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Helm chart dependency updates and support for extraVolumes and -Mounts (#766)

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* Helm chart updates

* set target branch to master for chart testing
This commit is contained in:
chgl
2025-02-16 08:45:11 +01:00
committed by GitHub
parent ef28875939
commit 98bfad07b3
9 changed files with 128 additions and 30 deletions
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9
charts/hapi-fhir-jpaserver/Chart.lock
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@@ -1,6 +1,9 @@
dependencies:
- name: postgresql
repository: oci://registry-1.docker.io/bitnamicharts
version: 15.5.22
digest: sha256:513750151f1497acfe6ba07fb1833b8d945ca19094f83018d34b339b666a2d56
generated: "2024-08-18T18:30:23.392457144+02:00"
version: 16.3.2
- name: common
repository: oci://registry-1.docker.io/bitnamicharts
version: 2.28.0
digest: sha256:99587bb3481cd94c1679d9dd23cb8c816701a1c6f0d458c77c71e7e541dd2f55
generated: "2024-12-17T12:51:15.601470579+01:00"

21
charts/hapi-fhir-jpaserver/Chart.yaml
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@@ -7,11 +7,14 @@ sources:
- https://github.com/hapifhir/hapi-fhir-jpaserver-starter
dependencies:
- name: postgresql
version: 15.5.22
version: 16.3.2
repository: oci://registry-1.docker.io/bitnamicharts
condition: postgresql.enabled
appVersion: 7.2.0
version: 0.17.1
- name: common
repository: oci://registry-1.docker.io/bitnamicharts
version: 2.28.0
appVersion: 7.6.0
version: 0.18.0
annotations:
artifacthub.io/license: Apache-2.0
artifacthub.io/containsSecurityUpdates: "false"
@@ -24,6 +27,14 @@ annotations:
# When using the list of objects option the valid supported kinds are
# added, changed, deprecated, removed, fixed, and security.
- kind: changed
description: updated curlimages/curl to 8.9.1
description: "updated postgresql sub-chart to 16.3.2"
- kind: changed
description: "updated postgresql sub-chart to 15.5.22."
description: "updated curlimages/curl to 8.11.1"
- kind: changed
description: "updated hapiproject/hapi to 7.6.0"
- kind: added
description: "support for setting resource limits and requests from presets. With a default set for all containers"
- kind: added
description: "support for setting extra volumes and volume mounts"
- kind: changed
description: "set default pod security context for main and test pods"

