merge master
This commit is contained in:
Justin McKelvy
2
.github/ct/config.yaml
vendored
2
.github/ct/config.yaml
vendored
@@ -11,6 +11,4 @@ helm-extra-args: --timeout 300s
|
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upgrade: true
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skip-missing-values: true
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release-label: release
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||||
chart-repos:
|
||||
- bitnami=https://charts.bitnami.com/bitnami
|
||||
release-name-template: "helm-v{{ .Version }}"
|
||||
|
||||
13
.github/workflows/chart-release.yaml
vendored
13
.github/workflows/chart-release.yaml
vendored
@@ -9,10 +9,14 @@ on:
|
||||
|
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jobs:
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release:
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runs-on: ubuntu-20.04
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runs-on: ubuntu-22.04
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steps:
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- name: Add workspace as safe directory
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run: |
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git config --global --add safe.directory /__w/hapi-fhir-jpaserver-starter/hapi-fhir-jpaserver-starter
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|
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- name: Checkout
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uses: actions/checkout@v2
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uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # v3.5.2
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with:
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fetch-depth: 0
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|
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@@ -21,14 +25,11 @@ jobs:
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git config user.name "$GITHUB_ACTOR"
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git config user.email "$GITHUB_ACTOR@users.noreply.github.com"
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- name: Add bitnami repo
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run: helm repo add bitnami https://charts.bitnami.com/bitnami
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||||
|
||||
- name: Update dependencies
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run: find charts/ ! -path charts/ -maxdepth 1 -type d -exec helm dependency update {} \;
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||||
- name: Run chart-releaser
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uses: helm/chart-releaser-action@v1.2.0
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uses: helm/chart-releaser-action@be16258da8010256c6e82849661221415f031968 # v1.5.0
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with:
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config: .github/ct/config.yaml
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env:
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||||
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||||
26
.github/workflows/chart-test.yaml
vendored
26
.github/workflows/chart-test.yaml
vendored
@@ -9,8 +9,8 @@ on:
|
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|
||||
jobs:
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lint:
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runs-on: ubuntu-20.04
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container: quay.io/helmpack/chart-testing:v3.4.0
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runs-on: ubuntu-22.04
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container: quay.io/helmpack/chart-testing:v3.8.0@sha256:f058c660a28d99a9394ae081d98921efe068079531f247c86b8054e3c9d407aa
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steps:
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- name: Install helm-docs
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||||
working-directory: /tmp
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||||
@@ -22,11 +22,14 @@ jobs:
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chmod +x /usr/local/bin/helm-docs && \
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helm-docs --version
|
||||
|
||||
- name: Add workspace as safe directory
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||||
run: |
|
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git config --global --add safe.directory /__w/hapi-fhir-jpaserver-starter/hapi-fhir-jpaserver-starter
|
||||
|
||||
- name: Checkout
|
||||
uses: actions/checkout@v2
|
||||
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # v3.5.2
|
||||
with:
|
||||
fetch-depth: 0
|
||||
|
||||
- name: Check if documentation is up-to-date
|
||||
run: helm-docs && git diff --exit-code HEAD
|
||||
|
||||
@@ -34,20 +37,20 @@ jobs:
|
||||
run: ct lint --config .github/ct/config.yaml
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||||
|
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test:
|
||||
runs-on: ubuntu-20.04
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||||
runs-on: ubuntu-22.04
|
||||
strategy:
|
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matrix:
|
||||
k8s-version: [1.22.9, 1.23.6, 1.24.1]
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k8s-version: [1.25.9, 1.26.4, 1.27.2]
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needs:
|
||||
- lint
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steps:
|
||||
- name: Checkout
|
||||
uses: actions/checkout@v3
|
||||
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # v3.5.2
|
||||
with:
|
||||
fetch-depth: 0
|
||||
|
||||
- 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)
|
||||
id: list-changed
|
||||
@@ -58,13 +61,12 @@ jobs:
|
||||
fi
|
||||
|
||||
- name: Create k8s Kind Cluster
|
||||
uses: helm/kind-action@v1.2.0
|
||||
if: steps.list-changed.outputs.changed == 'true'
|
||||
uses: helm/kind-action@fa81e57adff234b2908110485695db0f181f3c67 # v1.7.0
|
||||
if: ${{ steps.list-changed.outputs.changed == 'true' }}
|
||||
with:
|
||||
version: v0.14.0
|
||||
cluster_name: kind-cluster-k8s-${{ matrix.k8s-version }}
|
||||
node_image: kindest/node:v${{ matrix.k8s-version }}
|
||||
|
||||
- name: Run chart-testing (install)
|
||||
run: ct install --config .github/ct/config.yaml
|
||||
if: steps.list-changed.outputs.changed == 'true'
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||||
if: ${{ steps.list-changed.outputs.changed == 'true' }}
|
||||
|
||||
10
Dockerfile
10
Dockerfile
@@ -1,7 +1,7 @@
|
||||
FROM maven:3.8-openjdk-17-slim as build-hapi
|
||||
FROM docker.io/library/maven:3.9.2-eclipse-temurin-17 AS build-hapi
|
||||
WORKDIR /tmp/hapi-fhir-jpaserver-starter
|
||||
|
||||
ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.17.0
|
||||
ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.26.0
|
||||
RUN curl -LSsO https://github.com/open-telemetry/opentelemetry-java-instrumentation/releases/download/v${OPENTELEMETRY_JAVA_AGENT_VERSION}/opentelemetry-javaagent.jar
|
||||
|
||||
COPY pom.xml .
|
||||
@@ -18,7 +18,7 @@ RUN mkdir /app && cp /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.
|
||||
|
||||
########### 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
|
||||
FROM bitnami/tomcat:9.0 AS tomcat
|
||||
|
||||
RUN rm -rf /opt/bitnami/tomcat/webapps/ROOT && \
|
||||
mkdir -p /opt/bitnami/hapi/data/hapi/lucenefiles && \
|
||||
@@ -36,7 +36,7 @@ COPY --from=build-hapi --chown=1001:1001 /tmp/hapi-fhir-jpaserver-starter/opente
|
||||
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-debian11:nonroot as default
|
||||
FROM gcr.io/distroless/java17-debian11:nonroot AS default
|
||||
# 65532 is the nonroot user's uid
|
||||
# used here instead of the name to allow Kubernetes to easily detect that the container
|
||||
# is running as a non-root (uid != 0) user.
|
||||
@@ -46,4 +46,4 @@ WORKDIR /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
|
||||
|
||||
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"]
|
||||
|
||||
16
README.md
16
README.md
@@ -235,7 +235,7 @@ Server will then be accessible at http://localhost:8080/ and eg. http://localhos
|
||||
```bash
|
||||
mvn clean package spring-boot:repackage -Pboot && java -jar target/ROOT.war
|
||||
```
|
||||
Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust you overlay configuration in the application.yaml to eg.
|
||||
Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to eg.
|
||||
|
||||
```yaml
|
||||
tester:
|
||||
@@ -250,7 +250,7 @@ Server will then be accessible at http://localhost:8080/ and eg. http://localhos
|
||||
```bash
|
||||
mvn clean package com.google.cloud.tools:jib-maven-plugin:dockerBuild -Dimage=distroless-hapi && docker run -p 8080:8080 distroless-hapi
|
||||
```
|
||||
Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust you overlay configuration in the application.yaml to eg.
|
||||
Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to eg.
|
||||
|
||||
```yaml
|
||||
tester:
|
||||
@@ -266,7 +266,7 @@ Server will then be accessible at http://localhost:8080/ and eg. http://localhos
|
||||
```bash
|
||||
./build-docker-image.sh && docker run -p 8080:8080 hapi-fhir/hapi-fhir-jpaserver-starter:latest
|
||||
```
|
||||
Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust you overlay configuration in the application.yaml to eg.
|
||||
Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to eg.
|
||||
|
||||
```yaml
|
||||
tester:
|
||||
@@ -307,7 +307,7 @@ spring:
|
||||
# Then comment all hibernate.search.backend.*
|
||||
```
|
||||
|
||||
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.
|
||||
Because the integration tests within the project rely on the default H2 database configuration, it is important to either explicitly 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
|
||||
|
||||
@@ -322,14 +322,14 @@ spring:
|
||||
driverClassName: com.microsoft.sqlserver.jdbc.SQLServerDriver
|
||||
```
|
||||
|
||||
Also, make sure you are not setting the Hibernate dialect explicitly, in other words remove any lines similar to:
|
||||
Also, make sure you are not setting the Hibernate dialect explicitly, in other words, remove any lines similar to:
|
||||
|
||||
```
|
||||
hibernate.dialect: {some none Microsoft SQL dialect}
|
||||
```
|
||||
|
||||
|
||||
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.
