initial commit

charts/opal/templates/NOTES.txt

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+1. Get the application URL by running these commands:
+{{- if .Values.ingress.enabled }}
+{{- range .Values.ingress.hosts }}
+  http{{ if $.Values.ingress.tls }}s{{ end }}://{{ . }}{{ $.Values.ingress.path }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ template "molgenis.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get svc -w {{ template "molgenis.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ template "molgenis.fullname" . }} -o jsonpath='{.status.loadBalancer.ingress[0].ip}')
+  echo http://$SERVICE_IP:{{ .Values.service.port }}
+{{- else if contains "ClusterIP" .Values.service.type }}
+  export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app={{ template "molgenis.name" . }},release={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+  echo "Visit http://127.0.0.1:8080 to use your application"
+  kubectl port-forward $POD_NAME 8080:80
+{{- end }}

charts/opal/templates/_helpers.tpl

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+{{/* vim: set filetype=mustache: */}}
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "opal.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "opal.fullname" -}}
+{{- if .Values.fullnameOverride -}}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
+{{- else -}}
+{{- $name := default .Chart.Name .Values.nameOverride -}}
+{{- if contains $name .Release.Name -}}
+{{- .Release.Name | trunc 63 | trimSuffix "-" -}}
+{{- else -}}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+{{- end -}}
+{{- end -}}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "opal.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
+{{- end -}}

charts/opal/templates/deployment.yaml

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+apiVersion: apps/v1beta2
+kind: Deployment
+metadata:
+  {{- with .Values.ingress.annotations }}
+  annotations:
+{{ toYaml . | indent 4 }}
+  {{- end }}
+  name: {{ template "opal.fullname" . }}
+  labels:
+    app: {{ template "opal.name" . }}
+    chart: {{ template "opal.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app: {{ template "opal.name" . }}
+      release: {{ .Release.Name }}
+  strategy:
+    type: Recreate
+  template:
+    metadata:
+      labels:
+        app: {{ template "opal.name" . }}
+        release: {{ .Release.Name }}
+    spec:
+      containers:
+        - name: opal
+        {{- with .Values.opal }}
+          image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}
+          imagePullPolicy: {{ .image.pullPolicy }}
+          env:
+            - name: opal.home
+              value: /home/opal
+            - name: db_uri
+              value: jdbc:postgresql://localhost/opal
+            - name: db_user
+              value: opal
+            - name: db_password
+              value: opal
+            - name: admin.password
+              value: "{{ .adminPassword }}"
+            - name: CATALINA_OPTS
+            {{- if eq .type.kind "small" }}
+              value: "-Xmx{{ .type.small.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
+            {{- else if eq .type.kind "medium"}}
+              value: "-Xmx{{ .type.medium.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
+            {{- else }}
+              value: "-Xmx{{ .type.large.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
+            {{- end }}
+          ports:
+            - containerPort: 8080
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: opal-nfs
+            mountPath: /home/opal
+          {{- 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:
+          {{- if eq .type.kind "small" }}
+{{ toYaml .type.small.resources | indent 12 }}
+          {{- else if eq .type.kind "medium" }}
+{{ toYaml .type.medium.resources | indent 12 }}
+          {{- else }}
+{{ toYaml .type.large.resources | indent 12 }}
+          {{- end }}
+        {{- end }}
+
+{{- if .Values.persistence.enabled }}
+      volumes:
+        - name: opal-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.opal.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 }}

charts/opal/templates/ingress.yaml

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+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "opal.fullname" . -}}
+{{- $ingressPath := .Values.ingress.path -}}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: "{{ $.Release.Name }}-ingress"
+  labels:
+    app: {{ template "opal.name" . }}
+    chart: {{ template "opal.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+{{- with .Values.ingress.annotations }}
+  annotations:
+{{ toYaml . | indent 4 }}
+{{- end }}
+spec:
+{{- if .Values.ingress.tls }}
+  tls:
+  {{- range .Values.ingress.tls }}
+    - hosts:
+      {{- range .hosts }}
+        - {{ . }}
+      {{- end }}
+      secretName: {{ .secretName }}
+  {{- end }}
+{{- end }}
+  rules:
+    {{- if eq $.Values.opal.environment "development" }}
+    - host: {{ .Release.Name }}.dev.opal.org
+    {{- else if eq $.Values.opal.environment "test" }}
+    - host: {{ .Release.Name }}.test.opal.org
+    {{- else if eq $.Values.opal.environment "acceptance" }}
+    - host: {{ .Release.Name }}.accept.opal.org
+    {{- else }}
+    - host: {{ .Release.Name }}.opal.org
+    {{- end }}
+      http:
+        paths:
+          - path: {{ $ingressPath }}
+            backend:
+              serviceName: {{ $fullName }}
+              servicePort: {{ $.Values.service.port }}
+{{- end }}

charts/opal/templates/persistence/mysqlPVC.yaml

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+{{- if .Values.persistence.enabled }}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.mysql.persistence.claim }}
+  annotations:
+    {{- if .Values.persistence.retain }}
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
+    {{- else }}
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
+    {{- end }}
+spec:
+  accessModes:
+    - ReadWriteMany
+  resources:
+    requests:
+    {{- if eq .Values.persistence.mysql.size "default" }}
+      {{- if eq .Values.opal.type.kind "small" }}
+      storage: {{ .Values.mysql.type.small.persistence.size }}
+      {{- else if eq .Values.opal.type.kind "medium" }}
+      storage: {{ .Values.mysql.type.medium.persistence.size }}
+      {{- else }}
+      storage: {{ .Values.mysql.type.large.persistence.size }}
+      {{- end }}
+    {{ else }}
+        storage: {{ .Values.persistence.mysql.size }}
+    {{- end }}
+{{- end }}

charts/opal/templates/persistence/opalPVC.yaml

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+{{- if .Values.persistence.enabled -}}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.opal.persistence.claim }}
+  annotations:
+    {{- if .Values.persistence.retain }}
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
+    {{- else }}
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
+    {{- end }}
+spec:
+  accessModes:
+    - ReadWriteMany
+  resources:
+    requests:
+    {{- if eq .Values.persistence.opal.size "default" }}
+      {{- if eq .Values.opal.type.kind "small" }}
+      storage: {{ .Values.opal.type.small.persistence.size }}
+      {{- else if eq .Values.opal.type.kind "medium" }}
+      storage: {{ .Values.opal.type.medium.persistence.size }}
+      {{- else }}
+      storage: {{ .Values.opal.type.large.persistence.size }}
+      {{- end }}
+    {{ else }}
+      storage: {{ .Values.persistence.opal.size }}
+    {{- end }}
+{{- end }}

charts/opal/templates/service.yaml

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+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ template "opal.fullname" . }}
+  labels:
+    app: {{ template "opal.name" . }}
+    chart: {{ template "opal.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - name: opal
+      port: {{ .Values.service.port }}
+  selector:
+    app: {{ template "opal.name" . }}
+    release: {{ .Release.Name }}