[NRL-829] WIP Add todos for remaining changes

mattdean3-nhs · mattdean3-nhs · commit c0dc2004930c · 2024-10-17T10:17:22.000+01:00
diff --git a/api/consumer/readDocumentReference/read_document_reference.py b/api/consumer/readDocumentReference/read_document_reference.py
@@ -57,6 +57,7 @@ def handler(
         )
 
     try:
+        # TODO-NOW - Fix deprecated parse_raw usage
         document_reference = DocumentReference.parse_raw(result.document)
     except ValidationError as exc:
         logger.log(
diff --git a/api/consumer/searchDocumentReference/search_document_reference.py b/api/consumer/searchDocumentReference/search_document_reference.py
@@ -91,9 +91,11 @@ def handler(
         pointer_types=pointer_types,
     ):
         try:
+            # TODO-NOW - Fix deprecated parse_raw usage
             document_reference = DocumentReference.parse_raw(result.document)
             bundle["total"] += 1
             bundle["entry"].append(
+                # TODO-NOW - Fix deprecated dict usage
                 {"resource": document_reference.dict(exclude_none=True)}
             )
             logger.log(
@@ -114,6 +116,7 @@ def handler(
                 diagnostics="An error occurred whilst parsing the document reference search results",
             ) from exc
 
+    # TODO-NOW - Fix deprecated parse_obj
     response = Response.from_resource(Bundle.parse_obj(bundle))
     logger.log(LogReference.CONSEARCH999)
 
diff --git a/api/consumer/searchPostDocumentReference/search_post_document_reference.py b/api/consumer/searchPostDocumentReference/search_post_document_reference.py
@@ -92,6 +92,7 @@ def handler(
         nhs_number=body.nhs_number, custodian=custodian_id, pointer_types=pointer_types
     ):
         try:
+            # TODO-NOW - Fix deprecated parse_raw usage
             document_reference = DocumentReference.parse_raw(result.document)
             bundle["total"] += 1
             bundle["entry"].append(
@@ -115,6 +116,7 @@ def handler(
                 diagnostics="An error occurred whilst parsing the document reference search results",
             ) from exc
 
+    # TODO-NOW - Fix deprecated parse_obj usage
     response = Response.from_resource(Bundle.parse_obj(bundle))
     logger.log(LogReference.CONPOSTSEARCH999)
 
diff --git a/api/producer/readDocumentReference/read_document_reference.py b/api/producer/readDocumentReference/read_document_reference.py
@@ -56,6 +56,7 @@ def handler(
         )
 
     try:
+        # TODO-NOW - Fix deprecated parse_raw usage
         document_reference = DocumentReference.parse_raw(result.document)
     except ValidationError as exc:
         logger.log(
diff --git a/api/producer/searchDocumentReference/search_document_reference.py b/api/producer/searchDocumentReference/search_document_reference.py
@@ -77,6 +77,7 @@ def handler(
         pointer_types=pointer_types,
     ):
         try:
+            # TODO-NOW - Fix deprecated parse_raw usage
             document_reference = DocumentReference.parse_raw(result.document)
             bundle["total"] += 1
             bundle["entry"].append(
@@ -100,6 +101,7 @@ def handler(
                 diagnostics="An error occurred whilst parsing the document reference search results",
             )
 
+    # TODO-NOW - Fix deprecated parse_obj usage
     response = Response.from_resource(Bundle.parse_obj(bundle))
     logger.log(LogReference.PROSEARCH999)
     return response
diff --git a/api/producer/searchPostDocumentReference/search_post_document_reference.py b/api/producer/searchPostDocumentReference/search_post_document_reference.py
@@ -71,6 +71,7 @@ def handler(
         pointer_types=pointer_types,
     ):
         try:
+            # TODO-NOW - Fix deprecated parse_raw usage
             document_reference = DocumentReference.parse_raw(result.document)
             bundle["total"] += 1
             bundle["entry"].append(
@@ -95,4 +96,5 @@ def handler(
             )
 