|
||||
Because the integration tests within the project rely on the default H2 database configuration, it is important to either explicitly 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.
|
||||
@@ -373,7 +373,7 @@ Again, browse to the following link to use the server (note that the port 8080 m
|
||||
|
||||
[http://localhost:8080/](http://localhost:8080/)
|
||||
|
||||
You will then be able access the JPA server e.g. using http://localhost:8080/fhir/metadata.
|
||||
You will then be able to access the JPA server e.g. using http://localhost:8080/fhir/metadata.
|
||||
|
||||
If you would like it to be hosted at eg. hapi-fhir-jpaserver, eg. http://localhost:8080/hapi-fhir-jpaserver/ or http://localhost:8080/hapi-fhir-jpaserver/fhir/metadata - then rename the WAR file to ```hapi-fhir-jpaserver.war``` and adjust the overlay configuration accordingly e.g.
|
||||
|
||||
@@ -390,7 +390,7 @@ If you would like it to be hosted at eg. hapi-fhir-jpaserver, eg. http://localho
|
||||
|
||||
## Deploy with docker compose
|
||||
|
||||
Docker compose is a simple option to build and deploy container. To deploy with docker compose, you should build the project
|
||||
Docker compose is a simple option to build and deploy containers. To deploy with docker compose, you should build the project
|
||||
with `mvn clean install` and then bring up the containers with `docker-compose up -d --build`. The server can be
|
||||
reached at http://localhost:8080/.
|
||||
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
dependencies:
|
||||
- name: postgresql
|
||||
repository: https://charts.bitnami.com/bitnami
|
||||
version: 12.1.2
|
||||
digest: sha256:525689611a29f90b0bc8cd674df5d97024c99eda8104216390f6747904fd0208
|
||||
generated: "2022-11-21T22:55:45.1699395+01:00"
|
||||
repository: oci://registry-1.docker.io/bitnamicharts
|
||||
version: 12.5.6
|
||||
digest: sha256:4d21dbc02bbdb55b957b0093e37376853727de82396abfadfaf1d738bd51b8e6
|
||||
generated: "2023-06-03T20:58:45.922102213+02:00"
|
||||
|
||||
@@ -7,17 +7,21 @@ sources:
|
||||
- https://github.com/hapifhir/hapi-fhir-jpaserver-starter
|
||||
dependencies:
|
||||
- name: postgresql
|
||||
version: 12.1.2
|
||||
repository: https://charts.bitnami.com/bitnami
|
||||
version: 12.5.6
|
||||
repository: oci://registry-1.docker.io/bitnamicharts
|
||||
condition: postgresql.enabled
|
||||
appVersion: 6.2.2
|
||||
version: 0.11.1
|
||||
appVersion: 6.6.0
|
||||
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 v6.2.2
|
||||
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 v7.87.0
|
||||
description: allow disabling the liveness-, readiness-, and startup-probes entirely
|
||||
|
||||
@@ -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.
|
||||
|
||||
@@ -8,11 +8,14 @@ This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes e
|
||||
|
||||
```sh
|
||||
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)
|
||||
> 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)).
|
||||
## Requirements
|
||||
|
||||
| Repository | Name | Version |
|
||||
|------------|------|---------|
|
||||
| oci://registry-1.docker.io/bitnamicharts | postgresql | 12.5.6 |
|
||||
|
||||
## Values
|
||||
|
||||
@@ -27,12 +30,13 @@ helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpas
|
||||
| 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 | `"v6.2.2@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 |
|
||||
| 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 |
|
||||
@@ -40,11 +44,6 @@ helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpas
|
||||
| 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 |
|
||||
@@ -62,11 +61,6 @@ helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpas
|
||||
| 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` | |
|
||||
@@ -79,18 +73,14 @@ helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpas
|
||||
| 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
|
||||
|
||||
@@ -8,18 +8,17 @@ This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes e
|
||||
|
||||
```sh
|
||||
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)
|
||||
> 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.requirementsSection" . }}
|
||||
|
||||
{{ template "chart.valuesSection" . }}
|
||||
|
||||
## 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
17
charts/hapi-fhir-jpaserver/ci/extra-config-values.yaml
Normal file
@@ -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
11
charts/hapi-fhir-jpaserver/templates/application-config.yaml
Normal 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 }}
|
||||
@@ -30,7 +30,7 @@ spec:
|
||||
{{- toYaml .Values.podSecurityContext | nindent 8 }}
|
||||
initContainers:
|
||||
- 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
|
||||
{{- with .Values.restrictedContainerSecurityContext }}
|
||||
securityContext:
|
||||
@@ -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 }}
|
||||
|
||||
@@ -11,20 +11,17 @@ spec:
|
||||
restartPolicy: Never
|
||||
containers:
|
||||
- name: test-metadata-endpoint
|
||||
image: docker.io/curlimages/curl:7.87.0@sha256:f7f265d5c64eb4463a43a99b6bf773f9e61a50aaa7cefaf564f43e42549a01dd
|
||||
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:7.87.0@sha256:f7f265d5c64eb4463a43a99b6bf773f9e61a50aaa7cefaf564f43e42549a01dd
|
||||
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:7.87.0@sha256:f7f265d5c64eb4463a43a99b6bf773f9e61a50aaa7cefaf564f43e42549a01dd
|
||||
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"]
|
||||
|
||||
@@ -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: "v6.2.2@sha256:9c4e8af94d81ac0049dbb589e4cd855bf78c9c13be6f6844e814c63d63545b44"
|
||||
tag: "v6.6.0@sha256:c00367865ae5dad4e171cbb68bfc1c39818854079d1565bee4c86a45e78335d0"
|
||||
# -- image pullPolicy to use
|
||||
pullPolicy: IfNotPresent
|
||||
|
||||
@@ -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
|
||||
|
||||
6
pom.xml
6
pom.xml
@@ -247,6 +247,12 @@
|
||||
</dependency>
|
||||
|
||||
<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
|
||||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-jpaserver-test-utilities</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.eclipse.jetty</groupId>
|
||||
<artifactId>jetty-servlets</artifactId>
|
||||
|
||||
@@ -1,32 +1,32 @@
|
||||
package ca.uhn.fhir.jpa.starter;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Objects;
|
||||
|
||||
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings.ClientIdStrategyEnum;
|
||||
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
|
||||
import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
|
||||
import ca.uhn.fhir.rest.api.EncodingEnum;
|
||||
import org.cqframework.cql.cql2elm.CqlCompilerException;
|
||||
import org.cqframework.cql.cql2elm.CqlTranslator;
|
||||
import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
|
||||
import org.cqframework.cql.cql2elm.LibraryBuilder;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.springframework.boot.context.properties.ConfigurationProperties;
|
||||
import org.springframework.boot.context.properties.EnableConfigurationProperties;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
|
||||
import com.google.common.collect.ImmutableList;
|
||||
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings.ClientIdStrategyEnum;
|
||||
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
|
||||
import ca.uhn.fhir.rest.api.EncodingEnum;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Objects;
|
||||
import java.util.Set;
|
||||
|
||||
@ConfigurationProperties(prefix = "hapi.fhir")
|
||||
@Configuration
|
||||
@EnableConfigurationProperties
|
||||
public class AppProperties {
|
||||
|
||||
private Boolean cr_enabled = false;
|
||||
//cql settings
|
||||
private Boolean cql_use_embedded_libraries = true;
|
||||
private Boolean cql_runtime_debug_logging_enabled = false;
|
||||
@@ -56,7 +56,6 @@ public class AppProperties {
|
||||
// Care-gaps Settings
|
||||
private String caregaps_reporter = "default";
|
||||
private String caregaps_section_author = "default";
|
||||
private Boolean cr_enabled = false;
|
||||
private Boolean ips_enabled = false;
|
||||
private Boolean openapi_enabled = false;
|
||||
private Boolean mdm_enabled = false;
|
||||
@@ -68,6 +67,7 @@ public class AppProperties {
|
||||
private Boolean allow_multiple_delete = false;
|
||||
private Boolean allow_override_default_search_params = true;
|
||||
private Boolean auto_create_placeholder_reference_targets = false;
|
||||
private final Set<String> auto_version_reference_at_paths = new HashSet<>();
|
||||
private Boolean dao_scheduling_enabled = true;
|
||||
private Boolean delete_expunge_enabled = false;
|
||||
private Boolean enable_index_missing_fields = false;
|
||||
@@ -98,17 +98,21 @@ public class AppProperties {
|
||||
private List<String> supported_resource_types = new ArrayList<>();
|
||||
private List<Bundle.BundleType> allowed_bundle_types = null;
