Handle subject parameter separately

Author: ruscoder

app/aidbox/operations.py

@@ -12,15 +12,11 @@
     resolve_expression,
 )
 from ..sdc.exception import MissingParamOperationOutcome
-from ..sdc.utils import parameter_to_env, parse_parameter_value, validate_context
+from ..sdc.utils import get_external_fhir_base_url_from_resource, parameter_to_env, validate_context
 from ..utils import get_extract_services
 from .settings import settings
 from .utils import AidboxSdcRequest, aidbox_operation, get_user_sdk_client, prepare_args
 
-# TODO: it's outside from spec, if it's only for data fetching,
-# TODO: better to use dataEndpoint and it should be handled in `parameter_to_env` function
-EXTERNAL_FHIR_BASE_URL_PARAM_KEY = "externalFhirBaseUrl"
-
 
 @aidbox_operation(["GET"], ["Questionnaire", {"name": "id"}, "$assemble"])
 @prepare_args
@@ -52,7 +48,7 @@ async def constraint_check_operation(request: AidboxSdcRequest):
     client = get_user_sdk_client(
         request.request,
         request.client,
-        _get_external_fhir_base_url_from_resource(request.resource, request.is_fhir),
+        get_external_fhir_base_url_from_resource(request.resource, request.is_fhir),
     )
     env = await parameter_to_env(client, request.resource, request.is_fhir)
 
@@ -79,7 +75,7 @@ async def get_questionnaire_context_operation(request: AidboxSdcRequest):
     client = get_user_sdk_client(
         request.request,
         request.client,
-        _get_external_fhir_base_url_from_resource(request.resource, request.is_fhir),
+        get_external_fhir_base_url_from_resource(request.resource, request.is_fhir),
     )
     env = await parameter_to_env(client, request.resource, request.is_fhir)
 
@@ -100,7 +96,7 @@ async def extract_questionnaire_operation(request: AidboxSdcRequest):
     client = get_user_sdk_client(
         request.request,
         request.client,
-        _get_external_fhir_base_url_from_resource(resource, request.is_fhir),
+        get_external_fhir_base_url_from_resource(resource, request.is_fhir),
     )
     if resource["resourceType"] == "QuestionnaireResponse":
         env = {}
@@ -159,7 +155,7 @@ async def extract_questionnaire_instance_operation(request: AidboxSdcRequest):
     extract_client = get_user_sdk_client(
         request.request,
         request.client,
-        _get_external_fhir_base_url_from_resource(resource, request.is_fhir),
+        get_external_fhir_base_url_from_resource(resource, request.is_fhir),
     )
     fhir_questionnaire = (
         await request.fhir_client.resources("Questionnaire")
@@ -233,7 +229,7 @@ async def populate_questionnaire(request: AidboxSdcRequest):
     client = get_user_sdk_client(
         request.request,
         request.client,
-        _get_external_fhir_base_url_from_resource(request.resource, request.is_fhir),
+        get_external_fhir_base_url_from_resource(request.resource, request.is_fhir),
     )
     env = await parameter_to_env(client, request.resource, request.is_fhir)
 
@@ -250,7 +246,7 @@ async def populate_questionnaire_instance(request: AidboxSdcRequest):
     client = get_user_sdk_client(
         request.request,
         request.client,
-        _get_external_fhir_base_url_from_resource(request.resource, request.is_fhir),
+        get_external_fhir_base_url_from_resource(request.resource, request.is_fhir),
     )
     fhir_questionnaire = (
         await request.fhir_client.resources("Questionnaire")
@@ -269,16 +265,3 @@ async def populate_questionnaire_instance(request: AidboxSdcRequest):
 @aidbox_operation(["POST"], ["Questionnaire", "$resolve-expression"], public=True)
 def resolve_expression_operation(_operation, request):
     return web.json_response(resolve_expression(request["resource"]), dumps=json.dumps)
-
-
-def _get_external_fhir_base_url_from_resource(resource: dict | None, is_fhir: bool):
-    if not resource or resource.get("resourceType") != "Parameters":
-        return None
-    for param in resource.get("parameter", []):
-        if param.get("name") != EXTERNAL_FHIR_BASE_URL_PARAM_KEY:
-            continue
-        if "resource" in param:
-            continue
-        value = parse_parameter_value(param, is_fhir)
-        return value or None
-    return None

app/sdc/utils.py

@@ -19,6 +19,10 @@
 
 r4 = models["r4"]
 
+# TODO: it's outside from spec, if it's only for data fetching,
+# TODO: better to use dataEndpoint and it should be handled in `parameter_to_env` function
+EXTERNAL_FHIR_BASE_URL_PARAM_KEY = "externalFhirBaseUrl"
+
 
 def get_type(item, data):
     type = item["type"]
@@ -172,9 +176,15 @@ async def parameter_to_env(
         elif "resource" in param:
             env[param["name"]] = param["resource"]
         else:
-            value = parse_parameter_value(param, is_fhir)
+            value, kind = parse_parameter_value(param, is_fhir)
             if value:
-                env[param["name"]] = value
+                if param["name"] == "subject" and kind == "Reference":
+                    env[param["name"]] = await client.reference(
+                        reference=value["reference"]
+                    ).to_resource()
+                    env["useSDCAPI"] = True
+                else:
+                    env[param["name"]] = value
     # Mapping parameters to fhir resource names
     questionnaire = env.get("questionnaire")
     if questionnaire:
@@ -185,14 +195,27 @@ async def parameter_to_env(
     return env
 