     logger.log(LogReference.PROPOSTSEARCH999)
+    # TODO-NOW - Fix deprecated parse_obj usage
     return Response.from_resource(Bundle.parse_obj(bundle))
diff --git a/api/producer/updateDocumentReference/update_document_reference.py b/api/producer/updateDocumentReference/update_document_reference.py
@@ -79,6 +79,7 @@ def handler(
         )
 
     try:
+        # TODO-NOW - Fix deprecated parse_raw usage
         existing_resource = DocumentReference.parse_raw(existing_model.document)
     except ValidationError as exc:
         logger.log(LogReference.PROUPDATE002, error=exc)
diff --git a/layer/nrlf/consumer/fhir/r4/model.py b/layer/nrlf/consumer/fhir/r4/model.py
@@ -9,6 +9,8 @@
 
 from nrlf.core.constants import PointerTypes
 
+# TODO-NOW - Do we need to regenerate this file?
+
 
 class LocationItem(BaseModel):
     __root__: Annotated[
diff --git a/layer/nrlf/core/config.py b/layer/nrlf/core/config.py
@@ -1,4 +1,5 @@
-from pydantic import BaseSettings, Field
+from pydantic import Field
+from pydantic_settings import BaseSettings
 
 
 class Config(BaseSettings):
@@ -13,10 +14,10 @@ class Config(BaseSettings):
     logic to be supported.
     """
 
-    AWS_REGION: str = Field(default=..., env="AWS_REGION")
-    PREFIX: str = Field(default=..., env="PREFIX")
-    ENVIRONMENT: str = Field(default=..., env="ENVIRONMENT")
-    SPLUNK_INDEX: str = Field(default=..., env="SPLUNK_INDEX")
-    SOURCE: str = Field(default=..., env="SOURCE")
-    AUTH_STORE: str = Field(default=..., env="AUTH_STORE")
-    TABLE_NAME: str = Field(default=..., env="TABLE_NAME")
+    AWS_REGION: str = Field(default=...)
+    PREFIX: str = Field(default=...)
+    ENVIRONMENT: str = Field(default=...)
+    SPLUNK_INDEX: str = Field(default=...)
+    SOURCE: str = Field(default=...)
+    AUTH_STORE: str = Field(default=...)
+    TABLE_NAME: str = Field(default=...)
diff --git a/layer/nrlf/core/decorators.py b/layer/nrlf/core/decorators.py
@@ -42,16 +42,19 @@ def wrapper(*args, **kwargs) -> Dict[str, Any]:
             return wrapped_func(*args, **kwargs)
 
         except OperationOutcomeError as exc:
+            # TODO-NOW - Fix deprecated dict usage
             response = exc.response.dict(exclude_none=True)
             logger.log(LogReference.ERROR001, error=str(exc), response=response)
             return response
 
         except ParseError as exc:
+            # TODO-NOW - Fix deprecated dict usage
             response = exc.response.dict(exclude_none=True)
             logger.log(LogReference.ERROR002, error=str(exc), response=response)
             return response
 
         except Exception as exc:
+            # TODO-NOW - Fix deprecated dict usage
             response = Response.from_exception(exc).dict(exclude_none=True)
             logger.exception(
                 "An unhandled exception occurred whilst processing the request",
@@ -210,8 +213,10 @@ def basic_handler(
     logger.log(
         LogReference.HANDLER999,
         status_code=response.statusCode,
+        # TODO-NOW - Fix deprecated dict usage
         response=response.dict(),
     )
+    # TODO-NOW - Fix deprecated dict usage
     return response.dict()
 
 
@@ -253,6 +258,7 @@ def wrapper(*args, **kwargs):
             verify_request_ids(event)
 
             config = Config()
+            # TODO-NOW - Fix deprecated dict usage
             logger.log(LogReference.HANDLER001, config=config.dict())
             metadata = load_connection_metadata(event.headers, config)
 
