Add Helm chart and new entrypoint

deployment/helm/pathling/Chart.yaml

@@ -0,0 +1,5 @@
+apiVersion: v2
+name: pathling
+description: A Helm chart for Pathling Server
+type: application
+version: 1.0.0

deployment/helm/pathling/templates/deployment.yaml

@@ -0,0 +1,87 @@
+kind: Deployment
+apiVersion: apps/v1
+metadata:
+  name: pathling-deployment
+spec:
+  selector:
+    matchLabels:
+      app: pathling-server
+  template:
+    metadata:
+      labels:
+        app: pathling-server
+    spec:
+      containers:
+        - name: pathling-server
+          image: {{ .Values.pathling.image | quote }}
+          imagePullPolicy: {{ .Values.pathling.deployment.imagePullPolicy }}
+          ports:
+            - containerPort: 8080
+            - containerPort: 8081
+            - containerPort: 4040
+            - containerPort: 7077
+            - containerPort: 7078
+          resources:
+            requests: {{ toJson .Values.pathling.resources.requests }}
+            limits: {{ toJson .Values.pathling.resources.limits }}
+          startupProbe:
+            httpGet:
+              path: /actuator/health/liveness
+              port: 8081
+            periodSeconds: 5
+            failureThreshold: 36
+          livenessProbe:
+            httpGet:
+              path: /actuator/health/liveness
+              port: 8081
+            periodSeconds: 5
+            failureThreshold: 12
+          readinessProbe:
+            httpGet:
+              path: /actuator/health/readiness
+              port: 8081
+            periodSeconds: 5
+            failureThreshold: 3
+          volumeMounts: {{ toJson .Values.pathling.volumeMounts }}
+          {{- if gt (add (len .Values.pathling.config) (len .Values.pathling.secretConfig)) 0 }}
+          env:
+            - name: JAVA_TOOL_OPTIONS
+              value: {{ printf "-Xmx%s %s" .Values.pathling.resources.maxHeapSize .Values.pathling.additionalJavaOptions }}
+            - name: spark.driver.host
+              value: pathling-driver
+            - name: spark.driver.port
+              value: "7077"
+            - name: spark.blockManager.port
+              value: "7078"
+            - name: spark.driver.bindAddress
+              value: 0.0.0.0
+            {{- range $configKey, $configValue := .Values.pathling.config }}
+            - name: {{ $configKey }}
+              value: {{ $configValue | quote }}
+            {{- end }}
+            {{- range $configKey, $configValue := .Values.pathling.secretConfig }}
+            - name: {{ $configKey }}
+              valueFrom:
+                secretKeyRef:
+                  name: pathling-secrets
+                  key: {{ $configKey }}
+            {{- end }}
+          {{- end }}
+      volumes: {{ toJson .Values.pathling.volumes }}
+      serviceAccountName: {{ .Values.pathling.serviceAccount }}
+      imagePullSecrets: {{ toJson .Values.pathling.imagePullSecrets }}
+      tolerations: {{ toJson .Values.pathling.tolerations }}
+      affinity: {{ toJson .Values.pathling.affinity }}
+  strategy:
+    type: {{ .Values.pathling.deployment.strategy }}
+{{- if gt (len .Values.pathling.secretConfig) 0 }}
+---
+apiVersion: v1
+kind: Secret
+metadata:
+  name: pathling-secrets
+data:
+  {{- range $configKey, $configValue := .Values.pathling.secretConfig }}
+  {{ $configKey }}: {{ $configValue | b64enc }}
+  {{- end }}
+{{- end }}

deployment/helm/pathling/templates/role-binding.yaml

@@ -0,0 +1,11 @@
+apiVersion: rbac.authorization.k8s.io/v1
+kind: RoleBinding
+metadata:
+  name: spark-role-binding
+subjects:
+  - kind: ServiceAccount
+    name: spark-service-account
+roleRef:
+  kind: Role
+  name: spark-role
+  apiGroup: rbac.authorization.k8s.io

deployment/helm/pathling/templates/role.yaml

@@ -0,0 +1,14 @@
+apiVersion: rbac.authorization.k8s.io/v1
+kind: Role
+metadata:
+  name: spark-role
+rules:
+  - apiGroups: [""]
+    resources: ["pods", "services", "configmaps"]
+    verbs: ["create", "get", "list", "watch", "delete"]
+  - apiGroups: [""]
+    resources: ["pods/log"]
+    verbs: ["get", "list", "watch"]
+  - apiGroups: [""]
+    resources: ["pods"]
+    verbs: ["watch"]

deployment/helm/pathling/templates/service-account.yaml

@@ -0,0 +1,4 @@
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  name: spark-service-account

deployment/helm/pathling/templates/service.yaml

@@ -0,0 +1,52 @@
+kind: Service
+apiVersion: v1
+metadata:
+  name: pathling-fhir
+spec:
+  type: ClusterIP
+  ports:
+    - port: 8080
+      targetPort: 8080
+  selector:
+    app: pathling-server
+---
+kind: Service
+apiVersion: v1
+metadata:
+  name: pathling-management
+spec:
+  type: ClusterIP
+  ports:
+    - port: 8081
+      targetPort: 8081
+  selector:
+    app: pathling-server
+---
+kind: Service
+apiVersion: v1
+metadata:
+  name: pathling-spark-ui
+spec:
+  type: ClusterIP
+  ports:
+    - port: 4040
+      targetPort: 4040
+  selector:
+    app: pathling-server
+---
+kind: Service
+apiVersion: v1
+metadata:
+  name: pathling-driver
+spec:
+  type: ClusterIP
+  ports:
+    - name: driver
+      port: 7077
+      targetPort: 7077
+    - name: block-manager
+      port: 7078
+      targetPort: 7078
+  selector:
+    app: pathling-server
+  publishNotReadyAddresses: true

deployment/helm/pathling/values.yaml

@@ -0,0 +1,21 @@
+pathling:
+  image: aehrc/pathling:latest
+  resources:
+    requests:
+      cpu: 2
+      memory: 4G
+    limits:
+      memory: 4G
+    maxHeapSize: 2800m
+  additionalJavaOptions: -Duser.timezone=UTC
+  deployment:
+    strategy: Recreate
+    imagePullPolicy: Always
+  volumes: [ ]
+  volumeMounts: [ ]
+  serviceAccount: ~
+  imagePullSecrets: [ ]
+  tolerations: [ ]
+  affinity: ~
+  config: { }
+  secretConfig: { }

fhir-server/pom.xml

@@ -388,8 +388,21 @@
                 <port>8080</port>
                 <port>8081</port>
                 <port>4040</port>
+                <port>7077</port>
               </ports>
+              <entrypoint>
+                <command>/usr/bin/entrypoint.sh</command>
+              </entrypoint>
             </container>
+            <extraDirectories>
+              <paths>src/main/jib</paths>
+              <permissions>
+                <permission>
+                  <file>/usr/bin/entrypoint.sh</file>
+                  <mode>755</mode>
+                </permission>
+              </permissions>
+            </extraDirectories>
           </configuration>
         </plugin>
       </plugins>

fhir-server/src/main/jib/usr/bin/entrypoint.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+#
+# Copyright 2023 Commonwealth Scientific and Industrial Research
+# Organisation (CSIRO) ABN 41 687 119 230.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# Modified from the Kubernetes Docker image entrypoint script: 
+# https://github.com/apache/spark/blob/v3.3.2/resource-managers/kubernetes/docker/src/main/dockerfiles/spark/entrypoint.sh
+
+set -xe
+
+case "$1" in
+  # If the command is "executor", run the container as a Kubernetes executor.
+  executor)
+    env | grep SPARK_JAVA_OPT_ | sort -t_ -k4 -n | sed 's/[^=]*=\(.*\)/\1/g' > /tmp/java_opts.txt
+    readarray -t SPARK_EXECUTOR_JAVA_OPTS < /tmp/java_opts.txt
+    CMD=(
+      java
+      "${SPARK_EXECUTOR_JAVA_OPTS[@]}"
+      -Xms$SPARK_EXECUTOR_MEMORY
+      -Xmx$SPARK_EXECUTOR_MEMORY
+      -cp @/app/jib-classpath-file
+      org.apache.spark.scheduler.cluster.k8s.KubernetesExecutorBackend
+      --driver-url $SPARK_DRIVER_URL
+      --executor-id $SPARK_EXECUTOR_ID
+      --cores $SPARK_EXECUTOR_CORES
+      --app-id $SPARK_APPLICATION_ID
+      --hostname $SPARK_EXECUTOR_POD_IP
+      --resourceProfileId $SPARK_RESOURCE_PROFILE_ID
+      --podName $SPARK_EXECUTOR_POD_NAME
+    )
+    ;;
+
+  # If the command is anything else, run the FHIR server.
+  *)
+    CMD=(
+      java
+      -cp @/app/jib-classpath-file
+      au.csiro.pathling.PathlingServer
+    )
+    ;;
+esac
+
+exec "${CMD[@]}"