|
||||
private Boolean narrative_enabled = true;
|
||||
|
||||
private Validation validation = new Validation();
|
||||
private Map<String, Tester> tester = new HashMap<>();
|
||||
private Map<String, Tester> tester = null;
|
||||
private Logger logger = new Logger();
|
||||
private Subscription subscription = new Subscription();
|
||||
private Cors cors = null;
|
||||
private Partitioning partitioning = null;
|
||||
private Boolean install_transitive_ig_dependencies = true;
|
||||
private Boolean reload_existing_implementationguides = false;
|
||||
private Map<String, ImplementationGuide> implementationGuides = null;
|
||||
private Map<String, PackageInstallationSpec> implementationGuides = null;
|
||||
|
||||
private String staticLocation = null;
|
||||
|
||||
private String staticLocationPrefix = "/static";
|
||||
|
||||
private Boolean lastn_enabled = false;
|
||||
private boolean store_resource_in_lucene_index_enabled = false;
|
||||
private NormalizedQuantitySearchLevel normalized_quantity_search_level = NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED;
|
||||
@@ -118,14 +122,24 @@ public class AppProperties {
|
||||
|
||||
private Integer bundle_batch_pool_size = 20;
|
||||
private Integer bundle_batch_pool_max_size = 100;
|
||||
private final List<String> local_base_urls = new ArrayList<>();
|
||||
private final Set<String> local_base_urls = new HashSet<>();
|
||||
|
||||
private final List<String> custom_interceptor_classes = new ArrayList<>();
|
||||
|
||||
public String getStaticLocationPrefix() {
|
||||
return staticLocationPrefix;
|
||||
}
|
||||
|
||||
public void setStaticLocationPrefix(String staticLocationPrefix) {
|
||||
this.staticLocationPrefix = staticLocationPrefix;
|
||||
}
|
||||
|
||||
|
||||
public List<String> getCustomInterceptorClasses() {
|
||||
return custom_interceptor_classes;
|
||||
}
|
||||
|
||||
|
||||
public String getStaticLocation() {
|
||||
return staticLocation;
|
||||
}
|
||||
@@ -134,6 +148,7 @@ public class AppProperties {
|
||||
this.staticLocation = staticLocation;
|
||||
}
|
||||
|
||||
|
||||
public Boolean getOpenapi_enabled() {
|
||||
return openapi_enabled;
|
||||
}
|
||||
@@ -166,11 +181,11 @@ public class AppProperties {
|
||||
this.defer_indexing_for_codesystems_of_size = defer_indexing_for_codesystems_of_size;
|
||||
}
|
||||
|
||||
public Map<String, ImplementationGuide> getImplementationGuides() {
|
||||
public Map<String, PackageInstallationSpec> getImplementationGuides() {
|
||||
return implementationGuides;
|
||||
}
|
||||
|
||||
public void setImplementationGuides(Map<String, ImplementationGuide> implementationGuides) {
|
||||
public void setImplementationGuides(Map<String, PackageInstallationSpec> implementationGuides) {
|
||||
this.implementationGuides = implementationGuides;
|
||||
}
|
||||
|
||||
@@ -182,6 +197,14 @@ public class AppProperties {
|
||||
this.partitioning = partitioning;
|
||||
}
|
||||
|
||||
public Boolean getCr_enabled() {
|
||||
return cr_enabled;
|
||||
}
|
||||
|
||||
public void setCr_enabled(Boolean cr_enabled) {
|
||||
this.cr_enabled = cr_enabled;
|
||||
}
|
||||
|
||||
public boolean isCqlUseEmbeddedLibraries() {
|
||||
return cql_use_embedded_libraries;
|
||||
}
|
||||
@@ -382,14 +405,6 @@ public class AppProperties {
|
||||
this.cql_compiler_translator_format = cqlTranslatorFormat;
|
||||
}
|
||||
|
||||
|
||||
public Boolean getCr_enabled() {
|
||||
return cr_enabled;
|
||||
}
|
||||
|
||||
public void setCr_enabled(Boolean cr_enabled) {
|
||||
this.cr_enabled = cr_enabled;
|
||||
}
|
||||
public String getCareGapsReporter() {
|
||||
return caregaps_reporter;
|
||||
}
|
||||
@@ -401,6 +416,7 @@ public class AppProperties {
|
||||
public void setCareGapsReporter(String theCareGapsReporter) {
|
||||
this.caregaps_reporter = theCareGapsReporter;
|
||||
}
|
||||
|
||||
public Boolean getIps_enabled() {
|
||||
return ips_enabled;
|
||||
}
|
||||
@@ -409,6 +425,7 @@ public class AppProperties {
|
||||
this.ips_enabled = ips_enabled;
|
||||
}
|
||||
|
||||
|
||||
public Boolean getMdm_enabled() {
|
||||
return mdm_enabled;
|
||||
}
|
||||
@@ -486,7 +503,7 @@ public class AppProperties {
|
||||
}
|
||||
|
||||
public void setClient_id_strategy(
|
||||
ClientIdStrategyEnum client_id_strategy) {
|
||||
ClientIdStrategyEnum client_id_strategy) {
|
||||
this.client_id_strategy = client_id_strategy;
|
||||
}
|
||||
|
||||
@@ -535,7 +552,7 @@ public class AppProperties {
|
||||
}
|
||||
|
||||
public void setAllow_override_default_search_params(
|
||||
Boolean allow_override_default_search_params) {
|
||||
Boolean allow_override_default_search_params) {
|
||||
this.allow_override_default_search_params = allow_override_default_search_params;
|
||||
}
|
||||
|
||||
@@ -544,10 +561,14 @@ public class AppProperties {
|
||||
}
|
||||
|
||||
public void setAuto_create_placeholder_reference_targets(
|
||||
Boolean auto_create_placeholder_reference_targets) {
|
||||
Boolean auto_create_placeholder_reference_targets) {
|
||||
this.auto_create_placeholder_reference_targets = auto_create_placeholder_reference_targets;
|
||||
}
|
||||
|
||||
public Set<String> getAuto_version_reference_at_paths() {
|
||||
return auto_version_reference_at_paths;
|
||||
}
|
||||
|
||||
public Integer getDefault_page_size() {
|
||||
return default_page_size;
|
||||
}
|
||||
@@ -601,7 +622,7 @@ public class AppProperties {
|
||||
}
|
||||
|
||||
public void setEnforce_referential_integrity_on_delete(
|
||||
Boolean enforce_referential_integrity_on_delete) {
|
||||
Boolean enforce_referential_integrity_on_delete) {
|
||||
this.enforce_referential_integrity_on_delete = enforce_referential_integrity_on_delete;
|
||||
}
|
||||
|
||||
@@ -610,7 +631,7 @@ public class AppProperties {
|
||||
}
|
||||
|
||||
public void setEnforce_referential_integrity_on_write(
|
||||
Boolean enforce_referential_integrity_on_write) {
|
||||
Boolean enforce_referential_integrity_on_write) {
|
||||
this.enforce_referential_integrity_on_write = enforce_referential_integrity_on_write;
|
||||
}
|
||||
|
||||
@@ -746,11 +767,13 @@ public class AppProperties {
|
||||
this.tester = tester;
|
||||
}
|
||||
|
||||
public Boolean getNarrative_enabled() {
|
||||
public Boolean getNarrative_enabled()
|
||||
{
|
||||
return narrative_enabled;
|
||||
}
|
||||
|
||||
public void setNarrative_enabled(Boolean narrative_enabled) {
|
||||
public void setNarrative_enabled(Boolean narrative_enabled)
|
||||
{
|
||||
this.narrative_enabled = narrative_enabled;
|
||||
}
|
||||
|
||||
@@ -810,13 +833,13 @@ public class AppProperties {
|
||||
this.bundle_batch_pool_max_size = bundle_batch_pool_max_size;
|
||||
}
|
||||
|
||||
public List<String> getLocal_base_urls() {
|
||||
public Set<String> getLocal_base_urls() {
|
||||
return local_base_urls;
|
||||
}
|
||||
|
||||
public static class Cors {
|
||||
private Boolean allow_Credentials = true;
|
||||
private List<String> allowed_origin = ImmutableList.of("*");
|
||||
private List<String> allowed_origin = List.of("*");
|
||||
|
||||
public List<String> getAllowed_origin() {
|
||||
return allowed_origin;
|
||||
@@ -834,6 +857,7 @@ public class AppProperties {
|
||||
this.allow_Credentials = allow_Credentials;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
public static class Logger {
|
||||
@@ -876,6 +900,7 @@ public class AppProperties {
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public static class Tester {
|
||||
|
||||
private String name;
|
||||
@@ -916,35 +941,6 @@ public class AppProperties {
|
||||
}
|
||||
}
|
||||
|
||||
public static class ImplementationGuide {
|
||||
private String url;
|
||||
private String name;
|
||||
private String version;
|
||||
|
||||
public String getUrl() {
|
||||
return url;
|
||||
}
|
||||
|
||||
public void setUrl(String url) {
|
||||
this.url = url;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
public void setName(String name) {
|
||||
this.name = name;
|
||||
}
|
||||
|
||||
public String getVersion() {
|
||||
return version;
|
||||
}
|
||||
|
||||
public void setVersion(String version) {
|
||||
this.version = version;
|
||||
}
|
||||
}
|
||||
|
||||
public static class Validation {
|
||||
|
||||
@@ -980,7 +976,6 @@ public class AppProperties {
|
||||
public void setPartitioning_include_in_search_hashes(Boolean partitioning_include_in_search_hashes) {
|
||||
this.partitioning_include_in_search_hashes = partitioning_include_in_search_hashes;
|
||||
}
|
||||
|
||||
public Boolean getAllow_references_across_partitions() {
|
||||
return allow_references_across_partitions;
|
||||
}
|
||||
@@ -1020,6 +1015,7 @@ public class AppProperties {
|
||||
this.email = email;
|
||||
}
|
||||
|
||||
|
||||
public static class Email {
|
||||
public String getFrom() {
|
||||
return from;
|
||||
@@ -1112,4 +1108,4 @@ public class AppProperties {
|
||||
public void setEnable_index_of_type(boolean enable_index_of_type) {
|
||||
