feat: Pvc auto deletion logic

helm/blueapi/README.md

@@ -32,8 +32,12 @@ A Helm chart deploying a worker pod that runs Bluesky plans
 | podAnnotations | object | `{}` |  |
 | podLabels | object | `{}` |  |
 | podSecurityContext | object | `{}` |  |
+| pvcAutoDeletion.enabled | bool | `true` |  |
 | readinessProbe | object | `{"failureThreshold":2,"httpGet":{"path":"/healthz","port":"http"},"periodSeconds":10}` | Readiness probe, if configured kubernetes will not route traffic to this pod if failed consecutively. This could allow the service time to recover if it is being overwhelmed by traffic, but without the to ability to load balance or scale up/outwards, upstream services will need to know to back off. This is automatically disabled when in debug mode. |
-| resources | object | `{"limits":{"cpu":"2000m","memory":"4000Mi"},"requests":{"cpu":"200m","memory":"400Mi"}}` | Sets the compute resources available to the pod. These defaults are appropriate when using debug mode or an internal PVC and therefore running VS Code server in the pod. In the Diamond cluster, requests must be >= 0.1*limits When not using either of the above, the limits may be lowered. When idle but connected, blueapi consumes ~400MB of memory and 1% cpu and may struggle when allocated less. |
+| resources.limits.cpu | string | `"2000m"` |  |
+| resources.limits.memory | string | `"4000Mi"` |  |
+| resources.requests.cpu | string | `"200m"` |  |
+| resources.requests.memory | string | `"400Mi"` |  |
 | restartOnConfigChange | bool | `true` | If enabled the blueapi pod will restart on changes to `worker` |
 | securityContext.runAsNonRoot | bool | `true` |  |
 | securityContext.runAsUser | int | `1000` |  |
@@ -44,13 +48,13 @@ A Helm chart deploying a worker pod that runs Bluesky plans
 | serviceAccount.create | bool | `false` |  |
 | serviceAccount.name | string | `""` |  |
 | startupProbe | object | `{"failureThreshold":5,"httpGet":{"path":"/healthz","port":"http"},"periodSeconds":10}` | A more lenient livenessProbe to allow the service to start fully. This is automatically disabled when in debug mode. |
+| timeStampCron.enabled | bool | `true` |  |
 | tolerations | list | `[]` | May be required to run on specific nodes (e.g. the control machine) |
 | tracing | object | `{"fastapi":{"excludedURLs":"/healthz"},"otlp":{"enabled":false,"protocol":"http/protobuf","server":{"host":"http://opentelemetry-collector.tracing","port":4318}}}` | Exclude health probe requests from tracing by default to prevent spamming |
 | volumeMounts | list | `[{"mountPath":"/config","name":"worker-config","readOnly":true}]` | Additional volumeMounts on the output StatefulSet definition. Define how volumes are mounted to the container referenced by using the same name. |
 | volumes | list | `[]` | Additional volumes on the output StatefulSet definition. Define volumes from e.g. Secrets, ConfigMaps or the Filesystem |
 | worker | object | `{"api":{"url":"http://0.0.0.0:8000/"},"env":{"sources":[{"kind":"planFunctions","module":"dodal.plans"},{"kind":"planFunctions","module":"dodal.plan_stubs.wrapped"}]},"logging":{"graylog":{"enabled":false,"url":"tcp://graylog-log-target.diamond.ac.uk:12231/"},"level":"INFO"},"scratch":{"repositories":[],"root":"/workspace"},"stomp":{"auth":{"password":"guest","username":"guest"},"enabled":false,"url":"tcp://rabbitmq:61613/"}}` | Config for the worker goes here, will be mounted into a config file |
 | worker.api.url | string | `"http://0.0.0.0:8000/"` | 0.0.0.0 required to allow non-loopback traffic If using hostNetwork, the port must be free on the host |
 | worker.env.sources | list | `[{"kind":"planFunctions","module":"dodal.plans"},{"kind":"planFunctions","module":"dodal.plan_stubs.wrapped"}]` | modules (must be installed in the venv) to fetch devices/plans from |
-| worker.logging | object | `{"graylog":{"enabled":false,"url":"tcp://graylog-log-target.diamond.ac.uk:12231/"},"level":"INFO"}` | Configures logging. Port 12231 is the `dodal` input on graylog which will be renamed `blueapi` |
 | worker.scratch | object | `{"repositories":[],"root":"/workspace"}` | If initContainer is enabled the default branch of python projects in this section are installed into the venv *without their dependencies* |
 | worker.stomp | object | `{"auth":{"password":"guest","username":"guest"},"enabled":false,"url":"tcp://rabbitmq:61613/"}` | Message bus configuration for returning status to GDA/forwarding documents downstream Password may be in the form ${ENV_VAR} to be fetched from an environment variable e.g. mounted from a SealedSecret |

helm/blueapi/files/scripts/pvc-deletion.sh

@@ -0,0 +1,26 @@
+#!/bin/sh
+# Get all PVCs by running pods
+ALL_PVCS=$(kubectl get pvc -n  $RELEASE_NAMESPACE  -o=jsonpath='{.items[*].metadata.name}' | tr ' ' '\n' | sort -u)
+BLUEAPI_PVCS=$( echo $ALL_PVCS | tr ' ' '\n' | grep blueapi-scratch)
+NOW=$(date +%s)
+#loop through all pvcs.
+for pvc in $BLUEAPI_PVCS; do
+    #check if pvc has last-used annotation 
+        #get last used annotation 
+        LAST_USED=$(kubectl get pvc "$pvc" -n  $RELEASE_NAMESPACE  -o=jsonpath='{.metadata.annotations.last-used}')
+        #checking if its not null
+        if [ -n "$LAST_USED"  ]; then
+            #check if last_used is older than 3 months
+            if [ $(($NOW - LAST_USED)) -gt 7884000 ]; then
+                #checking if the pvc is protected, if it is protected skip deletion
+                if  [ "$(kubectl get pvc "$pvc" -n  $RELEASE_NAMESPACE  -o=jsonpath='{.metadata.annotations.protected}')" = "true" ]; then
+                    echo " PVC $pvc is protected, skipping deletion"
+                    continue
+                fi
+                #PVC has not been used for more than three months, delete it
+                kubectl delete pvc "$pvc" -n  $RELEASE_NAMESPACE
+            fi
+        else
+            echo " $pvc has no last-used annotation"
+    fi
+done

helm/blueapi/files/scripts/time-stamper.sh

@@ -0,0 +1,10 @@
+#!/bin/sh
+# Get all PVCs currently mounted by running pods
+MOUNTED_PVCS=$(kubectl get pods -n  $RELEASE_NAMESPACE  \
+  -o=jsonpath='{.items[*].spec.volumes[*].persistentVolumeClaim.claimName}' | tr ' ' '\n' | sort -u)
+BLUEAPI_PVCS=$( echo $MOUNTED_PVCS | tr ' ' '\n' | grep blueapi-scratch)
+#loop through all the pvcs annotating ones thare are mounted
+NOW=$(date +%s)
+for pvc in $BLUEAPI_PVCS; do
+    kubectl annotate --overwrite pvc "$pvc" -n  $RELEASE_NAMESPACE  last-used="$NOW"
+done

helm/blueapi/templates/configmap.yaml

@@ -31,6 +31,6 @@ data:
   init_config.yaml: |-
     scratch:
       {{- toYaml .Values.worker.scratch | nindent 6 }}
-{{- end }}
 
----
+---    
+{{- end }}

helm/blueapi/templates/cronjob-configmaps.yaml

@@ -0,0 +1,22 @@
+{{- if .Values.timeStampCron.enabled }}
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name : {{include "blueapi.fullname" . }}-pvc-stamper-script
+data:
+  {{- $files := .Files }}
+  time-stamper.sh: |-
+{{ $files.Get "files/scripts/time-stamper.sh" | indent 4 }}
+---
+{{- end }}
+
+{{- if .Values.pvcAutoDeletion.enabled }}
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name : {{include "blueapi.fullname" . }}-pvc-auto-deletion-script
+data:
+  {{- $files := .Files }}
+  pvc-deletion.sh: |-
+{{ $files.Get "files/scripts/pvc-deletion.sh" | indent 4 }}
+{{- end }}

