Unable to add new path and value using patch operation

[dominicfollett]

Describe the bug

"Add" patch does not add new path and value to Daemonset manifest.

Files that can reproduce the issue

Example:

kustomization.yaml

patches:
  - patch: |-
      - op: add
        path: /spec/template/spec/nodeSelector
        value: {"non-existing":true}
    target:
      kind: DaemonSet
      labelSelector: "app=datadog-agent"

Or

patches:
  - patch: |-
      - op: add
        path: /spec/template/spec/nodeSelector
        value:
           non-existing: true
    target:
      kind: DaemonSet
      labelSelector: "app=datadog-agent"

resources.yaml

apiVersion: apps/v1
kind: DaemonSet
metadata:
  name: datadog-agent
  namespace: default
spec:
  selector:
    matchLabels:
      app: datadog-agent
  template:
    metadata:
      labels:
        app: datadog-agent
      name: datadog-agent
    spec:
      serviceAccountName: datadog-agent
      containers:
      - image: datadog/agent:latest
        imagePullPolicy: IfNotPresent
        name: datadog-agent
...

...
-->

Expected output

apiVersion: apps/v1
kind: DaemonSet
metadata:
  name: datadog-agent
  namespace: default
spec:
  selector:
    matchLabels:
      app: datadog-agent
  template:
    metadata:
      labels:
        app: datadog-agent
      name: datadog-agent
    spec:
      nodeSelector:
          non-existing: "true"
      serviceAccountName: datadog-agent
      containers:
      - image: datadog/agent:latest
        imagePullPolicy: IfNotPresent
        name: datadog-agent

Actual output

apiVersion: apps/v1
kind: DaemonSet
metadata:
  name: datadog-agent
  namespace: default
spec:
  selector:
    matchLabels:
      app: datadog-agent
  template:
    metadata:
      labels:
        app: datadog-agent
      name: datadog-agent
    spec:
      serviceAccountName: datadog-agent
      containers:
      - image: datadog/agent:latest
        imagePullPolicy: IfNotPresent
        name: datadog-agent

Kustomize version

Kustomize Version: v4.5.4

Platform

MacOS Monterey 12.5.1

Additional context

[seh]

Your DaemonSet is lacking the "app" label mentioned in your patch's label selector. You have that label in the DaemonSet's pod spec template, but not on the DaemonSet itself.

[thecooldrop]

I am seeing this issue with following resources as well:

kustomization.yaml with patches:

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
namespace: argocd
resources:
  - https://raw.githubusercontent.com/argoproj/argo-cd/v2.4.15/manifests/install.yaml
configMapGenerator:
  - name: argocd-cm
    behavior: merge
    literals:
      - admin.enabled=true
  - name: http-proxies-config
    behavior: create
    literals:
      - HTTP_PROXY=http://anonymized.com
      - HTTPS_PROXY=http://anonymized.com
      - NO_PROXY=192.168.0.0/16
patches:
  - target:
      group: apps
      version: v1
      kind: Deployment
      namespace: argocd
      name: argocd-repo-server
    patch: |-
      - op: add
        path: "/spec/template/spec/containers/0/envFrom"
        value:
          - configMapRef:
              name: http-proxies-config
              optional: false

The output is (as you can see the envFrom is not included in first container of targeted Deployment):

