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Updated helm chart with additional config settings (#566)

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chgl
2023-07-21 16:26:10 +02:00
committed by GitHub
parent 5bd43b29c9
commit 8ef50832d3
8 changed files with 126 additions and 80 deletions
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12
charts/hapi-fhir-jpaserver/Chart.yaml
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@@ -11,15 +11,17 @@ dependencies:
repository: oci://registry-1.docker.io/bitnamicharts
condition: postgresql.enabled
appVersion: 6.6.0
version: 0.12.0
version: 0.13.0
annotations:
artifacthub.io/license: Apache-2.0
artifacthub.io/changes: |
# When using the list of objects option the valid supported kinds are
# added, changed, deprecated, removed, fixed, and security.
- kind: added
description: allow specifying application properties via yaml config
- kind: added
description: allow setting resource limits and requests for the Helm test pods
- kind: changed
description: updated HAPI FHIR JPA Server app image version to v6.6.0
description: updated curl used by helm tests to version to v8.2.0
- kind: changed
description: updated curl used by helm tests to version to v8.1.1
- kind: changed
description: updated postgresql sub-chart to v12.5.6
description: allow disabling the liveness-, readiness-, and startup-probes entirely

21
charts/hapi-fhir-jpaserver/README.md
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@@ -1,6 +1,6 @@
# HAPI FHIR JPA Server Starter Helm Chart
![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)
![Version: 0.13.0](https://img.shields.io/badge/Version-0.13.0-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.
@@ -30,6 +30,7 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| externalDatabase.password | string | `""` | database password |
| externalDatabase.port | int | `5432` | database port number |
| externalDatabase.user | string | `"fhir"` | username for the external database |
| extraConfig | string | `""` | additional Spring Boot application config. Mounted as a file and automatically loaded by the application. |
| extraEnv | list | `[]` | extra environment variables to set on the server container |
| fullnameOverride | string | `""` | override the chart fullname |
| image.pullPolicy | string | `"IfNotPresent"` | image pullPolicy to use |
@@ -43,11 +44,6 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| ingress.hosts[0].pathType | string | `"ImplementationSpecific"` | |
| ingress.hosts[0].paths[0] | string | `"/"` | |
| ingress.tls | list | `[]` | ingress TLS config |
| livenessProbe.failureThreshold | int | `5` | |
| livenessProbe.initialDelaySeconds | int | `30` | |
| livenessProbe.periodSeconds | int | `20` | |
| livenessProbe.successThreshold | int | `1` | |
| livenessProbe.timeoutSeconds | int | `30` | |
| metrics.service.port | int | `8081` | |
| metrics.serviceMonitor.additionalLabels | object | `{}` | additional labels to apply to the ServiceMonitor object, e.g. `release: prometheus` |
| metrics.serviceMonitor.enabled | bool | `false` | if enabled, creates a ServiceMonitor instance for Prometheus Operator-based monitoring |
@@ -65,11 +61,6 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| postgresql.primary.containerSecurityContext.capabilities.drop[0] | string | `"ALL"` | |
| postgresql.primary.containerSecurityContext.runAsNonRoot | bool | `true` | |
| postgresql.primary.containerSecurityContext.seccompProfile.type | string | `"RuntimeDefault"` | |
| readinessProbe.failureThreshold | int | `5` | |
| readinessProbe.initialDelaySeconds | int | `30` | |
| readinessProbe.periodSeconds | int | `20` | |
| readinessProbe.successThreshold | int | `1` | |
| readinessProbe.timeoutSeconds | int | `20` | |
| replicaCount | int | `1` | number of replicas to deploy |
| resources | object | `{}` | configure the FHIR server's resource requests and limits |
| securityContext.allowPrivilegeEscalation | bool | `false` | |
@@ -82,18 +73,14 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| securityContext.seccompProfile.type | string | `"RuntimeDefault"` | |
| service.port | int | `8080` | port where the server will be exposed at |
| service.type | string | `"ClusterIP"` | service type |
| startupProbe.failureThreshold | int | `10` | |
| startupProbe.initialDelaySeconds | int | `30` | |
| startupProbe.periodSeconds | int | `30` | |
| startupProbe.successThreshold | int | `1` | |
| startupProbe.timeoutSeconds | int | `30` | |
| tests.resources | object | `{}` | configure the test pods resource requests and limits |
| tolerations | list | `[]` | pod tolerations |
| topologySpreadConstraints | list | `[]` | pod topology spread configuration see: https://kubernetes.io/docs/concepts/workloads/pods/pod-topology-spread-constraints/#api |
## Development
To update the Helm chart when a new version of the `hapiproject/hapi` image is released, [values.yaml](values.yaml) `image.tag` and the [Chart.yaml](Chart.yaml)'s
`version` and optionally the `appVersion` field on major releases need to be updated. Afterwards, re-generate the [README.md](README.md)
`version` and optionally the `appVersion` field need to be updated. Afterwards, re-generate the [README.md](README.md)
by running:
```sh

2
charts/hapi-fhir-jpaserver/README.md.gotmpl
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@@ -18,7 +18,7 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
## Development
To update the Helm chart when a new version of the `hapiproject/hapi` image is released, [values.yaml](values.yaml) `image.tag` and the [Chart.yaml](Chart.yaml)'s
`version` and optionally the `appVersion` field on major releases need to be updated. Afterwards, re-generate the [README.md](README.md)
`version` and optionally the `appVersion` field need to be updated. Afterwards, re-generate the [README.md](README.md)
by running:
```sh