helm/blueapi/templates/cronjob.yaml

@@ -0,0 +1,169 @@
+{{- if .Values.timeStampCron.enabled }}
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  name: {{ include "blueapi.fullname" . }}-last-used-stamper
+  namespace: {{ .Release.Namespace }}
+automountServiceAccountToken: true
+---
+apiVersion: rbac.authorization.k8s.io/v1
+kind: Role
+metadata:
+  name: {{ include "blueapi.fullname" . }}-last-used-stamper
+  namespace: {{ .Release.Namespace }}
+rules:
+- apiGroups: [""]
+  resources: ["pods", "persistentvolumeclaims"]
+  verbs: ["get", "list", "patch"]
+---
+apiVersion: rbac.authorization.k8s.io/v1
+kind: RoleBinding
+metadata:
+  name: {{ include "blueapi.fullname" . }}-last-used-stamper
+  namespace: {{ .Release.Namespace }}
+subjects:
+- kind: ServiceAccount
+  name: {{ include "blueapi.fullname" . }}-last-used-stamper
+  namespace: {{ .Release.Namespace }}
+roleRef:
+  kind: Role
+  name: {{ include "blueapi.fullname" . }}-last-used-stamper
+  apiGroup: rbac.authorization.k8s.io
+---
+apiVersion: batch/v1
+kind: CronJob
+metadata:
+  name: {{ include "blueapi.fullname" . }}-last-used-stamper
+  namespace: {{ .Release.Namespace }}
+spec:
+  concurrencyPolicy: Forbid
+  successfulJobsHistoryLimit: 1
+  failedJobsHistoryLimit: 1
+  schedule: "*/5 * * * *"
+
+  jobTemplate:
+    spec:
+      # amount of attempts of labeling a pvc
+      backoffLimit: 3
+      # job stops after 180 seconds
+      activeDeadlineSeconds: 180
+      template:
+        spec:
+          serviceAccountName: {{ include "blueapi.fullname" . }}-last-used-stamper
+          {{- with .Values.tolerations }}
+          tolerations:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.nodeSelector }}
+          nodeSelector:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.affinity }}
+          affinity:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          volumes:
+            - name: {{include "blueapi.fullname" . }}-pvc-stamper-script
+              configMap:
+                name: {{include "blueapi.fullname" . }}-pvc-stamper-script
+                defaultMode: 0555
+          containers:
+          - name: last-used-stamper
+            env:
+              - name: RELEASE_NAME
+                value: {{ .Release.Name }}
+              - name: RELEASE_NAMESPACE
+                value: {{ .Release.Namespace }}
+            volumeMounts:
+              - name: {{include "blueapi.fullname" . }}-pvc-stamper-script
+                mountPath: /scripts
+            image: bitnami/kubectl:latest
+            imagePullPolicy: IfNotPresent
+            command: ["/scripts/time-stamper.sh"]
+          restartPolicy: OnFailure
+{{- end }}
+{{- if .Values.pvcAutoDeletion.enabled }}
+---
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  name: {{ include "blueapi.fullname" . }}-pvc-auto-deletion
+  namespace: {{ .Release.Namespace }}
+automountServiceAccountToken: true
+---
+apiVersion: rbac.authorization.k8s.io/v1
+kind: Role
+metadata:
+  name: {{ include "blueapi.fullname" . }}-pvc-auto-deletion
+  namespace: {{ .Release.Namespace }}
+rules:
+- apiGroups: [""]
+  resources: ["pods", "persistentvolumeclaims"]
+  verbs: ["get", "list", "patch","delete"]
+---
+apiVersion: rbac.authorization.k8s.io/v1
+kind: RoleBinding
+metadata:
+  name: {{ include "blueapi.fullname" . }}-pvc-auto-deletion
+  namespace: {{ .Release.Namespace }}
+subjects:
+- kind: ServiceAccount
+  name: {{ include "blueapi.fullname" . }}-pvc-auto-deletion
+  namespace: {{ .Release.Namespace }}
+roleRef:
+  kind: Role
+  name: {{ include "blueapi.fullname" . }}-pvc-auto-deletion
+  apiGroup: rbac.authorization.k8s.io
+---
+apiVersion: batch/v1
+kind: CronJob
+metadata:
+  name: {{ include "blueapi.fullname" . }}-pvc-auto-deletion
+  namespace: {{ .Release.Namespace }}
+spec:
+  concurrencyPolicy: Forbid
+  successfulJobsHistoryLimit: 1
+  failedJobsHistoryLimit: 1
+  schedule: "@weekly"
+
+  jobTemplate:
+    spec:
+      # amount of attempts for pvc deletion 
+      backoffLimit: 3
+      # job stops after 300 seconds
+      activeDeadlineSeconds: 300
+      template:
+        spec:
+          serviceAccountName: {{ include "blueapi.fullname" . }}-pvc-auto-deletion
+          {{- with .Values.tolerations }}
+          tolerations:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.nodeSelector }}
+          nodeSelector:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.affinity }}
+          affinity:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          volumes:
+            - name: {{include "blueapi.fullname" . }}-pvc-auto-deletion-script
+              configMap:
+                name: {{include "blueapi.fullname" . }}-pvc-auto-deletion-script
+                defaultMode: 0555
+          containers:
+          - name: pvc-auto-deletion
+            env:
+              - name: RELEASE_NAME
+                value: {{ .Release.Name }}
+              - name: RELEASE_NAMESPACE
+                value: {{ .Release.Namespace }}
+            volumeMounts:
+              - name: {{include "blueapi.fullname" . }}-pvc-auto-deletion-script
+                mountPath: /scripts
+            image: bitnami/kubectl:latest
+            imagePullPolicy: IfNotPresent
+            command: ["/scripts/pvc-deletion.sh"]
+          restartPolicy: OnFailure
+{{- end }}

helm/blueapi/values.schema.json

@@ -174,6 +174,14 @@
         "podSecurityContext": {
             "type": "object"
         },
+        "pvcAutoDeletion": {
+            "type": "object",
+            "properties": {
+                "enabled": {
+                    "type": "boolean"
+                }
+            }
+        },
         "readinessProbe": {
             "description": "Readiness probe, if configured kubernetes will not route traffic to this pod if failed consecutively. This could allow the service time to recover if it is being overwhelmed by traffic, but without the to ability to load balance or scale up/outwards, upstream services will need to know to back off. This is automatically disabled when in debug mode.",
             "type": "object",
@@ -198,7 +206,6 @@
             }
         },
         "resources": {
-            "description": "Sets the compute resources available to the pod. These defaults are appropriate when using debug mode or an internal PVC and therefore running VS Code server in the pod. In the Diamond cluster, requests must be \u003e= 0.1*limits When not using either of the above, the limits may be lowered. When idle but connected, blueapi consumes ~400MB of memory and 1% cpu and may struggle when allocated less.",
             "type": "object",
             "properties": {
                 "limits": {
@@ -292,6 +299,14 @@
                 }
             }
         },
+        "timeStampCron": {
+            "type": "object",
+            "properties": {
+                "enabled": {
+                    "type": "boolean"
+                }
+            }
+        },
         "tolerations": {
             "description": "May be required to run on specific nodes (e.g. the control machine)",
             "type": "array"
@@ -389,7 +404,6 @@
                     }
                 },
                 "logging": {
-                    "description": "Configures logging. Port 12231 is the `dodal` input on graylog which will be renamed `blueapi`",
                     "type": "object",
                     "properties": {
                         "graylog": {

helm/blueapi/values.yaml

@@ -36,8 +36,7 @@ podAnnotations: {}
 # For more information checkout: https://kubernetes.io/docs/concepts/overview/working-with-objects/labels/
 podLabels: {}
 
-podSecurityContext: {}
-  # fsGroup: 2000
+podSecurityContext: {} # fsGroup: 2000
 
 securityContext:
   # https://github.com/DiamondLightSource/blueapi/issues/1096
@@ -48,7 +47,7 @@ securityContext:
   #   drop:
   #   - ALL
 
-# This is for setting up a service more information can be found here: https://kubernetes.io/docs/concepts/services-networking/service/
+  # This is for setting up a service more information can be found here: https://kubernetes.io/docs/concepts/services-networking/service/
 service:
   # This sets the service type more information can be found here: https://kubernetes.io/docs/concepts/services-networking/service/#publishing-services-service-types
   # -- To make blueapi available on an IP outside of the cluster prior to an Ingress being created, change this to LoadBalancer
@@ -76,13 +75,13 @@ ingress:
   #    hosts:
   #      - chart-example.local
 
-# -- Sets the compute resources available to the pod.
-# These defaults are appropriate when using debug mode or an internal PVC and therefore
-# running VS Code server in the pod.
-# In the Diamond cluster, requests must be >= 0.1*limits
-# When not using either of the above, the limits may be lowered.
-# When idle but connected, blueapi consumes ~400MB of memory and 1% cpu
-# and may struggle when allocated less.
+  # -- Sets the compute resources available to the pod.
+  # These defaults are appropriate when using debug mode or an internal PVC and therefore
+  # running VS Code server in the pod.
+  # In the Diamond cluster, requests must be >= 0.1*limits
+  # When not using either of the above, the limits may be lowered.
+  # When idle but connected, blueapi consumes ~400MB of memory and 1% cpu
+  # and may struggle when allocated less.
 resources:
   # We usually recommend not to specify default resources and to leave this as a conscious
   # choice for the user. This also increases chances charts run on environments with little
@@ -205,7 +204,7 @@ worker:
     repositories: []
     # - name: "dodal"
     #   remote_url: https://github.com/DiamondLightSource/dodal.git
-  # -- Configures logging. Port 12231 is the `dodal` input on graylog which will be renamed `blueapi`
+    # -- Configures logging. Port 12231 is the `dodal` input on graylog which will be renamed `blueapi`
   logging:
     level: "INFO"
     graylog:
@@ -224,6 +223,12 @@ initContainer:
     # -- Size of persistent volume
     size: "1Gi"
 
+timeStampCron:
+  enabled: true
+
+pvcAutoDeletion:
+  enabled: true
+
 debug:
   # -- If enabled, runs debugpy, allowing port-forwarding to expose port 5678 or attached vscode instance
   enabled: false