kustomize does not remove items of an array using strategic merge

[oliver-goetz]

Describe the bug

Deleting items from an array using strategic merge patch does not work as expected in my base-overlay scenario. Instead of removing the items from the list, it replaces the list content.

Please see my example below. The outputs are those of kustomize build ./001 command.

Files that can reproduce the issue

Base layer - directory ./000

kustomization.yaml

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization

resources:
- prometheus-rules.yaml

prometheus-rules.yaml

apiVersion: monitoring.coreos.com/v1
kind: PrometheusRule
metadata:
  labels:
    app.kubernetes.io/name: kube-prometheus
    app.kubernetes.io/part-of: kube-prometheus
    prometheus: k8s
    role: alert-rules
  name: kubernetes-monitoring-rules
  namespace: monitoring
spec:
  groups:
  - name: kubernetes-system-scheduler
    rules:
    - alert: KubeSchedulerDown
      annotations:
        description: KubeScheduler has disappeared from Prometheus target discovery.
        runbook_url: https://runbooks.prometheus-operator.dev/runbooks/kubernetes/kubeschedulerdown
        summary: Target disappeared from Prometheus target discovery.
      expr: |
        absent(up{job="kube-scheduler"} == 1)
      for: 15m
      labels:
        severity: critical
  - name: kubernetes-system-controller-manager
    rules:
    - alert: KubeControllerManagerDown
      annotations:
        description: KubeControllerManager has disappeared from Prometheus target
          discovery.
        runbook_url: https://runbooks.prometheus-operator.dev/runbooks/kubernetes/kubecontrollermanagerdown
        summary: Target disappeared from Prometheus target discovery.
      expr: |
        absent(up{job="kube-controller-manager"} == 1)
      for: 15m
      labels:
        severity: critical
  - name: kubernetes-system-kube-proxy
    rules:
    - alert: KubeProxyDown
      annotations:
        description: KubeProxy has disappeared from Prometheus target discovery.
        runbook_url: https://runbooks.prometheus-operator.dev/runbooks/kubernetes/kubeproxydown
        summary: Target disappeared from Prometheus target discovery.
      expr: |
        absent(up{job="kube-proxy"} == 1)
      for: 15m
      labels:
        severity: critical

Overlay - directory ./001

kustomization.yaml

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization

bases:
- ../000

patchesStrategicMerge:
- prometheus-rules-merge.yaml

prometheus-rules-merge.yaml

apiVersion: monitoring.coreos.com/v1
kind: PrometheusRule
metadata:
  name: kubernetes-monitoring-rules
  namespace: monitoring
spec:
  groups:
  - $patch: delete
    name: kubernetes-system-scheduler
  - $patch: delete
    name: kubernetes-system-controller-manager

Expected output

apiVersion: monitoring.coreos.com/v1
kind: PrometheusRule
metadata:
  labels:
    app.kubernetes.io/name: kube-prometheus
    app.kubernetes.io/part-of: kube-prometheus
    prometheus: k8s
    role: alert-rules
  name: kubernetes-monitoring-rules
  namespace: monitoring
spec:
  groups:
  - name: kubernetes-system-kube-proxy
    rules:
    - alert: KubeProxyDown
      annotations:
        description: KubeProxy has disappeared from Prometheus target discovery.
        runbook_url: https://runbooks.prometheus-operator.dev/runbooks/kubernetes/kubeproxydown
        summary: Target disappeared from Prometheus target discovery.
      expr: |
        absent(up{job="kube-proxy"} == 1)
      for: 15m
      labels:
        severity: critical

Actual output

apiVersion: monitoring.coreos.com/v1
kind: PrometheusRule
metadata:
  labels:
    app.kubernetes.io/name: kube-prometheus
    app.kubernetes.io/part-of: kube-prometheus
    prometheus: k8s
    role: alert-rules
  name: kubernetes-monitoring-rules
  namespace: monitoring
spec:
  groups:
  - $patch: delete
    name: kubernetes-system-scheduler
  - $patch: delete
    name: kubernetes-system-controller-manager

Kustomize version

{Version:kustomize/v4.5.4 GitCommit:cf3a452ddd6f83945d39d582243b8592ec627ae3 BuildDate:2022-03-28T23:06:20Z GoOs:darwin GoArch:amd64}

Platform macOS

Additional context

[k8s-ci-robot]

@oliver-goetz: This issue is currently awaiting triage.

SIG CLI takes a lead on issue triage for this repo, but any Kubernetes member can accept issues by applying the triage/accepted label.

The triage/accepted label can be added by org members by writing /triage accepted in a comment.

Instructions for interacting with me using PR comments are available here. If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository.

[RafalMaleska]

stumbled about exactly the same issue when trying to paste away (exactly the same) elements in a list.

[pjastrzabek]

There is really no easy and reliable way of removing elements from lists with kustomize. What I ended up doing was patching via reference to an index

/spec/groups/5

which will cause problems as soon as upstream project will reorder elements.

What would be usefull is to support field expressions in delete patches /spec/groups/.[name=kubernetes-system-controller-manager]

[alexis-wefight]

Is there any workaround for this (without using the index number, which is not reliable)? I have exactly the same issue (with the same Prometheus rules I want to remove).

[KnVerey]

I suspect the problem here is that you're trying to patch a custom resource without providing the schema for it (via the openapi field). By default, SMPs replace arrays. If you provide a schema with the extensions for spec.groups specified and that doesn't fix it, please reopen.

/triage duplicate of https://github.com/kubernetes-sigs/kustomize/issues/4175, https://github.com/kubernetes-sigs/kustomize/issues/4514 and others /kind support /remove-kind bug /triage resolved

[k8s-ci-robot]

@KnVerey: The label(s) triage/of, triage/https://github.com/kubernetes-sigs/kustomize/issues/4175,, triage/https://github.com/kubernetes-sigs/kustomize/issues/4514, triage/and, triage/others cannot be applied, because the repository doesn't have them.

In response to this:

I suspect the problem here is that you're trying to patch a custom resource without providing the schema for it (via the openapi field). By default, SMPs replace arrays. If you provide a schema with the extensions for spec.groups specified and that doesn't fix it, please reopen.

/triage duplicate of https://github.com/kubernetes-sigs/kustomize/issues/4175, https://github.com/kubernetes-sigs/kustomize/issues/4514 and others /kind support /remove-kind bug /triage resolved

Instructions for interacting with me using PR comments are available here. If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository.