v9.4.0

.github/workflows/fhirpath-lab-api-release.yml

@@ -0,0 +1,57 @@
+# This workflow builds and publishes the FHIRPath Lab API Docker image to GHCR.
+
+name: Release FHIRPath Lab API
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [main]
+    paths:
+      - "fhirpath-lab-api/**"
+      - "deployment/fhirpath-lab-api/**"
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  release:
+    name: Build and push Docker image
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: ./.github/actions/setup-build-tools
+        with:
+          java: "false"
+          python: "true"
+
+      - name: Run tests
+        working-directory: fhirpath-lab-api
+        run: |
+          uv sync --extra dev
+          uv run pytest -v
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GHCR
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: fhirpath-lab-api
+          push: true
+          platforms: linux/amd64,linux/arm64
+          tags: |
+            ghcr.io/aehrc/fhirpath-lab-api:latest
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

deployment/fhirpath-lab-api/chart/Chart.yaml

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+# Copyright © 2026, Commonwealth Scientific and Industrial Research Organisation (CSIRO)
+# ABN 41 687 119 230. Licensed under the Apache License, Version 2.0.
+#
+# Author: John Grimes
+
+apiVersion: v2
+name: fhirpath-lab-api
+description: A FHIRPath Lab server backed by the Pathling FHIRPath engine
+icon: https://raw.githubusercontent.com/aehrc/pathling/main/media/logo-icon-colour-detail.svg
+type: application
+version: 1.0.0
+maintainers:
+  - name: John Grimes
+    email: John.Grimes@csiro.au
+sources:
+  - https://github.com/aehrc/pathling
+keywords:
+  - fhir
+  - fhirpath
+  - pathling

deployment/fhirpath-lab-api/chart/README.md

@@ -0,0 +1,64 @@
+# FHIRPath Lab API Helm chart
+
+A Helm chart for deploying the FHIRPath Lab API server on Kubernetes.
+
+## Prerequisites
+
+- Kubernetes 1.26+
+- Helm 3.x
+
+## Installation
+
+```bash
+helm install fhirpath-lab-api ./deployment/fhirpath-lab-api/chart/
+```
+
+With custom values:
+
+```bash
+helm install fhirpath-lab-api ./deployment/fhirpath-lab-api/chart/ \
+  -f my-values.yaml
+```
+
+## Configuration
+
+| Parameter                        | Description                             | Default                                 |
+| -------------------------------- | --------------------------------------- | --------------------------------------- |
+| `fhirpathLabApi.image`           | Container image                         | `ghcr.io/aehrc/fhirpath-lab-api:latest` |
+| `fhirpathLabApi.imagePullPolicy` | Image pull policy                       | `Always`                                |
+| `fhirpathLabApi.replicas`        | Number of replicas                      | `1`                                     |
+| `fhirpathLabApi.service.type`    | Kubernetes service type                 | `ClusterIP`                             |
+| `fhirpathLabApi.service.port`    | Service port                            | `8080`                                  |
+| `fhirpathLabApi.resources`       | CPU/memory resource requests and limits | `{}`                                    |
+| `fhirpathLabApi.config`          | Environment variables for the container | `{}`                                    |
+| `fhirpathLabApi.tolerations`     | Pod tolerations                         | `[]`                                    |
+| `fhirpathLabApi.affinity`        | Pod affinity rules                      | `{}`                                    |
+| `fhirpathLabApi.nodeSelector`    | Pod node selector                       | `{}`                                    |
+
+## Examples
+
+### Basic deployment with resource limits
+
+```yaml
+fhirpathLabApi:
+    resources:
+        requests:
+            memory: "4Gi"
+            cpu: "1"
+        limits:
+            memory: "4Gi"
+```
+
+### Additional CORS origins
+
+```yaml
+fhirpathLabApi:
+    config:
+        CORS_ALLOWED_ORIGINS: "https://my-app.example.com,https://staging.example.com"
+```
+
+## Uninstalling
+
+```bash
+helm uninstall fhirpath-lab-api
+```

deployment/fhirpath-lab-api/chart/templates/deployment.yaml

@@ -0,0 +1,60 @@
+# Copyright © 2026, Commonwealth Scientific and Industrial Research Organisation (CSIRO)
+# ABN 41 687 119 230. Licensed under the Apache License, Version 2.0.
+#
+# Author: John Grimes
+
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ .Release.Name }}-deployment
+  labels:
+    app: {{ .Release.Name }}
+spec:
+  replicas: {{ .Values.fhirpathLabApi.replicas }}
+  selector:
+    matchLabels:
+      app: {{ .Release.Name }}
+  template:
+    metadata:
+      labels:
+        app: {{ .Release.Name }}
+    spec:
+      containers:
+        - name: fhirpath-lab-api
+          image: {{ .Values.fhirpathLabApi.image | quote }}
+          imagePullPolicy: {{ .Values.fhirpathLabApi.imagePullPolicy | quote }}
+          ports:
+            - name: http
+              containerPort: 8080
+              protocol: TCP
+          {{- if gt (len .Values.fhirpathLabApi.config) 0 }}
+          env:
+            {{- range $key, $value := .Values.fhirpathLabApi.config }}
+            - name: {{ $key }}
+              value: {{ $value | quote }}
+            {{- end }}
+          {{- end }}
+          startupProbe:
+            httpGet:
+              path: /healthcheck
+              port: http
+            periodSeconds: 5
+            failureThreshold: 36
+          livenessProbe:
+            httpGet:
+              path: /healthcheck
+              port: http
+            periodSeconds: 30
+            failureThreshold: 3
+          readinessProbe:
+            httpGet:
+              path: /healthcheck
+              port: http
+            periodSeconds: 10
+            failureThreshold: 3
+          {{- if .Values.fhirpathLabApi.resources }}
+          resources: {{ toYaml .Values.fhirpathLabApi.resources | nindent 12 }}
+          {{- end }}
+      tolerations: {{ toJson .Values.fhirpathLabApi.tolerations }}
+      affinity: {{ toJson .Values.fhirpathLabApi.affinity }}
+      nodeSelector: {{ toJson .Values.fhirpathLabApi.nodeSelector }}

