Merge branch 'master' into rel_6_0_0_mergeback
This commit is contained in:
Tadgh
24
.github/workflows/build-images.yaml
vendored
24
.github/workflows/build-images.yaml
vendored
@@ -19,25 +19,24 @@ jobs:
|
||||
name: Build
|
||||
runs-on: ubuntu-20.04
|
||||
steps:
|
||||
- name: Docker meta
|
||||
- name: Container meta for default (distroless) image
|
||||
id: docker_meta
|
||||
uses: docker/metadata-action@v3
|
||||
with:
|
||||
images: ${{ env.IMAGES }}
|
||||
tags: |
|
||||
type=match,pattern=image-(.*),group=1,enable=${{github.event_name != 'pull_request'}}
|
||||
type=sha
|
||||
|
||||
- name: Docker distroless meta
|
||||
id: docker_distroless_meta
|
||||
|
||||
- name: Container meta for tomcat image
|
||||
id: docker_tomcat_meta
|
||||
uses: docker/metadata-action@v3
|
||||
with:
|
||||
images: ${{ env.IMAGES }}
|
||||
tags: |
|
||||
type=match,pattern=image-(.*),group=1,enable=${{github.event_name != 'pull_request'}}
|
||||
type=sha
|
||||
flavor: |
|
||||
suffix=-distroless,onlatest=true
|
||||
suffix=-tomcat,onlatest=true
|
||||
|
||||
- name: Set up QEMU
|
||||
uses: docker/setup-qemu-action@v1
|
||||
@@ -60,7 +59,7 @@ jobs:
|
||||
restore-keys: |
|
||||
${{ runner.os }}-buildx-
|
||||
|
||||
- name: Build and push
|
||||
- name: Build and push default (distroless) image
|
||||
id: docker_build
|
||||
uses: docker/build-push-action@v2
|
||||
with:
|
||||
@@ -70,15 +69,16 @@ jobs:
|
||||
tags: ${{ steps.docker_meta.outputs.tags }}
|
||||
labels: ${{ steps.docker_meta.outputs.labels }}
|
||||
platforms: ${{ env.PLATFORMS }}
|
||||
target: default
|
||||
|
||||
- name: Build and push distroless
|
||||
id: docker_build_distroless
|
||||
- name: Build and push tomcat image
|
||||
id: docker_build_tomcat
|
||||
uses: docker/build-push-action@v2
|
||||
with:
|
||||
cache-from: type=local,src=/tmp/.buildx-cache
|
||||
cache-to: type=local,dest=/tmp/.buildx-cache
|
||||
push: ${{ github.event_name != 'pull_request' }}
|
||||
tags: ${{ steps.docker_distroless_meta.outputs.tags }}
|
||||
labels: ${{ steps.docker_distroless_meta.outputs.labels }}
|
||||
tags: ${{ steps.docker_tomcat_meta.outputs.tags }}
|
||||
labels: ${{ steps.docker_tomcat_meta.outputs.labels }}
|
||||
platforms: ${{ env.PLATFORMS }}
|
||||
target: release-distroless
|
||||
target: tomcat
|
||||
|
||||
40
Dockerfile
40
Dockerfile
@@ -1,4 +1,4 @@
|
||||
FROM maven:3.8.2-jdk-11-slim as build-hapi
|
||||
FROM maven:3.8-openjdk-17-slim as build-hapi
|
||||
WORKDIR /tmp/hapi-fhir-jpaserver-starter
|
||||
|
||||
COPY pom.xml .
|
||||
@@ -6,14 +6,34 @@ COPY server.xml .
