ArgoCD tries to delete the contents of argocd-cm.yaml with kustomize bases

[cullenmcdermott]

Describe the bug
When using the provide Kustomize Manifests and configuring Argo CD to manage itself, every hard refresh will switch between In Sync and Out of Sync. It tries to delete the data block from the argo-cm.yaml configmap.

Here is a redacted version of my argocd-cm.yaml. It tries to remove everything under the data key.

apiVersion: v1
data:
  repositories: |
    - passwordSecret:
        key: password
        name: git-credentials
      url: https://gitlab.example.com/user/kubernetes
      usernameSecret:
        key: username
        name: git-credentials
  url: http://localhost:4000
kind: ConfigMap
metadata:
  name: argocd-cm
  namespace: argocd
  labels:
    app.kubernetes.io/instance: argocd
    app.kubernetes.io/name: argocd-cm
    app.kubernetes.io/part-of: argocd

To Reproduce

1. Create an "ArgoCD" Application in ArgoCD and configure it with a kustomization.yaml similar to this:

bases:
  - github.com/argoproj/argo-cd//manifests/cluster-install?ref=v1.1.2
namespace: argocd
patchesJson6902:
  - path: container_arg_patch.yaml
    target:
      group: apps
      kind: Deployment
      name: argocd-server
      version: v1
resources:
  - ingress.yaml
  - argocd-cm.yaml
commonLabels:
  app.kubernetes.io/instance: argocd
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization

2. Make sure it is in sync with your git provider.
3. In the UI click Hard Refresh it will go out of sync
4. Click hard refresh again it will go out of sync

It doesn't happen every time but I'm able to replicate it about 1/4 to 2/3 of the time.

Expected behavior
It should stay In Sync

Version

$ argocd version 
argocd: v1.1.2+567fcc3.dirty
  BuildDate: 2019-07-30T17:45:54Z
  GitCommit: 567fcc33140ec93051fdf8d0af7ea404deb64f20
  GitTreeState: dirty
  GoVersion: go1.11.4
  Compiler: gc
  Platform: linux/amd64
argocd-server: v1.1.2+567fcc3.dirty
  BuildDate: 2019-07-30T17:47:02Z
  GitCommit: 567fcc33140ec93051fdf8d0af7ea404deb64f20
  GitTreeState: dirty
  GoVersion: go1.11.4
  Compiler: gc
  Platform: linux/amd64
  Ksonnet Version: 0.13.1

[alexmt]

Thank you for providing clear steps to reproduce, @cullenmcdermott ! Got exact same behavior using https://github.com/alexmt/argocd-example-apps/tree/2173/bug .

I believe this is kustomize 2.0.3 bug. The argocd-cm config map already defined in the remote base, so config map should be modified using patch instead of added as a new resource. E.g.

bases:
  - github.com/argoproj/argo-cd//manifests/cluster-install?ref=v1.1.2
namespace: argocd
patchesJson6902:
  - path: container_arg_patch.yaml
    target:
      group: apps
      kind: Deployment
      name: argocd-server
      version: v1
resources:
  - ingress.yaml
patchesStrategicMerge:
  - argocd-cm.yaml
commonLabels:
  app.kubernetes.io/instance: argocd
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization

I think kustomize should return error in this case, but kustomize 2.0.3 just ignore conflicting resource and return unmodified version from the remote base. The kustomize 3.x returns error. It also panics but at least it is clear that kustomization.yaml has an error.

[alexmt]

I guess we can close it. Please feel free to reopen if solution does not help