this.enable_index_of_type = enable_index_of_type;
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -1,6 +1,5 @@
|
||||
package ca.uhn.fhir.jpa.starter;
|
||||
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import org.springframework.core.Ordered;
|
||||
@@ -14,25 +13,37 @@ import java.net.URI;
|
||||
@ConditionalOnProperty(prefix = "hapi.fhir", name = "staticLocation")
|
||||
public class ExtraStaticFilesConfigurer implements WebMvcConfigurer {
|
||||
|
||||
public static final String ROOT_CONTEXT_PATH = "/static";
|
||||
@Autowired
|
||||
AppProperties appProperties;
|
||||
private String staticLocation;
|
||||
private String rootContextPath;
|
||||
|
||||
@Override
|
||||
public ExtraStaticFilesConfigurer(AppProperties appProperties) {
|
||||
|
||||
rootContextPath = appProperties.getStaticLocationPrefix();
|
||||
if(rootContextPath.endsWith("/"))
|
||||
rootContextPath = rootContextPath.substring(0, rootContextPath.lastIndexOf('/'));
|
||||
|
||||
staticLocation = appProperties.getStaticLocation();
|
||||
if(staticLocation.endsWith("/"))
|
||||
staticLocation = staticLocation.substring(0, staticLocation.lastIndexOf('/'));
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public void addResourceHandlers(ResourceHandlerRegistry theRegistry) {
|
||||
theRegistry.addResourceHandler(ROOT_CONTEXT_PATH + "/**").addResourceLocations(appProperties.getStaticLocation());
|
||||
theRegistry.addResourceHandler(rootContextPath + "/**").addResourceLocations(staticLocation);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void addViewControllers(ViewControllerRegistry registry) {
|
||||
String path = URI.create(appProperties.getStaticLocation()).getPath();
|
||||
String path = URI.create(staticLocation).getPath();
|
||||
String lastSegment = path.substring(path.lastIndexOf('/') + 1);
|
||||
|
||||
registry.addViewController(ROOT_CONTEXT_PATH).setViewName("redirect:" + ROOT_CONTEXT_PATH + "/" + lastSegment + "/index.html");
|
||||
registry.addViewController(rootContextPath).setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
|
||||
|
||||
registry.addViewController(ROOT_CONTEXT_PATH + "/*").setViewName("redirect:" + ROOT_CONTEXT_PATH + "/" + lastSegment + "/index.html");
|
||||
registry.addViewController(rootContextPath + "/*").setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
|
||||
|
||||
registry.addViewController(ROOT_CONTEXT_PATH + "/" + lastSegment + "/").setViewName("redirect:" + ROOT_CONTEXT_PATH + "/" + lastSegment + "/index.html");
|
||||
registry.addViewController(rootContextPath + "/" + lastSegment + "/").setViewName("redirect:" + rootContextPath + "/" + lastSegment + "/index.html");
|
||||
|
||||
registry.setOrder(Ordered.HIGHEST_PRECEDENCE);
|
||||
}
|
||||
|
||||
@@ -29,7 +29,6 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
|
||||
import org.springframework.transaction.annotation.EnableTransactionManagement;
|
||||
|
||||
import java.util.HashSet;
|
||||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
/**
|
||||
@@ -41,23 +40,16 @@ public class FhirServerConfigCommon {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
|
||||
|
||||
public FhirServerConfigCommon(AppProperties appProperties) {
|
||||
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");
|
||||
ourLog.info("Server configured to "
|
||||
+ (appProperties.getAuto_create_placeholder_reference_targets() ? "allow" : "disable")
|
||||
+ " auto-creating placeholder references");
|
||||
public FhirServerConfigCommon(AppProperties appProperties) {
|
||||
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");
|
||||
ourLog.info("Server configured to " + (appProperties.getAuto_create_placeholder_reference_targets() ? "allow" : "disable") + " auto-creating placeholder references");
|
||||
ourLog.info("Server configured to auto-version references at paths {}", appProperties.getAuto_version_reference_at_paths());
|
||||
|
||||
if (appProperties.getSubscription().getEmail() != null) {
|
||||
AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
|
||||
@@ -94,23 +86,19 @@ public class FhirServerConfigCommon {
|
||||
public JpaStorageSettings jpaStorageSettings(AppProperties appProperties) {
|
||||
JpaStorageSettings jpaStorageSettings = new JpaStorageSettings();
|
||||
|
||||
jpaStorageSettings.setIndexMissingFields(
|
||||
appProperties.getEnable_index_missing_fields() ? JpaStorageSettings.IndexEnabledEnum.ENABLED
|
||||
: JpaStorageSettings.IndexEnabledEnum.DISABLED);
|
||||
jpaStorageSettings
|
||||
.setAutoCreatePlaceholderReferenceTargets(appProperties.getAuto_create_placeholder_reference_targets());
|
||||
jpaStorageSettings
|
||||
.setEnforceReferentialIntegrityOnWrite(appProperties.getEnforce_referential_integrity_on_write());
|
||||
jpaStorageSettings
|
||||
.setEnforceReferentialIntegrityOnDelete(appProperties.getEnforce_referential_integrity_on_delete());
|
||||
jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
|
||||
jpaStorageSettings.setAllowMultipleDelete(appProperties.getAllow_multiple_delete());
|
||||
jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
|
||||
jpaStorageSettings.setSchedulingDisabled(!appProperties.getDao_scheduling_enabled());
|
||||
jpaStorageSettings.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
|
||||
jpaStorageSettings.setExpungeEnabled(appProperties.getExpunge_enabled());
|
||||
if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
|
||||
jpaStorageSettings.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
|
||||
jpaStorageSettings.setIndexMissingFields(appProperties.getEnable_index_missing_fields() ? StorageSettings.IndexEnabledEnum.ENABLED : StorageSettings.IndexEnabledEnum.DISABLED);
|
||||
jpaStorageSettings.setAutoCreatePlaceholderReferenceTargets(appProperties.getAuto_create_placeholder_reference_targets());
|
||||
jpaStorageSettings.setAutoVersionReferenceAtPaths(appProperties.getAuto_version_reference_at_paths());
|
||||
jpaStorageSettings.setEnforceReferentialIntegrityOnWrite(appProperties.getEnforce_referential_integrity_on_write());
|
||||
jpaStorageSettings.setEnforceReferentialIntegrityOnDelete(appProperties.getEnforce_referential_integrity_on_delete());
|
||||
jpaStorageSettings.setAllowContainsSearches(appProperties.getAllow_contains_searches());
|
||||
jpaStorageSettings.setAllowMultipleDelete(appProperties.getAllow_multiple_delete());
|
||||
jpaStorageSettings.setAllowExternalReferences(appProperties.getAllow_external_references());
|
||||
jpaStorageSettings.setSchedulingDisabled(!appProperties.getDao_scheduling_enabled());
|
||||
jpaStorageSettings.setDeleteExpungeEnabled(appProperties.getDelete_expunge_enabled());
|
||||
jpaStorageSettings.setExpungeEnabled(appProperties.getExpunge_enabled());
|
||||
if(appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null)
|
||||
jpaStorageSettings.setEmailFromAddress(appProperties.getSubscription().getEmail().getFrom());
|
||||
|
||||
Integer maxFetchSize = appProperties.getMax_page_size();
|
||||
jpaStorageSettings.setFetchSizeDefaultMaximum(maxFetchSize);
|
||||
@@ -143,13 +131,13 @@ public class FhirServerConfigCommon {
|
||||
}
|
||||
}
|
||||
|
||||
jpaStorageSettings.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
|
||||
jpaStorageSettings.setAdvancedHSearchIndexing(appProperties.getAdvanced_lucene_indexing());
|
||||
jpaStorageSettings.setTreatBaseUrlsAsLocal(new HashSet<>(appProperties.getLocal_base_urls()));
|
||||
jpaStorageSettings.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
|
||||
jpaStorageSettings.setAdvancedHSearchIndexing(appProperties.getAdvanced_lucene_indexing());
|
||||
jpaStorageSettings.setTreatBaseUrlsAsLocal(new HashSet<>(appProperties.getLocal_base_urls()));
|
||||
|
||||
if (appProperties.getLastn_enabled()) {
|
||||
jpaStorageSettings.setLastNEnabled(true);
|
||||
}
|
||||
if (appProperties.getLastn_enabled()) {
|
||||
jpaStorageSettings.setLastNEnabled(true);
|
||||
}
|
||||
|
||||
if (appProperties.getInline_resource_storage_below_size() != 0) {
|
||||
jpaStorageSettings.setInlineResourceTextBelowSize(appProperties.getInline_resource_storage_below_size());
|
||||
|
||||
@@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
|
||||
import ca.uhn.fhir.to.FhirTesterMvcConfig;
|
||||
import ca.uhn.fhir.to.TesterConfig;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Conditional;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import org.springframework.context.annotation.Import;
|
||||
|
||||
@@ -18,6 +19,7 @@ import org.springframework.context.annotation.Import;
|
||||
*/
|
||||
@Configuration
|
||||
@Import(FhirTesterMvcConfig.class)
|
||||
@Conditional(FhirTesterConfigCondition.class)
|
||||
public class FhirTesterConfig {
|
||||
|
||||
/**
|
||||
@@ -26,7 +28,7 @@ public class FhirTesterConfig {
|
||||
* server, as well as one public server. If you are creating a project to
|
||||
* deploy somewhere else, you might choose to only put your own server's
|
||||
* address here.