@@ -291,8 +297,10 @@ def wrapper(*args, **kwargs):
             logger.log(
                 LogReference.HANDLER999,
                 status_code=response.statusCode,
+                # TODO-NOW - Fix deprecated dict usage
                 response=response.dict(),
             )
+            # TODO-NOW - Fix deprecated dict usage
             return response.dict()
 
         decorators = [
diff --git a/layer/nrlf/core/dynamodb/model.py b/layer/nrlf/core/dynamodb/model.py
@@ -134,6 +134,7 @@ def from_document_reference(
             category_id=category_id,
             source="NRLF",
             version=1,
+            # TODO-NOW - Fix deprecated json usage
             document=resource.json(exclude_none=True),
             created_on=created_on or create_fhir_instant(),
         )
@@ -146,6 +147,7 @@ def from_document_reference(
         )
         return core_model
 
+    # TODO-NOW - Fix deprecated root_validator usage
     @root_validator(pre=True)
     @classmethod
     def extract_custodian_suffix(cls, values: Dict[str, Any]) -> Dict[str, Any]:
@@ -176,6 +178,7 @@ def extract_custodian_suffix(cls, values: Dict[str, Any]) -> Dict[str, Any]:
 
         return values
 
+    # TODO-NOW - Fix deprecated root_validator usage
     @root_validator(pre=True)
     @classmethod
     def inject_producer_id(cls, values: Dict[str, Any]) -> Dict[str, Any]:
@@ -206,6 +209,7 @@ def inject_producer_id(cls, values: Dict[str, Any]) -> Dict[str, Any]:
         )
         return values
 
+    # TODO-NOW - Fix deprecated validator usage
     @validator("id")
     @classmethod
     def validate_id(cls, id_: str) -> str:
@@ -220,6 +224,7 @@ def validate_id(cls, id_: str) -> str:
 
         return id_
 
+    # TODO-NOW - Fix deprecated validator usage
     @validator("producer_id")
     @classmethod
     def validate_producer_id(cls, producer_id: str, values: Dict[str, Any]) -> str:
@@ -242,6 +247,7 @@ def validate_producer_id(cls, producer_id: str, values: Dict[str, Any]) -> str:
 
         return producer_id
 
+    # TODO-NOW - Fix deprecated validator usage
     @validator("type")
     @classmethod
     def validate_type(cls, type: str) -> str:
@@ -254,6 +260,7 @@ def validate_type(cls, type: str) -> str:
 
         return type
 
+    # TODO-NOW - Fix deprecated validator usage
     @validator("nhs_number")
     @classmethod
     def validate_nhs_number(cls, nhs_number: str) -> str:
@@ -266,6 +273,7 @@ def validate_nhs_number(cls, nhs_number: str) -> str:
 
         return nhs_number
 
+    # TODO-NOW - Fix deprecated validator usage
     @validator("source")
     @classmethod
     def validate_source(cls, source: str) -> str:
@@ -278,6 +286,7 @@ def validate_source(cls, source: str) -> str:
 
         return source
 
+    # TODO-NOW - Fix deprecated validator usage
     @validator("created_on")
     @classmethod
     def validate_created_on(cls, created_on: str) -> str:
@@ -294,6 +303,7 @@ def validate_created_on(cls, created_on: str) -> str:
 
         return created_on
 
+    # TODO-NOW - Fix deprecated validator usage
     @validator("updated_on")
     @classmethod
     def validate_updated_on(cls, updated_on: Optional[str]) -> Optional[str]:
diff --git a/layer/nrlf/core/dynamodb/repository.py b/layer/nrlf/core/dynamodb/repository.py
@@ -119,8 +119,10 @@ def get_by_id(self, id: str) -> Optional[DocumentPointer]:
 
