operator-sdk generate kustomize manifests -q generates invalid config/manifests/kustomization.yaml

[mdbooth]

Bug Report

Trying to work out why my generated CSV was incomplete after executing make bundle:

$ make bundle
/home/mbooth/go/bin/controller-gen "crd:trivialVersions=true" rbac:roleName=manager-role webhook paths="./..." output:crd:artifacts:config=config/crd/bases
operator-sdk generate kustomize manifests -q
cd config/manager && /usr/bin/kustomize edit set image controller=ovn-central-controller:latest
/usr/bin/kustomize build config/manifests | operator-sdk generate bundle -q --overwrite --version 0.0.1
Error: rawResources failed to read Resources: Load from path ../default failed: '../default' must be a file (got d='/home/mbooth/src/osp-k8s/ovn-central-operator/config/default')

INFO[0000] Building annotations.yaml
INFO[0000] Writing annotations.yaml in /home/mbooth/src/osp-k8s/ovn-central-operator/bundle/metadata
INFO[0000] Building Dockerfile
INFO[0000] Writing bundle.Dockerfile in /home/mbooth/src/osp-k8s/ovn-central-operator
operator-sdk bundle validate ./bundle
INFO[0000] Found annotations file                        bundle-dir=bundle container-tool=docker
INFO[0000] Could not find optional dependencies file     bundle-dir=bundle container-tool=docker
ERRO[0000] error validating content in bundle/manifests: error loading objs in directory: bundle manifests dir has hidden file: bundle/manifests/.ovn-central-operator.clusterserviceversion.yaml.swp
make: *** [Makefile:125: bundle] Error 1

From the above, failed to read Resources: Load from path ../default failed appears to be because the generated config/manifests/kustomization.yaml is invalid. The contents of this file are:

resources:
- ../default
- ../samples
- ../scorecard

This file is generated by operator-sdk generate kustomize manifests -q. Guessing resources should be bases there, but there's a secondary issue. I fixed the file manually to contain:

bases:
- ../default
- ../samples
- ../scorecard

but then I get:

$ kustomize build config/manifests
Error: AccumulateTarget: found conflict between different patches
&resource.Resource{Kunstructured:(*kunstruct.UnstructAdapter)(0xc000010168), options:(*types.GenArgs)(0xc0003bb700)} doesn't deep equal &resource.Resource{Kunstructured:(*kunstruct.UnstructAdapter)(0xc0000102c0), options:(*types.GenArgs)(0xc0003bb700)}

AFAICT this is a limitation of kustomize: (kubernetes-sigs/kustomize#642)

To work round it I commented out scorecard:

bases:
- ../default
- ../samples
#- ../scorecard

And now it works and make bundle generates a complete CSV.

Environment

Operator type:

/language go

Kubernetes cluster type:

OpenShift

$ operator-sdk version

operator-sdk version: "v1.0.1", commit: "4169b318b578156ed56530f373d328276d040a1b", kubernetes version: "v1.18.2", go version: "go1.13.15 linux/amd64", GOOS: "linux", GOARCH: "amd64"

$ go version (if language is Go)

go version go1.13.15 linux/amd64

$ kubectl version

Client Version: version.Info{Major:"1", Minor:"15+", GitVersion:"v1.15.8-beta.0", GitCommit:"6c143d35bb11d74970e7bc0b6c45b6bfdffc0bd4", GitTreeState:"archive", BuildDate:"2020-01-02T00:00:00Z", GoVersion:"go1.13.5", Compiler:"gc", Platform:"linux/amd64"}
Server Version: version.Info{Major:"1", Minor:"18+", GitVersion:"v1.18.3+b0068a8", GitCommit:"b0068a8", GitTreeState:"clean", BuildDate:"2020-09-11T20:03:06Z", GoVersion:"go1.13.4", Compiler:"gc", Platform:"linux/amd64"}

[ukclivecox]

So this default is wrong? Missing bases ?

operator-sdk/internal/cmd/operator-sdk/generate/kustomize/manifests.go

Lines 154 to 159 in adcef86

	// kustomization.yaml file contents for manifests. this should always be written to
	// config/manifests/kustomization.yaml since it only references files in config.
	const manifestsKustomization = `resources:
	- ../default
	- ../samples
	- ../scorecard

[ukclivecox]

Actually looks like the bases folder is just used in operator-sdk generate bundle where assumes the name of the csv file from the project name.

[estroz]

@mdbooth the kustomization.yaml file is not invalid; the bases directive has been deprecated since kustomize v2.1.0, and is superseded by resources. What kustomize version are you using? Can you try doing:

rm -f $(command -v kustomize)
make kustomize bundle

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[openshift-ci]

@openshift-bot: Closing this issue.

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