Merge branch 'master' into VED-350-Dose-Unit-Code-Validation

Author: Akol125

.github/workflows/continuous-integration.yml

@@ -8,7 +8,7 @@ jobs:
     if: github.ref == 'refs/heads/master'
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0  # This causes all history to be fetched, which is required for calculate-version to function	
 

.github/workflows/deploy-template.yml

@@ -24,7 +24,7 @@ jobs:
         run: aws sts get-caller-identity
 
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 
@@ -53,7 +53,7 @@ jobs:
       name: int
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - uses: aws-actions/configure-aws-credentials@v4
         with:
@@ -85,7 +85,7 @@ jobs:
       contents: read
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - uses: aws-actions/configure-aws-credentials@v4
         with:

.github/workflows/sonarcloud.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 

backend/poetry.lock

@@ -3,6 +3,7 @@
 import boto3
 import time
 import simplejson as json
+from clients import logger
 from dataclasses import dataclass
 import botocore.exceptions
 from boto3.dynamodb.conditions import Key, Attr
@@ -34,7 +35,7 @@ def _query_identifier(table, index, pk, identifier, is_present):
                 return queryresponse
 
             if retries > 6:
-                print(f"{identifier}: Crossed {retries} retries")
+                logger.info(f"{identifier}: Crossed {retries} retries")
 
             retries += 1
             # Delay time in milliseconds

backend/src/fhir_batch_repository.py

@@ -10,6 +10,7 @@
 from aws_lambda_typing.events import APIGatewayProxyEventV1
 from fhir.resources.R4B.immunization import Immunization
 from boto3 import client as boto3_client
+from clients import logger
 
 from authorization import Authorization, UnknownPermission
 from fhir_repository import ImmunizationRepository, create_table
@@ -625,7 +626,7 @@ def check_vaccine_type_permissions(self, aws_event):
             if len(supplier_system) == 0:
                 raise UnauthorizedSystemError()
             imms_vax_type_perms = get_supplier_permissions(supplier_system)
-            print(f" update imms = {imms_vax_type_perms}")
+            logger.info(f" update imms = {imms_vax_type_perms}")
             if len(imms_vax_type_perms) == 0:
                 raise UnauthorizedVaxError()
             # Return the values needed for later use

backend/src/fhir_controller.py

@@ -1,3 +1,5 @@
+from urllib import response
+from responses import logger
 import simplejson as json
 import os
 import time
@@ -397,20 +399,46 @@ def find_immunizations(self, patient_identifier: str, vaccine_types: list):
         condition = Key("PatientPK").eq(_make_patient_pk(patient_identifier))
         is_not_deleted = Attr("DeletedAt").not_exists() | Attr("DeletedAt").eq("reinstated")
 
-        response = self.table.query(
-            IndexName="PatientGSI",
-            KeyConditionExpression=condition,
-            FilterExpression=is_not_deleted,
-        )
+        raw_items = self.get_all_items(condition, is_not_deleted)
 
-        if "Items" in response:
+        if raw_items:    
             # Filter the response to contain only the requested vaccine types
-            items = [x for x in response["Items"] if x["PatientSK"].split("#")[0] in vaccine_types]
+            items = [x for x in raw_items if x["PatientSK"].split("#")[0] in vaccine_types]
 
             # Return a list of the FHIR immunization resource JSON items
-            return [json.loads(item["Resource"]) for item in items]
+            final_resources = [json.loads(item["Resource"]) for item in items]
+
+            return final_resources
         else:
-            raise UnhandledResponseError(message=f"Unhandled error. Query failed", response=response)
+            logger.warning("no items matched patient_identifier filter!")
+            return []
+
+    def get_all_items(self, condition, is_not_deleted):
+        """Query DynamoDB and paginate through all results."""
+        all_items = []
+        last_evaluated_key = None
+
+        while True:
+            query_args = {
+                "IndexName": "PatientGSI",
+                "KeyConditionExpression": condition,
+                "FilterExpression": is_not_deleted,
+            }
+            if last_evaluated_key:
+                query_args["ExclusiveStartKey"] = last_evaluated_key
+
+            response = self.table.query(**query_args)
+            if "Items" not in response:
+                raise UnhandledResponseError(message="No Items in DynamoDB response", response=response)
+  
+            items = response.get("Items", [])
+            all_items.extend(items)
+
+            last_evaluated_key = response.get("LastEvaluatedKey")
+            if not last_evaluated_key:
+                break
+
+        return all_items
 
