Personal-Twin/hapi-fhir-jpaserver-starter
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Updated helm chart and dockerfile dependencies (#540)

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* Updated Helm chart to use hapi fhir image v6.6.0

* Updated maven base image due to openjdk deprecation

* Removed superfluous app/main.war in entrypoint

* Update curlimages/curl to 8.1.2
This commit is contained in:
chgl
2023-06-25 23:59:09 +02:00
committed by GitHub
parent a06c0b9ce4
commit fdcd021e66
11 changed files with 51 additions and 46 deletions
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2
.github/ct/config.yaml vendored
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@@ -11,6 +11,4 @@ helm-extra-args: --timeout 300s
upgrade: true upgrade: true
skip-missing-values: true skip-missing-values: true
release-label: release release-label: release
chart-repos:
- bitnami=https://charts.bitnami.com/bitnami
release-name-template: "helm-v{{ .Version }}" release-name-template: "helm-v{{ .Version }}"

13
.github/workflows/chart-release.yaml vendored
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@@ -9,10 +9,14 @@ on:
jobs: jobs:
release: release:
runs-on: ubuntu-20.04 runs-on: ubuntu-22.04
steps: steps:
- name: Add workspace as safe directory
run: |
git config --global --add safe.directory /__w/hapi-fhir-jpaserver-starter/hapi-fhir-jpaserver-starter
- name: Checkout - name: Checkout
uses: actions/checkout@v2 uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # v3.5.2
with: with:
fetch-depth: 0 fetch-depth: 0
@@ -21,14 +25,11 @@ jobs:
git config user.name "$GITHUB_ACTOR" git config user.name "$GITHUB_ACTOR"
git config user.email "$GITHUB_ACTOR@users.noreply.github.com" git config user.email "$GITHUB_ACTOR@users.noreply.github.com"
- name: Add bitnami repo
run: helm repo add bitnami https://charts.bitnami.com/bitnami
- name: Update dependencies - name: Update dependencies
run: find charts/ ! -path charts/ -maxdepth 1 -type d -exec helm dependency update {} \; run: find charts/ ! -path charts/ -maxdepth 1 -type d -exec helm dependency update {} \;
- name: Run chart-releaser - name: Run chart-releaser
uses: helm/chart-releaser-action@v1.2.0 uses: helm/chart-releaser-action@be16258da8010256c6e82849661221415f031968 # v1.5.0
with: with:
config: .github/ct/config.yaml config: .github/ct/config.yaml
env: env:

26
.github/workflows/chart-test.yaml vendored
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@@ -9,8 +9,8 @@ on:
jobs: jobs:
lint: lint:
runs-on: ubuntu-20.04 runs-on: ubuntu-22.04
container: quay.io/helmpack/chart-testing:v3.4.0 container: quay.io/helmpack/chart-testing:v3.8.0@sha256:f058c660a28d99a9394ae081d98921efe068079531f247c86b8054e3c9d407aa
steps: steps:
- name: Install helm-docs - name: Install helm-docs
working-directory: /tmp working-directory: /tmp
@@ -22,11 +22,14 @@ jobs:
chmod +x /usr/local/bin/helm-docs && \ chmod +x /usr/local/bin/helm-docs && \
helm-docs --version helm-docs --version
- name: Add workspace as safe directory
run: |
git config --global --add safe.directory /__w/hapi-fhir-jpaserver-starter/hapi-fhir-jpaserver-starter
- name: Checkout - name: Checkout
uses: actions/checkout@v2 uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # v3.5.2
with: with:
fetch-depth: 0 fetch-depth: 0
- name: Check if documentation is up-to-date - name: Check if documentation is up-to-date
run: helm-docs && git diff --exit-code HEAD run: helm-docs && git diff --exit-code HEAD
@@ -34,20 +37,20 @@ jobs:
run: ct lint --config .github/ct/config.yaml run: ct lint --config .github/ct/config.yaml
test: test:
runs-on: ubuntu-20.04 runs-on: ubuntu-22.04
strategy: strategy:
matrix: matrix:
k8s-version: [1.22.9, 1.23.6, 1.24.1] k8s-version: [1.25.9, 1.26.4, 1.27.2]
needs: needs:
- lint - lint
steps: steps:
- name: Checkout - name: Checkout
uses: actions/checkout@v3 uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # v3.5.2
with: with:
fetch-depth: 0 fetch-depth: 0
- name: Set up chart-testing - name: Set up chart-testing
uses: helm/chart-testing-action@v2.2.1 uses: helm/chart-testing-action@e8788873172cb653a90ca2e819d79d65a66d4e76 # v2.4.0
- name: Run chart-testing (list-changed) - name: Run chart-testing (list-changed)
id: list-changed id: list-changed
@@ -58,13 +61,12 @@ jobs:
fi fi
- name: Create k8s Kind Cluster - name: Create k8s Kind Cluster
uses: helm/kind-action@v1.2.0 uses: helm/kind-action@fa81e57adff234b2908110485695db0f181f3c67 # v1.7.0
if: steps.list-changed.outputs.changed == 'true' if: ${{ steps.list-changed.outputs.changed == 'true' }}
with: with:
version: v0.14.0
cluster_name: kind-cluster-k8s-${{ matrix.k8s-version }} cluster_name: kind-cluster-k8s-${{ matrix.k8s-version }}
node_image: kindest/node:v${{ matrix.k8s-version }} node_image: kindest/node:v${{ matrix.k8s-version }}
- name: Run chart-testing (install) - name: Run chart-testing (install)
run: ct install --config .github/ct/config.yaml run: ct install --config .github/ct/config.yaml
if: steps.list-changed.outputs.changed == 'true' if: ${{ steps.list-changed.outputs.changed == 'true' }}