deployment/fhirpath-lab-api/chart/templates/service.yaml

@@ -0,0 +1,20 @@
+# Copyright © 2026, Commonwealth Scientific and Industrial Research Organisation (CSIRO)
+# ABN 41 687 119 230. Licensed under the Apache License, Version 2.0.
+#
+# Author: John Grimes
+
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Release.Name }}-service
+  labels:
+    app: {{ .Release.Name }}
+spec:
+  type: {{ .Values.fhirpathLabApi.service.type | quote }}
+  ports:
+    - port: {{ .Values.fhirpathLabApi.service.port }}
+      targetPort: http
+      protocol: TCP
+      name: http
+  selector:
+    app: {{ .Release.Name }}

deployment/fhirpath-lab-api/chart/values.schema.json

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+{
+  "$schema": "https://json-schema.org/draft-07/schema#",
+  "title": "FHIRPath Lab API Helm Chart Values",
+  "description": "Configuration values for deploying the FHIRPath Lab API server on Kubernetes",
+  "type": "object",
+  "properties": {
+    "fhirpathLabApi": {
+      "type": "object",
+      "description": "FHIRPath Lab API server configuration",
+      "properties": {
+        "image": {
+          "type": "string",
+          "description": "Docker image for the FHIRPath Lab API server",
+          "default": "ghcr.io/aehrc/fhirpath-lab-api:latest"
+        },
+        "imagePullPolicy": {
+          "type": "string",
+          "description": "Image pull policy for the container",
+          "enum": ["Always", "IfNotPresent", "Never"],
+          "default": "Always"
+        },
+        "replicas": {
+          "type": "integer",
+          "description": "Number of replicas to deploy",
+          "minimum": 1,
+          "default": 1
+        },
+        "service": {
+          "type": "object",
+          "description": "Kubernetes service configuration",
+          "properties": {
+            "type": {
+              "type": "string",
+              "description": "Service type",
+              "enum": ["ClusterIP", "NodePort", "LoadBalancer"],
+              "default": "ClusterIP"
+            },
+            "port": {
+              "type": "integer",
+              "description": "Service port",
+              "default": 8080
+            }
+          }
+        },
+        "resources": {
+          "type": "object",
+          "description": "Resource requests and limits for the server pod",
+          "properties": {
+            "requests": {
+              "type": "object",
+              "properties": {
+                "cpu": {
+                  "type": ["string", "integer"],
+                  "description": "CPU request"
+                },
+                "memory": {
+                  "type": "string",
+                  "description": "Memory request"
+                }
+              }
+            },
+            "limits": {
+              "type": "object",
+              "properties": {
+                "memory": {
+                  "type": "string",
+                  "description": "Memory limit"
+                }
+              }
+            }
+          },
+          "default": {}
+        },
+        "config": {
+          "type": "object",
+          "description": "Environment variables passed to the server container",
+          "additionalProperties": {
+            "type": ["string", "integer", "boolean", "null"]
+          },
+          "default": {}
+        },
+        "tolerations": {
+          "type": "array",
+          "description": "Tolerations for pod scheduling",
+          "items": {
+            "type": "object"
+          },
+          "default": []
+        },
+        "affinity": {
+          "type": "object",
+          "description": "Affinity rules for pod scheduling",
+          "default": {}
+        },
+        "nodeSelector": {
+          "type": "object",
+          "description": "Node selector for pod scheduling",
+          "default": {}
+        }
+      }
+    }
+  }
+}

deployment/fhirpath-lab-api/chart/values.yaml

@@ -0,0 +1,27 @@
+# Copyright © 2026, Commonwealth Scientific and Industrial Research Organisation (CSIRO)
+# ABN 41 687 119 230. Licensed under the Apache License, Version 2.0.
+#
+# Author: John Grimes
+
+fhirpathLabApi:
+  image: "ghcr.io/aehrc/fhirpath-lab-api:latest"
+  imagePullPolicy: "Always"
+  replicas: 1
+
+  service:
+    type: "ClusterIP"
+    port: 8080
+
+  resources:
+    {}
+    # requests:
+    #   memory: "4Gi"
+    #   cpu: "1"
+    # limits:
+    #   memory: "4Gi"
+
+  config: {}
+
+  tolerations: []
+  affinity: {}
+  nodeSelector: {}

encoders/pom.xml

@@ -31,7 +31,7 @@
   <parent>
     <groupId>au.csiro.pathling</groupId>
     <artifactId>pathling</artifactId>
-    <version>9.3.1</version>
+    <version>9.4.0-SNAPSHOT</version>
   </parent>
   <artifactId>encoders</artifactId>
   <packaging>jar</packaging>