|
||||
RUN mvn -ntp dependency:go-offline
|
||||
|
||||
COPY src/ /tmp/hapi-fhir-jpaserver-starter/src/
|
||||
RUN mvn clean install -DskipTests
|
||||
RUN mvn clean install -DskipTests -Djdk.lang.Process.launchMechanism=vfork
|
||||
|
||||
FROM build-hapi AS build-distroless
|
||||
RUN mvn package spring-boot:repackage -Pboot
|
||||
RUN mkdir /app && \
|
||||
cp /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.war
|
||||
RUN mkdir /app && cp /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.war
|
||||
|
||||
FROM gcr.io/distroless/java-debian11:11 AS release-distroless
|
||||
|
||||
########### bitnami tomcat version is suitable for debugging and comes with a shell
|
||||
########### it can be built using eg. `docker build --target tomcat .`
|
||||
FROM bitnami/tomcat:9.0 as tomcat
|
||||
|
||||
RUN rm -rf /opt/bitnami/tomcat/webapps/ROOT && \
|
||||
rm -rf /opt/bitnami/tomcat/webapps_default/ROOT && \
|
||||
mkdir -p /opt/bitnami/hapi/data/hapi/lucenefiles && \
|
||||
chmod 775 /opt/bitnami/hapi/data/hapi/lucenefiles
|
||||
|
||||
USER root
|
||||
RUN mkdir -p /target && chown -R 1001:1001 target
|
||||
USER 1001
|
||||
|
||||
COPY --chown=1001:1001 catalina.properties /opt/bitnami/tomcat/conf/catalina.properties
|
||||
COPY --chown=1001:1001 server.xml /opt/bitnami/tomcat/conf/server.xml
|
||||
COPY --from=build-hapi --chown=1001:1001 /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /opt/bitnami/tomcat/webapps_default/ROOT.war
|
||||
|
||||
ENV ALLOW_EMPTY_PASSWORD=yes
|
||||
|
||||
########### distroless brings focus on security and runs on plain spring boot - this is the default image
|
||||
FROM gcr.io/distroless/java17:nonroot as default
|
||||
COPY --chown=nonroot:nonroot --from=build-distroless /app /app
|
||||
# 65532 is the nonroot user's uid
|
||||
# used here instead of the name to allow Kubernetes to easily detect that the container
|
||||
@@ -21,13 +41,3 @@ COPY --chown=nonroot:nonroot --from=build-distroless /app /app
|
||||
USER 65532:65532
|
||||
WORKDIR /app
|
||||
CMD ["/app/main.war"]
|
||||
|
||||
FROM tomcat:9.0.53-jdk11-openjdk-slim-bullseye
|
||||
|
||||
RUN mkdir -p /data/hapi/lucenefiles && chmod 775 /data/hapi/lucenefiles
|
||||
COPY --from=build-hapi /tmp/hapi-fhir-jpaserver-starter/target/*.war /usr/local/tomcat/webapps/
|
||||
|
||||
COPY catalina.properties /usr/local/tomcat/conf/catalina.properties
|
||||
COPY server.xml /usr/local/tomcat/conf/server.xml
|
||||
|
||||
CMD ["catalina.sh", "run"]
|
||||
|
||||
29
README.md
29
README.md
@@ -189,6 +189,13 @@ spring:
|
||||
password: admin
|
||||
driverClassName: com.mysql.jdbc.Driver
|
||||
```
|
||||
|
||||
Also, make sure you are not setting the Hibernate dialect explicitly, in other words remove any lines similar to:
|
||||
|
||||
```
|
||||
hibernate.dialect: {some none MySQL dialect}
|
||||
```
|
||||
|
||||
On some systems, it might be necessary to override hibernate's default naming strategy. The naming strategy must be set using spring.jpa.hibernate.physical_naming_strategy.
|
||||
|
||||
```yaml
|
||||
@@ -215,6 +222,26 @@ spring:
|
||||
|
||||
Because the integration tests within the project rely on the default H2 database configuration, it is important to either explicity skip the integration tests during the build process, i.e., `mvn install -DskipTests`, or delete the tests altogether. Failure to skip or delete the tests once you've configured PostgreSQL for the datasource.driver, datasource.url, and hibernate.dialect as outlined above will result in build errors and compilation failure.
|
||||
|
||||
### Microsoft SQL Server configuration
|
||||
|
||||
To configure the starter app to use MS SQL Server, instead of the default H2, update the application.yaml file to have the following:
|
||||
|
||||
```yaml
|
||||
spring:
|
||||
datasource:
|
||||
url: 'jdbc:sqlserver://<server>:<port>;databaseName=<databasename>'
|
||||
username: admin
|
||||
password: admin
|
||||
driverClassName: com.microsoft.sqlserver.jdbc.SQLServerDriver
|
||||
```
|
||||
|
||||
|
||||
Because the integration tests within the project rely on the default H2 database configuration, it is important to either explicity skip the integration tests during the build process, i.e., `mvn install -DskipTests`, or delete the tests altogether. Failure to skip or delete the tests once you've configured PostgreSQL for the datasource.driver, datasource.url, and hibernate.dialect as outlined above will result in build errors and compilation failure.