6
Dockerfile
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@@ -1,7 +1,7 @@
FROM maven:3.8-openjdk-17-slim as build-hapi FROM docker.io/library/maven:3.9.2-eclipse-temurin-17 as build-hapi
WORKDIR /tmp/hapi-fhir-jpaserver-starter WORKDIR /tmp/hapi-fhir-jpaserver-starter
ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.17.0 ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.26.0
RUN curl -LSsO https://github.com/open-telemetry/opentelemetry-java-instrumentation/releases/download/v${OPENTELEMETRY_JAVA_AGENT_VERSION}/opentelemetry-javaagent.jar RUN curl -LSsO https://github.com/open-telemetry/opentelemetry-java-instrumentation/releases/download/v${OPENTELEMETRY_JAVA_AGENT_VERSION}/opentelemetry-javaagent.jar
COPY pom.xml . COPY pom.xml .
@@ -46,4 +46,4 @@ WORKDIR /app
COPY --chown=nonroot:nonroot --from=build-distroless /app /app COPY --chown=nonroot:nonroot --from=build-distroless /app /app
COPY --chown=nonroot:nonroot --from=build-hapi /tmp/hapi-fhir-jpaserver-starter/opentelemetry-javaagent.jar /app COPY --chown=nonroot:nonroot --from=build-hapi /tmp/hapi-fhir-jpaserver-starter/opentelemetry-javaagent.jar /app
ENTRYPOINT ["java", "--class-path", "/app/main.war", "-Dloader.path=main.war!/WEB-INF/classes/,main.war!/WEB-INF/,/app/extra-classes", "org.springframework.boot.loader.PropertiesLauncher", "app/main.war"] ENTRYPOINT ["java", "--class-path", "/app/main.war", "-Dloader.path=main.war!/WEB-INF/classes/,main.war!/WEB-INF/,/app/extra-classes", "org.springframework.boot.loader.PropertiesLauncher"]

8
charts/hapi-fhir-jpaserver/Chart.lock
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@@ -1,6 +1,6 @@
dependencies: dependencies:
- name: postgresql - name: postgresql
repository: https://charts.bitnami.com/bitnami repository: oci://registry-1.docker.io/bitnamicharts
version: 12.1.2 version: 12.5.6
digest: sha256:525689611a29f90b0bc8cd674df5d97024c99eda8104216390f6747904fd0208 digest: sha256:4d21dbc02bbdb55b957b0093e37376853727de82396abfadfaf1d738bd51b8e6
generated: "2022-11-21T22:55:45.1699395+01:00" generated: "2023-06-03T20:58:45.922102213+02:00"

