This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
helm repo add hapifhir https://hapifhir.github.io/hapi-fhir-jpaserver-starter/
helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver| Repository | Name | Version |
|---|---|---|
| oci:https://registry-1.docker.io/bitnamicharts | postgresql | 13.2.27 |
| Key | Type | Default | Description |
|---|---|---|---|
| affinity | object | {} |
pod affinity |
| deploymentAnnotations | object | {} |
annotations applied to the server deployment |
| externalDatabase.database | string | "fhir" |
database name |
| externalDatabase.existingSecret | string | "" |
name of an existing secret resource containing the DB password in the existingSecretKey key |
| externalDatabase.existingSecretKey | string | "postgresql-password" |
name of the key inside the existingSecret |
| externalDatabase.host | string | "localhost" |
external database host used with postgresql.enabled=false |
| 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 |
| 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 | "v6.10.1@sha256:4eac1b3481180b028616d1fab7e657e368538063d75f7ed3be2032e34c657dd4" |
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 |
| ingress.hosts[0].host | string | "fhir-server.127.0.0.1.nip.io" |
|
| ingress.hosts[0].pathType | string | "ImplementationSpecific" |
|
| ingress.hosts[0].paths[0] | string | "/" |
|
| ingress.tls | list | [] |
ingress TLS config |
| 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 |
| nameOverride | string | "" |
override the chart name |
| nodeSelector | object | {} |
node selector for the pod |
| podAnnotations | object | {} |
annotations applied to the server pod |
| 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 |
| 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 |
| securityContext.allowPrivilegeEscalation | bool | false |
|
| securityContext.capabilities.drop[0] | string | "ALL" |
|
| securityContext.privileged | bool | false |
|
| securityContext.readOnlyRootFilesystem | bool | true |
|
| securityContext.runAsGroup | int | 65532 |
|
| securityContext.runAsNonRoot | bool | true |
|
| securityContext.runAsUser | int | 65532 |
|
| securityContext.seccompProfile.type | string | "RuntimeDefault" |
|
| service.port | int | 8080 |
port where the server will be exposed at |
| service.type | string | "ClusterIP" |
service type |
| serviceAccount.annotations | object | {} |
Annotations to add to the service account |
| serviceAccount.automount | bool | true |
Automatically mount a ServiceAccount's API credentials? |
| serviceAccount.create | bool | false |
Specifies whether a service account should be created. |
| 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.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 |
To update the Helm chart when a new version of the hapiproject/hapi image is released, values.yaml image.tag and the Chart.yaml's
version and optionally the appVersion field need to be updated. Afterwards, re-generate the README.md
by running:
$ helm-docs
INFO[2021-11-20T12:38:04Z] Found Chart directories [charts/hapi-fhir-jpaserver]
INFO[2021-11-20T12:38:04Z] Generating README Documentation for chart /usr/src/app/charts/hapi-fhir-jpaserverThe container image includes the OpenTelemetry Java agent JAR which can be used to enable distributed tracing. It can be configured entirely using environment variables, see https://opentelemetry.io/docs/instrumentation/java/automatic/agent-config/ for details.
Here's an example setup deploying Jaeger as a tracing backend:
# required by the Jaeger Operator
kubectl apply -f https://github.com/cert-manager/cert-manager/releases/download/v1.9.1/cert-manager.yaml
kubectl create namespace observability
kubectl create -f https://github.com/jaegertracing/jaeger-operator/releases/download/v1.37.0/jaeger-operator.yaml -n observability
cat <<EOF | kubectl apply -n observability -f -
# simple, all-in-one Jaeger installation. Not suitable for production use.
apiVersion: jaegertracing.io/v1
kind: Jaeger
metadata:
name: simplest
EOFUse this chart's extraEnv value to set the required environment variables:
extraEnv:
- name: JAVA_TOOL_OPTIONS
value: "-javaagent:/app/opentelemetry-javaagent.jar"
- name: OTEL_METRICS_EXPORTER
value: "none"
- name: OTEL_LOGS_EXPORTER
value: "none"
- name: OTEL_TRACES_EXPORTER
value: "jaeger"
- name: OTEL_SERVICE_NAME
value: "hapi-fhir-jpaserver"
- name: OTEL_EXPORTER_JAEGER_ENDPOINT
value: "http:https://simplest-collector.observability.svc:14250"Finally, you can open the Jaeger query UI by running:
kubectl port-forward -n observability service/simplest-query 16686:16686and opening http:https://localhost:16686/ in your browser.
Autogenerated from chart metadata using helm-docs v1.11.3