Error: json: unknown field "env"

[andrewm4894]

/kind bug

I'm trying to install metadata onto my gcp kubeflow following the docs here.

However when i run

cd manifests/metadata/base
kustomize build . | kubectl apply -n kubeflow -f -

I get this error:

$:~/manifests/metadata/base$ kustomize build . | kubectl apply -n kubeflow -f -
Error: json: unknown field "env"
error: no objects passed to apply

I found this issue which seems to suggest whats going on. But i have no idea how to implement a work around to get metadata install on my cluster.

It feels like might be easy enough but unfortunately i really don't know what i'm doing when it comes to kubeflow and kubernetes troubleshooting.

Has anyone else run into this?

Enviornment

• Metadata version: metadata-v0.7.0
• Kubeflow version: kubeflow-v0.7.0
• Kubernetes version: (use kubectl version): 1.14.9-gke.2

[zhenghuiwang]

I think you're right: It is kustomize issue as I tried to run it locally and it works.

My version:

$ kustomize version                                                                    
Version: {KustomizeVersion:3.1.0 GitCommit:95f3303493fdea243ae83b767978092396169baf BuildDate:2019-07-26T19:21:45+01:00 GoOs:darwin GoArch:amd64}

What version do you use?

Also, you can try the new overlay to install it:

cd manifests/metadata
kustomize build overlays/db | kubectl apply -n kubeflow -f -

[parthmishra]

Changing instances of env to envs and putting the values in a list resolved this issue for me.

[andrewm4894]

Changing instances of env to envs and putting the values in a list resolved this issue for me.

@parthmishra would you be able to give me some info/tips/pointers on how to do this? Apologies but i'm a total newbie here so not sure how/where to change these references.

[parthmishra]

Sure, in overlays/db/kustomization.yaml file (edit: and in base/kustomization.yaml), I commented out the env and replaced with envs as shown below:

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
commonLabels:
  kustomize.component: metadata
namespace: kubeflow
generatorOptions:
  # name suffix hash is not propagated correctly to base resources
  disableNameSuffixHash: true
configMapGenerator:
  - name: metadata-db-parameters
    # env: params.env
    envs:
      - params.env
secretGenerator:
  - name: metadata-db-secrets
    # env: secrets.env
    envs:
      - secrets.env
...

And then I re-ran the kustomize command and it should work.

[andrewm4894]

Thanks!

Unfortunately i'm now getting this error:

Error: json: cannot unmarshal string into Go struct field ConfigMapArgs.envs of type []string
error: no objects passed to apply

My overlays/db/kustomization.yaml looks like this:

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
commonLabels:
  kustomize.component: metadata
namespace: kubeflow
generatorOptions:
  # name suffix hash is not propagated correctly to base resources
  disableNameSuffixHash: true
configMapGenerator:
- name: metadata-db-parameters
  envs: params.env
secretGenerator:
- name: metadata-db-secrets
  envs: secrets.env
bases:
- ../../base
resources:
- metadata-db-pvc.yaml
- metadata-db-deployment.yaml
- metadata-db-service.yaml
patchesStrategicMerge:
- metadata-deployment.yaml
images:
- name: mysql
  newName: mysql
  newTag: 8.0.3
vars:
- name: metadata-db-service
  objref:
    kind: Service
    name: metadata-db
    apiVersion: v1
  fieldref:
    fieldpath: metadata.name

If i run kustomize version i see:

Version: {Version:unknown GitCommit:$Format:%H$ BuildDate:1970-01-01T00:00:00Z GoOs:linux GoArch:amd64}

I think that might be because i installed it via these instructions but i believe that should be the latest.

[andrewm4894]

Seems like this issue is related to my new error. Googling furiously.

[parthmishra]

You need to change

envs: secrets.env

to

envs:
  - secrets.env

And repeat for envs: params.env

The top portion is interpreted as a string and thus causing the error when it's supposed to be a list.

[andrewm4894]

Now i'm getting:

Error: accumulating resources: couldn't make target for path '../../base': json: unknown field "env"
error: no objects passed to apply

overlays/db/kustomization.yaml:

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
commonLabels:
  kustomize.component: metadata
namespace: kubeflow
generatorOptions:
  # name suffix hash is not propagated correctly to base resources
  disableNameSuffixHash: true
configMapGenerator:
- name: metadata-db-parameters
  envs: 
    - params.env
secretGenerator:
- name: metadata-db-secrets
  envs: 
    - secrets.env
bases:
- ../../base
resources:
- metadata-db-pvc.yaml
- metadata-db-deployment.yaml
- metadata-db-service.yaml
patchesStrategicMerge:
- metadata-deployment.yaml
images:
- name: mysql
  newName: mysql
  newTag: 8.0.3
vars:
- name: metadata-db-service
  objref:
    kind: Service
    name: metadata-db
    apiVersion: v1
  fieldref:
    fieldpath: metadata.name

Apologies for the back and forth, hopefully might be useful for others who might run into this.

