use only FHIR format

Author: alexlipovka

app/aidbox/operations.py

@@ -1,7 +1,7 @@
 import simplejson as json
 from aiohttp import web
 
-from app.converter.aidbox import from_first_class_extension, to_first_class_extension
+from app.sdc.getters import get_launch_context, get_questionnaire_mapper
 
 from ..sdc import (
     assemble,
@@ -26,24 +26,14 @@
 @aidbox_operation(["GET"], ["Questionnaire", {"name": "id"}, "$assemble"])
 @prepare_args
 async def assemble_op(request: AidboxSdcRequest):
-    def get_to_first_class_extension(fhir_resource):
-        return to_first_class_extension(fhir_resource, request.aidbox_client)
-
     fhir_questionnaire = (
         await request.fhir_client.resources("Questionnaire")
         .search(_id=request.route_params["id"])
         .get()
     )
-    fce_questionnaire = await get_to_first_class_extension(fhir_questionnaire)
 
-    assembled_questionnaire_lazy = await assemble(
-        request.fhir_client, fce_questionnaire, get_to_first_class_extension
-    )
+    assembled_questionnaire_lazy = await assemble(request.fhir_client, dict(fhir_questionnaire))
     assembled_questionnaire = json.loads(json.dumps(assembled_questionnaire_lazy, default=list))
-    if request.is_fhir:
-        assembled_questionnaire = await from_first_class_extension(
-            assembled_questionnaire, request.aidbox_client
-        )
     return web.json_response(assembled_questionnaire, dumps=json.dumps)
 
 
@@ -57,16 +47,10 @@ async def constraint_check_operation(request: AidboxSdcRequest):
     )
     env = await parameter_to_env(client, request.resource, request.is_fhir)
 
-    fce_questionnaire = (
-        await to_first_class_extension(env["Questionnaire"], request.aidbox_client)
-        if request.is_fhir
-        else env["Questionnaire"]
-    )
-
     return web.json_response(
         await constraint_check(
             client,
-            fce_questionnaire,
+            env["Questionnaire"],
             env,
             legacy_behavior=settings.CONSTRAINT_LEGACY_BEHAVIOR,
         ),
@@ -84,12 +68,7 @@ async def get_questionnaire_context_operation(request: AidboxSdcRequest):
     )
     env = await parameter_to_env(client, request.resource, request.is_fhir)
 
-    fce_questionnaire = (
-        await to_first_class_extension(env["Questionnaire"], request.aidbox_client)
-        if request.is_fhir
-        else env["Questionnaire"]
-    )
-    result = await get_questionnaire_context(client, fce_questionnaire, env)
+    result = await get_questionnaire_context(client, env["Questionnaire"], env)
 
     return web.json_response(result, dumps=json.dumps)
 
@@ -106,44 +85,36 @@ async def extract_questionnaire_operation(request: AidboxSdcRequest):
     if resource["resourceType"] == "QuestionnaireResponse":
         env = {}
         env_questionnaire_response = resource
-        fhir_questionnaire = (
+        questionnaire = (
             await request.fhir_client.resources("Questionnaire")
             .search(_id=resource["questionnaire"])
             .get()
         )
-        fce_questionnaire = await to_first_class_extension(
-            fhir_questionnaire, request.aidbox_client
-        )
-        env_questionnaire = fhir_questionnaire if request.is_fhir else fce_questionnaire
     elif resource["resourceType"] == "Parameters":
         env = await parameter_to_env(client, resource, request.is_fhir)
         if "Questionnaire" not in env:
             raise MissingParamOperationOutcome("`Questionnaire` parameter is required")
         if "QuestionnaireResponse" not in env:
             raise MissingParamOperationOutcome("`QuestionnaireResponse` parameter is required")
 
-        fce_questionnaire = (
-            await to_first_class_extension(env["Questionnaire"], request.aidbox_client)
-            if request.is_fhir
-            else env["Questionnaire"]
-        )
-        env_questionnaire = env["Questionnaire"]
+        questionnaire = env["Questionnaire"]
         env_questionnaire_response = env["QuestionnaireResponse"]
 
