molgenis-ops-docker-helm/charts/molgenis/templates/deployment.yaml

apiVersion: apps/v1beta2
kind: Deployment
metadata:
  {{- with .Values.ingress.annotations }}
  annotations:
{{ toYaml . | indent 4 }}
  {{- end }}
  name: {{ template "molgenis.fullname" . }}
  labels:
    app: {{ template "molgenis.name" . }}
    chart: {{ template "molgenis.chart" . }}
    release: {{ .Release.Name }}
    heritage: {{ .Release.Service }}
spec:
  replicas: {{ .Values.replicaCount }}
  selector:
    matchLabels:
      app: {{ template "molgenis.name" . }}
      release: {{ .Release.Name }}
  strategy:
    type: Recreate
  template:
    metadata:
      labels:
        app: {{ template "molgenis.name" . }}
        release: {{ .Release.Name }}
    spec:
      containers:
        - name: molgenis
        {{- with .Values.molgenis }}
          image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}
          imagePullPolicy: {{ .image.pullPolicy }}
          env:
            - name: molgenis.home
              value: /home/molgenis
            - name: opencpu.uri.host
              value: {{ .services.opencpu.host }}
            - name: elasticsearch.transport.addresses
              value: {{ .services.elasticsearch.transportAddresses }}
            - name: elasticsearch.cluster.name
              value: {{ .services.elasticsearch.clusterName }}
            - name: db_uri
              value: jdbc:postgresql://{{ .services.postgres.host }}/{{ .services.postgres.scheme }}
            - name: db_user
              value: {{ .services.postgres.user }}
            - name: db_password
              value: {{ .services.postgres.password }}
            - name: admin.password
              value: {{ .adminPassword }}
            - name: CATALINA_OPTS
              value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
          ports:
            - containerPort: 8080
          {{- if $.Values.persistence.enabled }}
          volumeMounts:
          - name: molgenis-nfs
            mountPath: /home/molgenis
          {{- end }}
          livenessProbe:
            httpGet:
              path: /
              port: 8080
            initialDelaySeconds: 60
            periodSeconds: 5
            failureThreshold: 25
            successThreshold: 1
          readinessProbe:
            httpGet:
              path: /api/v2/version
              port: 8080
            initialDelaySeconds: 120
            periodSeconds: 30
            failureThreshold: 3
            successThreshold: 1
          resources:
{{ toYaml .resources | indent 12 }}
        {{- end }}

        - name: elasticsearch
        {{- with .Values.elasticsearch }}
          image: "{{ .image.repository }}:{{ .image.tag }}"
          imagePullPolicy: {{ .image.pullPolicy }}
          env:
            - name: cluster.name
              value: {{ .clusterName }}
            - name: bootstrap.memory_lock
              value: "true"
            - name: ES_JAVA_OPTS
              value: "{{ .javaOpts }}"
            - name: xpack.security.enabled
              value: "false"
            - name: discovery.type
              value: single-node
          ports:
            - containerPort: 9200
            - containerPort: 9300
          {{- if $.Values.persistence.enabled }}
          volumeMounts:
          - name: elasticsearch-nfs
            mountPath: /usr/share/elasticsearch/data
          {{- end }}
          resources:
{{ toYaml .resources | indent 12 }}
        {{- end }}

        - name: postgres
        {{- with .Values.postgres }}
          image: "{{ .image.repository }}:{{ .image.tag }}"
          imagePullPolicy: {{ .image.pullPolicy }}
          env:
            - name: POSTGRES_USER
              value: {{ $.Values.molgenis.services.postgres.user }}
            - name: POSTGRES_PASSWORD
              value: {{ $.Values.molgenis.services.postgres.password }}
            - name: POSTGRES_DB
              value: {{ $.Values.molgenis.services.postgres.scheme }}
          ports:
            - containerPort: 5432
          resources:
{{ toYaml .resources | indent 12 }}
          {{- if $.Values.persistence.enabled }}
          volumeMounts:
          - name: postgres-nfs
            mountPath: /var/lib/postgresql/data
          {{- end }}
        {{- end }}


{{- if .Values.persistence.enabled }}
      volumes:
        - name: molgenis-nfs
          persistentVolumeClaim:
            claimName: {{ .Values.molgenis.persistence.claim }}
        - name: elasticsearch-nfs
          persistentVolumeClaim:
            claimName: {{ .Values.elasticsearch.persistence.claim }}
        - name: postgres-nfs
          persistentVolumeClaim:
            claimName: {{ .Values.postgres.persistence.claim }}
{{- end }}

    {{- with .Values.nodeSelector }}
      nodeSelector:
{{ toYaml . | indent 8 }}
    {{- end }}
    {{- with .Values.affinity }}
      affinity:
{{ toYaml . | indent 8 }}
    {{- end }}
    {{- with .Values.tolerations }}
      tolerations:
{{ toYaml . | indent 8 }}
    {{- end }}