
+
+def _remove_nulls(d: dict):
+    return {key: value for key, value in d.items() if not _is_null(value)}
+
+
+def _is_empty(d: Any):
+    if isinstance(d, (dict, list)):
+        return not d
+    return False
+
+
+def _is_null(d: Any):
+    return d is None
 
 
 def _is_serializable_dict_like(item):

run_test.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 
-export TEST_COMMAND="pipenv run pytest ${@:-tests/}"
+export TEST_COMMAND="pipenv run pytest ${@:-tests/} -vv"
 docker compose -f docker-compose.tests.yaml up --quiet-pull --exit-code-from app app

tests/test_lib_base.py

@@ -32,6 +32,25 @@ def test_serialize_with_dict_null_values(self, client: Union[SyncFHIRClient, Asy
             "id": "patient",
         }
 
+    def test_serialize_with_empty_array(self, client: Union[SyncFHIRClient, AsyncFHIRClient]):
+        patient = client.resource("Patient", id="patient", generalPractitioner=[])
+        assert patient.serialize() == {
+            "resourceType": "Patient",
+            "id": "patient",
+        }
+
+    def test_serialize_with_empty_dict(self, client: Union[SyncFHIRClient, AsyncFHIRClient]):
+        patient = client.resource(
+            "Patient",
+            id="patient",
+            name=[{"given": ["Name"], "_given": [{}], "text": "Name", "_text": {}}],
+        )
+        assert patient.serialize() == {
+            "resourceType": "Patient",
+            "id": "patient",
+            "name": [{"given": ["Name"], "_given": [None], "text": "Name"}],
+        }
+
     def test_serialize(self, client: Union[SyncFHIRClient, AsyncFHIRClient]):
         practitioner1 = client.resource("Practitioner", id="pr1")
         practitioner2 = client.resource("Practitioner", id="pr2")