Added HAPI FHIR server Helm chart (#24)

* removed test values * added first draft of a HAPI FHIR helm chart * added missing fields to Chart.yaml * updated docs
chgl · Feb 5, 2021 · f944ea0 · f944ea0
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diff --git a/charts/hapi-fhir-jpaserver/.helmignore b/charts/hapi-fhir-jpaserver/.helmignore
@@ -0,0 +1,23 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/
diff --git a/charts/hapi-fhir-jpaserver/Chart.lock b/charts/hapi-fhir-jpaserver/Chart.lock
@@ -0,0 +1,6 @@
+dependencies:
+- name: postgresql
+  repository: https://charts.bitnami.com/bitnami
+  version: 10.2.0
+digest: sha256:ffc74acdb2350c12e199b3cf080130440bb1e137d1cf10dec1fbdbe597d40510
+generated: "2021-02-05T15:35:39.0212888+01:00"
diff --git a/charts/hapi-fhir-jpaserver/Chart.yaml b/charts/hapi-fhir-jpaserver/Chart.yaml
@@ -0,0 +1,16 @@
+apiVersion: v2
+name: hapi-fhir-jpaserver
+description: A Helm chart for deploying the HAPI FHIR JPA server starter on Kubernetes.
+type: application
+home: https://github.com/hapifhir/hapi-fhir-jpaserver-starter
+sources:
+  - https://github.com/hapifhir/hapi-fhir-jpaserver-starter
+maintainers:
+  - name: chgl
+dependencies:
+  - name: postgresql
+    version: 10.2.0
+    repository: https://charts.bitnami.com/bitnami
+    condition: postgresql.enabled
+appVersion: 5.2.0
+version: 0.1.0
diff --git a/charts/hapi-fhir-jpaserver/README.md b/charts/hapi-fhir-jpaserver/README.md
diff --git a/charts/hapi-fhir-jpaserver/doc.yaml b/charts/hapi-fhir-jpaserver/doc.yaml
@@ -0,0 +1,19 @@
+project:
+  name: HAPI FHIR JPA Server
+  shortName: hapi-fhir-jpaserver
+  url: https://github.com/hapifhir/hapi-fhir-jpaserver-starter
+  description: Helm chart for deploying the HAPI FHIR JPA starter server
+  app: the HAPI FHIR JPA starter server.
+repository:
+  url: https://chgl.github.io/charts
+  name: chgl
+chart:
+  name: hapi-fhir-jpaserver
+  values: "-- generate from values file --"
+  valuesExample: "-- generate from values file --"
+prerequisites:
+  - "Kubernetes v1.16+"
+  - "Helm v3"
+release:
+  name: hapi-fhir-jpaserver
+  namespace: fhir
diff --git a/charts/hapi-fhir-jpaserver/templates/NOTES.txt b/charts/hapi-fhir-jpaserver/templates/NOTES.txt
@@ -0,0 +1,22 @@
+1. Get the application URL by running these commands:
+{{- if .Values.ingress.enabled }}
+{{- range $host := .Values.ingress.hosts }}
+  {{- range .paths }}
+  http{{ if $.Values.ingress.tls }}s{{ end }}://{{ $host.host }}{{ . }}
+  {{- end }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "hapi-fhir-jpaserver.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "hapi-fhir-jpaserver.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "hapi-fhir-jpaserver.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
+  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.kubernetes.io/name={{ include "hapi-fhir-jpaserver.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+  export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $POD_NAME -o jsonpath="{.spec.containers[0].ports[0].containerPort}")
+  echo "Visit http://127.0.0.1:8080 to use your application"
+  kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:$CONTAINER_PORT
+{{- end }}
diff --git a/charts/hapi-fhir-jpaserver/templates/_helpers.tpl b/charts/hapi-fhir-jpaserver/templates/_helpers.tpl
@@ -0,0 +1,80 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "hapi-fhir-jpaserver.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 "hapi-fhir-jpaserver.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 "hapi-fhir-jpaserver.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "hapi-fhir-jpaserver.labels" -}}
+helm.sh/chart: {{ include "hapi-fhir-jpaserver.chart" . }}
+{{ include "hapi-fhir-jpaserver.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "hapi-fhir-jpaserver.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "hapi-fhir-jpaserver.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the JDBC URL from the host, port and database name.