         item = result["Item"]
         try:
+            # TODO-NOW - Fix deprecated parse_obj usage
             parsed_item = self.ITEM_TYPE.parse_obj({"_from_dynamo": True, **item})
             logger.log(LogReference.REPOSITORY011)
+            # TODO-NOW - Fix deprecated dict usage
             logger.log(LogReference.REPOSITORY011a, result=parsed_item.dict())
             return parsed_item
         except ValidationError as exc:
@@ -379,6 +381,7 @@ def _query(self, **kwargs) -> Iterator[DocumentPointer]:
 
                 for item in page["Items"]:
                     try:
+                        # TODO-NOW - Fix deprecated parse_obj usage
                         yield self.ITEM_TYPE.parse_obj({"_from_dynamo": True, **item})
 
                     except ValidationError as exc:
@@ -412,6 +415,7 @@ def update(self, item: DocumentPointer) -> DocumentPointer:
         """
         try:
             result = self.table.put_item(
+                # TODO-NOW - Fix deprecated dict usage
                 Item=item.dict(),
                 ConditionExpression="attribute_exists(pk) AND attribute_exists(sk)",
                 ReturnConsumedCapacity="INDEXES",
diff --git a/layer/nrlf/core/errors.py b/layer/nrlf/core/errors.py
@@ -40,6 +40,7 @@ def __init__(  # noqa: PLR0913
     def response(self) -> Response:
         return Response(
             statusCode=self.status_code,
+            # TODO-NOW - Fix deprecated json usage
             body=self.operation_outcome.json(exclude_none=True, indent=2),
         )
 
@@ -74,5 +75,6 @@ def response(self):
             body=producer_model.OperationOutcome(
                 resourceType="OperationOutcome",
                 issue=self.issues,
+                # TODO-NOW - Fix deprecated json usage
             ).json(exclude_none=True, indent=2),
         )
diff --git a/layer/nrlf/core/model.py b/layer/nrlf/core/model.py
@@ -1,7 +1,7 @@
-from typing import Union
+from typing import Literal, Union
 
 from nhs_number import is_valid as is_valid_nhs_number
-from pydantic import BaseModel, Extra, Field, StrictStr
+from pydantic import BaseModel, Field, StrictStr
 
 import nrlf.consumer.fhir.r4.model as consumer_model
 import nrlf.producer.fhir.r4.model as producer_model
@@ -27,7 +27,7 @@ class ProducerRequestParams(producer_model.RequestParams, _NhsNumberMixin):
 
 class ConsumerRequestParams(consumer_model.RequestParams, _NhsNumberMixin):
     class Config:
-        extra = Extra.forbid
+        extra = Literal["forbid"]
 
 
 class CountRequestParams(consumer_model.CountRequestParams, _NhsNumberMixin):
diff --git a/layer/nrlf/core/request.py b/layer/nrlf/core/request.py
@@ -24,7 +24,9 @@ def parse_headers(headers: Dict[str, str]) -> ConnectionMetadata:
             case_insensitive_headers.get(CLIENT_RP_DETAILS, "{}")
         )
 
+        # TODO-NOW - Fix deprecated parse_obj usage
         client_rp_details = ClientRpDetails.parse_obj(raw_client_rp_details)
+        # TODO-NOW - Fix deprecated parse_obj usage
         return ConnectionMetadata.parse_obj(
             {**raw_connection_metadata, "client_rp_details": client_rp_details}
         )
@@ -56,7 +58,9 @@ def parse_params(
     )
 
     try:
+        # TODO-NOW - Fix deprecated parse_obj usage
         result = model.parse_obj(query_string_params or {})
+        # TODO-NOW - Fix deprecated dict usage
         logger.log(LogReference.HANDLER007, parsed_params=result.dict())
         return result
 
@@ -87,7 +91,9 @@ def parse_body(
         )
 
     try:
+        # TODO-NOW - Fix deprecated parse_raw usage
         result = model.parse_raw(body)
+        # TODO-NOW - Fix deprecated dict usage
         logger.log(LogReference.HANDLER009, parsed_body=result.dict())
         return result
 