|
||||
|
||||
|
||||
NOTE: MS SQL Server by default uses a case-insensitive codepage. This will cause errors with some operations - such as when expanding case-sensitive valuesets (UCUM) as there are unique indexes defined on the terminology tables for codes.
|
||||
It is recommended to deploy a case-sensitive database prior to running HAPI FHIR when using MS SQL Server to avoid these and potentially other issues.
|
||||
|
||||
## Customizing The Web Testpage UI
|
||||
|
||||
The UI that comes with this server is an exact clone of the server available at [http://hapi.fhir.org](http://hapi.fhir.org). You may skin this UI if you'd like. For example, you might change the introductory text or replace the logo with your own.
|
||||
@@ -279,6 +306,8 @@ spring:
|
||||
driverClassName: com.mysql.jdbc.Driver
|
||||
```
|
||||
|
||||
Also, make sure you are not setting the Hibernate Dialect explicitly, see more details in the section about MySQL.
|
||||
|
||||
## Running hapi-fhir-jpaserver directly from IntelliJ as Spring Boot
|
||||
Make sure you run with the maven profile called ```boot``` and NOT also ```jetty```. Then you are ready to press debug the project directly without any extra Application Servers.
|
||||
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
dependencies:
|
||||
- name: postgresql
|
||||
repository: https://charts.bitnami.com/bitnami
|
||||
version: 10.12.2
|
||||
digest: sha256:38ee315eae1af3e3f6eb20e1dd8ffd60d4ab7ee0c51bf26941b56c8bcb376c11
|
||||
generated: "2021-10-07T00:19:18.9743522+02:00"
|
||||
version: 11.1.19
|
||||
digest: sha256:5bb38230bfa62c63547851e6f46f66a61441a4a4f18e3689827546277e34d192
|
||||
generated: "2022-04-08T21:55:34.6868891+02:00"
|
||||
|
||||
@@ -7,20 +7,23 @@ sources:
|
||||
- https://github.com/hapifhir/hapi-fhir-jpaserver-starter
|
||||
dependencies:
|
||||
- name: postgresql
|
||||
version: 10.12.2
|
||||
version: 11.1.19
|
||||
repository: https://charts.bitnami.com/bitnami
|
||||
condition: postgresql.enabled
|
||||
annotations:
|
||||
artifacthub.io/license: Apache-2.0
|
||||
artifacthub.io/prerelease: "true"
|
||||
artifacthub.io/changes: |
|
||||
# When using the list of objects option the valid supported kinds are
|
||||
# added, changed, deprecated, removed, fixed, and security.
|
||||
- kind: changed
|
||||
description: |
|
||||
updated HAPI FHIR starter image to 5.6.0
|
||||
- kind: added
|
||||
updated HAPI FHIR starter image to 5.7.0
|
||||
- kind: changed
|
||||
description: |
|
||||
added support for configuring PodDisruptionBudget for the server pods
|
||||
appVersion: v5.6.0
|
||||
version: 0.7.0
|
||||
BREAKING CHANGE: updated included PostgreSQL-subchart to v11
|
||||
- kind: changed
|
||||
description: |
|
||||
BREAKING CHANGE: removed ability to override the image flavor.
|
||||
The one based on distroless is now the new default.