     @staticmethod
     def _handle_dynamo_response(response):

backend/src/fhir_repository.py

@@ -6,24 +6,47 @@
 
 from log_firehose import FirehoseLogger
 
+from models.utils.validation_utils import get_vaccine_type
+
 logging.basicConfig()
 logger = logging.getLogger()
 logger.setLevel("INFO")
 
 
 firehose_logger = FirehoseLogger()
 
+def _log_data_from_body(event) -> dict:
+    log_data = {}
+    if event.get("body") is None:
+        return log_data
+    try:
+        imms = json.loads(event["body"])
+    except json.decoder.JSONDecodeError:
+        return log_data
+    try:
+        vaccine_type = get_vaccine_type(imms)
+        log_data["vaccine_type"] = vaccine_type
+    except Exception:
+        pass
+    try:
+        local_id = imms["identifier"][0]["value"] + "^" + imms["identifier"][0]["system"]
+        log_data["local_id"] = local_id
+    except Exception:
+        pass
+    return log_data
+
 
 def function_info(func):
     """This decorator prints the execution information for the decorated function."""
 
     @wraps(func)
     def wrapper(*args, **kwargs):
         event = args[0] if args else {}
-        print(f"Event: {event}")
+        logger.info(f"Event: {event}")
         headers = event.get("headers", {})
         correlation_id = headers.get("X-Correlation-ID", "X-Correlation-ID not passed")
         request_id = headers.get("X-Request-ID", "X-Request-ID not passed")
+        supplier_system = headers.get("SupplierSystem", "SupplierSystem not passed")
         actual_path = event.get("path", "Unknown")
         resource_path = event.get("requestContext", {}).get("resourcePath", "Unknown")
         logger.info(f"Starting {func.__name__} with X-Correlation-ID: {correlation_id} and X-Request-ID: {request_id}")
@@ -32,6 +55,7 @@ def wrapper(*args, **kwargs):
             "date_time": str(datetime.now()),
             "X-Correlation-ID": correlation_id,
             "X-Request-ID": request_id,
+            "supplier": supplier_system,
             "actual_path": actual_path,
             "resource_path": resource_path,
         }
@@ -40,9 +64,10 @@ def wrapper(*args, **kwargs):
         start = time.time()
         try:
             result = func(*args, **kwargs)
-            print(f"Result:{result}")
+            logger.info(f"Result:{result}")
             end = time.time()
             log_data["time_taken"] = f"{round(end - start, 5)}s"
+            log_data.update(_log_data_from_body(event))
             status = "500"
             status_code = "Exception"
             diagnostics = str()
@@ -56,7 +81,7 @@ def wrapper(*args, **kwargs):
                         record = result_headers["Location"]
                 if result.get("body"):
                     ops_outcome = json.loads(result["body"])
-                    print(f"ops_outcome: {ops_outcome}")
+                    logger.info(f"ops_outcome: {ops_outcome}")
                     if ops_outcome.get("issue"):
                         outcome_body = ops_outcome["issue"][0]
                         status_code = outcome_body["code"]
@@ -78,6 +103,7 @@ def wrapper(*args, **kwargs):
             log_data["error"] = str(e)
             end = time.time()
             log_data["time_taken"] = f"{round(end - start, 5)}s"
+            log_data.update(_log_data_from_body(event))
             logger.exception(json.dumps(log_data))
             firehose_log["event"] = log_data
             firehose_logger.send_log(firehose_log)

backend/src/log_structure.py

@@ -1,4 +1,5 @@
 from enum import StrEnum
+from clients import logger
 
 class ApiOperationCode(StrEnum):
     CREATE = "c"
@@ -22,7 +23,7 @@ def _expand_permissions(permissions: list[str]) -> dict[str, list[ApiOperationCo
 
 def validate_permissions(permissions: list[str], operation: ApiOperationCode, vaccine_types: list[str]):
     expanded_permissions = _expand_permissions(permissions)
-    print(f"operation: {operation}, expanded_permissions: {expanded_permissions}, vaccine_types: {vaccine_types}")
+    logger.info(f"operation: {operation}, expanded_permissions: {expanded_permissions}, vaccine_types: {vaccine_types}")
     return all(
         operation in expanded_permissions.get(vaccine_type.lower(), [])
         for vaccine_type in vaccine_types

backend/src/models/utils/permission_checker.py

@@ -6,7 +6,7 @@
 from typing import Optional
 from urllib.parse import parse_qs, urlencode, quote
 
-from clients import redis_client
+from clients import redis_client, logger
 from models.errors import ParameterException
 from models.constants import Constants