15
charts/hapi-fhir-jpaserver/README.md
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@@ -1,6 +1,6 @@
# HAPI FHIR JPA Server Starter Helm Chart
![Version: 0.17.1](https://img.shields.io/badge/Version-0.17.1-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 7.2.0](https://img.shields.io/badge/AppVersion-7.2.0-informational?style=flat-square)
![Version: 0.18.0](https://img.shields.io/badge/Version-0.18.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 7.6.0](https://img.shields.io/badge/AppVersion-7.6.0-informational?style=flat-square)
This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
@@ -15,7 +15,8 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| Repository | Name | Version |
|------------|------|---------|
| oci://registry-1.docker.io/bitnamicharts | postgresql | 15.5.22 |
| oci://registry-1.docker.io/bitnamicharts | common | 2.28.0 |
| oci://registry-1.docker.io/bitnamicharts | postgresql | 16.3.2 |
## Values
@@ -32,11 +33,13 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| 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 |
| extraVolumeMounts | list | `[]` | Optionally specify extra list of additional volumeMounts |
| extraVolumes | list | `[]` | Optionally specify extra list of additional volumes |
| fullnameOverride | string | `""` | override the chart fullname |
| image.pullPolicy | string | `"IfNotPresent"` | image pullPolicy to use |
| 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.tag | string | `"v7.2.0@sha256:9bcafa8342b572eee248cb7c48c496863d352bbd0347e1d98ea238d09620e89b"` | 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 | `"v7.6.0@sha256:4771a178e764896c83881c1b3a52bd487e53d06e1acc3653ea0db0c6f6b2b8a1"` | 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 |
| 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 |
@@ -44,6 +47,8 @@ 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 |
| initContainers.resources | object | `{}` | configure the init containers pods resource requests and limits |
| initContainers.resourcesPreset | string | `"nano"` | set container resources according to one common preset (allowed values: none, nano, micro, small, medium, large, xlarge, 2xlarge). This is ignored if `resources` is set (`resources` is recommended for production). More information: <https://github.com/bitnami/charts/blob/main/bitnami/common/templates/_resources.tpl#L15> |
| 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 |
@@ -53,12 +58,13 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| podDisruptionBudget.enabled | bool | `false` | Enable PodDisruptionBudget for the server pods. uses policy/v1/PodDisruptionBudget thus requiring k8s 1.21+ |
| podDisruptionBudget.maxUnavailable | string | `""` | maximum unavailable instances |
| podDisruptionBudget.minAvailable | int | `1` | minimum available instances |
| podSecurityContext | object | `{}` | pod security context |
| podSecurityContext | object | `{"fsGroup":65532,"fsGroupChangePolicy":"OnRootMismatch","runAsGroup":65532,"runAsNonRoot":true,"runAsUser":65532,"seccompProfile":{"type":"RuntimeDefault"}}` | pod security context |
| postgresql.auth.database | string | `"fhir"` | name for a custom database to create |
| postgresql.auth.existingSecret | string | `""` | Name of existing secret to use for PostgreSQL credentials `auth.postgresPassword`, `auth.password`, and `auth.replicationPassword` will be ignored and picked up from this secret The secret must contain the keys `postgres-password` (which is the password for "postgres" admin user), `password` (which is the password for the custom user to create when `auth.username` is set), and `replication-password` (which is the password for replication user). The secret might also contains the key `ldap-password` if LDAP is enabled. `ldap.bind_password` will be ignored and picked from this secret in this case. The value is evaluated as a template. |
| postgresql.enabled | bool | `true` | enable an included PostgreSQL DB. see <https://github.com/bitnami/charts/tree/master/bitnami/postgresql> for details if set to `false`, the values under `externalDatabase` are used |
| replicaCount | int | `1` | number of replicas to deploy |
| resources | object | `{}` | configure the FHIR server's resource requests and limits |
| resourcesPreset | string | `"medium"` | set container resources according to one common preset (allowed values: none, nano, micro, small, medium, large, xlarge, 2xlarge). This is ignored if `resources` is set (`resources` is recommended for production). More information: <https://github.com/bitnami/charts/blob/main/bitnami/common/templates/_resources.tpl#L15> |
| securityContext.allowPrivilegeEscalation | bool | `false` | |
| securityContext.capabilities.drop[0] | string | `"ALL"` | |
| securityContext.privileged | bool | `false` | |
@@ -75,6 +81,7 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| serviceAccount.name | string | `""` | The name of the service account to use. If not set and create is true, a name is generated using the fullname template |
| tests.automountServiceAccountToken | bool | `false` | whether the service account token should be auto-mounted for the test pods |
| tests.resources | object | `{}` | configure the test pods resource requests and limits |
| tests.resourcesPreset | string | `"nano"` | set container resources according to one common preset (allowed values: none, nano, micro, small, medium, large, xlarge, 2xlarge). This is ignored if `resources` is set (`resources` is recommended for production). More information: <https://github.com/bitnami/charts/blob/main/bitnami/common/templates/_resources.tpl#L15> |
| tolerations | list | `[]` | pod tolerations |
| topologySpreadConstraints | list | `[]` | pod topology spread configuration see: https://kubernetes.io/docs/concepts/workloads/pods/pod-topology-spread-constraints/#api |

11
charts/hapi-fhir-jpaserver/ci/extra-volumes-values.yaml Normal file
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@@ -0,0 +1,11 @@
extraVolumes:
- name: config-kube-root-ca
configMap:
name: kube-root-ca.crt
items:
- key: ca.crt
path: ca.crt
extraVolumeMounts:
- name: config-kube-root-ca
mountPath: /etc/test