|
||||
appVersion: v5.7.0
|
||||
version: 0.8.0
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
# HAPI FHIR JPA Server Starter Helm Chart
|
||||
|
||||
  
|
||||
  
|
||||
|
||||
This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
|
||||
|
||||
@@ -29,11 +29,10 @@ helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpas
|
||||
| externalDatabase.user | string | `"fhir"` | username for the external database |
|
||||
| extraEnv | list | `[]` | extra environment variables to set on the server container |
|
||||
| fullnameOverride | string | `""` | override the chart fullname |
|
||||
| image.flavor | string | `"distroless"` | the flavor or variant of the image to use. appended to the image tag by `-`. |
|
||||
| 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 | `""` | defaults to `Chart.appVersion` |
|
||||
| image.tag | string | `""` | defaults to `Chart.appVersion`. As of v5.7.0, this is the `distroless` flavor |
|
||||
| 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 |
|
||||
@@ -51,11 +50,11 @@ helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpas
|
||||
| podDisruptionBudget.maxUnavailable | string | `""` | maximum unavailable instances |
|
||||
| podDisruptionBudget.minAvailable | int | `1` | minimum available instances |
|
||||
| podSecurityContext | object | `{}` | pod security context |
|
||||
| postgresql.containerSecurityContext.allowPrivilegeEscalation | bool | `false` | |
|
||||
| postgresql.containerSecurityContext.capabilities.drop[0] | string | `"ALL"` | |
|
||||
| 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 |
|
||||
| postgresql.existingSecret | string | `""` | Name of existing secret to use for PostgreSQL passwords. The secret has to contain the keys `postgresql-password` which is the password for `postgresqlUsername` when it is different of `postgres`, `postgresql-postgres-password` which will override `postgresqlPassword`, `postgresql-replication-password` which will override `replication.password` and `postgresql-ldap-password` which will be sed to authenticate on LDAP. The value is evaluated as a template. |
|
||||
| postgresql.postgresqlDatabase | string | `"fhir"` | name of the database to create see: <https://github.com/bitnami/bitnami-docker-postgresql/blob/master/README.md#creating-a-database-on-first-run> |
|
||||
| postgresql.primary.containerSecurityContext.allowPrivilegeEscalation | bool | `false` | |
|
||||
| postgresql.primary.containerSecurityContext.capabilities.drop[0] | string | `"ALL"` | |
|
||||
| readinessProbe.failureThreshold | int | `5` | |
|
||||
| readinessProbe.initialDelaySeconds | int | `30` | |
|
||||
| readinessProbe.periodSeconds | int | `20` | |
|
||||
|
||||
@@ -0,0 +1,6 @@
|
||||
ingress:
|
||||
enabled: true
|
||||
|
||||
postgresql:
|
||||
auth:
|
||||
postgresPassword: secretpassword
|
||||
@@ -30,18 +30,6 @@ Create chart name and version as used by the chart label.
|
||||
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
|
||||
{{- end }}
|
||||
|
||||
{{/*
|
||||
Create image tag
|
||||
*/}}
|
||||
{{- define "hapi-fhir-jpaserver.imageTag" -}}
|
||||
{{- $version := default .Chart.AppVersion .Values.image.tag -}}
|
||||
{{- if .Values.image.flavor }}
|
||||
{{- printf "%s-%s" $version .Values.image.flavor }}
|
||||
{{- else }}
|
||||
{{- printf "%s" $version }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
|
||||
{{/*
|
||||
Common labels
|
||||
*/}}
|
||||
@@ -75,10 +63,10 @@ We truncate at 63 chars because some Kubernetes name fields are limited to this
|
||||
Get the Postgresql credentials secret name.
|
||||
*/}}
|
||||
{{- define "hapi-fhir-jpaserver.postgresql.secretName" -}}
|
||||
{{- if and (.Values.postgresql.enabled) (not .Values.postgresql.existingSecret) -}}
|
||||
{{- if and (.Values.postgresql.enabled) (not .Values.postgresql.auth.existingSecret) -}}
|
||||
{{- printf "%s" (include "hapi-fhir-jpaserver.postgresql.fullname" .) -}}
|
||||
{{- else if and (.Values.postgresql.enabled) (.Values.postgresql.existingSecret) -}}
|
||||
{{- printf "%s" .Values.postgresql.existingSecret -}}
|
||||
{{- else if and (.Values.postgresql.enabled) (.Values.postgresql.auth.existingSecret) -}}
|
||||
{{- printf "%s" .Values.postgresql.auth.existingSecret -}}
|
||||
{{- else }}
|
||||
{{- if .Values.externalDatabase.existingSecret -}}
|
||||
{{- printf "%s" .Values.externalDatabase.existingSecret -}}
|
||||
@@ -95,7 +83,7 @@ Get the Postgresql credentials secret key.