[parthmishra]

Ah that's my bad, I forgot to say that you need to do this in the base file as well (base/kustomization.yaml). Edit any instances of env to envs like you did with the overlays.

[andrewm4894]

Thanks! I got a load of output so looks like it did something :)

Will try work through one of the metadata pipelines to confirm.

[andrewm4894]

Although last line of output said:

for: "STDIN": Deployment.apps "metadata-ui" is invalid: spec.selector: Invalid value: v1.LabelSelector{MatchLabels:map[string]string{"app":"metadata-ui", "kustomize
.component":"metadata"}, MatchExpressions:[]v1.LabelSelectorRequirement(nil)}: field is immutable

But not sure if that's a non issue or not.

Some other output that suggests maybe did not work:

serviceaccount/metadata-ui unchanged
role.rbac.authorization.k8s.io/metadata-ui unchanged
rolebinding.rbac.authorization.k8s.io/metadata-ui unchanged
configmap/metadata-db-parameters unchanged
configmap/metadata-metadata-grpc-configmap-2dd6h7mhg6 unchanged
configmap/metadata-ui-parameters-b6c8ghff7c unchanged
secret/metadata-db-secrets unchanged
service/metadata-db unchanged
service/metadata-envoy-service unchanged
service/metadata-grpc-service unchanged
service/metadata-service unchanged
service/metadata-ui unchanged
persistentvolumeclaim/metadata-mysql unchanged
serviceaccount/metadata-ui unchanged
role.rbac.authorization.k8s.io/metadata-ui unchanged
rolebinding.rbac.authorization.k8s.io/metadata-ui unchanged
configmap/metadata-db-parameters unchanged
configmap/metadata-metadata-grpc-configmap-2dd6h7mhg6 unchanged
configmap/metadata-ui-parameters-b6c8ghff7c unchanged
secret/metadata-db-secrets unchanged
service/metadata-db unchanged
service/metadata-envoy-service unchanged
service/metadata-grpc-service unchanged
service/metadata-service unchanged
service/metadata-ui unchanged
persistentvolumeclaim/metadata-mysql unchanged
...
for: "STDIN": Deployment.apps "metadata-deployment" is invalid: spec.selector: Invalid value: v1.LabelSelector{MatchLabels:map[string]string{"component":"server", "
kustomize.component":"metadata"}, MatchExpressions:[]v1.LabelSelectorRequirement(nil)}: field is immutable
...
for: "STDIN": Deployment.apps "metadata-envoy-deployment" is invalid: spec.selector: Invalid value: v1.LabelSelector{MatchLabels:map[string]string{"component":"envo
y", "kustomize.component":"metadata"}, MatchExpressions:[]v1.LabelSelectorRequirement(nil)}: field is immutable
...
for: "STDIN": Deployment.apps "metadata-grpc-deployment" is invalid: spec.selector: Invalid value: v1.LabelSelector{MatchLabels:map[string]string{"component":"grpc-
server", "kustomize.component":"metadata"}, MatchExpressions:[]v1.LabelSelectorRequirement(nil)}: field is immutable
...
for: "STDIN": Deployment.apps "metadata-ui" is invalid: spec.selector: Invalid value: v1.LabelSelector{MatchLabels:map[string]string{"app":"metadata-ui", "kustomize
.component":"metadata"}, MatchExpressions:[]v1.LabelSelectorRequirement(nil)}: field is immutable

[squaricdot]

okay moving to envs worked. is this just happening because i downloaded the latest available kustomize ? is there any up to date documentation about what keys to use, or are valid in regards of latest version or updates.

it was rather unclear.

{Version:kustomize/v3.5.4 GitCommit:3af514fa9f85430f0c1557c4a0291e62112ab026 BuildDate:2020-01-11T03:12:59Z GoOs:linux GoArch:amd64}

[Manvi07]

Hi @parthmishra

I am facing a similar issue, (#2650)

kustomize build overlays/db
Error: json: cannot unmarshal array into Go struct field ConfigMapArgs.configMapGenerator.env of type string

Please let me know how I should change my file.

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
commonLabels:
  kustomize.component: metadata
namespace: kubeflow
generatorOptions:
  # name suffix hash is not propagated correctly to base resources
  disableNameSuffixHash: true
configMapGenerator:
- name: metadata-db-parameters
  env:
  - param.env
secretGenerator:
- name: metadata-db-secrets
  env:
  - secret.env
bases:
- ../../base
resources:
- metadata-db-pvc.yaml
- metadata-db-deployment.yaml
- metadata-db-service.yaml
patchesStrategicMerge:
- metadata-deployment.yaml
images:
- name: mysql
  newName: mysql
  newTag: 8.0.3
vars:
- name: metadata-db-service
  objref:
    kind: Service
    name: metadata-db
    apiVersion: v1
  fieldref:
    fieldpath: metadata.name

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