|
||||
*
|
||||
* <p>
|
||||
* Note the use of the ${serverBase} variable below. This will be replaced with
|
||||
* the base URL as reported by the server itself. Often for a simple Tomcat
|
||||
* (or other container) installation, this will end up being something
|
||||
|
||||
@@ -0,0 +1,16 @@
|
||||
package ca.uhn.fhir.jpa.starter.common;
|
||||
|
||||
import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
|
||||
import org.springframework.context.annotation.Condition;
|
||||
import org.springframework.context.annotation.ConditionContext;
|
||||
import org.springframework.core.env.ConfigurableEnvironment;
|
||||
import org.springframework.core.type.AnnotatedTypeMetadata;
|
||||
|
||||
public class FhirTesterConfigCondition implements Condition {
|
||||
@Override
|
||||
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
|
||||
|
||||
var properties = EnvironmentHelper.getPropertiesStartingWith((ConfigurableEnvironment) conditionContext.getEnvironment(), "hapi.fhir.tester");
|
||||
return !properties.isEmpty();
|
||||
}
|
||||
}
|
||||
@@ -1,7 +1,6 @@
|
||||
package ca.uhn.fhir.jpa.starter.common;
|
||||
|
||||
import ca.uhn.fhir.batch2.coordinator.JobDefinitionRegistry;
|
||||
import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
|
||||
import ca.uhn.fhir.batch2.jobs.imprt.BulkDataImportProvider;
|
||||
import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
|
||||
import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
|
||||
@@ -10,6 +9,7 @@ import ca.uhn.fhir.context.ConfigurationException;
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.FhirVersionEnum;
|
||||
import ca.uhn.fhir.context.support.IValidationSupport;
|
||||
|
||||
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
|
||||
import ca.uhn.fhir.jpa.api.IDaoRegistry;
|
||||
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
|
||||
@@ -18,6 +18,7 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
|
||||
import ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor;
|
||||
import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
|
||||
import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
|
||||
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
|
||||
import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
|
||||
import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
|
||||
@@ -60,7 +61,6 @@ import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
|
||||
import ca.uhn.fhir.validation.IValidatorModule;
|
||||
import ca.uhn.fhir.validation.ResultSeverityEnum;
|
||||
import com.google.common.base.Strings;
|
||||
import com.google.common.collect.ImmutableList;
|
||||
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
|
||||
import org.springframework.beans.factory.NoSuchBeanDefinitionException;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
@@ -73,26 +73,23 @@ import org.springframework.http.HttpHeaders;
|
||||
import org.springframework.orm.jpa.JpaTransactionManager;
|
||||
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
|
||||
import org.springframework.web.cors.CorsConfiguration;
|
||||
|
||||
import javax.persistence.EntityManagerFactory;
|
||||
import javax.sql.DataSource;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
import static ca.uhn.fhir.context.FhirVersionEnum.DSTU3;
|
||||
import static ca.uhn.fhir.context.FhirVersionEnum.R4;
|
||||
import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
|
||||
|
||||
@Configuration
|
||||
// allow users to configure custom packages to scan for additional beans
|
||||
//allow users to configure custom packages to scan for additional beans
|
||||
@ComponentScan(basePackages = { "${hapi.fhir.custom-bean-packages:}" })
|
||||
@Import({ ThreadPoolFactoryConfig.class })
|
||||
@Import(
|
||||
ThreadPoolFactoryConfig.class
|
||||
)
|
||||
public class StarterJpaConfig {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(StarterJpaConfig.class);
|
||||
|
||||
public StarterJpaConfig() {
|
||||
}
|
||||
|
||||
@Bean
|
||||
public IFulltextSearchSvc fullTextSearchSvc() {
|
||||
return new FulltextSearchSvcImpl();
|
||||
@@ -109,12 +106,14 @@ public class StarterJpaConfig {
|
||||
return ValidationSupportConfigUtil.newCachingValidationSupport(theJpaValidationSupportChain);
|
||||
}
|
||||
|
||||
|
||||
@Autowired
|
||||
private ConfigurableEnvironment configurableEnvironment;
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Customize the default/max page sizes for search results. You can set these
|
||||
* however
|
||||
* Customize the default/max page sizes for search results. You can set these however
|
||||
* you want, although very large page sizes will require a lot of RAM.
