Migrate FHIR gateway chart (#84)

* migrate fhir-gateway helm chart * add sentry configuration support
opensrp · May 21, 2024 · fa997f1 · fa997f1
1 parent 59f1012
commit fa997f1
Show file tree

Hide file tree

Showing 16 changed files with 738 additions and 0 deletions.
diff --git a/README.md b/README.md
@@ -14,6 +14,7 @@ This is the OpenSRP community's official repository for [Helm](https://helm.sh)
 8. [OpenHIM Mediator Mapping](https://github.com/jembi/openhim-mediator-mapping)
 9. OpenHIE Helper Tools: FHIR Extractor, OpenCR, MCSD Mock Service
 10. [DHIS2 FHIR Adapter](https://github.com/opensrp/dhis2-fhir-adapter)
+11. [FHIR Gateway](https://github.com/onaio/fhir-gateway-extension)
 
 ## Usage
 

diff --git a/charts/fhir-gateway/.helmignore b/charts/fhir-gateway/.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/fhir-gateway/Chart.yaml b/charts/fhir-gateway/Chart.yaml
@@ -0,0 +1,32 @@
+apiVersion: v2
+name: fhir-gateway
+description: |
+  This is a simple access-control proxy that sits in front of a
+  [FHIR](https://www.hl7.org/fhir/) store (e.g., a
+  [HAPI FHIR](https://hapifhir.io/) server,
+  [GCP FHIR store](https://cloud.google.com/healthcare-api/docs/concepts/fhir),
+  etc.) and controls access to FHIR resources.
+icon: https://avatars2.githubusercontent.com/u/7898027?s=200&v=4
+maintainers:
+  - name: opensrp
+    email: [email protected]
+# A chart can be either an 'application' or a 'library' chart.
+#
+# Application charts are a collection of templates that can be packaged into versioned archives
+# to be deployed.
+#
+# Library charts provide useful utilities or functions for the chart developer. They're included as
+# a dependency of application charts to inject those utilities and functions into the rendering
+# pipeline. Library charts do not define any templates and therefore cannot be deployed.
+type: application
+
+# This is the chart version. This version number should be incremented each time you make changes
+# to the chart and its templates, including the app version.
+# Versions are expected to follow Semantic Versioning (https://semver.org/)
+version: 0.1.0
+
+# This is the version number of the application being deployed. This version number should be
+# incremented each time you make changes to the application. Versions are not expected to
+# follow Semantic Versioning. They should reflect the version the application is using.
+# It is recommended to use it with quotes.
+appVersion: "v1.0.13"
diff --git a/charts/fhir-gateway/README.md b/charts/fhir-gateway/README.md
diff --git a/charts/fhir-gateway/templates/NOTES.txt b/charts/fhir-gateway/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 }}://{{ $host.host }}{{ .path }}
+  {{- end }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "fhir-gateway.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "fhir-gateway.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "fhir-gateway.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 "fhir-gateway.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/fhir-gateway/templates/_helpers.tpl b/charts/fhir-gateway/templates/_helpers.tpl
@@ -0,0 +1,74 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "fhir-gateway.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 "fhir-gateway.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 "fhir-gateway.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "fhir-gateway.labels" -}}
+helm.sh/chart: {{ include "fhir-gateway.chart" . }}
+{{ include "fhir-gateway.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "fhir-gateway.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "fhir-gateway.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "fhir-gateway.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "fhir-gateway.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}
+
+{{/*
+Populate the pod annotations
+*/}}
+{{- define "fhir-gateway.podAnnotations" -}}
+{{- range $index, $element:=.Values.podAnnotations }}
+{{ $index }}: {{ $element | quote }}
+{{- end }}
+{{- if .Values.recreatePodsWhenConfigMapChange }}
+checksum/config: {{ include (print $.Template.BasePath "/configmap.yaml") . | sha256sum }}
+{{- end }}
+{{- end }}
diff --git a/charts/fhir-gateway/templates/configmap.yaml b/charts/fhir-gateway/templates/configmap.yaml
@@ -0,0 +1,13 @@
+{{ $scope := .}}
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ include "fhir-gateway.fullname" . }}
+  labels:
+    {{- include "fhir-gateway.labels" . | nindent 4 }}
+data:
+  {{ range $value := .Values.configMaps -}}
+  {{ $value.name }}: |
+  {{ tpl $value.contents $scope | nindent 8 }}
+  {{ end }}
+
diff --git a/charts/fhir-gateway/templates/deployment.yaml b/charts/fhir-gateway/templates/deployment.yaml
@@ -0,0 +1,76 @@
+{{ $scope := .}}
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "fhir-gateway.fullname" . }}
+  labels:
+    {{- include "fhir-gateway.labels" . | nindent 4 }}
+spec:
+  {{- if not .Values.autoscaling.enabled }}
+  replicas: {{ .Values.replicaCount }}
+  {{- end }}
+  selector:
+    matchLabels:
+      {{- include "fhir-gateway.selectorLabels" . | nindent 6 }}
+  template:
+    metadata:
+      annotations:
+        {{- include "fhir-gateway.podAnnotations" . | indent 8 }}
+      labels:
+        {{- include "fhir-gateway.selectorLabels" . | nindent 8 }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      serviceAccountName: {{ include "fhir-gateway.serviceAccountName" . }}
