Merge pull request #498 from NilsKrattinger/imrpove_cvmfs_fix_configu…

…rability

Make CVMFS fix configurable

README.md

@@ -167,6 +167,7 @@ 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. |
 | `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 +41,7 @@
 | 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. |
 | 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 +1,4 @@
+{{- if and .Values.cvmfs.deployPostInstallFix .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }}
 ---
 apiVersion: v1
 kind: ConfigMap
@@ -17,3 +18,4 @@ data:
     echo "Deleting nodeplugin pods..."
     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 }}

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
@@ -37,4 +37,3 @@ spec:
         configMap:
           name: "{{ .Release.Name }}-configmap-cvmfs-fix"
 {{- end }}
-

galaxy/values.yaml

@@ -429,6 +429,8 @@ 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
   storageClassName: "{{ $.Release.Name }}-cvmfs"
   cvmfscsi:
     cache: