Fix input/output duplication in file_mapper

[lbeckman314]

Important

This PR is built off of PR #1407 and can be merged to develop (after #1407 is merged)

Overview 🌀

This PR resolves the following file_mapper error introduced when merging Commit 5b95fa0:

Current Behavior ❌

Error: kubernetes system error (JobCreationFailed):
Failed to create Kubernetes job: Job.batch "<TASK ID>-0" is invalid:
spec.template.spec.containers[0].volumeMounts[2].mountPath: Invalid value: "/data": must be unique

volumeMounts:
  - name: funnel-storage-<TASK ID>
    mountPath: /tmp
    subPath: <TASK ID>/tmp

  - name: funnel-storage-<TASK ID>
    mountPath: /work          <----- Duplicate mountPath ⚠️
    subPath: <TASK ID>/work

  - name: funnel-storage-<TASK ID>
    mountPath: /work          <----- Duplicate mountPath ⚠️
    subPath: <TASK ID>/work

  - name: funnel-storage-<TASK ID>
    mountPath: /local/work/tmp/.../bin
    subPath: <TASK ID>/local/work/tmp/.../bin

volumes:
- name: funnel-storage-<TASK ID>
persistentVolumeClaim:
  claimName: funnel-worker-pvc-<TASK ID>

This duplication is only happening if we have both inputs and outputs (regardless of the number).

Steps to Reproduce

To test it, create any TES task with at least one input and output.

New Behavior ✔️

Tip

No duplicated volumes!

volumeMounts:
  - name: funnel-storage-<TASK ID>
    mountPath: /tmp
    subPath: <TASK ID>/tmp

  - name: funnel-storage-<TASK ID>
    mountPath: /work
    subPath: <TASK ID>/work

  - name: funnel-storage-<TASK ID>
    mountPath: /local/work/tmp/.../bin
    subPath: <TASK ID>/local/work/.../bin

volumes:
- name: funnel-storage-<TASK ID>
  persistentVolumeClaim:
    claimName: funnel-worker-pvc-<TASK ID>

Credits 🤝

This issue was first identified and documented by @nss10 and the CTDS team, thank you!

[lbeckman314]

• Temp. enabling bypass for merging this PR in order to unblock integration tests (then disabling after merge)

• Moving forward this ruleset should remain as-is (no bypass allowed)!