14
charts/hapi-fhir-jpaserver/Chart.yaml
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@@ -7,17 +7,19 @@ sources:
- https://github.com/hapifhir/hapi-fhir-jpaserver-starter - https://github.com/hapifhir/hapi-fhir-jpaserver-starter
dependencies: dependencies:
- name: postgresql - name: postgresql
version: 12.1.2 version: 12.5.6
repository: https://charts.bitnami.com/bitnami repository: oci://registry-1.docker.io/bitnamicharts
condition: postgresql.enabled condition: postgresql.enabled
appVersion: 6.2.2 appVersion: 6.6.0
version: 0.11.1 version: 0.12.0
annotations: annotations:
artifacthub.io/license: Apache-2.0 artifacthub.io/license: Apache-2.0
artifacthub.io/changes: | artifacthub.io/changes: |
# When using the list of objects option the valid supported kinds are # When using the list of objects option the valid supported kinds are
# added, changed, deprecated, removed, fixed, and security. # added, changed, deprecated, removed, fixed, and security.
- kind: changed - kind: changed
description: updated HAPI FHIR JPA Server app image version to v6.2.2 description: updated HAPI FHIR JPA Server app image version to v6.6.0
- kind: changed - kind: changed
description: updated curl used by helm tests to version to v7.87.0 description: updated curl used by helm tests to version to v8.1.1
- kind: changed
description: updated postgresql sub-chart to v12.5.6

13
charts/hapi-fhir-jpaserver/README.md
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@@ -1,6 +1,6 @@
# HAPI FHIR JPA Server Starter Helm Chart # HAPI FHIR JPA Server Starter Helm Chart
![Version: 0.11.1](https://img.shields.io/badge/Version-0.11.1-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 6.2.2](https://img.shields.io/badge/AppVersion-6.2.2-informational?style=flat-square) ![Version: 0.12.0](https://img.shields.io/badge/Version-0.12.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 6.6.0](https://img.shields.io/badge/AppVersion-6.6.0-informational?style=flat-square)
This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment. This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
@@ -8,11 +8,14 @@ This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes e
```sh ```sh
helm repo add hapifhir https://hapifhir.github.io/hapi-fhir-jpaserver-starter/ helm repo add hapifhir https://hapifhir.github.io/hapi-fhir-jpaserver-starter/
helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
``` ```
> ⚠ By default, the included [PostgreSQL Helm chart](https://github.com/bitnami/charts/tree/master/bitnami/postgresql#upgrading) ## Requirements
> auto-generates a random password for the database which may cause problems when upgrading the chart (see [here for details](https://github.com/bitnami/charts/tree/master/bitnami/postgresql#upgrading)).
| Repository | Name | Version |
|------------|------|---------|
| oci://registry-1.docker.io/bitnamicharts | postgresql | 12.5.6 |
## Values ## Values
@@ -32,7 +35,7 @@ helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpas
| image.pullPolicy | string | `"IfNotPresent"` | image pullPolicy to use | | image.pullPolicy | string | `"IfNotPresent"` | image pullPolicy to use |
| image.registry | string | `"docker.io"` | registry where the HAPI FHIR server image is hosted | | image.registry | string | `"docker.io"` | registry where the HAPI FHIR server image is hosted |
| image.repository | string | `"hapiproject/hapi"` | the path inside the repository | | image.repository | string | `"hapiproject/hapi"` | the path inside the repository |
| image.tag | string | `"v6.2.2@sha256:9c4e8af94d81ac0049dbb589e4cd855bf78c9c13be6f6844e814c63d63545b44"` | the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image. | | image.tag | string | `"v6.6.0@sha256:c00367865ae5dad4e171cbb68bfc1c39818854079d1565bee4c86a45e78335d0"` | the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image. |
| imagePullSecrets | list | `[]` | image pull secrets to use when pulling the image | | imagePullSecrets | list | `[]` | image pull secrets to use when pulling the image |
| ingress.annotations | object | `{}` | provide any additional annotations which may be required. Evaluated as a template. | | ingress.annotations | object | `{}` | provide any additional annotations which may be required. Evaluated as a template. |
| ingress.enabled | bool | `false` | whether to create an Ingress to expose the FHIR server HTTP endpoint | | ingress.enabled | bool | `false` | whether to create an Ingress to expose the FHIR server HTTP endpoint |

5
charts/hapi-fhir-jpaserver/README.md.gotmpl
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@@ -8,11 +8,10 @@ This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes e
```sh ```sh
helm repo add hapifhir https://hapifhir.github.io/hapi-fhir-jpaserver-starter/ helm repo add hapifhir https://hapifhir.github.io/hapi-fhir-jpaserver-starter/
helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
``` ```
> ⚠ By default, the included [PostgreSQL Helm chart](https://github.com/bitnami/charts/tree/master/bitnami/postgresql#upgrading) {{ template "chart.requirementsSection" . }}
> auto-generates a random password for the database which may cause problems when upgrading the chart (see [here for details](https://github.com/bitnami/charts/tree/master/bitnami/postgresql#upgrading)).
{{ template "chart.valuesSection" . }} {{ template "chart.valuesSection" . }}

