Improve documentation and add some TODOs for code improvements

Author: nss10

docs/architecture.md

@@ -97,7 +97,7 @@ This ensures Funnel always has valid credentials to authenticate with Fence with
   * Ensure only authorized pods and services can communicate with Funnel
   * Reduce the blast radius of misconfigurations or compromised workloads
 
-* The diagram below illustrates the Funnel network policy model:
+* The diagram below illustrates the Funnel network policy model when deployed with MongoDB as funnel backend:
 
 ![Funnel Network Policies diagram](funnel_network_policies.jpg)
 

docs/gen3-deployment.md

@@ -31,11 +31,7 @@ Deploying Gen3Workflow automatically creates a **funnel-oidc-job**, which:
 
 > **Note:**
 > The value `gen3-workflow.externalSecrets.funnelOidcClient` can be overridden to use a different secret name when external secrets are enabled.
-> This is typically configured by the PE team using the pattern:
->
-> ```
-> <env_name>-funnel-oidc-client
-> ```
+> This is typically configured by the PE team using the pattern: `<env_name>-funnel-oidc-client`
 
 ---
 

gen3workflow/routes/ga4gh_tes.py

@@ -93,6 +93,7 @@ async def create_task(request: Request, auth=Depends(Auth)) -> dict:
     """
     await auth.authorize("create", ["/services/workflow/gen3-workflow/tasks"])
 
+    # TODO: Return a 400 error instead of 500 when there is any decode exception while getting request body
     body = await get_request_body(request)
     logger.debug(f"Incoming task creation request body: {body}")
 

gen3workflow/routes/s3.py

@@ -307,6 +307,8 @@ async def s3_endpoint(path: str, request: Request):
     )
     s3_api_url = f"https://{user_bucket}.s3.{region}.amazonaws.com/{api_endpoint}"
     logger.debug(f"Outgoing S3 request: '{request.method} {s3_api_url}'")
+
+    # TODO: Enclose this with a retry if S3 response with a 500 error ( which is possible! Failing fast can break a whole nextflow workflow)
     response = await request.app.async_client.request(
         method=request.method,
         url=s3_api_url,