|
||||
*/
|
||||
@Bean
|
||||
@@ -125,6 +124,7 @@ public class StarterJpaConfig {
|
||||
return pagingProvider;
|
||||
}
|
||||
|
||||
|
||||
@Bean
|
||||
public IResourceSupportedSvc resourceSupportedSvc(IDaoRegistry theDaoRegistry) {
|
||||
return new DaoRegistryResourceSupportedSvc(theDaoRegistry);
|
||||
@@ -137,10 +137,8 @@ public class StarterJpaConfig {
|
||||
|
||||
@Primary
|
||||
@Bean
|
||||
public LocalContainerEntityManagerFactoryBean entityManagerFactory(DataSource myDataSource,
|
||||
ConfigurableListableBeanFactory myConfigurableListableBeanFactory, FhirContext theFhirContext) {
|
||||
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil
|
||||
.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
|
||||
public LocalContainerEntityManagerFactoryBean entityManagerFactory(DataSource myDataSource, ConfigurableListableBeanFactory myConfigurableListableBeanFactory, FhirContext theFhirContext) {
|
||||
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
|
||||
retVal.setPersistenceUnitName("HAPI_PU");
|
||||
|
||||
try {
|
||||
@@ -148,8 +146,7 @@ public class StarterJpaConfig {
|
||||
} catch (Exception e) {
|
||||
throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
|
||||
}
|
||||
retVal.setJpaProperties(
|
||||
EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
|
||||
retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@@ -166,10 +163,10 @@ public class StarterJpaConfig {
|
||||
return new HSearchSortHelperImpl(mySearchParamRegistry);
|
||||
}
|
||||
|
||||
|
||||
@Bean
|
||||
@ConditionalOnProperty(prefix = "hapi.fhir", name = ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR, havingValue = "true")
|
||||
public RepositoryValidatingInterceptor repositoryValidatingInterceptor(
|
||||
IRepositoryValidationInterceptorFactory factory) {
|
||||
public RepositoryValidatingInterceptor repositoryValidatingInterceptor(IRepositoryValidationInterceptorFactory factory) {
|
||||
return factory.buildUsingStoredStructureDefinitions();
|
||||
}
|
||||
|
||||
@@ -191,23 +188,20 @@ public class StarterJpaConfig {
|
||||
@Bean("packageInstaller")
|
||||
@Primary
|
||||
@Conditional(OnImplementationGuidesPresent.class)
|
||||
public IPackageInstallerSvc packageInstaller(AppProperties appProperties,
|
||||
JobDefinition<ReindexJobParameters> reindexJobParametersJobDefinition,
|
||||
JobDefinitionRegistry jobDefinitionRegistry, IPackageInstallerSvc packageInstallerSvc) {
|
||||
public IPackageInstallerSvc packageInstaller(AppProperties appProperties, JobDefinition<ReindexJobParameters> reindexJobParametersJobDefinition, JobDefinitionRegistry jobDefinitionRegistry, IPackageInstallerSvc packageInstallerSvc)
|
||||
{
|
||||
jobDefinitionRegistry.addJobDefinitionIfNotRegistered(reindexJobParametersJobDefinition);
|
||||
|
||||
if (appProperties.getImplementationGuides() != null) {
|
||||
Map<String, AppProperties.ImplementationGuide> guides = appProperties.getImplementationGuides();
|
||||
for (Map.Entry<String, AppProperties.ImplementationGuide> guide : guides.entrySet()) {
|
||||
PackageInstallationSpec packageInstallationSpec = new PackageInstallationSpec()
|
||||
.setPackageUrl(guide.getValue().getUrl()).setName(guide.getValue().getName())
|
||||
.setVersion(guide.getValue().getVersion())
|
||||
.setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
|
||||
packageInstallationSpec.setReloadExisting(appProperties.getReload_existing_implementationguides());
|
||||
Map<String, PackageInstallationSpec> guides = appProperties.getImplementationGuides();
|
||||
for (Map.Entry<String, PackageInstallationSpec> guidesEntry : guides.entrySet()) {
|
||||
PackageInstallationSpec packageInstallationSpec = guidesEntry.getValue();
|
||||
if (appProperties.getInstall_transitive_ig_dependencies()) {
|
||||
packageInstallationSpec.setFetchDependencies(true);
|
||||
packageInstallationSpec.setDependencyExcludes(
|
||||
ImmutableList.of("hl7.fhir.r2.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core", "hl7.fhir.r5.core"));
|
||||
|
||||
packageInstallationSpec.addDependencyExclude("hl7.fhir.r2.core")
|
||||
.addDependencyExclude("hl7.fhir.r3.core")
|
||||
.addDependencyExclude("hl7.fhir.r4.core")
|
||||
.addDependencyExclude("hl7.fhir.r5.core");
|
||||
}
|
||||
packageInstallerSvc.install(packageInstallationSpec);
|
||||
}
|
||||
@@ -247,24 +241,7 @@ public class StarterJpaConfig {
|
||||
}
|
||||
|
||||
@Bean
|
||||
public RestfulServer restfulServer(IFhirSystemDao<?, ?> fhirSystemDao, AppProperties appProperties,
|
||||
DaoRegistry daoRegistry,
|
||||
Optional<MdmProviderLoader> mdmProviderProvider, IJpaSystemProvider jpaSystemProvider,
|
||||
ResourceProviderFactory resourceProviderFactory, JpaStorageSettings jpaStorageSettings,
|
||||
ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport,
|
||||
DatabaseBackedPagingProvider databaseBackedPagingProvider, LoggingInterceptor loggingInterceptor,
|
||||
Optional<TerminologyUploaderProvider> terminologyUploaderProvider,
|
||||
Optional<SubscriptionTriggeringProvider> subscriptionTriggeringProvider,
|
||||
Optional<CorsInterceptor> corsInterceptor, IInterceptorBroadcaster interceptorBroadcaster,
|
||||
Optional<BinaryAccessProvider> binaryAccessProvider, BinaryStorageInterceptor binaryStorageInterceptor,
|
||||
IValidatorModule validatorModule, Optional<GraphQLProvider> graphQLProvider,
|
||||
BulkDataExportProvider bulkDataExportProvider, BulkDataImportProvider bulkDataImportProvider,
|
||||
ValueSetOperationProvider theValueSetOperationProvider, ReindexProvider reindexProvider,
|
||||
PartitionManagementProvider partitionManagementProvider,
|
||||
Optional<RepositoryValidatingInterceptor> repositoryValidatingInterceptor,
|
||||
IPackageInstallerSvc packageInstallerSvc, ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc,
|
||||
ApplicationContext appContext,
|
||||
Optional<IpsOperationProvider> theIpsOperationProvider) {
|
||||
public RestfulServer restfulServer(IFhirSystemDao<?, ?> fhirSystemDao, AppProperties appProperties, DaoRegistry daoRegistry, Optional<MdmProviderLoader> mdmProviderProvider, IJpaSystemProvider jpaSystemProvider, ResourceProviderFactory resourceProviderFactory, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport, DatabaseBackedPagingProvider databaseBackedPagingProvider, LoggingInterceptor loggingInterceptor, Optional<TerminologyUploaderProvider> terminologyUploaderProvider, Optional<SubscriptionTriggeringProvider> subscriptionTriggeringProvider, Optional<CorsInterceptor> corsInterceptor, IInterceptorBroadcaster interceptorBroadcaster, Optional<BinaryAccessProvider> binaryAccessProvider, BinaryStorageInterceptor binaryStorageInterceptor, IValidatorModule validatorModule, Optional<GraphQLProvider> graphQLProvider, BulkDataExportProvider bulkDataExportProvider, BulkDataImportProvider bulkDataImportProvider, ValueSetOperationProvider theValueSetOperationProvider, ReindexProvider reindexProvider, PartitionManagementProvider partitionManagementProvider, Optional<RepositoryValidatingInterceptor> repositoryValidatingInterceptor, IPackageInstallerSvc packageInstallerSvc, ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc, ApplicationContext appContext, Optional<IpsOperationProvider> theIpsOperationProvider) {
|
||||
RestfulServer fhirServer = new RestfulServer(fhirSystemDao.getContext());
|
||||
|
||||
List<String> supportedResourceTypes = appProperties.getSupported_resource_types();
|
||||
@@ -282,21 +259,18 @@ public class StarterJpaConfig {
|
||||
fhirSystemDao.getContext().setNarrativeGenerator(new NullNarrativeGenerator());
|
||||
}
|
||||
|
||||
if (appProperties.getMdm_enabled()) {
|
||||
mdmProviderProvider.get().loadProvider();
|
||||
}
|
||||
if (appProperties.getMdm_enabled()) mdmProviderProvider.get().loadProvider();
|
||||
|
||||
fhirServer.registerProviders(resourceProviderFactory.createProviders());
|
||||
fhirServer.registerProvider(jpaSystemProvider);
|
||||
fhirServer.setServerConformanceProvider(calculateConformanceProvider(fhirSystemDao, fhirServer,
|
||||
jpaStorageSettings, searchParamRegistry, theValidationSupport));
|
||||
fhirServer.setServerConformanceProvider(calculateConformanceProvider(fhirSystemDao, fhirServer, jpaStorageSettings, searchParamRegistry, theValidationSupport));
|
||||
|
||||
/*
|
||||
* ETag Support
|
||||
*/
|
||||
|
||||
if (!appProperties.getEtag_support_enabled())
|
||||
fhirServer.setETagSupport(ETagSupportEnum.DISABLED);
|
||||
if (!appProperties.getEtag_support_enabled()) fhirServer.setETagSupport(ETagSupportEnum.DISABLED);
|
||||
|
||||
|
||||
/*
|
||||
* Default to JSON and pretty printing
|
||||
@@ -333,8 +307,7 @@ public class StarterJpaConfig {
|
||||
/*
|
||||
* If you are hosting this server at a specific DNS name, the server will try to
|
||||
* figure out the FHIR base URL based on what the web container tells it, but
|
||||
* this doesn't always work. If you are setting links in your search bundles
|
||||
* that
|
||||
* this doesn't always work. If you are setting links in your search bundles that
|
||||
* just refer to "localhost", you might want to use a server address strategy:
|
||||
*/
|
||||
String serverAddress = appProperties.getServer_address();
|
||||
@@ -342,24 +315,19 @@ public class StarterJpaConfig {
|
||||
fhirServer.setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
|
||||
} else if (appProperties.getUse_apache_address_strategy()) {
|
||||
boolean useHttps = appProperties.getUse_apache_address_strategy_https();
|
||||
fhirServer.setServerAddressStrategy(
|
||||
useHttps ? ApacheProxyAddressStrategy.forHttps() : ApacheProxyAddressStrategy.forHttp());
|
||||
fhirServer.setServerAddressStrategy(useHttps ? ApacheProxyAddressStrategy.forHttps() : ApacheProxyAddressStrategy.forHttp());
|
||||
} else {
|
||||
fhirServer.setServerAddressStrategy(new IncomingRequestAddressStrategy());
|
||||
}
|
||||
|
||||
/*
|
||||
* If you are using DSTU3+, you may want to add a terminology uploader, which
|
||||
* allows
|
||||
* uploading of external terminologies such as Snomed CT. Note that this
|
||||
* uploader
|
||||
* does not have any security attached (any anonymous user may use it by
|
||||
* default)
|
||||
* so it is a potential security vulnerability. Consider using an
|
||||
* AuthorizationInterceptor
|
||||
* If you are using DSTU3+, you may want to add a terminology uploader, which allows
|
||||
* uploading of external terminologies such as Snomed CT. Note that this uploader
|
||||
* does not have any security attached (any anonymous user may use it by default)
|
||||
* so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
|
||||
* with this feature.
