Cron job maintenance

README.md

@@ -417,6 +417,10 @@ The Galaxy application can be horizontally scaled for the web, job, or workflow
 by setting the desired values of the `webHandlers.replicaCount`,
 `jobHandlers.replicaCount`, and `workflowHandlers.replicaCount` configuration options.
 
+## Cron jobs
+
+Two Cron jobs are defined to clean up Galaxy's database and the `tmp` directory.  By default these
+jobs run at 02:05 (the database maintenance script) and 02:15 (`tmp` directyory cleanup). Users 
 ## Galaxy versions
 
 Some changes introduced in the chart sometimes rely on changes in the Galaxy

galaxy/templates/cronjob-maintenance.yaml

@@ -1,47 +1,67 @@
+{{ range $key, $cronjob := .Values.cronJobs }}
+---
 apiVersion: batch/v1
 kind: CronJob
 metadata:
-  name: {{ include "galaxy.fullname" . }}-maintenance
+  name: {{ include "galaxy.fullname" $ }}-cron-{{ $key }}
   labels:
-    {{- include "galaxy.labels" . | nindent 4 }}
+    {{- include "galaxy.labels" $ | nindent 4 }}
 spec:
-  schedule: "0 2 * * *"
+  schedule: {{ $cronjob.schedule | quote }}
   jobTemplate:
     spec:
       template:
         spec:
+          {{- if $cronjob.securityContext }}
           securityContext:
-            {{- toYaml .Values.securityContext | nindent 12 }}
-          {{- with .Values.nodeSelector }}
+            {{- toYaml $cronjob.securityContext | nindent 12 }}
+          {{- end}}
+          {{- if $cronjob.nodeSelector }}
           nodeSelector:
-            {{- toYaml . | nindent 16 }}
+            {{- toYaml $cronjob.nodeSelector | nindent 12 }}
+          {{- else if $.Values.nodeSelector }}
+          nodeSelector:
+            {{- toYaml $.Values.nodeSelector | nindent 12 }}
           {{- end }}
           containers:
-          - name: galaxy-maintenance
-            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
-            imagePullPolicy: {{ .Values.image.pullPolicy }}
-            # delete all tmp files older than walltime limit
+          - name: galaxy-cron-{{ $key }}
+            image: "{{ $.Values.image.repository }}:{{ $.Values.image.tag }}"
+            imagePullPolicy: {{ $.Values.image.pullPolicy }}
             command:
-              - find
-              - {{ .Values.persistence.mountPath }}/tmp
-              - '!'
-              - -newermt
-              - -{{ (index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800) }} seconds
-              - -type
-              - f
-              - -exec
-              - rm
-              - '{}'
-              - ;
+            {{- range $cmd := $cronjob.command }}
+              - {{ tpl $cmd $ | quote }}
+            {{- end}}
+            {{- if $cronjob.args }}
+            args:
+              {{- range $arg := $cronjob.args }}
+              - {{ tpl $arg $ | quote }}
+              {{- end }}
+            {{- end }}
             volumeMounts:
             - name: galaxy-data
-              mountPath: {{ .Values.persistence.mountPath }}
+              mountPath: {{ $.Values.persistence.mountPath }}
+            {{- range $key, $entry := $cronjob.extraFileMappings -}}
+            - name: {{ include "galaxy.getExtraFilesUniqueName" $key }}
+              mountPath: {{ $key }}
+              subPath: {{ include "galaxy.getFilenameFromPath" $key }}
+            {{- end }}
           volumes:
           - name: galaxy-data
-            {{- if .Values.persistence.enabled }}
+            {{- if $.Values.persistence.enabled }}
             persistentVolumeClaim:
-              claimName: {{ template "galaxy.pvcname" . }}
+              claimName: {{ template "galaxy.pvcname" $ }}
             {{- else }}
             emptyDir: {}
             {{- end }}
+        {{- range $key, $entry := $cronjob.extraFileMappings -}}
+        - name: {{ include "galaxy.getExtraFilesUniqueName" $key }}
+          {{- if $entry.useSecret }}
+          secret:
+            secretName: {{ printf "%s-%s" (include "galaxy.fullname" $) (include "galaxy.getExtraFilesUniqueName" $key) }}
+          {{- else }}
+          configMap:
+            name: {{ printf "%s-%s" (include "galaxy.fullname" $) (include "galaxy.getExtraFilesUniqueName" $key) }}
+          {{- end }}
+        {{- end }}
           restartPolicy: OnFailure
+{{- end }}

galaxy/templates/hook-cvmfs-fix.yaml

@@ -1,5 +1,5 @@
 {{- if and .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }}
-  # Include the code you want to run when both conditions are met
+# Include the code you want to run when both conditions are met
 apiVersion: batch/v1
 kind: Job
 metadata:

galaxy/values.yaml

@@ -267,6 +267,53 @@ extraEnv: []
   # - name: EXAMPLE_ENV
   #   value: MY_VALUE
 
+#- CronJobs to perform periodic maintenacne tasks
+cronJobs:
+  #- Runs the maintenance.sh script to clean up the Galaxy database.
+  maintenance:
+    schedule: "5 2 * * *"
+    extraSettings:
+      days: '7'
+    securityContext:
+      runAsUser: 0
+    command:
+      - "/bin/bash"
+      - "-c"
+    args:
+      - "/galaxy/server/scripts/maintenance.sh"
+      - "--no-dry-run"
+      - "--days"
+      - "{{ tpl .Values.cronJobs.maintenance.extraSettings.days $ }}"
+    extraFileMappings:
+      /galaxy/server/scripts/maintenance.sh:
+        tpl: true
+        content: |
+          {{ .Files.Get "files/source/maintenance.sh" }}
+      /galaxy/server/scripts/cleanup_datasets/cleanup_datasets.py:
+        tpl: true
+        content: |
+          {{ .Files.Get "files/source/cleanup_datasets.py" }}
+
+  #- Remove files from the tmp directory that are older than the allowable wall time for a job
+  tmpdir:
+    schedule: "15 2 * * *"
+    extraSettings:
+      last_modified: '{{ index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800 }}'
+    securityContext:
+      runAsUser: 0
+    command:
+      - /usr/bin/find
+    args:
+      - "{{ .Values.persistence.mountPath }}/tmp"
+      - "!"
+      - "-newermt"
+      - "{{ tpl .Values.cronJobs.tmpdir.extraSettings.last_modified $ }} seconds ago"
+      - "-type"
+      - "f"
+      - "-exec"
+      - "rm"
+      - "{}"
+      - ";"
 ingress:
   #- Should ingress be enabled. Defaults to `true`
   enabled: true