2
charts/hapi-fhir-jpaserver/templates/deployment.yaml
View File

@@ -30,7 +30,7 @@ spec:
{{- toYaml .Values.podSecurityContext | nindent 8 }} {{- toYaml .Values.podSecurityContext | nindent 8 }}
initContainers: initContainers:
- name: wait-for-db-to-be-ready - name: wait-for-db-to-be-ready
image: docker.io/bitnami/postgresql:15.1.0-debian-11-r0@sha256:27915588d5203a10a1c23624d9c81644437f33b7c224e25f79bcd9bd09bbb8e2 image: docker.io/bitnami/postgresql:15.3.0-debian-11-r7@sha256:cc301eef743685f4f69d1d719853988e8a9650c90fd9521f4742ce400b3fdf6a
imagePullPolicy: IfNotPresent imagePullPolicy: IfNotPresent
{{- with .Values.restrictedContainerSecurityContext }} {{- with .Values.restrictedContainerSecurityContext }}
securityContext: securityContext:

6
charts/hapi-fhir-jpaserver/templates/tests/test-endpoints.yaml
View File

@@ -11,7 +11,7 @@ spec:
restartPolicy: Never restartPolicy: Never
containers: containers:
- name: test-metadata-endpoint - name: test-metadata-endpoint
image: docker.io/curlimages/curl:7.87.0@sha256:f7f265d5c64eb4463a43a99b6bf773f9e61a50aaa7cefaf564f43e42549a01dd image: docker.io/curlimages/curl:8.1.2@sha256:ef501f5efa67be41da985b441bd63130ef39d4d6a4f9c035d737884357438b6c
command: ["curl", "--fail-with-body"] command: ["curl", "--fail-with-body"]
args: ["http://{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.service.port }}/fhir/metadata?_summary=true"] args: ["http://{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.service.port }}/fhir/metadata?_summary=true"]
{{- with .Values.restrictedContainerSecurityContext }} {{- with .Values.restrictedContainerSecurityContext }}
@@ -32,7 +32,7 @@ spec:
exec: exec:
command: ["true"] command: ["true"]
- name: test-patient-endpoint - name: test-patient-endpoint
image: docker.io/curlimages/curl:7.87.0@sha256:f7f265d5c64eb4463a43a99b6bf773f9e61a50aaa7cefaf564f43e42549a01dd image: docker.io/curlimages/curl:8.1.2@sha256:ef501f5efa67be41da985b441bd63130ef39d4d6a4f9c035d737884357438b6c
command: ["curl", "--fail-with-body"] command: ["curl", "--fail-with-body"]
args: ["http://{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.service.port }}/fhir/Patient?_count=1&_summary=true"] args: ["http://{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.service.port }}/fhir/Patient?_count=1&_summary=true"]
{{- with .Values.restrictedContainerSecurityContext }} {{- with .Values.restrictedContainerSecurityContext }}
@@ -53,7 +53,7 @@ spec:
exec: exec:
command: ["true"] command: ["true"]
- name: test-metrics-endpoint - name: test-metrics-endpoint
image: docker.io/curlimages/curl:7.87.0@sha256:f7f265d5c64eb4463a43a99b6bf773f9e61a50aaa7cefaf564f43e42549a01dd image: docker.io/curlimages/curl:8.1.2@sha256:ef501f5efa67be41da985b441bd63130ef39d4d6a4f9c035d737884357438b6c
command: ["curl", "--fail-with-body"] command: ["curl", "--fail-with-body"]
args: ["http://{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.metrics.service.port }}/actuator/prometheus"] args: ["http://{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.metrics.service.port }}/actuator/prometheus"]
{{- with .Values.restrictedContainerSecurityContext }} {{- with .Values.restrictedContainerSecurityContext }}

2
charts/hapi-fhir-jpaserver/values.yaml
View File

@@ -7,7 +7,7 @@ image:
# -- the path inside the repository # -- the path inside the repository
repository: hapiproject/hapi repository: hapiproject/hapi
# -- the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image. # -- the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image.
tag: "v6.2.2@sha256:9c4e8af94d81ac0049dbb589e4cd855bf78c9c13be6f6844e814c63d63545b44" tag: "v6.6.0@sha256:c00367865ae5dad4e171cbb68bfc1c39818854079d1565bee4c86a45e78335d0"
# -- image pullPolicy to use # -- image pullPolicy to use
pullPolicy: IfNotPresent pullPolicy: IfNotPresent