[NRL-1051] Allow non-conformant docref in a Bundle resource

Author: mattdean3-nhs

api/producer/processTransaction/process_transaction_bundle.py

@@ -1,3 +1,4 @@
+from typing import Any, Dict
 from uuid import uuid4
 
 from nrlf.core.codes import SpineErrorConcept
@@ -25,6 +26,24 @@
     OperationOutcomeIssue,
 )
 
+# TODO - Figure out sensible defaults
+# NOTE: while type, category and custodian are not required in MHDS profile, they will be required by NRLF
+DEFAULT_MHDS_AUTHOR = {
+    "identifier": {
+        "value": "X26",
+        "system": "https://fhir.nhs.uk/Id/ods-organization-code",
+    }
+}
+DEFAULT_MHDS_PRACTICE_SETTING_CODING = {
+    "system": "http://snomed.info/sct",
+    "code": "394802000",
+    "display": "General medical practice",
+}
+DEFAULT_MHDS_PROPERTIES: dict[str, Any] = {
+    "author": [DEFAULT_MHDS_AUTHOR],
+    "context": {"practiceSetting": {"coding": [DEFAULT_MHDS_PRACTICE_SETTING_CODING]}},
+}
+
 
 def _set_create_time_fields(
     create_time: str, document_reference: DocumentReference, nrl_permissions: list[str]
@@ -268,13 +287,27 @@ def create_document_reference(
 
 
 def _convert_document_reference(
-    document_reference: DocumentReference, requested_profile: str
+    raw_resource: Dict[str, Any], requested_profile: str
 ) -> DocumentReference:
     """
     Convert the DocumentReference to the requested profile
     """
-    # TODO - Implement conversion logic from MHDS profile to NRLF FHIR profile
-    return document_reference
+    if requested_profile.endswith(
+        "profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.UnContained.Comprehensive.ProvideBundle"
+    ):
+        docref_properties: dict[str, Any] = {}
+        docref_properties.update(DEFAULT_MHDS_PROPERTIES)
+        docref_properties.update(raw_resource)
+        docref_properties["status"] = "current"
+        return DocumentReference(**docref_properties)
+
+    raise OperationOutcomeError(
+        severity="error",
+        code="exception",
+        diagnostics="Unable to parse DocumentReference. Only IHE.MHD.UnContained.Comprehensive.ProvideBundle profile is supported",
+        expression=["meta.profile[0]"],
+        details=SpineErrorConcept.from_code("BAD_REQUEST"),
+    )
 
 
 @request_handler(body=Bundle)
@@ -322,12 +355,11 @@ def handler(
             resource=Bundle(resourceType="Bundle", type="transaction-response")
         )
 
-    document_references: list[DocumentReference] = []
-
+    entries: list[BundleEntry] = []
     issues: list[BaseModel] = []
 
     for entry in body.entry:
-        if not entry.resource or entry.resource.resourceType != "DocumentReference":
+        if not entry.resource or entry.resource["resourceType"] != "DocumentReference":
             issues.append(
                 OperationOutcomeIssue(
                     severity="error",
@@ -349,18 +381,29 @@ def handler(
                 )
             )
 
-        document_references.append(DocumentReference.model_validate(entry.resource))
+        entries.append(entry)
 
     if issues:
         return Response.from_issues(issues, statusCode="400")
 
     responses: list[Response] = []
-    for document_reference in document_references:
+    for entry in entries:
         try:
+            if not entry.resource:
+                raise OperationOutcomeError(
+                    severity="error",
+                    code="exception",
+                    diagnostics="No resource provided",
+                    expression=["entry.resource"],
+                    details=SpineErrorConcept.from_code("BAD_REQUEST"),
+                )
+
             if requested_profile:
                 document_reference = _convert_document_reference(
-                    document_reference, requested_profile
+                    entry.resource, requested_profile
                 )
+            else:
+                document_reference = DocumentReference(**(entry.resource))
 
             create_response = create_document_reference(
                 metadata, repository, document_reference

api/producer/processTransaction/tests/test_process_transaction_bundle.py

@@ -4,13 +4,17 @@
 from freezegun import freeze_time
 from moto import mock_aws
 
-from api.producer.processTransaction.process_transaction_bundle import handler
+from api.producer.processTransaction.process_transaction_bundle import (
+    DEFAULT_MHDS_PROPERTIES,
+    handler,
+)
 from nrlf.core.dynamodb.repository import DocumentPointerRepository
 from nrlf.producer.fhir.r4.model import (
     Bundle,
     BundleEntry,
     BundleEntryRequest,
-    DocumentReference,
+    Meta,
+    ProfileItem,
 )
 from nrlf.tests.data import load_document_reference
 from nrlf.tests.dynamodb import mock_repository
@@ -26,10 +30,12 @@
 @mock_repository
 @freeze_time("2024-03-21T12:34:56.789")
 @freeze_uuid("00000000-0000-0000-0000-000000000001")
-def test_create_single_document_reference_with_transaction_happy_path(
+def test_create_single_nrl_document_reference_with_transaction_happy_path(
     repository: DocumentPointerRepository,
 ):
-    doc_ref: DocumentReference = load_document_reference("Y05868-736253002-Valid")
+    doc_ref = load_document_reference("Y05868-736253002-Valid").model_dump(
+        exclude_none=True
+    )
 
     request_bundle = Bundle(
         entry=[
@@ -79,7 +85,86 @@ def test_create_single_document_reference_with_transaction_happy_path(
     assert created_doc_pointer.created_on == "2024-03-21T12:34:56.789Z"
     assert created_doc_pointer.updated_on is None
     assert json.loads(created_doc_pointer.document) == {
-        **(doc_ref.model_dump(exclude_none=True)),
+        **doc_ref,
+        "meta": {
+            "lastUpdated": "2024-03-21T12:34:56.789Z",
+        },
+        "date": "2024-03-21T12:34:56.789Z",
+        "id": "Y05868-00000000-0000-0000-0000-000000000001",
+    }
+
+
+@mock_aws
+@mock_repository
+@freeze_time("2024-03-21T12:34:56.789")
+@freeze_uuid("00000000-0000-0000-0000-000000000001")
+def test_create_single_mhds_document_reference_with_transaction_happy_path(
+    repository: DocumentPointerRepository,
+):
+    raw_doc_ref = load_document_reference("Y05868-736253002-Valid").model_dump(
+        exclude_none=True
+    )
+
+    raw_doc_ref.pop("author")
+    raw_doc_ref.pop("context")
+
+    request_bundle = Bundle(
+        meta=Meta(
+            profile=[
+                ProfileItem(
+                    "http://hl7.org/fhir/profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.UnContained.Comprehensive.ProvideBundle"
+                )
+            ]
+        ),
+        entry=[
+            BundleEntry(
+                resource=raw_doc_ref, request=BundleEntryRequest(url="/", method="POST")
+            )
+        ],
+        resourceType="Bundle",
+        type="transaction",
+    )
+
+    event = create_test_api_gateway_event(
+        headers=create_headers(),
+        body=request_bundle.model_dump_json(),
+    )
+
+    result = handler(event, create_mock_context())
+    body = result.pop("body")
+
+    assert result == {
+        "statusCode": "200",
+        "headers": {
+            **default_response_headers(),
+        },
+        "isBase64Encoded": False,
+    }
+
+    parsed_body = json.loads(body)
+    assert parsed_body == {
+        "resourceType": "Bundle",
+        "type": "transaction-response",
+        "entry": [
+            {
+                "response": {
+                    "status": "201",
+                    "location": "/producer/FHIR/R4/DocumentReference/Y05868-00000000-0000-0000-0000-000000000001",
+                },
+            },
+        ],
+    }
+
+    created_doc_pointer = repository.get_by_id(
+        "Y05868-00000000-0000-0000-0000-000000000001"
+    )
+
+    assert created_doc_pointer is not None
+    assert created_doc_pointer.created_on == "2024-03-21T12:34:56.789Z"
+    assert created_doc_pointer.updated_on is None
+    assert json.loads(created_doc_pointer.document) == {
+        **raw_doc_ref,
+        **DEFAULT_MHDS_PROPERTIES,
         "meta": {
             "lastUpdated": "2024-03-21T12:34:56.789Z",
         },

api/producer/swagger.yaml

@@ -1505,7 +1505,7 @@ components:
           pattern: \S*
           description: "The Absolute URL for the resource.  The fullUrl SHALL NOT disagree with the id in the resource – i.e. if the fullUrl is not a urn:uuid, the URL shall be version–independent URL consistent with the Resource.id. The fullUrl is a version independent reference to the resource. The fullUrl element SHALL have a value except that: \n* fullUrl can be empty on a POST (although it does not need to when specifying a temporary id for reference in the bundle)\n* Results from operations might involve resources that are not identified."
         resource:
-          $ref: "#/components/schemas/DocumentReference"
+          type: object
           description: The Resource for the entry. The purpose/meaning of the resource is determined by the Bundle.type.
         search:
           $ref: "#/components/schemas/BundleEntrySearch"

layer/nrlf/consumer/fhir/r4/model.py

@@ -1,6 +1,6 @@
 # generated by datamodel-codegen:
 #   filename:  swagger.yaml
-#   timestamp: 2024-11-20T09:43:58+00:00
+#   timestamp: 2024-12-02T21:57:23+00:00
 
 from __future__ import annotations
 

layer/nrlf/producer/fhir/r4/model.py

@@ -1,10 +1,10 @@
 # generated by datamodel-codegen:
 #   filename:  swagger.yaml
-#   timestamp: 2024-11-20T10:10:52+00:00
+#   timestamp: 2024-12-02T21:57:21+00:00
 
 from __future__ import annotations
 
-from typing import Annotated, List, Literal, Optional
+from typing import Annotated, Any, Dict, List, Literal, Optional
 
 from pydantic import BaseModel, ConfigDict, Field, RootModel
 
@@ -698,7 +698,7 @@ class BundleEntry(BaseModel):
         ),
     ] = None
     resource: Annotated[
-        Optional[DocumentReference],
+        Optional[Dict[str, Any]],
         Field(
             description="The Resource for the entry. The purpose/meaning of the resource is determined by the Bundle.type."
         ),

layer/nrlf/producer/fhir/r4/strict_model.py

@@ -1,10 +1,10 @@
 # generated by datamodel-codegen:
 #   filename:  swagger.yaml
-#   timestamp: 2024-11-20T10:10:54+00:00
+#   timestamp: 2024-12-02T21:57:22+00:00
 
 from __future__ import annotations
 
-from typing import Annotated, List, Literal, Optional
+from typing import Annotated, Any, Dict, List, Literal, Optional
 
 from pydantic import (
     BaseModel,
@@ -609,7 +609,7 @@ class BundleEntry(BaseModel):
         ),
     ] = None
     resource: Annotated[
-        Optional[DocumentReference],
+        Optional[Dict[str, Any]],
         Field(
             description="The Resource for the entry. The purpose/meaning of the resource is determined by the Bundle.type."
         ),