+    mapper_refs = get_questionnaire_mapper(questionnaire.get("extension", []))
     mappings = [
-        await request.aidbox_client.resources("Mapping").search(_id=m["id"]).get()
-        for m in fce_questionnaire.get("mapping", [])
+        await request.aidbox_client.resources("Mapping").search(_id=ref["reference"].split("/")[-1]).get()
+        for ref in mapper_refs
     ]
 
     context = {
-        "Questionnaire": env_questionnaire,
+        "Questionnaire": questionnaire,
         "QuestionnaireResponse": env_questionnaire_response,
         **env,
     }
 
     await constraint_check(
         client,
-        fce_questionnaire,
+        questionnaire,
         context,
         legacy_behavior=settings.CONSTRAINT_LEGACY_BEHAVIOR,
     )
@@ -162,23 +133,19 @@ async def extract_questionnaire_instance_operation(request: AidboxSdcRequest):
         request.client,
         get_external_fhir_base_url_from_resource(resource, request.is_fhir),
     )
-    fhir_questionnaire = (
+    questionnaire = (
         await request.fhir_client.resources("Questionnaire")
         .search(_id=request.route_params["id"])
         .get()
     )
-    fce_questionnaire = await to_first_class_extension(fhir_questionnaire, request.aidbox_client)
-    env_questionnaire = fhir_questionnaire if request.is_fhir else fce_questionnaire
 
     return web.json_response(
         await extract_questionnaire_instance(
             request.aidbox_client,
             extract_client,
-            fce_questionnaire,
-            env_questionnaire,
+            dict(questionnaire),
             resource,
             get_extract_services(request.request["app"]),
-            request.is_fhir,
         ),
         dumps=json.dumps,
     )
@@ -187,17 +154,15 @@ async def extract_questionnaire_instance_operation(request: AidboxSdcRequest):
 async def extract_questionnaire_instance(
     aidbox_client,
     extract_client,
-    fce_questionnaire,
-    env_questionnaire,
+    questionnaire,
     resource,
     extract_services,
-    is_fhir,
 ):
     if resource["resourceType"] == "QuestionnaireResponse":
         env = {}
         env_questionnaire_response = extract_client.resource("QuestionnaireResponse", **resource)
     elif resource["resourceType"] == "Parameters":
-        env = await parameter_to_env(extract_client, resource, is_fhir)
+        env = await parameter_to_env(extract_client, resource, True)
         if "QuestionnaireResponse" not in env:
             raise MissingParamOperationOutcome("`QuestionnaireResponse` parameter is required")
 
@@ -207,20 +172,23 @@ async def extract_questionnaire_instance(
             "Either `QuestionnaireResponse` resource or Parameters containing  QuestionnaireResponse are required",
         )
 
-    if "launchContext" in fce_questionnaire:
-        validate_context(fce_questionnaire["launchContext"], env)
+    launch_context = get_launch_context(questionnaire.get("extension", []))
+    if launch_context:
+        validate_context(launch_context, env)
+
     context = {
         "QuestionnaireResponse": env_questionnaire_response,
-        "Questionnaire": env_questionnaire,
+        "Questionnaire": questionnaire,
         **env,
     }
+    mapper_refs = get_questionnaire_mapper(questionnaire.get("extension", []))
     mappings = [
-        await aidbox_client.resources("Mapping").search(_id=m["id"]).get()
-        for m in fce_questionnaire.get("mapping", [])
+        await aidbox_client.resources("Mapping").search(_id=ref["reference"].split("/")[-1]).get()
+        for ref in mapper_refs
     ]
     await constraint_check(
         extract_client,
-        fce_questionnaire,
+        questionnaire,
         context,
         legacy_behavior=settings.CONSTRAINT_LEGACY_BEHAVIOR,
     )

app/fhir_server/operations.py

@@ -4,9 +4,8 @@
 from aiohttp import web
 from fhirpy.lib import AsyncFHIRClient
 
-from app.converter.fce_to_fhir import from_first_class_extension
-from app.converter.fhir_to_fce import to_first_class_extension
 from app.sdc.exception import ConstraintCheckOperationOutcome
+from app.sdc.getters import get_launch_context
 
 from ..sdc import (
     assemble,
@@ -25,46 +24,21 @@
 @routes.get("/Questionnaire/{id}/$assemble")
 async def assemble_handler(request: web.BaseRequest):
     client: AsyncFHIRClient = request.app["client"]
-    fce_converter_url = getattr(request.app["settings"], "FCE_CONVERTER_URL", None)
 
     questionnaire = (
         await client.resources("Questionnaire").search(_id=request.match_info["id"]).get()
     )
 
-    if fce_converter_url:
-        async with aiohttp.ClientSession() as session:
-
-            async def to_fce(fhir_resource):
-                async with session.post(
-                    f"{fce_converter_url}/to-fce", json=dict(fhir_resource)
-                ) as resp:
-                    return await resp.json()
-
-            fce_questionnaire = await to_fce(dict(questionnaire))
-            assembled_lazy = await assemble(client, fce_questionnaire, to_fce)
-            assembled = json.loads(json.dumps(assembled_lazy, default=list))
-
-            async with session.post(f"{fce_converter_url}/to-fhir", json=assembled) as resp:
-                return web.json_response(await resp.json())
-
-    async def get_to_first_class_extension(fhir_resource):
-        return to_first_class_extension(fhir_resource)
-
-    assembled_questionnaire_lazy = await assemble(
-        client, to_first_class_extension(questionnaire), get_to_first_class_extension
-    )
+    assembled_questionnaire_lazy = await assemble(client, dict(questionnaire))
     assembled_questionnaire = json.loads(json.dumps(assembled_questionnaire_lazy, default=list))
 