|
||||
*/
|
||||
if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(DSTU3)) { // <-- ENABLED RIGHT NOW
|
||||
if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) { // <-- ENABLED RIGHT NOW
|
||||
fhirServer.registerProvider(terminologyUploaderProvider.get());
|
||||
}
|
||||
|
||||
@@ -377,8 +345,7 @@ public class StarterJpaConfig {
|
||||
}
|
||||
|
||||
if (appProperties.getAllow_cascading_deletes()) {
|
||||
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(
|
||||
fhirSystemDao.getContext(), daoRegistry, interceptorBroadcaster, theThreadSafeResourceDeleterSvc);
|
||||
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(fhirSystemDao.getContext(), daoRegistry, interceptorBroadcaster, theThreadSafeResourceDeleterSvc);
|
||||
fhirServer.registerInterceptor(cascadingDeleteInterceptor);
|
||||
}
|
||||
|
||||
@@ -407,7 +374,7 @@ public class StarterJpaConfig {
|
||||
|
||||
// GraphQL
|
||||
if (appProperties.getGraphql_enabled()) {
|
||||
if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(DSTU3)) {
|
||||
if (fhirSystemDao.getContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
|
||||
fhirServer.registerProvider(graphQLProvider.get());
|
||||
}
|
||||
}
|
||||
@@ -421,15 +388,16 @@ public class StarterJpaConfig {
|
||||
fhirServer.registerProvider(bulkDataExportProvider);
|
||||
}
|
||||
|
||||
// Bulk Import
|
||||
//Bulk Import
|
||||
if (appProperties.getBulk_import_enabled()) {
|
||||
fhirServer.registerProvider(bulkDataImportProvider);
|
||||
}
|
||||
|
||||
|
||||
// valueSet Operations i.e $expand
|
||||
fhirServer.registerProvider(theValueSetOperationProvider);
|
||||
|
||||
// reindex Provider $reindex
|
||||
//reindex Provider $reindex
|
||||
fhirServer.registerProvider(reindexProvider);
|
||||
|
||||
// Partitioning
|
||||
@@ -443,7 +411,8 @@ public class StarterJpaConfig {
|
||||
// register custom interceptors
|
||||
registerCustomInterceptors(fhirServer, appContext, appProperties.getCustomInterceptorClasses());
|
||||
|
||||
// register the IPS Provider
|
||||
|
||||
//register the IPS Provider
|
||||
if (!theIpsOperationProvider.isEmpty()) {
|
||||
fhirServer.registerProvider(theIpsOperationProvider.get());
|
||||
}
|
||||
@@ -455,8 +424,7 @@ public class StarterJpaConfig {
|
||||
* check the properties for custom interceptor classes and registers them.
|
||||
*/
|
||||
@SuppressWarnings({ "unchecked", "rawtypes" })
|
||||
private void registerCustomInterceptors(RestfulServer fhirServer, ApplicationContext theAppContext,
|
||||
List<String> customInterceptorClasses) {
|
||||
private void registerCustomInterceptors(RestfulServer fhirServer, ApplicationContext theAppContext, List<String> customInterceptorClasses) {
|
||||
|
||||
if (customInterceptorClasses == null) {
|
||||
return;
|
||||
@@ -490,37 +458,30 @@ public class StarterJpaConfig {
|
||||
}
|
||||
}
|
||||
|
||||
public static IServerConformanceProvider<?> calculateConformanceProvider(IFhirSystemDao fhirSystemDao,
|
||||
RestfulServer fhirServer, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry,
|
||||
IValidationSupport theValidationSupport) {
|
||||
public static IServerConformanceProvider<?> calculateConformanceProvider(IFhirSystemDao fhirSystemDao, RestfulServer fhirServer, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport) {
|
||||
FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
|
||||
if (fhirVersion == FhirVersionEnum.DSTU2) {
|
||||
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(fhirServer, fhirSystemDao,
|
||||
jpaStorageSettings);
|
||||
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(fhirServer, fhirSystemDao, jpaStorageSettings);
|
||||
confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
|
||||
return confProvider;
|
||||
} else if (fhirVersion == DSTU3) {
|
||||
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
|
||||
|
||||
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(fhirServer, fhirSystemDao,
|
||||
jpaStorageSettings, searchParamRegistry);
|
||||
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry);
|
||||
confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
|
||||
return confProvider;
|
||||
} else if (fhirVersion == R4) {
|
||||
} else if (fhirVersion == FhirVersionEnum.R4) {
|
||||
|
||||
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao,
|
||||
jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
||||
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
||||
confProvider.setImplementationDescription("HAPI FHIR R4 Server");
|
||||
return confProvider;
|
||||
} else if (fhirVersion == FhirVersionEnum.R4B) {
|
||||
|
||||
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao,
|
||||
jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
||||
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
||||
confProvider.setImplementationDescription("HAPI FHIR R4B Server");
|
||||
return confProvider;
|
||||
} else if (fhirVersion == FhirVersionEnum.R5) {
|
||||
|
||||
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao,
|
||||
jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
||||
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, jpaStorageSettings, searchParamRegistry, theValidationSupport);
|
||||
confProvider.setImplementationDescription("HAPI FHIR R5 Server");
|
||||
return confProvider;
|
||||
} else {
|
||||
|
||||
@@ -47,12 +47,12 @@ public class RepositoryValidationInterceptorFactoryDstu3 implements IRepositoryV
|
||||
public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
|
||||
|
||||
IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
|
||||
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size())
|
||||
Map<String, List<StructureDefinition>> structureDefinitions = results.getResources(0, results.size())
|
||||
.stream()
|
||||
.map(StructureDefinition.class::cast)
|
||||
.collect(Collectors.groupingBy(StructureDefinition::getType));
|
||||
|
||||
structureDefintions.forEach((key, value) -> {
|
||||
structureDefinitions.forEach((key, value) -> {
|
||||
String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
|
||||
repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
|
||||
});
|
||||
|
||||
@@ -1,14 +1,16 @@
|
||||
package ca.uhn.fhir.jpa.starter.cr;
|
||||
|
||||
import ca.uhn.fhir.cr.config.r4.CrR4Config;
|
||||
import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
|
||||
import org.springframework.context.annotation.Conditional;
|
||||
import org.springframework.context.annotation.Import;
|
||||
|
||||
import ca.uhn.fhir.cr.common.CqlThreadFactory;
|
||||
import ca.uhn.fhir.cr.config.ApplyOperationConfig;
|
||||
import ca.uhn.fhir.cr.config.ExtractOperationConfig;
|
||||
import ca.uhn.fhir.cr.config.PackageOperationConfig;
|
||||
import ca.uhn.fhir.cr.config.PopulateOperationConfig;
|
||||
import ca.uhn.fhir.cr.config.r4.CrR4Config;
|
||||
import ca.uhn.fhir.jpa.starter.AppProperties;
|
||||
import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
|
||||
import org.cqframework.cql.cql2elm.CqlCompilerOptions;
|
||||
import org.cqframework.cql.cql2elm.model.CompiledLibrary;
|
||||
import org.cqframework.cql.cql2elm.model.Model;
|
||||
@@ -29,7 +31,6 @@ import java.util.Map;
|
||||
import java.util.Set;
|
||||
import java.util.concurrent.ExecutorService;
|
||||
import java.util.concurrent.Executors;
|
||||
import java.util.function.Function;
|
||||
|
||||
@Configuration
|
||||
@Conditional({ OnR4Condition.class, CrConfigCondition.class })
|
||||
|
||||
@@ -15,18 +15,18 @@ import ca.uhn.fhir.jpa.ips.generator.IpsGeneratorSvcImpl;
|
||||
@Conditional(IpsConfigCondition.class)
|
||||
public class StarterIpsConfig {
|
||||
@Bean
|
||||
IIpsGenerationStrategy IpsGenerationStrategy()
|
||||
IIpsGenerationStrategy ipsGenerationStrategy()