@@ -113,7 +119,9 @@ def parse_path(
     )
 
     try:
+        # TODO-NOW - Fix deprecated parse_obj usage
         result = model.parse_obj(path_params or {})
+        # TODO-NOW - Fix deprecated dict usage
         logger.log(LogReference.HANDLER011, parsed_path=result.dict())
         return result
 
diff --git a/layer/nrlf/core/response.py b/layer/nrlf/core/response.py
@@ -16,14 +16,15 @@ class Response(BaseModel):
 
     statusCode: str
     body: str
-    headers: dict = Field(default_factory=dict)
+    headers: dict[str, str] = Field(default_factory=dict[str, str])
     isBase64Encoded: bool = Field(default=False)
 
     @classmethod
     def from_resource(cls, resource: BaseModel, **kwargs) -> "Response":
         status_code = kwargs.pop("statusCode", "200")
         return cls(
             statusCode=status_code,
+            # TODO-NOW - Fix deprecated json usage
             body=resource.json(indent=2, exclude_none=True, exclude_defaults=True),
             **kwargs,
         )
@@ -34,6 +35,7 @@ def from_issues(cls, issues: List[BaseModel], **kwargs) -> "Response":
             body=producer_model.OperationOutcome(
                 resourceType="OperationOutcome",
                 issue=issues,  # type: ignore
+                # TODO-NOW - Fix deprecated json usage
             ).json(exclude_none=True, indent=2),
             **kwargs,
         )
@@ -52,6 +54,7 @@ def from_exception(cls, exc: Exception) -> "Response":
                         details=SpineErrorConcept.from_code("INTERNAL_SERVER_ERROR"),
                     )
                 ],
+                # TODO-NOW - Fix deprecated json usage
             ).json(exclude_none=True, indent=2),
         )
 
diff --git a/layer/nrlf/core/tests/test_errors.py b/layer/nrlf/core/tests/test_errors.py
diff --git a/layer/nrlf/core/validators.py b/layer/nrlf/core/validators.py
diff --git a/layer/nrlf/producer/fhir/r4/model.py b/layer/nrlf/producer/fhir/r4/model.py
diff --git a/layer/nrlf/producer/fhir/r4/strict_model.py b/layer/nrlf/producer/fhir/r4/strict_model.py
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/tests/performance/process_results.py b/tests/performance/process_results.py
diff --git a/tests/utilities/api_clients.py b/tests/utilities/api_clients.py

Original file line number	Diff line number	Diff line change
`@@ -57,6 +57,7 @@ def handler(`
`57`	`57`	`)`
`58`	`58`
`59`	`59`	`try:`
	`60`	`+ # TODO-NOW - Fix deprecated parse_raw usage`
`60`	`61`	`document_reference = DocumentReference.parse_raw(result.document)`
`61`	`62`	`except ValidationError as exc:`
`62`	`63`	`logger.log(`
Original file line number	Diff line number	Diff line change
`@@ -56,6 +56,7 @@ def handler(`
`56`	`56`	`)`
`57`	`57`
`58`	`58`	`try:`
	`59`	`+ # TODO-NOW - Fix deprecated parse_raw usage`
`59`	`60`	`document_reference = DocumentReference.parse_raw(result.document)`
`60`	`61`	`except ValidationError as exc:`
`61`	`62`	`logger.log(`
Original file line number	Diff line number	Diff line change
`@@ -79,6 +79,7 @@ def handler(`
`79`	`79`	`)`
`80`	`80`
`81`	`81`	`try:`
	`82`	`+ # TODO-NOW - Fix deprecated parse_raw usage`
`82`	`83`	`existing_resource = DocumentReference.parse_raw(existing_model.document)`
`83`	`84`	`except ValidationError as exc:`
`84`	`85`	`logger.log(LogReference.PROUPDATE002, error=exc)`