|
||||
{{- if (.Values.externalDatabase.existingSecret) -}}
|
||||
{{- printf "%s" .Values.externalDatabase.existingSecretKey -}}
|
||||
{{- else }}
|
||||
{{- printf "postgresql-password" -}}
|
||||
{{- printf "postgres-password" -}}
|
||||
{{- end -}}
|
||||
{{- end -}}
|
||||
|
||||
@@ -110,14 +98,14 @@ Add environment variables to configure database values
|
||||
Add environment variables to configure database values
|
||||
*/}}
|
||||
{{- define "hapi-fhir-jpaserver.database.user" -}}
|
||||
{{- ternary .Values.postgresql.postgresqlUsername .Values.externalDatabase.user .Values.postgresql.enabled -}}
|
||||
{{- ternary "postgres" .Values.externalDatabase.user .Values.postgresql.enabled -}}
|
||||
{{- end -}}
|
||||
|
||||
{{/*
|
||||
Add environment variables to configure database values
|
||||
*/}}
|
||||
{{- define "hapi-fhir-jpaserver.database.name" -}}
|
||||
{{- ternary .Values.postgresql.postgresqlDatabase .Values.externalDatabase.database .Values.postgresql.enabled -}}
|
||||
{{- ternary .Values.postgresql.auth.database .Values.externalDatabase.database .Values.postgresql.enabled -}}
|
||||
{{- end -}}
|
||||
|
||||
{{/*
|
||||
|
||||
@@ -60,7 +60,7 @@ spec:
|
||||
- name: {{ .Chart.Name }}
|
||||
securityContext:
|
||||
{{- toYaml .Values.securityContext | nindent 12 }}
|
||||
image: {{ .Values.image.registry }}/{{ .Values.image.repository }}:{{ include "hapi-fhir-jpaserver.imageTag" . }}
|
||||
image: {{ .Values.image.registry }}/{{ .Values.image.repository }}:{{ default .Chart.AppVersion .Values.image.tag }}
|
||||
imagePullPolicy: {{ .Values.image.pullPolicy }}
|
||||
ports:
|
||||
- name: http
|
||||
@@ -102,12 +102,10 @@ spec:
|
||||
key: {{ include "hapi-fhir-jpaserver.postgresql.secretKey" . }}
|
||||
- name: SPRING_DATASOURCE_DRIVERCLASSNAME
|
||||
value: org.postgresql.Driver
|
||||
- name: SPRING_JPA_PROPERTIES_HIBERNATE_DIALECT
|
||||
value: org.hibernate.dialect.PostgreSQL10Dialect
|
||||
- name: spring.jpa.properties.hibernate.dialect
|
||||
value: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
|
||||
- name: HAPI_FHIR_USE_APACHE_ADDRESS_STRATEGY
|
||||
value: "true"
|
||||
- name: SPRING_JPA_DATABASE_PLATFORM
|
||||
value: org.hibernate.dialect.PostgreSQLDialect
|
||||
{{- if .Values.extraEnv }}
|
||||
{{ toYaml .Values.extraEnv | nindent 12 }}
|
||||
{{- end }}
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
{{- if and (not .Values.postgresql.enabled) (not .Values.externalDatabase.existingSecret) (not .Values.postgresql.existingSecret) }}
|
||||
{{- if and (not .Values.postgresql.enabled) (not .Values.externalDatabase.existingSecret) (not .Values.postgresql.auth.existingSecret) }}
|
||||
apiVersion: v1
|
||||
kind: Secret
|
||||
metadata:
|
||||
@@ -7,5 +7,5 @@ metadata:
|
||||
{{- include "hapi-fhir-jpaserver.labels" . | nindent 4 }}
|
||||
type: Opaque
|
||||
data:
|
||||
postgresql-password: {{ .Values.externalDatabase.password | b64enc | quote }}
|
||||
postgres-password: {{ .Values.externalDatabase.password | b64enc | quote }}
|
||||
{{- end }}
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
apiVersion: v1
|
||||
kind: Pod
|
||||
metadata:
|
||||
name: "{{ include "hapi-fhir-jpaserver.fullname" . }}-test-connection"
|
||||
name: "{{ include "hapi-fhir-jpaserver.fullname" . }}-test-endpoints"
|
||||
labels:
|
||||
{{- include "hapi-fhir-jpaserver.labels" . | nindent 4 }}
|
||||
{{ include "hapi-fhir-jpaserver.fullname" . }}-client: "true"
|
||||
@@ -10,7 +10,32 @@ metadata:
|
||||
spec:
|
||||
restartPolicy: Never
|
||||
containers:
|
||||
- name: wget
|
||||
- name: test-metadata-endpoint
|
||||
image: busybox:1
|
||||
command: ['wget', '-O', '-']
|
||||
args: ['http://{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.service.port }}/fhir/metadata']
|
||||
securityContext:
|
||||
allowPrivilegeEscalation: false
|
||||
capabilities:
|
||||
drop:
|
||||
- ALL
|
||||
readOnlyRootFilesystem: true
|
||||
runAsUser: 22222
|
||||
runAsNonRoot: true
|
||||
resources:
|
||||
limits:
|
||||
cpu: 100m
|
||||
memory: 128Mi
|
||||
requests:
|
||||
cpu: 100m
|
||||
memory: 128Mi
|
||||
livenessProbe:
|
||||
exec:
|
||||
command: ["true"]
|
||||
readinessProbe:
|
||||
exec:
|
||||
command: ["true"]
|
||||
- name: test-patient-endpoint
|
||||
image: busybox:1
|
||||
command: ['wget', '-O', '-']
|
||||
args: ['http://{{ include "hapi-fhir-jpaserver.fullname" . }}:{{ .Values.service.port }}/fhir/Patient?_count=1']
|
||||
@@ -6,11 +6,8 @@ image:
|
||||
registry: docker.io
|
||||
# -- the path inside the repository
|
||||
repository: hapiproject/hapi
|
||||
# -- defaults to `Chart.appVersion`
|
||||
# -- defaults to `Chart.appVersion`. As of v5.7.0, this is the `distroless` flavor
|
||||
tag: ""
|
||||
# -- the flavor or variant of the image to use.
|
||||
# appended to the image tag by `-`.
|
||||
flavor: "distroless"
|
||||
# -- image pullPolicy to use
|
||||
pullPolicy: IfNotPresent
|
||||
|
||||
@@ -96,22 +93,24 @@ postgresql:
|
||||
# see <https://github.com/bitnami/charts/tree/master/bitnami/postgresql> for details
|
||||
# if set to `false`, the values under `externalDatabase` are used
|
||||
enabled: true
|
||||
# -- name of the database to create
|
||||
# see: <https://github.com/bitnami/bitnami-docker-postgresql/blob/master/README.md#creating-a-database-on-first-run>
|
||||
postgresqlDatabase: "fhir"
|
||||
# -- Name of existing secret to use for PostgreSQL passwords.
|
||||
# The secret has to contain the keys `postgresql-password`
|
||||
# which is the password for `postgresqlUsername` when it is
|
||||
# different of `postgres`, `postgresql-postgres-password` which
|
||||
# will override `postgresqlPassword`, `postgresql-replication-password`
|
||||
# which will override `replication.password` and `postgresql-ldap-password`
|
||||
# which will be sed to authenticate on LDAP. The value is evaluated as a template.
|
||||
existingSecret: ""
|
||||
containerSecurityContext:
|
||||
allowPrivilegeEscalation: false
|
||||
capabilities:
|
||||
drop:
|
||||
- ALL
|
||||
auth:
|
||||
# -- name for a custom database to create
|
||||
database: "fhir"
|
||||
# -- 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.
|
||||
existingSecret: ""
|
||||
primary:
|
||||
containerSecurityContext:
|
||||
allowPrivilegeEscalation: false
|
||||
capabilities:
|
||||
drop:
|
||||
- ALL
|
||||
|
||||
readinessProbe:
|
||||
failureThreshold: 5
|
||||
|
||||
30
pom.xml
30
pom.xml
@@ -61,6 +61,10 @@
|
||||
<groupId>org.postgresql</groupId>
|
||||
<artifactId>postgresql</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.microsoft.sqlserver</groupId>
|
||||
<artifactId>mssql-jdbc</artifactId>
|
||||
</dependency>
|
||||
|
||||
<!-- Needed for Email subscriptions -->
|
||||
<dependency>
|
||||
@@ -85,6 +89,12 @@
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-jpaserver-subscription</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>com.zaxxer</groupId>
|
||||
<artifactId>HikariCP-java7</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
|
||||
<!-- This dependency includes the JPA server itself, which is packaged separately from the rest of HAPI FHIR -->
|
||||
@@ -301,6 +311,26 @@
|
||||
<version>${spring_boot_version}</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.springframework.boot</groupId>
|
||||
<artifactId>spring-boot-starter-actuator</artifactId>
|
||||
<version>${spring_boot_version}</version>
|
||||
</dependency>
|
||||
|
||||
<!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-registry-prometheus -->
|
||||
<dependency>
|
||||
<groupId>io.micrometer</groupId>
|
||||
<artifactId>micrometer-registry-prometheus</artifactId>
|
||||
<version>1.8.5</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>com.zaxxer</groupId>
