From 287cf133f440a03b37cc3549e91462c745cf7844 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Mon, 19 Feb 2024 12:12:38 -0500
Subject: [PATCH] Define all cron jobs in the values.yaml file again, but
 allows time durations to be parameterized.

---
 galaxy/templates/cronjob-maintenance.yaml | 102 +---------------------
 galaxy/values.yaml                        |  46 +++++++---
 2 files changed, 35 insertions(+), 113 deletions(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 9df57386..3f626e35 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -1,101 +1,3 @@
-{{- if .Values.maintenance.tmp.enabled }}
----
-apiVersion: batch/v1
-kind: CronJob
-metadata:
-  name: {{ include "galaxy.fullname" . }}-maintenance-clean-tmp
-  labels:
-    {{- include "galaxy.labels" . | nindent 4 }}
-spec:
-  schedule: {{ .Values.maintenance.tmp.schedule | quote }}
-  jobTemplate:
-    spec:
-      template:
-        spec:
-          securityContext:
-            runAsUser: 0
-            {{- toYaml .Values.securityContext | nindent 12 }}
-          {{- with .Values.nodeSelector }}
-          nodeSelector:
-            {{- toYaml . | nindent 16 }}
-          {{- end }}
-          containers:
-          - name: galaxy-maintenance-clean-tmp
-            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
-            imagePullPolicy: {{ .Values.image.pullPolicy }}
-            # delete all tmp files older than walltime limit
-            command:
-              - find
-              - {{ .Values.persistence.mountPath }}/tmp
-              - '!'
-              - -newermt
-              - "{{ .Values.maintenance.tmp.seconds }} seconds"
-              - -type
-              - f
-              - -exec
-              - rm
-              - '{}'
-              - ;
-            volumeMounts:
-            - name: galaxy-data
-              mountPath: {{ .Values.persistence.mountPath }}
-          volumes:
-          - name: galaxy-data
-            {{- if .Values.persistence.enabled }}
-            persistentVolumeClaim:
-              claimName: {{ template "galaxy.pvcname" . }}
-            {{- else }}
-            emptyDir: {}
-            {{- end }}
-          restartPolicy: OnFailure
-{{- end }}
-{{- if .Values.maintenance.script.enabled }}
----
-apiVersion: batch/v1
-kind: CronJob
-metadata:
-  name: {{ include "galaxy.fullname" . }}-maintenance-script
-  labels:
-    {{- include "galaxy.labels" . | nindent 4 }}
-spec:
-  schedule: {{ .Values.maintenance.script.schedule | quote }}
-  jobTemplate:
-    spec:
-      template:
-        spec:
-          securityContext:
-            runAsUser: 0
-          {{- with .Values.nodeSelector }}
-          nodeSelector:
-            {{- toYaml . | nindent 16 }}
-          {{- end }}
-          containers:
-          - name: galaxy-maintenance-script
-            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
-            imagePullPolicy: {{ .Values.image.pullPolicy }}
-            # delete all tmp files older than walltime limit
-            command:
-              - "/bin/bash"
-              - "-c"
-            args:
-              - "/galaxy/server/scripts/maintenance.sh"
-              - "--no-dry-run"
-              - "--days"
-              - {{ .Values.maintenance.script.days | quote }}
-            volumeMounts:
-            - name: galaxy-data
-              mountPath: {{ .Values.persistence.mountPath }}
-          volumes:
-          - name: galaxy-data
-            {{- if .Values.persistence.enabled }}
-            persistentVolumeClaim:
-              claimName: {{ template "galaxy.pvcname" . }}
-            {{- else }}
-            emptyDir: {}
-            {{- end }}
-          restartPolicy: OnFailure
-{{- end }}
-{{ if .Values.cronJobs -}}
 {{ range $key, $cronjob := .Values.cronJobs }}
 ---
 apiVersion: batch/v1
@@ -116,13 +18,12 @@ spec:
           {{- end}}
           {{- with $.nodeSelector }}
           nodeSelector:
-            {{- toYaml . | nindent 16 }}
+            {{- toYaml . | nindent 12 }}
           {{- end }}
           containers:
           - name: galaxy-maintenance-{{ $key }}
             image: "{{ $.Values.image.repository }}:{{ $.Values.image.tag }}"
             imagePullPolicy: {{ $.Values.image.pullPolicy }}
-            # delete all tmp files older than walltime limit
             command:
             {{- range $cmd := $cronjob.command }}
               - {{ tpl $cmd $ | quote }}
@@ -146,4 +47,3 @@ spec:
             {{- end }}
           restartPolicy: OnFailure
 {{- end }}
-{{- end }}
diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index fd821f04..454215eb 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -279,19 +279,41 @@ cronJobs:
       - "-R"
       - "galaxy"
       - "/galaxy/server/database"
-#- Maintenance tasks that should be run periodically to prevent storage from being exhausted
-maintenance:
-  #- Remove files in the tmp directory.
-  tmp:
-    enabled: true
+  maintenance:
     schedule: "5 2 * * *"
-    seconds: "604800" # Default wall time for jobs
-  #- The maintenance script removes histories, datasets, and other Galaxy objects older than 7 days.
-  script:
-    enabled: true
-    schedule: "10 2 * * *"
-    days: "7"
-
+    extraSettings:
+      days: 7
+    securityContext:
+      runAsUser: 0
+    command:
+      - "/bin/bash"
+      - "-c"
+    args:
+      - "/galaxy/server/scripts/maintenance.sh"
+      - "--no-dry-run"
+      - "--days"
+      - "{{ .Values.cronJobs.maintenance.extraSettings.days }}"
+  #- Remove files from the tmp directory that are older than the allowable wall time for a job
+  tmp:
+    schedule: "15 2 * * *"
+    extraSettings:
+      seconds: 604800
+    securityContext:
+      runAsUser: 0
+    command:
+      - /usr/bin/find
+    args:
+      - "{{ .Values.persistence.mountPath }}/tmp"
+      - "!"
+      - "-newermt"
+      - "{{ .Values.cronJobs.tmp.extraSettings.seconds }}"
+      - "seconds"
+      - "-type"
+      - "f"
+      - "-exec"
+      - "rm"
+      - "{}"
+      - ";"
 ingress:
   #- Should ingress be enabled. Defaults to `true`
   enabled: true