-    return web.json_response(from_first_class_extension(assembled_questionnaire))
+    return web.json_response(assembled_questionnaire)
 
 
 @routes.post("/QuestionnaireResponse/$constraint-check")
 async def constraint_check_handler(request: web.BaseRequest):
     client = request.app["client"]
     env = await parameter_to_env(client, await request.json())
-    # TODO: I believe there's a bug, it should be in FHIR format
-    env["Questionnaire"] = to_first_class_extension(env["Questionnaire"])
-    env["QuestionnaireResponse"] = to_first_class_extension(env["QuestionnaireResponse"])
 
     return web.json_response(await constraint_check(client, env["Questionnaire"], env))
 
@@ -75,7 +49,7 @@ async def get_questionnaire_context_handler(request: web.BaseRequest):
     env = await parameter_to_env(client, await request.json())
 
     return web.json_response(
-        await get_questionnaire_context(client, to_first_class_extension(env["Questionnaire"]), env)
+        await get_questionnaire_context(client, env["Questionnaire"], env)
     )
 
 
@@ -92,7 +66,6 @@ async def extract_questionnaire_handler(request: web.BaseRequest):
         )
     elif resource["resourceType"] == "Parameters":
         env = await parameter_to_env(client, resource)
-        # TODO: Use FHIR spec questionnaire
         questionnaire = env.get("Questionnaire")
         questionnaire_response = env.get("QuestionnaireResponse")
 
@@ -119,14 +92,14 @@ async def extract_questionnaire_handler(request: web.BaseRequest):
             ]
         )
         jute_templates.append(json.loads(template_string))
-    # TODO: I believe there's a bug, it should be in FHIR
+
     context = {
-        "Questionnaire": to_first_class_extension(questionnaire),
-        "QuestionnaireResponse": to_first_class_extension(questionnaire_response),
+        "Questionnaire": questionnaire,
+        "QuestionnaireResponse": questionnaire_response,
         **env,
     }
 
-    await constraint_check(client, to_first_class_extension(questionnaire), context)
+    await constraint_check(client, questionnaire, context)
     extraction_result = await extract(
         client, jute_templates, context, get_extract_services(request.app)
     )
@@ -137,19 +110,17 @@ async def extract_questionnaire_handler(request: web.BaseRequest):
 async def extract_questionnaire_instance_operation(request: web.BaseRequest):
     resource = await request.json()
     client = request.app["client"]
-    fhir_questionnaire = (
+    questionnaire = (
         await client.resources("Questionnaire").search(_id=request.match_info["id"]).get()
     )
     jute_templates = []
     structure_map_extensions = [
         ext
-        for ext in fhir_questionnaire.get("extension", [])
+        for ext in questionnaire.get("extension", [])
         if ext["url"]
         == "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-targetStructureMap"
     ]
 
-    questionnaire = to_first_class_extension(fhir_questionnaire)
-
     for structure_map_extension in structure_map_extensions:
         structure_map_id = structure_map_extension["valueCanonical"].split("/")[-1]
         structure_map = await client.resources("StructureMap").search(_id=structure_map_id).get()
@@ -168,9 +139,8 @@ async def extract_questionnaire_instance_operation(request: web.BaseRequest):
 
     if resource["resourceType"] == "QuestionnaireResponse":
         questionnaire_response = client.resource("QuestionnaireResponse", **resource)
-        # TODO: I believe there's a bug, it should be in FHIR
         context = {
-            "Questionnaire": to_first_class_extension(questionnaire),
+            "Questionnaire": questionnaire,
             "QuestionnaireResponse": questionnaire_response,
         }
         await constraint_check(client, questionnaire, context)
@@ -196,8 +166,9 @@ async def extract_questionnaire_instance_operation(request: web.BaseRequest):
         questionnaire_response = client.resource(
             "QuestionnaireResponse", **questionnaire_response_data
         )
-        if "launchContext" in questionnaire:
-            validate_context(questionnaire["launchContext"], env)
+        launch_context = get_launch_context(questionnaire.get("extension", []))
+        if launch_context:
+            validate_context(launch_context, env)
         context = {
             "QuestionnaireResponse": questionnaire_response,
             "Questionnaire": questionnaire,
@@ -227,7 +198,6 @@ async def populate_questionnaire_handler(request: web.BaseRequest):
     env = await parameter_to_env(client, body)
     questionnaire_data = env["Questionnaire"]
     if not questionnaire_data:
-        # TODO: return OperationOutcome
         return web.json_response(
             {
                 "error": "bad_request",