Update breaks (500 error) when bundle was invalid

[Reinaard]

When a resource/bundle is invalid, it gives a 500 internal server error instead of nicer error handling

To Reproduce

1. POST invalid Endpoint to FHIR store like (everything is accidentally within "meta"):

{
    "resourceType": "Endpoint",
    "meta": {
        "versionId": "1",
        "lastUpdated": "2025-11-27T09:31:25.541+00:00",
        "status": "entered-in-error",
        "connectionType": {
            "system": "http://example.org/connection-type",
            "code": "hl7-fhir-messaging",
            "display": "HL7 FHIR Messaging"
        },
        "name": "Test BV",
        "payloadType": [
            {
                "coding": [
                    {
                        "system": "http://example.org/payload-type",
                        "code": "application/fhir+json",
                        "display": "FHIR XML"
                    }
                ]
            }
        ],
        "payloadMimeType": [
            "application/fhir+xml"
        ],
        "address": "http://lmr-noord:9500/fhir",
        "header": [
            "Authorization: Bearer token"
        ]
    },
    "search": {
        "mode": "match"
    }
}

2. GET the new Endpoint and notice the small body:

{
      "fullUrl": "http://localhost:9504/fhir/Endpoint/7",
      "resource": {
        "resourceType": "Endpoint",
        "id": "7",
        "meta": {
          "versionId": "1",
          "lastUpdated": "2025-12-09T15:20:35.421+00:00"
        }
      },
      "search": {
        "mode": "match"
      }
    },

3. Go to mcsd-update-client and update resource
4. We get an 500 internal server error:

INFO:     185.93.2.245:51378 - "POST /update_resources HTTP/1.1" 500 Internal Server Error
ERROR:    Exception in ASGI application
Traceback (most recent call last):
  File "/usr/local/lib/python3.11/site-packages/uvicorn/protocols/http/h11_impl.py", line 403, in run_asgi
    result = await app(  # type: ignore[func-returns-value]
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 60, in __call__
    return await self.app(scope, receive, send)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/fastapi/applications.py", line 1134, in __call__
    await super().__call__(scope, receive, send)
  File "/usr/local/lib/python3.11/site-packages/starlette/applications.py", line 113, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/usr/local/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__
    raise exc
  File "/usr/local/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__
    await self.app(scope, receive, _send)
  File "/usr/local/lib/python3.11/site-packages/opentelemetry/instrumentation/asgi/__init__.py", line 743, in __call__
    await self.app(scope, otel_receive, otel_send)
  File "/usr/local/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 63, in __call__
    await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
  File "/usr/local/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
    raise exc
  File "/usr/local/lib/python3.11/site-packages/starlette/_exception_handler.py", line 42, in wrapped_app
    await app(scope, receive, sender)
  File "/usr/local/lib/python3.11/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "/usr/local/lib/python3.11/site-packages/starlette/routing.py", line 716, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/usr/local/lib/python3.11/site-packages/starlette/routing.py", line 736, in app
    await route.handle(scope, receive, send)
  File "/usr/local/lib/python3.11/site-packages/starlette/routing.py", line 290, in handle
    await self.app(scope, receive, send)
  File "/usr/local/lib/python3.11/site-packages/fastapi/routing.py", line 125, in app
    await wrap_app_handling_exceptions(app, request)(scope, receive, send)
  File "/usr/local/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
    raise exc
  File "/usr/local/lib/python3.11/site-packages/starlette/_exception_handler.py", line 42, in wrapped_app
    await app(scope, receive, sender)
  File "/usr/local/lib/python3.11/site-packages/fastapi/routing.py", line 111, in app
    response = await f(request)
               ^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/fastapi/routing.py", line 391, in app
    raw_response = await run_endpoint_function(
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/fastapi/routing.py", line 292, in run_endpoint_function
    return await run_in_threadpool(dependant.call, **values)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/starlette/concurrency.py", line 38, in run_in_threadpool
    return await anyio.to_thread.run_sync(func)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync
    return await get_async_backend().run_sync_in_worker_thread(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2485, in run_sync_in_worker_thread
    return await future
           ^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 976, in run
    result = context.run(func, *args)
             ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/src/app/routers/update_router.py", line 35, in update_all_directories
    return [service.update(directory, since, ura_whitelist) for directory in directories]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/src/app/routers/update_router.py", line 35, in <listcomp>
    return [service.update(directory, since, ura_whitelist) for directory in directories]
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/src/app/services/update/update_client_service.py", line 166, in update
    self.update_resource(directory, res.value, cache_service, since, ura_whitelist)
  File "/src/app/services/update/update_client_service.py", line 209, in update_resource
    next_params, history = directory_fhir_api.get_history_batch(
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/src/app/services/api/fhir_api.py", line 199, in get_history_batch
    page_bundle = self.__fhir_service.create_bundle(response.json())
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/src/app/services/fhir/fhir_service.py", line 46, in create_bundle
    return create_bundle(data, self.fill_required_fields)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/src/app/services/fhir/bundle/parser.py", line 31, in create_bundle
    return Bundle.model_validate(data)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/pydantic/main.py", line 716, in model_validate
    return cls.__pydantic_validator__.validate_python(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pydantic_core._pydantic_core.ValidationError: 2 validation errors for Bundle
entry.0.resource.connectionType
  Field required [type=missing, input_value={'id': '7', 'meta': {'ver...09T15:20:35.421+00:00'}}, input_type=dict]
    For further information visit https://errors.pydantic.dev/2.12/v/missing
entry.0.resource.payloadType
  Field required [type=missing, input_value={'id': '7', 'meta': {'ver...09T15:20:35.421+00:00'}}, input_type=dict]
    For further information visit https://errors.pydantic.dev/2.12/v/missing

5. Not delete the invalid Endpoint using the id in the FHIR store
6. Try update resource again from mcsd_update_client
7. Still 500 internal server error

Expected behavior:

• Nicer error handling, application should not break!
• After deleting the invalid Endpoint, the error should disappear