Fix bug where user mounted files were being removed by agent

[bjee19]

Proposed changes

Fix bug where user mounted files were being removed by agent.

Problem: User mounted files are being removed by nginx agent.

Solution: Mark user mounted files as unmanaged so nginx agent doesn't remove them. To do so we use agent's UpdateOverview function to get all files referenced in the nginx conf. We compare that with the user added volumeMounts and mark any files that were user mounted as unmanaged, ensuring nginx agent doesn't remove them.

Testing: Added unit tests and manual testing.

Closes #3776

Checklist

Before creating a PR, run through this checklist and mark each as complete.

• I have read the CONTRIBUTING doc
• I have added tests that prove my fix is effective or that my feature works
• I have checked that all unit tests pass after adding my changes
• I have updated necessary documentation
• I have rebased my branch onto main
• I will ensure my PR is targeting the main branch and pulling from my branch from my own fork

Release notes

If this PR introduces a change that affects users and needs to be mentioned in the release notes,
please add a brief note that summarizes the change.

Fix bug where user mounted files were being removed by NGINX. 

[bjee19]

Will add more details on manual testing below, then will mark PR as ready to review.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.00%. Comparing base (5c78a60) to head (a736dd6).
⚠️ Report is 18 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #4178   +/-   ##
=======================================
  Coverage   85.99%   86.00%           
=======================================
  Files         131      131           
  Lines       14063    14144   +81     
  Branches       35       35           
=======================================
+ Hits        12093    12164   +71     
- Misses       1770     1775    +5     
- Partials      200      205    +5     

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[bjee19]

With these yamls:

apiVersion: gateway.networking.k8s.io/v1
kind: HTTPRoute
metadata:
  name: coffee
spec:
  parentRefs:
  - name: gateway
    sectionName: http
  hostnames:
  - "cafe.example.com"
  rules:
  - matches:
    - path:
        type: PathPrefix
        value: /coffee
    filters:
        - type: ExtensionRef
          extensionRef:
            group: gateway.nginx.org
            kind: SnippetsFilter
            name: test
    backendRefs:
    - name: coffee
      port: 80
---
apiVersion: apps/v1
kind: Deployment
metadata:
  name: coffee
spec:
  replicas: 1
  selector:
    matchLabels:
      app: coffee
  template:
    metadata:
      labels:
        app: coffee
    spec:
      containers:
      - name: coffee
        image: nginxdemos/nginx-hello:plain-text
        ports:
        - containerPort: 8080
---
apiVersion: v1
kind: Service
metadata:
  name: coffee
spec:
  ports:
  - port: 80
    targetPort: 8080
    protocol: TCP
    name: http
  selector:
    app: coffee
---
apiVersion: gateway.networking.k8s.io/v1
kind: Gateway
metadata:
  name: gateway
spec:
  gatewayClassName: nginx
  listeners:
  - name: http
    port: 80
    protocol: HTTP
    hostname: "*.example.com"
---
apiVersion: v1
kind: Secret
metadata:
  name: cafe-secret
type: kubernetes.io/tls
data:
  tls.crt: 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
  tls.key: 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
---
apiVersion: gateway.nginx.org/v1alpha1
kind: SnippetsFilter
metadata:
  name: test
spec:
  snippets:
  - context: http.server
    value: |
      client_header_buffer_size 2k;
      ssl_client_certificate /etc/nginx/certs/my-certs/tls.crt;
      ssl_verify_client optional;
      ssl_verify_depth 2;

      proxy_connect_timeout 60s;
      proxy_read_timeout 60s;
      proxy_send_timeout 60s;

And a modified NginxProxy:

spec:
  ipFamily: dual
  kubernetes:
    deployment:
      container:
        image:
          pullPolicy: Never
          repository: nginx-gateway-fabric/nginx
          tag: b.jee
        volumeMounts:
        - mountPath: /etc/nginx/my-certs/
          name: cafe-secret
      pod:
        volumes:
        - name: cafe-secret
          secret:
            secretName: cafe-secret
      replicas: 1
    service:
      externalTrafficPolicy: Local
      type: NodePort

I've verified that the certs are able to be mounted. (that tls key is the same we use in our public examples, not a real secret).

[bjee19]

@ciarams87 and other reviewers, one thing to note is if a user is to add a volumeMount that is an existing directory / other nginx conf files are in it, those will be marked as unmanaged and will make agent fail to startup (I tried /etc/nginx).

With our current constraints, I can't think of a way around this, so I think it is fine to require users to mount their files into a new directory. Any thoughts?

[ciarams87]

@ciarams87 and other reviewers, one thing to note is if a user is to add a volumeMount that is an existing directory / other nginx conf files are in it, those will be marked as unmanaged and will make agent fail to startup (I tried /etc/nginx).

With our current constraints, I can't think of a way around this, so I think it is fine to require users to mount their files into a new directory. Any thoughts?

@bjee19 So /etc/nginx won't work but /etc/nginx/my-folder will?

That makes a lot of sense, and we should absolutely require users mount their files into a new directory.

We should clearly document that new volume mounts cannot conflict with our internal volume mounts and folder structure.

[ciarams87]

lgtm!

[bjee19]

So /etc/nginx won't work but /etc/nginx/my-folder will?

yep

[sjberman]

Could have volume mounts on a DaemonSet as well.

[salonichf5]

great job 🥳