diff --git a/README.md b/README.md index ff4d89eb..3a1be528 100644 --- a/README.md +++ b/README.md @@ -168,7 +168,6 @@ current default values can be found in `values.yaml` file. | `cvmfs.enabled` | Enable use of CVMFS in configs, and deployment of CVMFS Persistent Volume Claims for Galaxy | | `cvmfs.pvc.{}` | Persistent Volume Claim to deploy for CVMFS repositories. See `values.yaml` for examples. | | `cvmfs.deployPostInstallFix` |Deploy the fix for Galaxy-CVMFS-CSI Helm Chart. | -| `cvmfs.externalCvmfsNamespace` | Define the namespace where the cvmfs NodePlugin is deployed, if cvmfs.deploy is true, this isn't used. | | `setupJob.ttlSecondsAfterFinished` | Sets `ttlSecondsAfterFinished` for the initialization jobs. See the [Kubernetes documentation](https://kubernetes.io/docs/concepts/workloads/controllers/ttlafterfinished/#ttl-controller) for more details. | | `setupJob.downloadToolConfs.enabled` | Download configuration files and the `tools` directory from an archive via a job at startup | | `setupJob.downloadToolConfs.archives.startup` | A URL to a `tar.gz` publicly accessible archive containing AT LEAST conf files and XML tool wrappers. Meant to be enough for Galaxy handlers to startup. | diff --git a/VALUES.md b/VALUES.md index 950ee381..319c31e8 100644 --- a/VALUES.md +++ b/VALUES.md @@ -42,7 +42,6 @@ | cvmfs | Configuration block if `cvmfs` is used as `refdata.type` | | cvmfs.deploy | Deploy the Galaxy-CVMFS-CSI Helm Chart. This is an optional dependency, and for production scenarios it should be deployed separately as a cluster-wide resource | | cvmfs.deployPostInstallFix| Deploy the fix for Galaxy-CVMFS-CSI Helm Chart. | -| cvmfs.externalCvmfsNamespace|Define the namespace where the cvmfs NodePlugin is deployed, if cvmfs.deploy is true, this isn't used. | | s3csi | Configuration block if `s3csi` is used as the `refdata.type` | | s3csi.deploy | Deploy the CSI-S3 Helm Chart. This is an optional dependency, and for production scenarios it should be deployed separately as a cluster-wide resource. | | useSecretConfigs | When this flag is set to true, all configs will be set in secrets, when it is set to false, all configs will be set in configmaps | diff --git a/galaxy/templates/configmap-cvmfs-fix.yaml b/galaxy/templates/configmap-cvmfs-fix.yaml index fc268b16..11178d85 100644 --- a/galaxy/templates/configmap-cvmfs-fix.yaml +++ b/galaxy/templates/configmap-cvmfs-fix.yaml @@ -1,5 +1,4 @@ {{- if and .Values.cvmfs.deployPostInstallFix .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }} -{{ $Namespace := .Values.cvmfs.deploy | ternary .Release.Namespace .Values.cvmfs.externalCvmfsNamespace }} --- apiVersion: v1 kind: ConfigMap @@ -10,13 +9,13 @@ metadata: data: cvmfs-fix.sh: | sleep 10; - status=`kubectl get pods -n {{ $Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o custom-columns=STATUS:.status.phase --no-headers | sort | uniq | tr -d '\n'` + status=`kubectl get pods -n {{ .Release.Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o custom-columns=STATUS:.status.phase --no-headers | sort | uniq | tr -d '\n'` while [ "$status" != "Running" ]; do echo "Waiting on nodeplugin pod to enter 'Running' status. Currently '$status'."; sleep 1; - status=`kubectl get pods -n {{ $Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o custom-columns=STATUS:.status.phase --no-headers | sort | uniq | tr -d '\n'` + status=`kubectl get pods -n {{ .Release.Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o custom-columns=STATUS:.status.phase --no-headers | sort | uniq | tr -d '\n'` done && \ echo "Deleting nodeplugin pods..." - kubectl get pods -n {{ $Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o name | xargs kubectl -n {{ $Namespace }} delete && \ + kubectl get pods -n {{ .Release.Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o name | xargs kubectl -n {{ .Release.Namespace }} delete && \ echo "Deleted nodeplugin pods." {{- end }} diff --git a/galaxy/templates/hook-cvmfs-fix.yaml b/galaxy/templates/hook-cvmfs-fix.yaml index 08d141f2..89150080 100644 --- a/galaxy/templates/hook-cvmfs-fix.yaml +++ b/galaxy/templates/hook-cvmfs-fix.yaml @@ -19,7 +19,7 @@ spec: labels: {{- include "galaxy.labels" . | nindent 8 }} spec: - serviceAccountName: {{ .Values.cvmfs.deploy | ternary ( include "galaxy.serviceAccountName" . ) (printf "%s-cvmfs-fix" (include "galaxy.fullname" .)) }} + serviceAccountName: {{ include "galaxy.serviceAccountName" . }} securityContext: {{- toYaml .Values.securityContext | nindent 8 }} restartPolicy: Never diff --git a/galaxy/templates/rbac-fix-cvmfs.yaml b/galaxy/templates/rbac-fix-cvmfs.yaml deleted file mode 100644 index 4cad7e7b..00000000 --- a/galaxy/templates/rbac-fix-cvmfs.yaml +++ /dev/null @@ -1,42 +0,0 @@ -{{- if and .Values.cvmfs.deployPostInstallFix (not .Values.cvmfs.deploy) .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }} ---- -apiVersion: v1 -kind: ServiceAccount -metadata: - name: {{ include "galaxy.fullname" . }}-cvmfs-fix - namespace: {{ .Release.Namespace }} - labels: - {{- include "galaxy.labels" . | nindent 4 }} - {{- with .Values.serviceAccount.annotations }} - annotations: - {{- toYaml . | nindent 4 }} - {{- end }} ---- -kind: Role -apiVersion: rbac.authorization.k8s.io/v1 -metadata: - namespace: {{ .Values.cvmfs.externalCvmfsNamespace }} - name: {{ include "galaxy.fullname" . }}-cvmfs-fix - labels: - {{- include "galaxy.labels" . | nindent 4 }} -rules: -- apiGroups: [""] - resources: ["pods"] - verbs: ["get", "list","watch","delete"] ---- -kind: RoleBinding -apiVersion: rbac.authorization.k8s.io/v1 -metadata: - name: {{ include "galaxy.fullname" . }}-cvmfs-fix - namespace: {{ .Values.cvmfs.externalCvmfsNamespace }} - labels: - {{- include "galaxy.labels" . | nindent 4 }} -subjects: -- kind: ServiceAccount - name: {{ include "galaxy.fullname" . }}-cvmfs-fix - namespace: {{ .Release.Namespace }} -roleRef: - kind: Role - name: {{ include "galaxy.fullname" . }}-cvmfs-fix - apiGroup: rbac.authorization.k8s.io -{{ end }} diff --git a/galaxy/values.yaml b/galaxy/values.yaml index 50529422..26921b69 100644 --- a/galaxy/values.yaml +++ b/galaxy/values.yaml @@ -431,8 +431,6 @@ cvmfs: deploy: true #- Deploy the CVMF post install fix, deployPostInstallFix: true - #- Define the namespace where the cvmfs NodePlugin is deployed, if cvmfs.deploy is true, this isn't used. - externalCvmfsNamespace: storageClassName: "{{ $.Release.Name }}-cvmfs" #- Configuration block if `s3csi` is used as the `refdata.type`