Make CVMFS fix configurable

README.md

@@ -167,6 +167,8 @@ current default values can be found in `values.yaml` file.
 | `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.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 <a href="galaxy/values.yaml">`values.yaml`</a> 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.                                                   |

VALUES.md

@@ -41,6 +41,8 @@
 | refdata.type | `s3fs` or `cvmfs`, determines the CSI to use for mounting reference data. `cvmfs` is the default and recommended for the time being. |
 | 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 |

galaxy/templates/configmap-cvmfs-fix.yaml

@@ -1,3 +1,5 @@
+{{- 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
@@ -8,12 +10,13 @@ metadata:
 data:
   cvmfs-fix.sh: |
     sleep 10;
-    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'`
+    status=`kubectl get pods -n {{ $Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o custom-columns=STATUS:.status.phase --no-headers | sort | uniq | tr -d '\n'`
     while [ "$status" != "Running" ]; do
       echo "Waiting on nodeplugin pod to enter 'Running' status. Currently '$status'.";
       sleep 1;
-      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'`
+      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'`
     done && \
     echo "Deleting nodeplugin pods..."
-    kubectl get pods -n {{ .Release.Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o name | xargs kubectl -n {{ .Release.Namespace }} delete && \
+    kubectl get pods -n {{ $Namespace }} -l 'app=cvmfscsi' -l 'component=nodeplugin' -o name | xargs kubectl -n {{ $Namespace }} delete && \
     echo "Deleted nodeplugin pods."
+{{- end }}

galaxy/templates/hook-cvmfs-fix.yaml

@@ -1,4 +1,4 @@
-{{- if and .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }}
+{{- if and .Values.cvmfs.deployPostInstallFix .Values.refdata.enabled (eq .Values.refdata.type "cvmfs")  }}
 ---
 # Include the code you want to run when both conditions are met
 apiVersion: batch/v1
@@ -19,7 +19,7 @@ spec:
       labels:
         {{- include "galaxy.labels" . | nindent 8 }}
     spec:
-      serviceAccountName: {{ include "galaxy.serviceAccountName" . }}
+      serviceAccountName: {{ .Values.cvmfs.deploy | ternary ( include "galaxy.serviceAccountName" . )  (printf "%s-cvmfs-fix" (include "galaxy.fullname" .))  }}
       securityContext:
         {{- toYaml .Values.securityContext | nindent 8 }}
       restartPolicy: Never
@@ -37,4 +37,3 @@ spec:
         configMap:
           name: "{{ .Release.Name }}-configmap-cvmfs-fix"
 {{- end }}
-

galaxy/templates/rbac-fix-cvmfs.yaml

@@ -0,0 +1,42 @@
+{{- 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 }}

galaxy/values.yaml

@@ -429,6 +429,10 @@ refdata:
 cvmfs:
   #- 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
   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`