+*/}}
+{{- define "hapi-fhir-jpaserver.jdbcUrl" -}}
+{{- if .Values.postgresql.enabled -}}
+{{- $pgServiceName := ( printf "%s-%s" .Release.Name "postgresql") -}}
+{{ printf "jdbc:postgresql://%s:%d/%s" $pgServiceName 5432 .Values.postgresql.postgresqlDatabase }}
+{{- else -}}
+{{ printf "jdbc:postgresql://%s:%d/%s" .Values.externalDatabase.host (int64 .Values.externalDatabase.port) .Values.externalDatabase.database }}
+{{- end -}}
+{{- end -}}
+
+{{/*
+Get the name of the secret containing the DB password
+*/}}
+{{- define "hapi-fhir-jpaserver.db-secretName" -}}
+{{- if .Values.postgresql.enabled -}}
+{{- if .Values.postgresql.existingSecret -}}
+    {{ .Values.postgresql.existingSecret | quote }}
+{{- else -}}
+    {{ printf "%s-%s" .Release.Name "postgresql" }}
+{{- end -}}
+{{- else if .Values.externalDatabase.existingSecret -}}
+    {{ .Values.externalDatabase.existingSecret | quote }}
+{{- else -}}
+    {{ printf "%s-%s" .Release.Name "externaldb" }}
+{{- end -}}
+{{- end -}}
diff --git a/charts/hapi-fhir-jpaserver/templates/deployment.yaml b/charts/hapi-fhir-jpaserver/templates/deployment.yaml
@@ -0,0 +1,106 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "hapi-fhir-jpaserver.fullname" . }}
+  labels:
+    {{- include "hapi-fhir-jpaserver.labels" . | nindent 4 }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      {{- include "hapi-fhir-jpaserver.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      {{- with .Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      labels:
+        {{- include "hapi-fhir-jpaserver.selectorLabels" . | nindent 8 }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      securityContext:
+        {{- toYaml .Values.podSecurityContext | nindent 8 }}
+      {{- if .Values.postgresql.enabled }}
+      initContainers:
+        - name: wait-for-db
+          image: busybox:1.32
+          imagePullPolicy: IfNotPresent
+          securityContext:
+            allowPrivilegeEscalation: false
+            readOnlyRootFilesystem: true
+            privileged: false
+            capabilities:
+              drop:
+                - ALL
+            runAsNonRoot: true
+            runAsUser: 11111
+            runAsGroup: 11111
+          command: ["sh", "-c", "while ! nc -z {{ .Release.Name }}-postgresql 5432 -w 5; do echo $(date) waiting for database; sleep 5; done;"]
+      {{- end }}
+      containers:
+        - name: {{ .Chart.Name }}
+          securityContext:
+            {{- toYaml .Values.securityContext | nindent 12 }}
+          image: "{{ .Values.image.registry }}/{{ .Values.image.repository }}:{{ .Values.image.tag }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          ports:
+            - name: http
+              containerPort: 8080
+              protocol: TCP
+          readinessProbe:
+            httpGet:
+              path: /fhir/metadata
+              port: http
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+          env:
+            - name: SPRING_DATASOURCE_URL
+              value: {{ include "hapi-fhir-jpaserver.jdbcUrl" $ }}
+            - name: SPRING_DATASOURCE_USERNAME
+              {{- if .Values.postgresql.enabled }}
+              value: {{ .Values.postgresql.postgresqlUsername }}
+              {{- else }}
+              value: {{ .Values.externalDatabase.user | quote }}
+              {{- end }}
+            - name: SPRING_DATASOURCE_PASSWORD
+              valueFrom:
+                secretKeyRef:
+                  name: {{ template "hapi-fhir-jpaserver.db-secretName" . }}
+                  key: postgresql-password
+            - name: SPRING_DATASOURCE_DRIVERCLASSNAME
+              value: org.postgresql.Driver
+            - name: SPRING_JPA_PROPERTIES_HIBERNATE_DIALECT
+              value: org.hibernate.dialect.PostgreSQL10Dialect
+            - name: HAPI_FHIR_USE_APACHE_ADDRESS_STRATEGY
+              value: "true"
+            - name: SPRING_JPA_DATABASE_PLATFORM
+              value: org.hibernate.dialect.PostgreSQLDialect
+            {{- if .Values.extraEnv }}
+            {{ toYaml .Values.extraEnv | nindent 12 }}
+            {{- end }}
+          volumeMounts:
+            - mountPath: /tmp
+              name: tmp-volume
+            - mountPath: /app/target