|
||||
<artifactId>HikariCP</artifactId>
|
||||
<version>5.0.1</version>
|
||||
</dependency>
|
||||
|
||||
|
||||
<dependency>
|
||||
<groupId>org.junit.jupiter</groupId>
|
||||
<artifactId>junit-jupiter-api</artifactId>
|
||||
|
||||
@@ -25,12 +25,14 @@ public class AppProperties {
|
||||
private Boolean openapi_enabled = false;
|
||||
private Boolean mdm_enabled = false;
|
||||
private boolean advanced_lucene_indexing = false;
|
||||
private boolean enable_index_of_type = false;
|
||||
private Boolean allow_cascading_deletes = false;
|
||||
private Boolean allow_contains_searches = true;
|
||||
private Boolean allow_external_references = false;
|
||||
private Boolean allow_multiple_delete = false;
|
||||
private Boolean allow_override_default_search_params = true;
|
||||
private Boolean auto_create_placeholder_reference_targets = false;
|
||||
private Boolean dao_scheduling_enabled = true;
|
||||
private Boolean delete_expunge_enabled = false;
|
||||
private Boolean enable_index_missing_fields = false;
|
||||
private Boolean enable_index_contained_resource = false;
|
||||
@@ -286,6 +288,14 @@ public class AppProperties {
|
||||
this.default_page_size = default_page_size;
|
||||
}
|
||||
|
||||
public Boolean getDao_scheduling_enabled() {
|
||||
return dao_scheduling_enabled;
|
||||
}
|
||||
|
||||
public void setDao_scheduling_enabled(Boolean dao_scheduling_enabled) {
|
||||
this.dao_scheduling_enabled = dao_scheduling_enabled;
|
||||
}
|
||||
|
||||
public Boolean getDelete_expunge_enabled() {
|
||||
return delete_expunge_enabled;
|
||||
}
|
||||
@@ -807,4 +817,12 @@ public class AppProperties {
|
||||
private Boolean quitWait = false;
|
||||
}
|
||||
}
|
||||
|
||||
public boolean getEnable_index_of_type() {
|
||||
return enable_index_of_type;
|
||||
}
|
||||
|
||||
public void setEnable_index_of_type(boolean enable_index_of_type) {
|
||||
this.enable_index_of_type = enable_index_of_type;
|
||||
}
|
||||
}
|
||||
|
||||
@@ -28,6 +28,7 @@ import ca.uhn.fhir.rest.openapi.OpenApiInterceptor;
|
||||
import ca.uhn.fhir.rest.server.*;
|
||||
import ca.uhn.fhir.rest.server.interceptor.*;
|
||||
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
|
||||
import ca.uhn.fhir.rest.server.provider.ReindexProvider;
|
||||
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
|
||||
import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
|
||||
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
|
||||
@@ -80,6 +81,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
|
||||
@Autowired
|
||||
ValueSetOperationProvider valueSetOperationProvider;
|
||||
@Autowired
|
||||
ReindexProvider reindexProvider;
|
||||
@Autowired
|
||||
BinaryStorageInterceptor binaryStorageInterceptor;
|
||||
@Autowired
|
||||
IPackageInstallerSvc packageInstallerSvc;
|
||||
@@ -113,8 +116,10 @@ public class BaseJpaRestfulServer extends RestfulServer {
|
||||
// Customize supported resource types
|
||||
List<String> supportedResourceTypes = appProperties.getSupported_resource_types();
|
||||
|
||||
if (!supportedResourceTypes.isEmpty() && !supportedResourceTypes.contains("SearchParameter")) {
|
||||
supportedResourceTypes.add("SearchParameter");
|
||||
if (!supportedResourceTypes.isEmpty()) {
|
||||
if (!supportedResourceTypes.contains("SearchParameter")) {
|
||||
supportedResourceTypes.add("SearchParameter");
|
||||
}
|
||||
daoRegistry.setSupportedResourceTypes(supportedResourceTypes);
|
||||
}
|
||||
|
||||
@@ -358,6 +363,9 @@ public class BaseJpaRestfulServer extends RestfulServer {
|
||||
// valueSet Operations i.e $expand
|
||||
registerProvider(valueSetOperationProvider);
|
||||
|
||||
//reindex Provider $reindex
|
||||
registerProvider(reindexProvider);
|
||||
|
||||
// Partitioning
|
||||
if (appProperties.getPartitioning() != null) {
|
||||
registerInterceptor(new RequestTenantPartitionInterceptor());
