fixes

src/adapter/bio_samples_adapter.py

@@ -160,7 +160,7 @@ async def get_sample(
     async def submit_sample(
         self,
         submission: dict[str, Any],
-        auth_token:Any,
+        auth_token: str | None,
     ) -> dict[str, Any]:
 
         if not auth_token:

src/middleware/cache_middleware.py

@@ -48,24 +48,32 @@ async def process(
 
         try:
             cached = await self.redis.get(cache_key)
-        except Exception:
+        except Exception as error:
+            logger.warning(
+                "Redis cache read failed. Proceeding without cache.",
+                extra={
+                    "extra_fields": {
+                        "event": "cache_read_failed",
+                        "tool": context.tool_name,
+                        "requestId": context.request_id,
+                        "error": str(error),
+                    }
+                },
+            )
             cached = None
 
         if cached:
             logger.info(
                 "Cache hit",
                 extra={
-                     "extra_fields": {
+                    "extra_fields": {
                         "event": "cache_hit",
                         "tool": context.tool_name,
-                         "requestId": context.request_id,
+                        "requestId": context.request_id,
                     }
                 },
             )
             return json.loads(cached)
-
-        cached_response = json.loads(cached)
-        return cached_response
 
         response = await next_handler(context)
 
@@ -88,15 +96,20 @@ async def process(
                 },
             )
 
-        logger.info({
-            "event": "cache_miss",
-            "tool": context.tool_name,
-            "cache": {
-            "hit": False,
-            "type": "redis",
-            "ttlSeconds": self.ttl_seconds,
-        },
-        })
+        logger.info(
+            "Cache miss",
+            extra={
+                "extra_fields": {
+                    "event": "cache_miss",
+                    "tool": context.tool_name,
+                    "cache": {
+                        "hit": False,
+                        "type": "redis",
+                        "ttlSeconds": self.ttl_seconds,
+                    },
+                }
+            },
+        )
         return response
 
     def _cache_key(self, context: RequestContext) -> str:

src/orchestrator/execution_pipeline.py

@@ -11,17 +11,15 @@ async def execute(
         self,
         context
     ):
-        async def call_next(index):
+        async def call_next(index, ctx=context):
             if index == len(self.middlewares):
-                return await self.executor.execute(
-                    context
-                )
+                return await self.executor.execute(ctx)
 
             middleware = self.middlewares[index]
 
             return await middleware.process(
-                context,
-                lambda ctx: call_next(index + 1)
+                ctx,
+                lambda next_ctx: call_next(index + 1, next_ctx)
             )
 
         return await call_next(0)