+              name: lucenefiles-volume
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      volumes:
+        - name: tmp-volume
+          emptyDir: {}
+        - name: lucenefiles-volume
+          emptyDir: {}
diff --git a/charts/hapi-fhir-jpaserver/templates/externaldb-secret.yaml b/charts/hapi-fhir-jpaserver/templates/externaldb-secret.yaml
@@ -0,0 +1,14 @@
+{{- if and (not .Values.postgresql.enabled) (not .Values.externalDatabase.existingSecret) (not .Values.postgresql.existingSecret)}}
+apiVersion: v1
+kind: Secret
+metadata:
+  name: {{ printf "%s-%s" .Release.Name "externaldb"  }}
+  labels:
+    app.kubernetes.io/name: {{ include "hapi-fhir-server.name" . }}
+    helm.sh/chart: {{ include "hapi-fhir-server.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+type: Opaque
+data:
+  postgresql-password: {{ .Values.externalDatabase.password | b64enc | quote }}
+{{- end }}
diff --git a/charts/hapi-fhir-jpaserver/templates/ingress.yaml b/charts/hapi-fhir-jpaserver/templates/ingress.yaml
@@ -0,0 +1,54 @@
+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "hapi-fhir-jpaserver.fullname" . -}}
+{{- $svcPort := .Values.service.port -}}
+{{- if semverCompare ">=1.19-0" .Capabilities.KubeVersion.GitVersion }}
+apiVersion: networking.k8s.io/v1
+{{- else if semverCompare ">=1.14-0" .Capabilities.KubeVersion.GitVersion }}
+apiVersion: networking.k8s.io/v1beta1
+{{ else }}
+apiVersion: extensions/v1beta1
+{{- end }}
+kind: Ingress
+metadata:
+  name: {{ $fullName }}
+  labels:
+    {{- include "hapi-fhir-jpaserver.labels" . | nindent 4 }}
+  {{- with .Values.ingress.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+spec:
+{{- if .Values.ingress.tls }}
+  tls:
+  {{- range .Values.ingress.tls }}
+    - hosts:
+      {{- range .hosts }}
+        - {{ . | quote }}
+      {{- end }}
+      secretName: {{ .secretName }}
+  {{- end }}
+{{- end }}
+  rules:
+  {{- range .Values.ingress.hosts }}
+    {{- $pathType := .pathType }}
+    - host: {{ .host | quote }}
+      http:
+        paths:
+        {{- range .paths }}
+          - path: {{ . }}
+            {{- if semverCompare ">=1.19-0" $.Capabilities.KubeVersion.GitVersion }}
+            pathType: {{ $pathType | default "ImplementationSpecific" }}
+            {{- end }}
+            backend:
+              {{- if semverCompare ">=1.19-0" $.Capabilities.KubeVersion.GitVersion }}
+              service:
+                name: {{ $fullName }}
+                port:
+                  number: {{ $svcPort }}
+              {{ else }}
+              serviceName: {{ $fullName }}
+              servicePort: {{ $svcPort }}
+              {{- end }}
+        {{- end }}
+  {{- end }}
+{{- end }}
diff --git a/charts/hapi-fhir-jpaserver/templates/service.yaml b/charts/hapi-fhir-jpaserver/templates/service.yaml
@@ -0,0 +1,15 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ include "hapi-fhir-jpaserver.fullname" . }}
+  labels:
+    {{- include "hapi-fhir-jpaserver.labels" . | nindent 4 }}
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - port: {{ .Values.service.port }}
+      targetPort: http
+      protocol: TCP
+      name: http
+  selector:
+    {{- include "hapi-fhir-jpaserver.selectorLabels" . | nindent 4 }}
diff --git a/charts/hapi-fhir-jpaserver/templates/tests/test-connection.yaml b/charts/hapi-fhir-jpaserver/templates/tests/test-connection.yaml
@@ -0,0 +1,32 @@
+apiVersion: v1
+kind: Pod
+metadata:
+  name: "{{ include "hapi-fhir-jpaserver.fullname" . }}-test-connection"
+  labels:
+    {{- include "hapi-fhir-jpaserver.labels" . | nindent 4 }}
+  annotations:
+    "helm.sh/hook": test
+spec:
+  restartPolicy: Never
+  containers:
+    - name: wget
+      image: busybox:1
+      command: ['wget']
+      args: ['{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.service.port }}/fhir/metadata']
+      securityContext:
+        readOnlyRootFilesystem: true
+        runAsUser: 22222
+        runAsNonRoot: true
+      resources:
+        limits:
+          cpu: 100m
+          memory: 128Mi
+        requests:
+          cpu: 100m
+          memory: 128Mi
+      livenessProbe:
+        exec:
+          command: ["true"]
+      readinessProbe:
+        exec:
+          command: ["true"]