Continue charm

Author: meier-rene

charts/custom-values.yaml

@@ -1,6 +1,16 @@
-# Overwrite ingress path properties for massbank3-frontend
+# hostneme of the public url serving massbank
 host: msbi.ipb-halle.de
+# base path of the public url serving massbank
 pathPrefix: MassBank3
+# release name of the helm install of massbank3-frontend, required for dbtool
+# to identify the hostname of the postgres database
+massbank3ReleaseName: massbank3
+
+# postgres settings for dbtool
+postgresPassword: "massbank3adminpassword"
+username: "massbank3"
+password: "massbank3password"
+database: "massbank3"
 
 massbank3-export-service:
   host: msbi.ipb-halle.de

charts/massbank3-dbtool/templates/job.yaml

@@ -7,32 +7,15 @@ metadata:
 spec:
   template:
     metadata:
-      {{- with .Values.podAnnotations }}
-      annotations:
-        {{- toYaml . | nindent 8 }}
-      {{- end }}
       labels:
         {{- include "massbank3-dbtool.labels" . | nindent 8 }}
         {{- with .Values.podLabels }}
         {{- toYaml . | nindent 8 }}
         {{- end }}
     spec:
       restartPolicy: Never
-      {{- with .Values.imagePullSecrets }}
-      imagePullSecrets:
-        {{- toYaml . | nindent 8 }}
-      {{- end }}
-      serviceAccountName: {{ include "massbank3-dbtool.serviceAccountName" . }}
-      {{- with .Values.podSecurityContext }}
-      securityContext:
-        {{- toYaml . | nindent 8 }}
-      {{- end }}
       containers:
         - name: {{ .Chart.Name }}
-          {{- with .Values.securityContext }}
-          securityContext:
-            {{- toYaml . | nindent 12 }}
-          {{- end }}
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
           env:
@@ -41,7 +24,7 @@ spec:
             - name: DB_PASSWORD
               value: {{ .Values.password }}
             - name: DB_HOST
-              value: "massbank3-postgresql"
+              value: {{ .Values.massbank3ReleaseName }}-postgresql
             - name: DB_NAME
               value: {{ .Values.database }}
             - name: DB_USER
@@ -56,12 +39,3 @@ spec:
               value: ""
             - name: MB_DROP_ALL
               value: "true"
-      {{- with .Values.nodeSelector }}
-      nodeSelector:
-        {{- toYaml . | nindent 8 }}
-      {{- end }}
-      {{- with .Values.affinity }}
-      affinity:
-        {{- toYaml . | nindent 8 }}
-      {{- end }}
-

charts/massbank3-dbtool/templates/serviceaccount.yaml

@@ -1,52 +1,19 @@
 # This will set the replicaset count more information can be found here: https://kubernetes.io/docs/concepts/workloads/controllers/replicaset/
 replicaCount: 1
 
-host: "msbi.ipb-halle.de"
-pathPrefix: "MassBank"
-
 postgresPassword: "massbank3adminpassword"
 username: "massbank3"
 password: "massbank3password"
 database: "massbank3"
 
+massbank3ReleaseName: massbank3
+
 image:
   repository: ipbhalle/massbank3-dbtool
   tag: "dev"
   pullPolicy: IfNotPresent
 
-# This is for the secrets for pulling an image from a private repository more information can be found here: https://kubernetes.io/docs/tasks/configure-pod-container/pull-image-private-registry/
-imagePullSecrets: []
-# This is to override the chart name.
-nameOverride: ""
-fullnameOverride: ""
-
-# This section builds out the service account more information can be found here: https://kubernetes.io/docs/concepts/security/service-accounts/
-serviceAccount:
-  # Specifies whether a service account should be created
-  create: true
-  # Automatically mount a ServiceAccount's API credentials?
-  automount: true
-  # Annotations to add to the service account
-  annotations: {}
-  # The name of the service account to use.
-  # If not set and create is true, a name is generated using the fullname template
-  name: ""
-
-# This is for setting Kubernetes Annotations to a Pod.
-# For more information checkout: https://kubernetes.io/docs/concepts/overview/working-with-objects/annotations/
-podAnnotations: {}
 # This is for setting Kubernetes Labels to a Pod.
 # For more information checkout: https://kubernetes.io/docs/concepts/overview/working-with-objects/labels/
 podLabels:
-  app: massbank3-dbtool
-
-podSecurityContext: {}
-  # fsGroup: 2000
-
-securityContext: {}
-  # capabilities:
-  #   drop:
-  #   - ALL
-  # readOnlyRootFilesystem: true
-  # runAsNonRoot: true
-  # runAsUser: 1000
+  app: massbank3-dbtool

charts/massbank3-dbtool/values.yaml

@@ -10,7 +10,7 @@ appVersion: "v0.1"
 dependencies:
   - name: postgresql
     repository: https://charts.bitnami.com/bitnami
-    version: 16.4.9
+    version: 16.6.2
   - name: massbank3-similarity-service
     repository: file://../massbank3-similarity-service
     version: 0.1.0

charts/massbank3-server/Chart.yaml

@@ -49,6 +49,15 @@ postgresql:
     extraVolumeMounts: |
       - name: bingo-volume
         mountPath: /opt/bingo-postgres
+    persistence:
+      size: 16Gi
+  resources:
+    requests:
+      memory: "2Gi"
+      cpu: "1"
+    limits:
+      memory: "4Gi"
+      cpu: "2"
 
 # This is for the secrets for pulling an image from a private repository more information can be found here: https://kubernetes.io/docs/tasks/configure-pod-container/pull-image-private-registry/
 imagePullSecrets: []