apiVersion: apps/v1
kind: Deployment
metadata:
  labels:
    app.kubernetes.io/component: repo-server
    app.kubernetes.io/name: argocd-repo-server
    app.kubernetes.io/part-of: argocd
  name: argocd-repo-server
  namespace: argocd
spec:
  selector:
    matchLabels:
      app.kubernetes.io/name: argocd-repo-server
  template:
    metadata:
      labels:
        app.kubernetes.io/name: argocd-repo-server
    spec:
      affinity:
        podAntiAffinity:
          preferredDuringSchedulingIgnoredDuringExecution:
          - podAffinityTerm:
              labelSelector:
                matchLabels:
                  app.kubernetes.io/name: argocd-repo-server
              topologyKey: kubernetes.io/hostname
            weight: 100
          - podAffinityTerm:
              labelSelector:
                matchLabels:
                  app.kubernetes.io/part-of: argocd
              topologyKey: kubernetes.io/hostname
            weight: 5
      automountServiceAccountToken: false
      containers:
      - command:
        - sh
        - -c
        - entrypoint.sh argocd-repo-server --redis argocd-redis:6379
        env:
        - name: ARGOCD_RECONCILIATION_TIMEOUT
          valueFrom:
            configMapKeyRef:
              key: timeout.reconciliation
              name: argocd-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_LOGFORMAT
          valueFrom:
            configMapKeyRef:
              key: reposerver.log.format
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_LOGLEVEL
          valueFrom:
            configMapKeyRef:
              key: reposerver.log.level
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_PARALLELISM_LIMIT
          valueFrom:
            configMapKeyRef:
              key: reposerver.parallelism.limit
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_DISABLE_TLS
          valueFrom:
            configMapKeyRef:
              key: reposerver.disable.tls
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_TLS_MIN_VERSION
          valueFrom:
            configMapKeyRef:
              key: reposerver.tls.minversion
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_TLS_MAX_VERSION
          valueFrom:
            configMapKeyRef:
              key: reposerver.tls.maxversion
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_TLS_CIPHERS
          valueFrom:
            configMapKeyRef:
              key: reposerver.tls.ciphers
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_CACHE_EXPIRATION
          valueFrom:
            configMapKeyRef:
              key: reposerver.repo.cache.expiration
              name: argocd-cmd-params-cm
              optional: true
        - name: REDIS_SERVER
          valueFrom:
            configMapKeyRef:
              key: redis.server
              name: argocd-cmd-params-cm
              optional: true
        - name: REDISDB
          valueFrom:
            configMapKeyRef:
              key: redis.db
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_DEFAULT_CACHE_EXPIRATION
          valueFrom:
            configMapKeyRef:
              key: reposerver.default.cache.expiration
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_OTLP_ADDRESS
          valueFrom:
            configMapKeyRef:
              key: otlp.address
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_MAX_COMBINED_DIRECTORY_MANIFESTS_SIZE
          valueFrom:
            configMapKeyRef:
              key: reposerver.max.combined.directory.manifests.size
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_PLUGIN_TAR_EXCLUSIONS
          valueFrom:
            configMapKeyRef:
              key: reposerver.plugin.tar.exclusions
              name: argocd-cmd-params-cm
              optional: true
        - name: HELM_CACHE_HOME
          value: /helm-working-dir
        - name: HELM_CONFIG_HOME
          value: /helm-working-dir
        - name: HELM_DATA_HOME
          value: /helm-working-dir
        image: quay.io/argoproj/argocd:v2.4.15
        imagePullPolicy: Always
        livenessProbe:
          failureThreshold: 3
          httpGet:
            path: /healthz?full=true
            port: 8084
          initialDelaySeconds: 30
          periodSeconds: 5
        name: argocd-repo-server
        ports:
        - containerPort: 8081
        - containerPort: 8084
        readinessProbe:
          httpGet:
            path: /healthz
            port: 8084
          initialDelaySeconds: 5
          periodSeconds: 10
        securityContext:
          allowPrivilegeEscalation: false
          capabilities:
            drop:
            - all
          readOnlyRootFilesystem: true
          runAsNonRoot: true
        volumeMounts:
        - mountPath: /app/config/ssh
          name: ssh-known-hosts
        - mountPath: /app/config/tls
          name: tls-certs
        - mountPath: /app/config/gpg/source
          name: gpg-keys
        - mountPath: /app/config/gpg/keys
          name: gpg-keyring
        - mountPath: /app/config/reposerver/tls
          name: argocd-repo-server-tls
        - mountPath: /tmp
          name: tmp
        - mountPath: /helm-working-dir
          name: helm-working-dir
        - mountPath: /home/argocd/cmp-server/plugins
          name: plugins
      initContainers:
      - command:
        - cp
        - -n
        - /usr/local/bin/argocd
        - /var/run/argocd/argocd-cmp-server
        image: quay.io/argoproj/argocd:v2.4.15
        name: copyutil
        securityContext:
          allowPrivilegeEscalation: false
          capabilities:
            drop:
            - all
          readOnlyRootFilesystem: true
          runAsNonRoot: true
        volumeMounts:
        - mountPath: /var/run/argocd
          name: var-files
      serviceAccountName: argocd-repo-server
      volumes:
      - configMap:
          name: argocd-ssh-known-hosts-cm
        name: ssh-known-hosts
      - configMap:
          name: argocd-tls-certs-cm
        name: tls-certs
      - configMap:
          name: argocd-gpg-keys-cm
        name: gpg-keys
      - emptyDir: {}
        name: gpg-keyring
      - emptyDir: {}
        name: tmp
      - emptyDir: {}
        name: helm-working-dir
      - name: argocd-repo-server-tls
        secret:
          items:
          - key: tls.crt
            path: tls.crt
          - key: tls.key
            path: tls.key
          - key: ca.crt
            path: ca.crt
          optional: true
          secretName: argocd-repo-server-tls
      - emptyDir: {}
        name: var-files
      - emptyDir: {}
        name: plugins

but if I use patchesJson6902 as in:

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
namespace: argocd
resources:
  - https://raw.githubusercontent.com/argoproj/argo-cd/v2.4.15/manifests/install.yaml
configMapGenerator:
  - name: argocd-cm
    behavior: merge
    literals:
      - admin.enabled=true
  - name: http-proxies-config
    behavior: create
    literals:
      - HTTP_PROXY=http://anonymized.com
      - HTTPS_PROXY=http://anonymized.com
      - NO_PROXY=192.168.0.0/16
patchesJson6902:
  - target:
      group: apps
      version: v1
      kind: Deployment
      namespace: argocd
      name: argocd-repo-server
    patch: |-
      - op: add
        path: "/spec/template/spec/containers/0/envFrom"
        value:
          - configMapRef:
              name: http-proxies-config
              optional: false

then output is:

apiVersion: apps/v1
kind: Deployment
metadata:
  labels:
    app.kubernetes.io/component: repo-server
    app.kubernetes.io/name: argocd-repo-server
    app.kubernetes.io/part-of: argocd
  name: argocd-repo-server
  namespace: argocd
spec:
  selector:
    matchLabels:
      app.kubernetes.io/name: argocd-repo-server
  template:
    metadata:
      labels:
        app.kubernetes.io/name: argocd-repo-server
    spec:
      affinity:
        podAntiAffinity:
          preferredDuringSchedulingIgnoredDuringExecution:
          - podAffinityTerm:
              labelSelector:
                matchLabels:
                  app.kubernetes.io/name: argocd-repo-server
              topologyKey: kubernetes.io/hostname
            weight: 100
          - podAffinityTerm:
              labelSelector:
                matchLabels:
                  app.kubernetes.io/part-of: argocd
              topologyKey: kubernetes.io/hostname
            weight: 5
      automountServiceAccountToken: false
      containers:
      - command:
        - sh
        - -c
        - entrypoint.sh argocd-repo-server --redis argocd-redis:6379
        env:
        - name: ARGOCD_RECONCILIATION_TIMEOUT
          valueFrom:
            configMapKeyRef:
              key: timeout.reconciliation
              name: argocd-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_LOGFORMAT
          valueFrom:
            configMapKeyRef:
              key: reposerver.log.format
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_LOGLEVEL
          valueFrom:
            configMapKeyRef:
              key: reposerver.log.level
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_PARALLELISM_LIMIT
          valueFrom:
            configMapKeyRef:
              key: reposerver.parallelism.limit
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_DISABLE_TLS
          valueFrom:
            configMapKeyRef:
              key: reposerver.disable.tls
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_TLS_MIN_VERSION
          valueFrom:
            configMapKeyRef:
              key: reposerver.tls.minversion
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_TLS_MAX_VERSION
          valueFrom:
            configMapKeyRef:
              key: reposerver.tls.maxversion
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_TLS_CIPHERS
          valueFrom:
            configMapKeyRef:
              key: reposerver.tls.ciphers
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_CACHE_EXPIRATION
          valueFrom:
            configMapKeyRef:
              key: reposerver.repo.cache.expiration
              name: argocd-cmd-params-cm
              optional: true
        - name: REDIS_SERVER
          valueFrom:
            configMapKeyRef:
              key: redis.server
              name: argocd-cmd-params-cm
              optional: true
        - name: REDISDB
          valueFrom:
            configMapKeyRef:
              key: redis.db
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_DEFAULT_CACHE_EXPIRATION
          valueFrom:
            configMapKeyRef:
              key: reposerver.default.cache.expiration
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_OTLP_ADDRESS
          valueFrom:
            configMapKeyRef:
              key: otlp.address
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_MAX_COMBINED_DIRECTORY_MANIFESTS_SIZE
          valueFrom:
            configMapKeyRef:
              key: reposerver.max.combined.directory.manifests.size
