Is there a way to make kustomize merge headings in a yaml file instead of completely replacing that heading with the overlay yaml - merge

Question

i have a base yaml and an overlay yaml and using "kustomize" i want to merge these two yaml. what happens with me is that on running kustomize build there comes an output but it is not expected why? because the kustomize instead of filling the custom information from the overlay yaml replaces the whole heading tag of the base with the overlay "containers" in my case. The intended behaviour that i need is the it should somehow fill in the missing information using the overlay yaml instead of replacement.
base yaml:
apiVersion: v1
kind: Pod
metadata:
name: temp
labels:
tier: temp
spec:
containers:
- name: temp
image: temp
imagePullPolicy: Always
command: temp
args:
temp
envFrom:
- configMapRef:
name: temp
volumeMounts:
volumes:
overlay yaml:
apiVersion: v1
kind: Pod
metadata:
name: temp
labels:
tier: temp
spec:
containers:
volumeMounts:
- name: temppathname
mountPath: /temppath
volumes:
- name: temppathname
hostPath:
type: temp
path: temppath
Expected result after kustomize build:
apiVersion: v1
kind: Pod
metadata:
name: temp
labels:
tier: temp
spec:
containers:
- name: temp
image: temp
imagePullPolicy: Always
command: temp
args:
["sleep 9000"]
envFrom:
- configMapRef:
name: temp
volumeMounts:
- name: temppathname
mountPath: /temppath
volumes:
- name: temppathname
hostPath:
type: temp
path: temppath
what i'm getting:
apiVersion: v1
kind: Pod
metadata:
labels:
tier: temp
name: temp
spec:
containers:
volumeMounts:
- name: temppathname
mountPath: /temppath
volumes:
- name: temppathname
hostPath:
type: temp
path: temppath

Answer 1

In your base.yaml the value for the key containers is a sequence (node). In your overlay.yaml the value for the key containers is a mapping. Of course those two cannot be merged.
Not knowing kustomize at all, it seems logical that because those cannot be merged, the overlay replaces that whole sequence node with the mapping node. Your expectation that the mapping of the overlay is merged with a mapping that happens to be an item (in this case the only item) in the sequence of the base seems completely arbitrary. Which item would need to be taken if there had been multiple items? The first? The last? The last one before item five that is a mapping?
If your overlay.yaml looked like:
apiVersion: v1
kind: Pod
metadata:
name: temp
labels:
tier: temp
spec:
containers:
- volumeMounts: # < created a sequence item here by inserting an item indicator
- name: temppathname
mountPath: /temppath
volumes:
- name: temppathname
hostPath:
type: temp
path: temppath
then I could understand your expectation (and maybe the above change can be applied to make it work, I don't have a way to test).

Answer 2

I find that the easiest way to deal with this is to use JSONPatch. I would remove the empty fields of the base as in:
apiVersion: v1
kind: Pod
metadata:
name: temp
labels:
tier: temp
spec:
containers:
- name: temp
image: temp
imagePullPolicy: Always
command: temp
args:
temp
envFrom:
- configMapRef:
name: temp
Then in your overlay create a new patch, for example named create_volume.yml:
- op: add
path: /spec/volumes/-
value:
name: temppathname
hostPath:
type: temp
path: temppath
- op: add
path: /spec/containers/0/volumeMounts/-
value:
name: temppathname
mountPath: /temppath
And finally in the overlay kustomization.yml add:
patchesJson6902:
- target:
version: v1
kind: Pod
name: temp
path: create_volume.yml
If it doesn't work you might have to play with the API group in the patch target. I only patched deployments until now and my target would be:
- target:
group: apps
version: v1
kind: Deployment
name: temp
path: create_volume.yml