feat: Add initial deny list for user mounted directories

[lbeckman314]

Overview ⚙️

This PR adds a default "deny list" to user-submitted task volumes to prevent errors related to trying to mount to system directories.

Current Behavior ⚠️

• Submitted task that mounts an input file to /dev:

➜ helm upgrade --install funnel calypr/funnel --version 0.1.99-rc.37 --values values.yaml

➜ kubectl get deployments -o wide
NAME            IMAGES
funnel-server   quay.io/ohsu-comp-bio/funnel:2026-05-27

➜ kubectl port-forward svc/funnel 8000:8000

➜ cat mount-test.json
{
  "name": "deny-input-dev",
  "description": "Issue #92: Input mounted to /dev (develop → accepted, feat/deny-lists → rejected)",
  "executors": [
    {
      "image": "alpine",
      "command": ["ls", "-la", "/dev"]
    }
  ],
  "inputs": [
    {
      "url": "https://raw.githubusercontent.com/calypr/funnel/refs/heads/develop/README.md",
      "path": "/dev"
    }
  ]
}

➜ funnel task create mount-test.json
d8pfs1s622hs739b7rh0

• Able to replicate EXECUTOR_ERROR stemming from OCI StartError: 🐛

➜ funnel task get d8pfs1s622hs739b7rh0

{
  ...
  "id":  "d8pfs1s622hs739b7rh0",
  "logs":  [
    {
      "logs":  [
        {
          "exitCode":  128,
        }
      ],
      "systemLogs":  [
         ...
        "level='error' msg='Exec error' error='executor job d8pfs1s622hs739b7rh0-0 failed with exit code 128 (StartError): failed to create containerd task: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: error during container init: error mounting \"/var/lib/kubelet/pods/64a9fb7a-5822-496c-992d-2c081d929297/containers/funnel-executor-d8pfs1s622hs739b7rh0/4dc52fb5\" to rootfs at \"/dev/termination-log\": open o_path procfd: open /run/containerd/io.containerd.runtime.v2.task/k8s.io/e4a407b35fca352200248175af22997988a90d0765dafbc358bc7fcf0f186d7c/rootfs/dev/termination-log: not a directory: unknown'"
      ]
    }
  ],
  "state":  "EXECUTOR_ERROR"
}

New Behavior ✔️

forbiddenPathPrefixes

• /dev
• /proc
• /sys
• /run
• /var/run

Tested against PR #1436 (funnel:6e404ed):

➜ helm upgrade --install funnel calypr/funnel --version 0.1.99-rc.37 --values values.yaml --set image.tag=6e404ed

➜ kubectl get deployments -o wide
NAME            IMAGES
funnel-server   quay.io/ohsu-comp-bio/funnel:6e404ed

➜ kubectl port-forward svc/funnel 8000:8000

• Getting 400 response code when attempting to submit tasks that mount /dev:

funnel

➜ funnel task create mount-test.json
Error: [STATUS CODE - 400]      {
  "error": "invalid task message:\nTask.Inputs[0].Path: \"/dev\" is not allowed as an input path\n"
} 

curl

➜ curl -X POST http://localhost:8000/v1/tasks --data @mount-test.json -w "\n[STATUS CODE - %{http_code}]\n"
{
  "error": "invalid task message:\nTask.Inputs[0].Path: \"/dev\" is not allowed as an input path\n"
}
[STATUS CODE - 400]

Breaking Changes? ❌

• This can technically be considered a breaking change since Funnel now rejects tasks that would previously run (and error) due to mounting inputs/outputs to system directories.

Next Steps 🌀

• Merge to develop
• Create new image/tag (e.g. 2026-06-23)
• Release in Helm Chart v0.1.99-rc.39

[github-actions]

Gen3 Integration Tests

filepath	passed	skipped	SUBTOTAL
tests/test_gen3_workflow.py	25	4	29
TOTAL	25	4	29

[github-actions]

Gen3 Integration Tests

filepath	passed	skipped	SUBTOTAL
tests/test_gen3_workflow.py	25	4	29
TOTAL	25	4	29

[github-actions]

Gen3 Integration Tests

filepath	passed	skipped	SUBTOTAL
tests/test_gen3_workflow.py	25	4	29
TOTAL	25	4	29

[github-actions]

Gen3 Integration Tests

filepath	passed	skipped	SUBTOTAL
tests/test_gen3_workflow.py	25	4	29
TOTAL	25	4	29