Merge pull request #420 from galaxyproject/sync-with-master

Sync anvil branch with master at 5.7.1

galaxy/Chart.yaml

@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.7.0-anvil.1
+version: 5.7.1-anvil.0
 appVersion: "23.0"
 description: Chart for Galaxy, an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
 icon: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo_square.png

galaxy/templates/configmap-cvmfs-fix.yaml

@@ -0,0 +1,18 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ .Release.Name }}-configmap-cvmfs-fix
+  labels:
+    {{- include "galaxy.labels" . | nindent 4 }}
+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'`
+    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'`
+    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 && \
+    echo "Deleted nodeplugin pods."

galaxy/templates/hook-cvmfs-fix.yaml

@@ -0,0 +1,35 @@
+apiVersion: batch/v1
+kind: Job
+metadata:
+  name: "{{ .Release.Name }}-post-install-cvmfs-fix-job"
+  labels:
+    {{- include "galaxy.labels" . | nindent 4 }}
+  annotations:
+    "helm.sh/hook": post-install
+    "helm.sh/hook-weight": "10"
+    "helm.sh/hook-delete-policy": hook-succeeded
+spec:
+  ttlSecondsAfterFinished: 120
+  template:
+    metadata:
+      name: "{{ .Release.Name }}-post-install-cvmfs-fix-job"
+      labels:
+        {{- include "galaxy.labels" . | nindent 8 }}
+    spec:
+      serviceAccountName: {{ include "galaxy.serviceAccountName" . }}
+      securityContext:
+        {{- toYaml .Values.securityContext | nindent 8 }}
+      restartPolicy: Never
+      containers:
+      - name: post-install-kubectl
+        image: bitnami/kubectl
+        command:
+          - "sh"
+          - "/script/cvmfs-fix.sh"
+        volumeMounts:
+            - name: kubectl-script
+              mountPath: "/script"
+      volumes:
+      - name: kubectl-script
+        configMap:
+          name: "{{ .Release.Name }}-configmap-cvmfs-fix"

galaxy/templates/rbac-job.yaml

@@ -9,7 +9,7 @@ metadata:
 rules:
 - apiGroups: [""]
   resources: ["pods", "pods/log"]
-  verbs: ["get", "list", "watch"]
+  verbs: ["get", "list", "watch", "delete"]
 - apiGroups: ["batch", "extensions"]
   resources: ["jobs"]
   verbs: ["get", "list", "watch", "create", "update", "patch", "delete"]