17
charts/hapi-fhir-jpaserver/ci/extra-config-values.yaml Normal file
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@@ -0,0 +1,17 @@
extraConfig: |
hapi:
fhir:
cr_enabled: true
tester:
home:
name: Hello HAPI FHIR
server_address: "http://fhir-server.127.0.0.1.nip.io/fhir"
refuse_to_fetch_third_party_urls: true
fhir_version: R4
ingress:
enabled: true
hosts:
- host: fhir-server.127.0.0.1.nip.io
pathType: ImplementationSpecific
paths: ["/"]

11
charts/hapi-fhir-jpaserver/templates/application-config.yaml Normal file
View File

@@ -0,0 +1,11 @@
{{- if .Values.extraConfig -}}
apiVersion: v1
kind: ConfigMap
metadata:
name: {{ include "hapi-fhir-jpaserver.fullname" . }}-application-config
labels:
{{- include "hapi-fhir-jpaserver.labels" . | nindent 4 }}
data:
application-extra.yaml: |-
{{ .Values.extraConfig | nindent 4 }}
{{- end }}

52
charts/hapi-fhir-jpaserver/templates/deployment.yaml
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@@ -63,38 +63,17 @@ spec:
- name: http-metrics
containerPort: 8081
protocol: TCP
startupProbe:
httpGet:
path: /readyz
port: http
{{- with .Values.startupProbe }}
initialDelaySeconds: {{ .initialDelaySeconds }}
periodSeconds: {{ .periodSeconds }}
timeoutSeconds: {{ .timeoutSeconds }}
successThreshold: {{ .successThreshold }}
failureThreshold: {{ .failureThreshold }}
startupProbe:
{{- toYaml . | nindent 12 }}
{{- end }}
readinessProbe:
httpGet:
path: /readyz
port: http
{{- with .Values.readinessProbe }}
initialDelaySeconds: {{ .initialDelaySeconds }}
periodSeconds: {{ .periodSeconds }}
timeoutSeconds: {{ .timeoutSeconds }}
successThreshold: {{ .successThreshold }}
failureThreshold: {{ .failureThreshold }}
{{- end }}
livenessProbe:
httpGet:
path: /livez
port: http
{{- with .Values.livenessProbe }}
initialDelaySeconds: {{ .initialDelaySeconds }}
periodSeconds: {{ .periodSeconds }}
timeoutSeconds: {{ .timeoutSeconds }}
successThreshold: {{ .successThreshold }}
failureThreshold: {{ .failureThreshold }}
livenessProbe:
{{- toYaml . | nindent 12 }}
{{- end }}
{{- with .Values.readinessProbe }}
readinessProbe:
{{- toYaml . | nindent 12 }}
{{- end }}
resources:
{{- toYaml .Values.resources | nindent 12 }}
@@ -118,6 +97,10 @@ spec:
value: "true"
- name: MANAGEMENT_SERVER_PORT
value: "8081"
{{- if .Values.extraConfig }}
- name: SPRING_CONFIG_IMPORT
value: "/app/config/application-extra.yaml"
{{- end }}
{{- if .Values.extraEnv }}
{{ toYaml .Values.extraEnv | nindent 12 }}
{{- end }}
@@ -126,6 +109,12 @@ spec:
name: tmp-volume
- mountPath: /app/target
name: lucenefiles-volume
{{- if .Values.extraConfig }}
- name: application-extra-config
mountPath: /app/config/application-extra.yaml
readOnly: true
subPath: application-extra.yaml
{{- end }}
{{- with .Values.nodeSelector }}
nodeSelector:
{{- toYaml . | nindent 8 }}
@@ -147,3 +136,8 @@ spec:
emptyDir: {}
- name: lucenefiles-volume
emptyDir: {}
{{- if .Values.extraConfig }}
- name: application-extra-config
configMap:
name: {{ include "hapi-fhir-jpaserver.fullname" . }}-application-config
{{- end }}

