Buil fails when using components and strategic merge patch and null node

[matthewhughes-uw]

What happened?

Given the following setup:

├── annotations.yaml
├── components
│   └── kustomization.yaml
├── kustomization.yaml
└── manifests.yaml

With contents:

# kustomization.yaml
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization

resources:
  - manifests.yaml

patches:
  - path: annotations.yaml

components:
  - components

# manifests.yaml
---
apiVersion: apps/v1
kind: Deployment
metadata:
  name: my-nginx
  namespace: my-namespace
spec:
  selector:
    matchLabels:
      run: my-nginx
  replicas: 2
  template:
    metadata:
      labels:
        run: my-nginx
    spec:
      # NOTE: empty initContainers
      initContainers:
      containers:
      - name: my-nginx
        image: nginx
        ports:
        - containerPort: 80
        env:
          - name: MY_POD_NAME
            valueFrom:
              fieldRef:
                fieldPath: metadata.name
      affinity:
        podAffinity:
          # imagine some complicated affinity setup
          # we want the component to strip these
          podAffinity: {}
---
apiVersion: v1
kind: Service
metadata:
  name: my-nginx
  namespace: my-namespace
  labels:
    run: my-nginx
spec:
  ports:
  - port: 80
    protocol: TCP
  selector:
    run: my-nginx

# annotations.yaml
# placeholder patch, just need any patch
---
apiVersion: apps/v1
kind: Deployment
metadata:
  name: my-nginx
  namespace: my-namespace
  annotations:
    example.com/my.tool: blah
---
apiVersion: v1
kind: Service
metadata:
  name: my-nginx
  namespace: my-namespace
  annotations:
    example.com/my.tool: blah

# components/kustomization.yaml
apiVersion: kustomize.config.k8s.io/v1alpha1
kind: Component

patches:
  - target:
      version: v1
      group: apps
    # example patch, just something that reaches inside /spec/template/spec
    patch: |-
      - op: remove
        path: /spec/template/spec/affinity/podAffinity

Then running kustomize build fails with:

Error: updating name reference in 'spec/template/spec/initContainers/env/valueFrom/configMapKeyRef/name' field of 'Deployment.v1.apps/my-nginx.my-namespace': considering field 'spec/template/spec/initContainers/env/valueFrom/configMapKeyRef/name' of object Deployment.v1.apps/my-nginx.my-namespace: expected sequence or mapping node

What did you expect to happen?

kustomize build would succeed

How can we reproduce it (as minimally and precisely as possible)?

See details above

Expected output

apiVersion: v1
kind: Service
metadata:
  annotations:
    example.com/my.tool: blah
  labels:
    run: my-nginx
  name: my-nginx
  namespace: my-namespace
spec:
  ports:
  - port: 80
    protocol: TCP
  selector:
    run: my-nginx
---
apiVersion: apps/v1
kind: Deployment
metadata:
  annotations:
    example.com/my.tool: blah
  name: my-nginx
  namespace: my-namespace
spec:
  replicas: 2
  selector:
    matchLabels:
      run: my-nginx
  template:
    metadata:
      labels:
        run: my-nginx
    spec:
      affinity: {}
      containers:
      - env:
        - name: MY_POD_NAME
          valueFrom:
            fieldRef:
              fieldPath: metadata.name
        image: nginx
        name: my-nginx
        ports:
        - containerPort: 80

Actual output

The error

Error: updating name reference in 'spec/template/spec/initContainers/env/valueFrom/configMapKeyRef/name' field of 'Deployment.v1.apps/my-nginx.my-namespace': considering field 'spec/template/spec/initContainers/env/valueFrom/configMapKeyRef/name' of object Deployment.v1.apps/my-nginx.my-namespace: expected sequence or mapping node

Note: things work as expected if the patches are provided as inline JSON6902 patches, i.e. update kustomization.yaml to:

  - target:
      version: v1
      group: apps
      kind: Deployment
    patch: |-
      - op: add
        path: /metadata/annotations/example.com~1my.tool
        value: blah
  - target:
      version: v1
      kind: Service
    patch: |-
      - op: add
        path: /metadata/annotations/example.com~1my.tool
        value: blah

Kustomize version

v5.3.0

Operating system

Linux

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[matthewhughes-uw]

This feels related to #5050

note in our case we have e.g. initContainers: (i.e. initContainers: null) because the manifests were built from some helm charts and that was what helm originally gave as output

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