 
-def parse_parameter_value(parameter, is_fhir: bool):
+def parse_parameter_value(parameter, is_fhir: bool) -> tuple[Any, str]:
     if is_fhir:
         _name_key, value_key = parameter.keys()
-        return parameter[value_key]
-    else:
-        value = parameter["value"]
-        polimorphic_key = first(value.keys())
-        return value[polimorphic_key] if polimorphic_key else None
+        return parameter[value_key], value_key.removeprefix("value")
+
+    value = parameter["value"]
+    polimorphic_key = first(value.keys())
+    return value[polimorphic_key] if polimorphic_key else None, polimorphic_key
+
+
+def get_external_fhir_base_url_from_resource(resource: dict | None, is_fhir: bool):
+    if not resource or resource.get("resourceType") != "Parameters":
+        return None
+    for param in resource.get("parameter", []):
+        if param.get("name") != EXTERNAL_FHIR_BASE_URL_PARAM_KEY:
+            continue
+        if "resource" in param:
+            continue
+        value, _key = parse_parameter_value(param, is_fhir)
+        return value or None
+    return None
 
 
 async def load_source_queries(client, fce_questionnaire, env):

tests/sdc/test_populate.py

@@ -1949,6 +1949,7 @@ async def test_named_item_population_context_parent_child_repeating_populate(fhi
         ],
     }
 
+
 @pytest.mark.asyncio
 async def test_initial_expression_populate_sdc_api(fhir_client, safe_db):
     q = await create_questionnaire(
@@ -1957,51 +1958,53 @@ async def test_initial_expression_populate_sdc_api(fhir_client, safe_db):
             "status": "active",
             "extension": [
                 make_launch_context_ext("LaunchPatient", "Patient"),
+                make_launch_context_ext("subject", "Patient"),
             ],
             "item": [
                 {
                     "type": "string",
                     "linkId": "patientGiven",
                     "extension": [make_initial_expression_ext("%LaunchPatient.name.given")],
                 },
+                {
+                    "type": "string",
+                    "linkId": "patientId",
+                    "extension": [make_initial_expression_ext("%subject.id")],
+                },
             ],
         },
     )
 
-    launch_patient = fhir_client.resource('Patient',
-        name= [{"given": ["John"]}]
+    launch_patient = fhir_client.resource(
+        "Patient",
+        name=[{"given": ["John"]}],
     )
     await launch_patient.save()
 
     patient_id = launch_patient["id"]
 
     patient_ref = {
         "reference": f"Patient/{patient_id}",
-        "display": "Dow, John"
+        "display": "Dow, John",
     }
 
-    p = await fhir_client.execute("Questionnaire/$populate", data={
-        "resourceType": "Parameters",
-        "parameter": [
-            {
-                "name": "questionnaire",
-                "resource": q
-            },
-            {
-                "name": "context",
-                "part": [
-                    {
-                        "name": "name",
-                        "valueString": "LaunchPatient"
-                    },
-                    {
-                        "name": "content",
-                        "valueReference": patient_ref
-                    }
-                ]
-            }
-        ]
-    })
+    p = await fhir_client.execute(
+        "Questionnaire/$populate",
+        data={
+            "resourceType": "Parameters",
+            "parameter": [
+                {"name": "questionnaire", "resource": q},
+                {
+                    "name": "context",
+                    "part": [
+                        {"name": "name", "valueString": "LaunchPatient"},
+                        {"name": "content", "valueReference": patient_ref},
+                    ],
+                },
+                {"name": "subject", "valueReference": patient_ref},
+            ],
+        },
+    )
 
     assert p == {
         "resourceType": "Parameters",
@@ -2016,9 +2019,13 @@ async def test_initial_expression_populate_sdc_api(fhir_client, safe_db):
                         {
                             "linkId": "patientGiven",
                             "answer": [{"valueString": "John"}],
-                        }
+                        },
+                        {
+                            "linkId": "patientId",
+                            "answer": [{"valueString": patient_id}],
+                        },
                     ],
-                }
-            }
-        ]
+                },
+            },
+        ],
     }

tests/test_utils.py

@@ -313,6 +313,26 @@ async def test_parameter_to_env_resolves_context_reference(fhir_client, safe_db)
     assert resolved["code"]["text"] == "parameter-to-env-integration"
 
 
+@pytest.mark.asyncio
+async def test_parameter_to_env_subject_resolves(fhir_client, safe_db):
+    patient = fhir_client.resource("Patient")
+    await patient.save()
+    patient_ref = {"reference": f"Patient/{patient.id}"}
+
+    parameters = {
+        "resourceType": "Parameters",
+        "parameter": [
+            {"name": "subject", "valueReference": patient_ref},
+        ],
+    }
+
+    env = await parameter_to_env(fhir_client, parameters, is_fhir=True)
+
+    assert env["useSDCAPI"] is True
+    assert env["subject"]["resourceType"] == "Patient"
+    assert env["subject"]["id"] == patient.id
+
+
 async def test_sdc_api_params():
     resolved_patient = {
         "resourceType": "Patient",