+      securityContext:
+        {{- toYaml .Values.podSecurityContext | nindent 8 }}
+      volumes:
+        {{- if .Values.volumes }}
+        {{- tpl (toYaml .Values.volumes) . | nindent 12 }}
+        {{- end }}
+      {{- if .Values.initContainers }}
+      initContainers:
+        {{- toYaml .Values.initContainers | nindent 12 }}
+      {{- end }}
+      containers:
+        - name: {{ .Chart.Name }}
+          securityContext:
+            {{- toYaml .Values.securityContext | nindent 12 }}
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          {{- if  .Values.env }}
+          env:
+            {{- if .Values.applicationConfig }}
+            - name: SPRING_APPLICATION_JSON
+              value: {{ tpl (toYaml .Values.applicationConfig) . | fromYaml | toJson | quote }}
+            {{- end }}
+            {{- tpl (toYaml .Values.env) .  | nindent 12 }}
+          {{- end }}
+          ports:
+            - name: http
+              containerPort: 8080
+              protocol: TCP
+          livenessProbe:
+          {{- toYaml .Values.livenessProbe | nindent 12 }}
+          readinessProbe:
+          {{- toYaml .Values.readinessProbe | nindent 12 }}
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+          volumeMounts:
+          {{- if .Values.volumeMounts }}
+          {{- toYaml .Values.volumeMounts | nindent 12 }}
+          {{- end }}
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
diff --git a/charts/fhir-gateway/templates/hpa.yaml b/charts/fhir-gateway/templates/hpa.yaml
@@ -0,0 +1,32 @@
+{{ if .Values.autoscaling.enabled }}
+apiVersion: autoscaling/v2
+kind: HorizontalPodAutoscaler
+metadata:
+  name: {{ include "fhir-gateway.fullname" . }}
+  labels:
+    {{- include "fhir-gateway.labels" . | nindent 4 }}
+spec:
+  scaleTargetRef:
+    apiVersion: apps/v1
+    kind: Deployment
+    name: {{ include "fhir-gateway.fullname" . }}
+  minReplicas: {{ .Values.autoscaling.minReplicas }}
+  maxReplicas: {{ .Values.autoscaling.maxReplicas }}
+  metrics:
+    {{- if .Values.autoscaling.targetCPUUtilizationPercentage }}
+    - type: Resource
+      resource:
+        name: cpu
+        target:
+          type: Utilization
+          averageUtilization: {{ .Values.autoscaling.targetCPUUtilizationPercentage }}
+    {{- end }}
+    {{- if .Values.autoscaling.targetMemoryUtilizationPercentage }}
+    - type: Resource
+      resource:
+        name: memory
+        target:
+          type: Utilization
+          averageUtilization: {{ .Values.autoscaling.targetMemoryUtilizationPercentage }}
+    {{- end }}
+{{- end }}
diff --git a/charts/fhir-gateway/templates/ingress.yaml b/charts/fhir-gateway/templates/ingress.yaml
@@ -0,0 +1,61 @@
+{{ if .Values.ingress.enabled -}}
+{{- $fullName := include "fhir-gateway.fullname" . -}}
+{{- $svcPort := .Values.service.port -}}
+{{- if and .Values.ingress.className (not (semverCompare ">=1.18-0" .Capabilities.KubeVersion.GitVersion)) }}
+  {{- if not (hasKey .Values.ingress.annotations "kubernetes.io/ingress.class") }}
+  {{- $_ := set .Values.ingress.annotations "kubernetes.io/ingress.class" .Values.ingress.className}}
+  {{- end }}
+{{- end }}
+{{- 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 "fhir-gateway.labels" . | nindent 4 }}
+  {{- with .Values.ingress.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+spec:
+  {{- if and .Values.ingress.className (semverCompare ">=1.18-0" .Capabilities.KubeVersion.GitVersion) }}
+  ingressClassName: {{ .Values.ingress.className }}
+  {{- end }}
+  {{- if .Values.ingress.tls }}
+  tls:
+    {{- range .Values.ingress.tls }}
+    - hosts:
+        {{- range .hosts }}
+        - {{ . | quote }}
+        {{- end }}
+      secretName: {{ .secretName }}
+    {{- end }}
+  {{- end }}
+  rules:
+    {{- range .Values.ingress.hosts }}
+    - host: {{ .host | quote }}
+      http:
+        paths:
+          {{- range .paths }}
+          - path: {{ .path }}
+            {{- if and .pathType (semverCompare ">=1.18-0" $.Capabilities.KubeVersion.GitVersion) }}
+            pathType: {{ .pathType }}
+            {{- 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/fhir-gateway/templates/pdb.yaml b/charts/fhir-gateway/templates/pdb.yaml
@@ -0,0 +1,22 @@
+{{ if .Values.pdb.enabled }}
+{{- if semverCompare "<1.21-0" .Capabilities.KubeVersion.GitVersion -}}
+apiVersion: "policy/v1beta1"
+{{- else -}}
+apiVersion: "policy/v1"
+{{- end }}
+kind: PodDisruptionBudget
+metadata:
+  name: {{ include "fhir-gateway.fullname" . }}
+  labels:
+    {{- include "fhir-gateway.labels" . | nindent 4 }}
+spec:
+  {{- if .Values.pdb.minAvailable }}
+  minAvailable: {{ .Values.pdb.minAvailable }}
+  {{- end }}
+  {{- if .Values.pdb.maxUnavailable }}
+  maxUnavailable: {{ .Values.pdb.maxUnavailable }}
+  {{- end }}
+  selector:
+    matchLabels:
+      {{- include "fhir-gateway.selectorLabels" . | nindent 6 }}
+{{- end }}
diff --git a/charts/fhir-gateway/templates/service.yaml b/charts/fhir-gateway/templates/service.yaml
@@ -0,0 +1,15 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ include "fhir-gateway.fullname" . }}
+  labels:
+    {{- include "fhir-gateway.labels" . | nindent 4 }}
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - port: {{ .Values.service.port }}
+      targetPort: http
+      protocol: TCP
+      name: http
+  selector:
+    {{- include "fhir-gateway.selectorLabels" . | nindent 4 }}