diff --git a/Dockerfile b/Dockerfile index 2ab344f..b2767a7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.11-bullseye +FROM python:3.12-bullseye RUN pip install pipenv RUN mkdir /app WORKDIR /app diff --git a/Pipfile b/Pipfile index a73361c..30bfcc1 100644 --- a/Pipfile +++ b/Pipfile @@ -28,7 +28,7 @@ sentry-sdk = "==1.14.0" aiocontextvars = "==0.2.2" coloredlogs = ">=15.0.1" aidbox-python-sdk = "==0.1.3" -fhirpathpy = "~=1.0" +fhirpathpy = "*" pytest-aiohttp = "==1.0.4" pytest-cov = "==4.0.0" pytest = "==7.2.2" @@ -41,4 +41,4 @@ pytest-asyncio = "*" aiohttp-cors = "~=0.7.0" [requires] -python_version = "3.11" +python_version = "3.12" diff --git a/Pipfile.lock b/Pipfile.lock index c5fa24f..0b21746 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "9ab5733baab2fd42cc62994025d27ba226ba264e3123d628647bfbda04e3cbdb" + "sha256": "a9203ec278d40db32cc4fa958bdd6298df94457694ee72c2fbe5bc7756dd8043" }, "pipfile-spec": 6, 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..utils import get_extract_services +from ..utils import get_extract_services, get_mapper_repository routes = web.RouteTableDef() @@ -56,7 +56,12 @@ async def get_questionnaire_context_handler(request: web.BaseRequest): @routes.post("/Questionnaire/$extract") async def extract_questionnaire_handler(request: web.BaseRequest): resource = await request.json() - client = request.app["client"] + original_client = request.app["client"] + client = AsyncFHIRClient( + original_client.url, + authorization=request.headers["Authorization"], + extra_headers=original_client.extra_headers, + ) if resource["resourceType"] == "QuestionnaireResponse": env = {} @@ -76,7 +81,7 @@ async def extract_questionnaire_handler(request: web.BaseRequest): if ext["url"] == "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-targetStructureMap" ] - jute_templates = [] + templates = [] for structure_map_extension in structure_map_extensions: structure_map_id = structure_map_extension["valueCanonical"].split("/")[-1] @@ -92,7 +97,21 @@ async def extract_questionnaire_handler(request: web.BaseRequest): "valueString", ] ) - jute_templates.append(json.loads(template_string)) + templates.append(json.loads(template_string)) + + mapper_extensions = [ + ext["valueReference"]["reference"] + for ext in questionnaire["extension"] + if ext["url"] == "http://beda.software/fhir-extensions/questionnaire-mapper" + ] + + mapper_service_url = get_mapper_repository(request.app) + async with ClientSession() as session: + for mapper_ref in mapper_extensions: + query = f"{mapper_service_url}/{mapper_ref}" + async with session.get(query) as result: + data = await result.text() + templates.append(json.loads(data)) context = { "Questionnaire": to_first_class_extension(questionnaire), @@ -101,9 +120,7 @@ async def extract_questionnaire_handler(request: web.BaseRequest): } await constraint_check(client, context) - extraction_result = await extract( - client, jute_templates, context, get_extract_services(request.app) - ) + extraction_result = await extract(client, templates, context, get_extract_services(request.app)) return web.json_response(extraction_result) @@ -114,7 +131,7 @@ async def extract_questionnaire_instance_operation(request: web.BaseRequest): fhir_questionnaire = ( await client.resources("Questionnaire").search(_id=request.match_info["id"]).get() ) - jute_templates = [] + templates = [] structure_map_extensions = [ ext for ext in fhir_questionnaire["extension"] @@ -138,7 +155,7 @@ async def extract_questionnaire_instance_operation(request: web.BaseRequest): "valueString", ] ) - jute_templates.append(json.loads(template_string)) + templates.append(json.loads(template_string)) if resource["resourceType"] == "QuestionnaireResponse": questionnaire_response = client.resource("QuestionnaireResponse", **resource) @@ -148,7 +165,7 @@ async def extract_questionnaire_instance_operation(request: web.BaseRequest): } await constraint_check(client, context) return web.json_response( - await extract(client, jute_templates, context, get_extract_services(request.app)) + await extract(client, templates, context, get_extract_services(request.app)) ) if resource["resourceType"] == "Parameters": @@ -178,7 +195,7 @@ async def extract_questionnaire_instance_operation(request: web.BaseRequest): } await constraint_check(client, context) return web.json_response( - await extract(client, jute_templates, context, get_extract_services(request.app)) + await extract(client, templates, context, get_extract_services(request.app)) ) raise ConstraintCheckOperationOutcome( @@ -216,11 +233,16 @@ async def populate_questionnaire_handler(request: web.BaseRequest): @routes.post("/Questionnaire/{id}/$populate") async def populate_questionnaire_instance(request: web.BaseRequest): - client = request.app["client"] + original_client = request.app["client"] + client = AsyncFHIRClient( + original_client.url, + authorization=request.headers["Authorization"], + extra_headers=original_client.extra_headers, + ) questionnaire = ( await client.resources("Questionnaire").search(_id=request.match_info["id"]).get() ) - env = parameter_to_env(request["resource"]) + env = parameter_to_env(await request.json()) converted = to_first_class_extension(questionnaire) env["Questionnaire"] = converted populated_resource = await populate(client, converted, env) diff --git a/app/fhir_server/settings.py b/app/fhir_server/settings.py index 23a41f7..308fe5a 100644 --- a/app/fhir_server/settings.py +++ b/app/fhir_server/settings.py @@ -15,4 +15,5 @@ def __init__(self, **custom_settings): BASE_URL=os.getenv("BASE_URL", "http://devbox:8080/fhir"), AUTH_TOKEN=os.getenv("AUTH_TOKEN"), FHIRPATH_MAPPING_SERVICE=os.getenv("FHIRPATH_MAPPING_SERVICE"), + MAPPER_REPOSITORY=os.getenv("MAPPER_REPOSITORY"), ) diff --git a/app/utils.py b/app/utils.py index 741e3bf..78f34cb 100644 --- a/app/utils.py +++ b/app/utils.py @@ -2,3 +2,8 @@ def get_extract_services(app): jute_service = app["settings"].JUTE_SERVICE fhir_mapping_service = app["settings"].FHIRPATH_MAPPING_SERVICE return {"JUTE": jute_service, "FHIRPath": fhir_mapping_service} + + +def get_mapper_repository(app): + mapper_repository = app["settings"].MAPPER_REPOSITORY or app["setting"].BASE_URL + return mapper_repository