|
||||
|
||||
@@ -40,6 +40,7 @@ public class FhirServerConfigCommon {
|
||||
ourLog.info("Server configured to " + (appProperties.getAllow_contains_searches() ? "allow" : "deny") + " contains searches");
|
||||
ourLog.info("Server configured to " + (appProperties.getAllow_multiple_delete() ? "allow" : "deny") + " multiple deletes");
|
||||
ourLog.info("Server configured to " + (appProperties.getAllow_external_references() ? "allow" : "deny") + " external references");
|
||||
ourLog.info("Server configured to " + (appProperties.getDao_scheduling_enabled() ? "enable" : "disable") + " DAO scheduling");
|
||||
ourLog.info("Server configured to " + (appProperties.getDelete_expunge_enabled() ? "enable" : "disable") + " delete expunges");
|
||||
ourLog.info("Server configured to " + (appProperties.getExpunge_enabled() ? "enable" : "disable") + " expunges");
|
||||
ourLog.info("Server configured to " + (appProperties.getAllow_override_default_search_params() ? "allow" : "deny") + " overriding default search params");
|
||||
@@ -86,6 +87,7 @@ public class FhirServerConfigCommon {
|
||||
retVal.setAllowContainsSearches(appProperties.getAllow_contains_searches());
|
||||
retVal.setAllowMultipleDelete(appProperties.getAllow_multiple_delete());
|
||||
retVal.setAllowExternalReferences(appProperties.getAllow_external_references());
|
||||
retVal.setSchedulingDisabled(!appProperties.getDao_scheduling_enabled());
|
||||
retVal.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
|
||||
retVal.setExpungeEnabled(appProperties.getExpunge_enabled());
|
||||
if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
|
||||
@@ -177,6 +179,7 @@ public class FhirServerConfigCommon {
|
||||
modelConfig.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
|
||||
|
||||
modelConfig.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
|
||||
modelConfig.setIndexIdentifierOfType(appProperties.getEnable_index_of_type());
|
||||
return modelConfig;
|
||||
}
|
||||
|
||||
|
||||
@@ -1,6 +1,14 @@
|
||||
#Adds the option to go to eg. http://localhost:8080/actuator/health for seeing the running configuration
|
||||
#see https://docs.spring.io/spring-boot/docs/current/reference/html/actuator.html#actuator.endpoints
|
||||
management:
|
||||
endpoints:
|
||||
web:
|
||||
exposure:
|
||||
include: "health,prometheus"
|
||||
spring:
|
||||
main:
|
||||
allow-circular-references: true
|
||||
#allow-bean-definition-overriding: true
|
||||
flyway:
|
||||
enabled: false
|
||||
check-location: false
|
||||
@@ -83,9 +91,13 @@ hapi:
|
||||
# delete_expunge_enabled: true
|
||||
# enable_repository_validating_interceptor: false
|
||||
# enable_index_missing_fields: false
|
||||
# enable_index_of_type: true
|
||||
# enable_index_contained_resource: false
|
||||
# This is an experimental feature, and does not fully support _total and other FHIR features.
|
||||
### !!Extended Lucene/Elasticsearch Indexing is still a experimental feature, expect some features (e.g. _total=accurate) to not work as expected!!
|
||||
### more information here: https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html
|
||||
advanced_lucene_indexing: false
|
||||
# enforce_referential_integrity_on_delete: false
|
||||
# This is an experimental feature, and does not fully support _total and other FHIR features.
|
||||
# enforce_referential_integrity_on_delete: false
|
||||
# enforce_referential_integrity_on_write: false
|
||||
# etag_support_enabled: true
|
||||
|
||||
@@ -15,6 +15,6 @@ public class Demo {
|
||||
System.setProperty("spring.batch.job.enabled", "false");
|
||||
SpringApplication.run(Demo.class, args);
|
||||
|
||||
//Server is now accessible at eg. http://localhost:8080/metadata
|
||||
//Server is now accessible at eg. http://localhost:8080/fhir/metadata
|
||||
}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user