33
charts/hapi-fhir-jpaserver/templates/tests/test-endpoints.yaml
View File

@@ -11,20 +11,17 @@ spec:
restartPolicy: Never
containers:
- name: test-metadata-endpoint
image: docker.io/curlimages/curl:8.1.2@sha256:ef501f5efa67be41da985b441bd63130ef39d4d6a4f9c035d737884357438b6c
image: "{{ .Values.curl.image.registry }}/{{ .Values.curl.image.repository }}:{{ .Values.curl.image.tag }}"
command: ["curl", "--fail-with-body"]
args: ["http://{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.service.port }}/fhir/metadata?_summary=true"]
{{- with .Values.restrictedContainerSecurityContext }}
securityContext:
{{- toYaml . | nindent 8 }}
{{- end }}
{{- with .Values.tests.resources }}
resources:
limits:
cpu: 100m
memory: 128Mi
requests:
cpu: 100m
memory: 128Mi
{{- toYaml . | nindent 8 }}
{{- end }}
livenessProbe:
exec:
command: ["true"]
@@ -32,20 +29,17 @@ spec:
exec:
command: ["true"]
- name: test-patient-endpoint
image: docker.io/curlimages/curl:8.1.2@sha256:ef501f5efa67be41da985b441bd63130ef39d4d6a4f9c035d737884357438b6c
image: "{{ .Values.curl.image.registry }}/{{ .Values.curl.image.repository }}:{{ .Values.curl.image.tag }}"
command: ["curl", "--fail-with-body"]
args: ["http://{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.service.port }}/fhir/Patient?_count=1&_summary=true"]
{{- with .Values.restrictedContainerSecurityContext }}
securityContext:
{{- toYaml . | nindent 8 }}
{{- end }}
{{- with .Values.tests.resources }}
resources:
limits:
cpu: 100m
memory: 128Mi
requests:
cpu: 100m
memory: 128Mi
{{- toYaml . | nindent 8 }}
{{- end }}
livenessProbe:
exec:
command: ["true"]
@@ -53,20 +47,17 @@ spec:
exec:
command: ["true"]
- name: test-metrics-endpoint
image: docker.io/curlimages/curl:8.1.2@sha256:ef501f5efa67be41da985b441bd63130ef39d4d6a4f9c035d737884357438b6c
image: "{{ .Values.curl.image.registry }}/{{ .Values.curl.image.repository }}:{{ .Values.curl.image.tag }}"
command: ["curl", "--fail-with-body"]
args: ["http://{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.metrics.service.port }}/actuator/prometheus"]
{{- with .Values.restrictedContainerSecurityContext }}
securityContext:
{{- toYaml . | nindent 8 }}
{{- end }}
{{- with .Values.tests.resources }}
resources:
limits:
cpu: 100m
memory: 128Mi
requests:
cpu: 100m
memory: 128Mi
{{- toYaml . | nindent 8 }}
{{- end }}
livenessProbe:
exec:
command: ["true"]

58
charts/hapi-fhir-jpaserver/values.yaml
View File

@@ -131,27 +131,42 @@ postgresql:
seccompProfile:
type: RuntimeDefault
# -- readiness probe
# @ignored
readinessProbe:
httpGet:
path: /readyz
port: http
failureThreshold: 5
initialDelaySeconds: 30
periodSeconds: 20
successThreshold: 1
timeoutSeconds: 20
startupProbe:
failureThreshold: 10
initialDelaySeconds: 30
periodSeconds: 30
successThreshold: 1
timeoutSeconds: 30
# -- liveness probe
# @ignored
livenessProbe:
httpGet:
path: /livez
port: http
failureThreshold: 5
initialDelaySeconds: 30
periodSeconds: 20
successThreshold: 1
timeoutSeconds: 30
# -- startup probe
# @ignored
startupProbe:
httpGet:
path: /readyz
port: http
failureThreshold: 10
initialDelaySeconds: 30
periodSeconds: 30
successThreshold: 1
timeoutSeconds: 30
externalDatabase:
# -- external database host used with `postgresql.enabled=false`
host: localhost
@@ -208,3 +223,32 @@ restrictedContainerSecurityContext:
runAsGroup: 65534
seccompProfile:
type: RuntimeDefault
# @ignored
curl:
image:
registry: docker.io
repository: curlimages/curl
tag: 8.2.0@sha256:daf3f46a2639c1613b25e85c9ee4193af8a1d538f92483d67f9a3d7f21721827
tests:
# -- configure the test pods resource requests and limits
resources: {}
# limits:
# cpu: 100m
# memory: 128Mi
# requests:
# cpu: 100m
# memory: 128Mi
# -- additional Spring Boot application config. Mounted as a file and automatically loaded by the application.
extraConfig: ""
# # For example:
# |
# hapi:
# fhir:
# implementationguides:
# gh_0_1_0:
# url: https://build.fhir.org/ig/hl7-eu/gravitate-health/package.tgz
# name: hl7.eu.fhir.gh
# version: 0.1.0