From e0b960dadf8dc2495d6f6067f2a886dd21b1ef0b Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 9 Feb 2024 16:20:10 -0500
Subject: [PATCH] First pass at defining cron jobs in the values.yaml file.

---
 galaxy/templates/cronjob-maintenance.yaml | 46 ++++++++---------
 galaxy/values.yaml                        | 63 ++++++++++++++++++++++-
 2 files changed, 85 insertions(+), 24 deletions(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 17b0219a..a9344494 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -1,47 +1,47 @@
+{{ if .Values.cronJobs -}}
+{{ range $key, $cronjob := .Values.cronJobs }}
+---
 apiVersion: batch/v1
 kind: CronJob
 metadata:
-  name: {{ include "galaxy.fullname" . }}-maintenance
+  name: {{ include "galaxy.fullname" $ }}-maintenance-{{ $key }}
   labels:
-    {{- include "galaxy.labels" . | nindent 4 }}
+    {{- include "galaxy.labels" $ | nindent 4 }}
 spec:
-  schedule: "0 2 * * *"
+  schedule: {{ $cronjob.schedule | quote }}
   jobTemplate:
     spec:
       template:
         spec:
           securityContext:
-            {{- toYaml .Values.securityContext | nindent 12 }}
-          {{- with .Values.nodeSelector }}
+            {{- toYaml $cronjob.securityContext | nindent 12 }}
+          {{- with $.nodeSelector }}
           nodeSelector:
             {{- toYaml . | nindent 16 }}
           {{- end }}
           containers:
-          - name: galaxy-maintenance
-            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
-            imagePullPolicy: {{ .Values.image.pullPolicy }}
+          - name: galaxy-maintenance-{{ $key }}
+            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
-              - -{{ (index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800) }} seconds
-              - -type
-              - f
-              - -exec
-              - rm
-              - '{}'
-              - ;
+            command: {{ $cronjob.command }}
+            {{- if $cronjob.args }}
+            args:
+              {{- range $arg := $cronjob.args }}
+              - {{ tpl $arg $ }}
+              {{- end }}
+            {{- end }}
             volumeMounts:
             - name: galaxy-data
-              mountPath: {{ .Values.persistence.mountPath }}
+              mountPath: {{ $.Values.persistence.mountPath }}
           volumes:
           - name: galaxy-data
-            {{- if .Values.persistence.enabled }}
+            {{- if $.Values.persistence.enabled }}
             persistentVolumeClaim:
-              claimName: {{ template "galaxy.pvcname" . }}
+              claimName: {{ template "galaxy.pvcname" $ }}
             {{- else }}
             emptyDir: {}
             {{- end }}
           restartPolicy: OnFailure
+{{- end }}
+{{- end }}
diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 9c85c0c0..ad8e3e25 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -267,6 +267,66 @@ extraEnv: []
   # - name: EXAMPLE_ENV
   #   value: MY_VALUE
 
+cronJobs:
+  clean-tmp:
+    schedule: "0 2 * * *"
+    securityContext:
+      runAsUser: 0
+    command: /bin/bash
+    args:
+      - "-c"
+      - "find"
+      - "{{ .Values.persistence.mountPath }}/tmp"
+      - "!"
+      - "-newermt"
+      - "-{{ (index .Values \"configs\" \"job_conf.yml\" \"runners\" \"k8s\" \"k8s_walltime_limit\" | default 604800) }} seconds"
+      - "-type"
+      - "f"
+      - "-exec"
+      - "rm"
+      - "{}"
+      - ";"
+  clean-jobs:
+    schedule: "10 2 * * *"
+    securityContext:
+      runAsUser: 0
+    command: /usr/bin/tmpwatch
+    args:
+      - "-v"
+      - "--all"
+      - "--mtime"
+      - "--dirmtime"
+      - "7d"
+      - "{{ .Values.persistence.mountPath }}/jobs_directory"
+  cleanup-datasets:
+    schedule: "20 2 * * *"
+    securityContext:
+      runAsUser: 0
+    command: /galaxy/server/.venv/bin/python
+    args:
+    - "/galaxy/server/scripts/cleanup_datasets/pgcleanup.py"
+    - "-c"
+    - "/galaxy/server/config/galaxy.yml"
+    - "-o"
+    - "7"
+    - "-l"
+    - "{{ .Values.persistence.mountPath }}/tmp"
+    - "-w"
+    - "128MB"
+    - "delete_userless_histories"
+    - "delete_exported_histories"
+  cleanup-tusd-store:
+    schedule: "30 2 * * *"
+    securityContext:
+      runAsUser: 0
+    command: /usr/bin/tmpwatch
+    args:
+    - "-v"
+    - "--all"
+    - "--mtime"
+    - "--dirmtime"
+    - "7d"
+    - "{{ .Values.persistence.mountPath }}/tmp/tus_upload_store"
 ingress:
   #- Should ingress be enabled. Defaults to `true`
   enabled: true
@@ -301,7 +361,8 @@ resources:
     memory: 7G
     ephemeral-storage: 10Gi
 
-nodeSelector: {}
+#nodeSelector: {}
+nodeSelector: "cloud:google:com/gke-nodepool: default-pool"
 
 tolerations: []