How to overwrite file at a deployment time in kubernetes?

Question

I'm trying to deploy Diffusion image in kubernetes and I need to overwrite one of Diffusion configuration files at deployment time.

Actually it is a SystemAuthentication.store file with default credentials in /opt/Diffusion6.0.3_01/etc/. I'm storing new file in secret and mount it into etc/test/ which can be seen in below deployment file.

template:
metadata:
  labels:
    run: diffusion
spec:
  serviceAccountName: diffusion-role
  volumes:
  - name: diffusion-secrets
    secret:
      secretName: diffusion-license
  - name: ssl-cert
    secret:
      secretName: ssl-certificate
  - name: system-authentication
    secret:
      secretName: system-authentication-store
  containers:
  - image: pushtechnology/diffusion:6.0.3
    imagePullPolicy: IfNotPresent
    name: diffusion
    ports:
    - containerPort: 8080
      protocol: TCP
    - containerPort: 8443
      protocol: TCP
    volumeMounts:
    - name: diffusion-secrets
      mountPath: /etc/diffusion-secrets
      readOnly: true
    - name: ssl-cert
      mountPath: /etc/test/
      readOnly: true
    - name: system-authentication
      mountPath: /etc/test/
    command: [ "/bin/sh", "-c", "cp etc/test/SystemAuthentication.store /opt/DIffusion6.0.3_01" ]

When I deploy this image pods are failing with

Events:
Type     Reason                 Age              From                                   Message
----     ------                 ----             ----                               -------
Normal   Scheduled              2m               default-scheduler                  Successfully assigned diffusion-db6d6df7b-f5tp4 to timmy.pushtechnology.com
Normal   SuccessfulMountVolume  2m               kubelet, timmy.pushtechnology.com  MountVolume.SetUp succeeded for volume "diffusion-role-token-n59ds"
Normal   SuccessfulMountVolume  2m               kubelet, timmy.pushtechnology.com  MountVolume.SetUp succeeded for volume "ssl-cert"
Normal   SuccessfulMountVolume  2m               kubelet, timmy.pushtechnology.com  MountVolume.SetUp succeeded for volume "system-authentication"
Normal   SuccessfulMountVolume  2m               kubelet, timmy.pushtechnology.com  MountVolume.SetUp succeeded for volume "diffusion-secrets"
Normal   Killing                1m (x2 over 1m)  kubelet, timmy.pushtechnology.com  Killing container with id docker://diffusion:FailedPostStartHook
Warning  BackOff                1m (x2 over 1m)  kubelet, timmy.pushtechnology.com  Back-off restarting failed container
Normal   Pulled                 1m (x3 over 2m)  kubelet, timmy.pushtechnology.com  Container image "pushtechnology/diffusion:6.0.3" already present on machine
Normal   Created                1m (x3 over 1m)  kubelet, timmy.pushtechnology.com  Created container
Normal   Started                1m (x3 over 1m)  kubelet, timmy.pushtechnology.com  Started container
Warning  FailedPostStartHook    1m (x3 over 1m)  kubelet, timmy.pushtechnology.com  
Warning  FailedSync             1m (x5 over 1m)  kubelet, timmy.pushtechnology.com  Error syncing pod

I have tried also workaruond described here: https://github.com/kubernetes/kubernetes/issues/19764#issuecomment-269879587

with same results.

Answer 1

I think @svenwtl answer might be correct, but a Dockerfile of the image I'm using has some complicated constructs that I had no idea how to use in the deployment file. The fix which has worked for me (after a long try/fail loop) was to actually use a container lifecycle hook:

    volumeMounts:
    - name: diffusion-secrets
      mountPath: /etc/diffusion-secrets
      readOnly: true
    - name: ssl-cert
      mountPath: /etc/test/
      readOnly: true
    - name: system-authentication
      mountPath: /etc/test1/
    lifecycle:
      postStart:
        exec:
          command: [ "/bin/sh", "-c", "cp -f /etc/test1/SystemAuthentication.store /opt/Diffusion6.0.3_01/etc/" ]

I also mounted SystemAuthentication in different folder /etc/test1, but I don't think this was part of the fix.