22
charts/hapi-fhir-jpaserver/templates/deployment.yaml
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@@ -31,12 +31,17 @@ spec:
{{- toYaml .Values.podSecurityContext | nindent 8 }}
initContainers:
- name: wait-for-db-to-be-ready
image: docker.io/bitnami/postgresql:16.4.0-debian-12-r1@sha256:fb3d0a34e7b9f3e59442aa1fa2e6377857147c09ae754ddd5d4bb3fc0dd137da
image: docker.io/bitnami/postgresql:17.2.0-debian-12-r3@sha256:4de5c47eb98dd8fe09abdcbc2264984486ee8196e90902fb354f5d2ab97e8921
imagePullPolicy: IfNotPresent
{{- with .Values.restrictedContainerSecurityContext }}
securityContext:
{{- toYaml . | nindent 12 }}
{{- end }}
{{- if .Values.initContainers.resources }}
resources: {{- toYaml .Values.initContainers.resources | nindent 12 }}
{{- else if ne .Values.initContainers.resourcesPreset "none" }}
resources: {{- include "common.resources.preset" (dict "type" .Values.initContainers.resourcesPreset) | nindent 12 }}
{{- end }}
env:
- name: PGHOST
value: "{{ include "hapi-fhir-jpaserver.database.host" . }}"
@@ -76,8 +81,11 @@ spec:
readinessProbe:
{{- toYaml . | nindent 12 }}
{{- end }}
resources:
{{- toYaml .Values.resources | nindent 12 }}
{{- if .Values.resources }}
resources: {{- toYaml .Values.resources | nindent 12 }}
{{- else if ne .Values.resourcesPreset "none" }}
resources: {{- include "common.resources.preset" (dict "type" .Values.resourcesPreset) | nindent 12 }}
{{- end }}
env:
- name: SPRING_DATASOURCE_URL
value: {{ include "hapi-fhir-jpaserver.database.jdbcUrl" $ }}
@@ -98,6 +106,8 @@ spec:
value: "true"
- name: MANAGEMENT_SERVER_PORT
value: "8081"
- name: MANAGEMENT_ENDPOINTS_WEB_EXPOSURE_INCLUDE
value: "health,prometheus"
{{- if .Values.extraConfig }}
- name: SPRING_CONFIG_IMPORT
value: "/app/config/application-extra.yaml"
@@ -116,6 +126,9 @@ spec:
readOnly: true
subPath: application-extra.yaml
{{- end }}
{{- if .Values.extraVolumeMounts }}
{{- include "common.tplvalues.render" (dict "value" .Values.extraVolumeMounts "context" $) | nindent 12 }}
{{- end }}
{{- with .Values.nodeSelector }}
nodeSelector:
{{- toYaml . | nindent 8 }}
@@ -142,3 +155,6 @@ spec:
configMap:
name: {{ include "hapi-fhir-jpaserver.fullname" . }}-application-config
{{- end }}
{{- if .Values.extraVolumes }}
{{- include "common.tplvalues.render" (dict "value" .Values.extraVolumes "context" $) | nindent 8 }}
{{- end }}

24
charts/hapi-fhir-jpaserver/templates/tests/test-endpoints.yaml
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@@ -5,11 +5,14 @@ metadata:
labels:
{{- include "hapi-fhir-jpaserver.labels" . | nindent 4 }}
{{ include "hapi-fhir-jpaserver.fullname" . }}-client: "true"
app.kubernetes.io/component: tests
annotations:
"helm.sh/hook": test
spec:
restartPolicy: Never
automountServiceAccountToken: {{ .Values.tests.automountServiceAccountToken }}
securityContext:
{{- toYaml .Values.tests.podSecurityContext | nindent 4 }}
containers:
- name: test-metadata-endpoint
image: "{{ .Values.curl.image.registry }}/{{ .Values.curl.image.repository }}:{{ .Values.curl.image.tag }}"
@@ -19,9 +22,10 @@ spec:
securityContext:
{{- toYaml . | nindent 8 }}
{{- end }}
{{- with .Values.tests.resources }}
resources:
{{- toYaml . | nindent 8 }}
{{- if .Values.tests.resources }}
resources: {{- toYaml .Values.tests.resources | nindent 10 }}
{{- else if ne .Values.tests.resourcesPreset "none" }}
resources: {{- include "common.resources.preset" (dict "type" .Values.tests.resourcesPreset) | nindent 10 }}
{{- end }}
livenessProbe:
exec:
@@ -37,9 +41,10 @@ spec:
securityContext:
{{- toYaml . | nindent 8 }}
{{- end }}
{{- with .Values.tests.resources }}
resources:
{{- toYaml . | nindent 8 }}
{{- if .Values.tests.resources }}
resources: {{- toYaml .Values.tests.resources | nindent 10 }}
{{- else if ne .Values.tests.resourcesPreset "none" }}
resources: {{- include "common.resources.preset" (dict "type" .Values.tests.resourcesPreset) | nindent 10 }}
{{- end }}
livenessProbe:
exec:
@@ -55,9 +60,10 @@ spec:
securityContext:
{{- toYaml . | nindent 8 }}
{{- end }}
{{- with .Values.tests.resources }}
resources:
{{- toYaml . | nindent 8 }}
{{- if .Values.tests.resources }}
resources: {{- toYaml .Values.tests.resources | nindent 10 }}
{{- else if ne .Values.tests.resourcesPreset "none" }}
resources: {{- include "common.resources.preset" (dict "type" .Values.tests.resourcesPreset) | nindent 10 }}
{{- end }}
livenessProbe:
exec:

51
charts/hapi-fhir-jpaserver/values.yaml
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@@ -7,7 +7,7 @@ image:
# -- the path inside the repository
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.
tag: "v7.2.0@sha256:9bcafa8342b572eee248cb7c48c496863d352bbd0347e1d98ea238d09620e89b"
tag: "v7.6.0@sha256:4771a178e764896c83881c1b3a52bd487e53d06e1acc3653ea0db0c6f6b2b8a1"
# -- image pullPolicy to use
pullPolicy: IfNotPresent
@@ -28,8 +28,13 @@ podAnnotations: {}
# -- pod security context
podSecurityContext:
{}
# fsGroup: 2000
fsGroupChangePolicy: OnRootMismatch
runAsNonRoot: true
runAsGroup: 65532
runAsUser: 65532
fsGroup: 65532
seccompProfile:
type: RuntimeDefault
securityContext:
allowPrivilegeEscalation: false
@@ -69,6 +74,11 @@ ingress:
# hosts:
# - chart-example.local
# -- set container resources according to one common preset (allowed values: none, nano, micro, small, medium, large, xlarge, 2xlarge).
# This is ignored if `resources` is set (`resources` is recommended for production).
# More information: <https://github.com/bitnami/charts/blob/main/bitnami/common/templates/_resources.tpl#L15>
resourcesPreset: "medium"
# -- configure the FHIR server's resource requests and limits
resources:
{}
@@ -231,11 +241,15 @@ curl:
image:
registry: docker.io
repository: curlimages/curl
tag: 8.9.1@sha256:8addc281f0ea517409209f76832b6ddc2cabc3264feb1ebbec2a2521ffad24e4
tag: 8.11.1@sha256:c1fe1679c34d9784c1b0d1e5f62ac0a79fca01fb6377cdd33e90473c6f9f9a69
tests:
# -- whether the service account token should be auto-mounted for the test pods
automountServiceAccountToken: false
# -- set container resources according to one common preset (allowed values: none, nano, micro, small, medium, large, xlarge, 2xlarge).
# This is ignored if `resources` is set (`resources` is recommended for production).
# More information: <https://github.com/bitnami/charts/blob/main/bitnami/common/templates/_resources.tpl#L15>
resourcesPreset: "nano"
# -- configure the test pods resource requests and limits
resources: {}
# limits:
@@ -244,6 +258,29 @@ tests:
# requests:
# cpu: 100m
# memory: 128Mi
# @ignored
podSecurityContext:
fsGroupChangePolicy: OnRootMismatch
runAsNonRoot: true
runAsGroup: 65532
runAsUser: 65532
fsGroup: 65532
seccompProfile:
type: RuntimeDefault
initContainers:
# -- set container resources according to one common preset (allowed values: none, nano, micro, small, medium, large, xlarge, 2xlarge).
# This is ignored if `resources` is set (`resources` is recommended for production).
# More information: <https://github.com/bitnami/charts/blob/main/bitnami/common/templates/_resources.tpl#L15>
resourcesPreset: "nano"
# -- configure the init containers 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:
@@ -257,3 +294,9 @@ extraConfig:
# url: https://build.fhir.org/ig/hl7-eu/gravitate-health/package.tgz
# name: hl7.eu.fhir.gh
# version: 0.1.0
# -- Optionally specify extra list of additional volumes
extraVolumes: []
# -- Optionally specify extra list of additional volumeMounts
extraVolumeMounts: []