              name: argocd-cmd-params-cm
              optional: true
        - name: ARGOCD_REPO_SERVER_PLUGIN_TAR_EXCLUSIONS
          valueFrom:
            configMapKeyRef:
              key: reposerver.plugin.tar.exclusions
              name: argocd-cmd-params-cm
              optional: true
        - name: HELM_CACHE_HOME
          value: /helm-working-dir
        - name: HELM_CONFIG_HOME
          value: /helm-working-dir
        - name: HELM_DATA_HOME
          value: /helm-working-dir
        envFrom:
        - configMapRef:
            name: http-proxies-config-5dth2d9c9g
            optional: false
        image: quay.io/argoproj/argocd:v2.4.15
        imagePullPolicy: Always
        livenessProbe:
          failureThreshold: 3
          httpGet:
            path: /healthz?full=true
            port: 8084
          initialDelaySeconds: 30
          periodSeconds: 5
        name: argocd-repo-server
        ports:
        - containerPort: 8081
        - containerPort: 8084
        readinessProbe:
          httpGet:
            path: /healthz
            port: 8084
          initialDelaySeconds: 5
          periodSeconds: 10
        securityContext:
          allowPrivilegeEscalation: false
          capabilities:
            drop:
            - all
          readOnlyRootFilesystem: true
          runAsNonRoot: true
        volumeMounts:
        - mountPath: /app/config/ssh
          name: ssh-known-hosts
        - mountPath: /app/config/tls
          name: tls-certs
        - mountPath: /app/config/gpg/source
          name: gpg-keys
        - mountPath: /app/config/gpg/keys
          name: gpg-keyring
        - mountPath: /app/config/reposerver/tls
          name: argocd-repo-server-tls
        - mountPath: /tmp
          name: tmp
        - mountPath: /helm-working-dir
          name: helm-working-dir
        - mountPath: /home/argocd/cmp-server/plugins
          name: plugins
      initContainers:
      - command:
        - cp
        - -n
        - /usr/local/bin/argocd
        - /var/run/argocd/argocd-cmp-server
        image: quay.io/argoproj/argocd:v2.4.15
        name: copyutil
        securityContext:
          allowPrivilegeEscalation: false
          capabilities:
            drop:
            - all
          readOnlyRootFilesystem: true
          runAsNonRoot: true
        volumeMounts:
        - mountPath: /var/run/argocd
          name: var-files
      serviceAccountName: argocd-repo-server
      volumes:
      - configMap:
          name: argocd-ssh-known-hosts-cm
        name: ssh-known-hosts
      - configMap:
          name: argocd-tls-certs-cm
        name: tls-certs
      - configMap:
          name: argocd-gpg-keys-cm
        name: gpg-keys
      - emptyDir: {}
        name: gpg-keyring
      - emptyDir: {}
        name: tmp
      - emptyDir: {}
        name: helm-working-dir
      - name: argocd-repo-server-tls
        secret:
          items:
          - key: tls.crt
            path: tls.crt
          - key: tls.key
            path: tls.key
          - key: ca.crt
            path: ca.crt
          optional: true
          secretName: argocd-repo-server-tls
      - emptyDir: {}
        name: var-files
      - emptyDir: {}
        name: plugins

[natasha41575]

According to https://www.rfc-editor.org/rfc/rfc6902#section-4.1:

If the target location specifies an object member that does not
already exist, a new member is added to the object.

What I think that means is that the JSON patch should be creating the new path/value if it is not already there. I'm doubtful that this is something we can fix in kustomize, as my guess is that we probably use some JSON patch library, but it would be helpful to have someone investigate.

/triage accepted

In the meantime, you may find replacements to be a better alternative to do this creation operation.

[thecooldrop]

In my case the issue is that patches stanza is not processing Json6902 patches as expected, and behaves differently from patchesJson6902 stanza, while documentation is saying that Json6902 patches are usable with patches stanza as well.

So the issue is actually the divergent behavior, where it should actually be the same, and not that Json6902 patch is not behaving as expected.

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/remove-triage accepted

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