|
||||
{
|
||||
return new DefaultIpsGenerationStrategy();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public IpsOperationProvider IpsOperationProvider(IIpsGeneratorSvc theIpsGeneratorSvc){
|
||||
public IpsOperationProvider ipsOperationProvider(IIpsGeneratorSvc theIpsGeneratorSvc){
|
||||
return new IpsOperationProvider(theIpsGeneratorSvc);
|
||||
}
|
||||
|
||||
@Bean
|
||||
public IIpsGeneratorSvc IpsGeneratorSvcImpl(FhirContext theFhirContext, IIpsGenerationStrategy theGenerationStrategy, DaoRegistry theDaoRegistry)
|
||||
public IIpsGeneratorSvc ipsGeneratorSvcImpl(FhirContext theFhirContext, IIpsGenerationStrategy theGenerationStrategy, DaoRegistry theDaoRegistry)
|
||||
{
|
||||
return new IpsGeneratorSvcImpl(theFhirContext, theGenerationStrategy, theDaoRegistry);
|
||||
}
|
||||
|
||||
@@ -6,7 +6,6 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
|
||||
import ca.uhn.fhir.mdm.api.IMdmSettings;
|
||||
import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
|
||||
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
|
||||
import com.google.common.base.Charsets;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
@@ -17,6 +16,7 @@ import org.springframework.core.io.DefaultResourceLoader;
|
||||
import org.springframework.core.io.Resource;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
|
||||
@Configuration
|
||||
@Conditional(MdmConfigCondition.class)
|
||||
@@ -27,7 +27,7 @@ public class MdmConfig {
|
||||
IMdmSettings mdmSettings(@Autowired MdmRuleValidator theMdmRuleValidator, AppProperties appProperties) throws IOException {
|
||||
DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
|
||||
Resource resource = resourceLoader.getResource("mdm-rules.json");
|
||||
String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
|
||||
String json = IOUtils.toString(resource.getInputStream(), StandardCharsets.UTF_8);
|
||||
return new MdmSettings(theMdmRuleValidator).setEnabled(appProperties.getMdm_enabled()).setScriptText(json);
|
||||
}
|
||||
}
|
||||
|
||||
@@ -17,7 +17,6 @@ import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
|
||||
import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
|
||||
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
|
||||
import org.springframework.boot.orm.jpa.hibernate.SpringImplicitNamingStrategy;
|
||||
import org.springframework.boot.orm.jpa.hibernate.SpringPhysicalNamingStrategy;
|
||||
import org.springframework.core.env.CompositePropertySource;
|
||||
import org.springframework.core.env.ConfigurableEnvironment;
|
||||
import org.springframework.core.env.EnumerablePropertySource;
|
||||
|
||||
@@ -68,7 +68,8 @@ hapi:
|
||||
### forces the use of the https:// protocol for the returned server address.
|
||||
### alternatively, it may be set using the X-Forwarded-Proto header.
|
||||
# use_apache_address_strategy_https: false
|
||||
### enables the server to host content like HTML, css, etc. under the url pattern of /static/**
|
||||
### enables the server to host content like HTML, css, etc. under the url pattern of eg. /static/**
|
||||
# staticLocationPrefix: /static
|
||||
### the deepest folder level will be used. E.g. - if you put file:/foo/bar/bazz as value then the files are resolved under /static/bazz/**
|
||||
#staticLocation: file:/foo/bar/bazz
|
||||
### enable to set the Server URL
|
||||
@@ -77,14 +78,15 @@ hapi:
|
||||
# install_transitive_ig_dependencies: true
|
||||
### tells the server whether to attempt to load IG resources that are already present
|
||||
# reload_existing_implementationGuides : false
|
||||
# implementationguides:
|
||||
#implementationguides:
|
||||
### example from registry (packages.fhir.org)
|
||||
# swiss:
|
||||
# name: swiss.mednet.fhir
|
||||
# version: 0.8.0
|
||||
# swiss:
|
||||
# name: swiss.mednet.fhir
|
||||
# version: 0.8.0
|
||||
# reloadExisting : false
|
||||
# example not from registry
|
||||
# ips_1_0_0:
|
||||
# url: https://build.fhir.org/ig/HL7/fhir-ips/package.tgz
|
||||
# packageUrl: https://build.fhir.org/ig/HL7/fhir-ips/package.tgz
|
||||
# name: hl7.fhir.uv.ips
|
||||
# version: 1.0.0
|
||||
# supported_resource_types:
|
||||
@@ -100,6 +102,8 @@ hapi:
|
||||
# allow_multiple_delete: true
|
||||
# allow_override_default_search_params: true
|
||||
# auto_create_placeholder_reference_targets: false
|
||||
### tells the server to automatically append the current version of the target resource to references at these paths
|
||||
# auto_version_reference_at_paths: Device.patient, Device.location, Device.parent, DeviceMetric.parent, DeviceMetric.source, Observation.device, Observation.subject
|
||||
# cr_enabled: true
|
||||
# ips_enabled: false
|
||||
# default_encoding: JSON
|
||||
|
||||
@@ -15,7 +15,7 @@ import org.springframework.boot.test.context.SpringBootTest;
|
||||
"hapi.fhir.subscription.websocket_enabled=false",
|
||||
"spring.main.allow-bean-definition-overriding=true"
|
||||
})
|
||||
public class CustomBeanTest {
|
||||
class CustomBeanTest {
|
||||
|
||||
@Autowired
|
||||
some.custom.pkg1.CustomBean customBean1;
|
||||
|
||||
@@ -22,7 +22,7 @@ import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
|
||||
"hapi.fhir.fhir_version=r4"
|
||||
})
|
||||
|
||||
public class CustomInterceptorTest {
|
||||
class CustomInterceptorTest {
|
||||
|
||||
@LocalServerPort
|
||||
private int port;
|
||||
|
||||
@@ -3,16 +3,23 @@ package ca.uhn.fhir.jpa.starter;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchRestClientFactory;
|
||||
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
|
||||
import ca.uhn.fhir.jpa.test.config.TestElasticsearchContainerHelper;
|
||||
import ca.uhn.fhir.rest.client.api.IGenericClient;
|
||||
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
|
||||
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
|
||||
import java.io.IOException;
|
||||
import java.time.Duration;
|
||||
import java.time.temporal.ChronoUnit;
|
||||
|
||||
import java.util.Date;
|
||||
import java.util.GregorianCalendar;
|
||||
import java.util.List;
|
||||
import javax.annotation.PreDestroy;
|
||||
|
||||
import org.elasticsearch.client.RequestOptions;
|
||||
import org.elasticsearch.client.RestHighLevelClient;
|
||||
import org.elasticsearch.client.indices.PutIndexTemplateRequest;
|
||||
import org.elasticsearch.common.settings.Settings;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.hl7.fhir.r4.model.DateTimeType;
|
||||
@@ -34,8 +41,11 @@ import org.springframework.context.ConfigurableApplicationContext;
|
||||
import org.springframework.test.context.ContextConfiguration;
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension;
|
||||
import org.testcontainers.elasticsearch.ElasticsearchContainer;
|
||||
import org.testcontainers.junit.jupiter.Container;
|
||||
import org.testcontainers.junit.jupiter.Testcontainers;
|
||||
|
||||
@ExtendWith(SpringExtension.class)
|
||||
@Testcontainers
|
||||
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties =
|
||||
{
|
||||
"spring.datasource.url=jdbc:h2:mem:dbr4",
|
||||
@@ -43,6 +53,7 @@ import org.testcontainers.elasticsearch.ElasticsearchContainer;
|
||||
"hapi.fhir.lastn_enabled=true",
|
||||
"hapi.fhir.store_resource_in_lucene_index_enabled=true",
|
||||
"hapi.fhir.advanced_lucene_indexing=true",
|
||||
|
||||
"elasticsearch.enabled=true",
|
||||
"hapi.fhir.cr_enabled=false",
|
||||
// Because the port is set randomly, we will set the rest_url using the Initializer.
|
||||
@@ -62,19 +73,31 @@ public class ElasticsearchLastNR4IT {
|
||||
private IGenericClient ourClient;
|
||||
private FhirContext ourCtx;
|
||||
|
||||
private static final String ELASTIC_VERSION = "7.16.3";
|
||||
private static final String ELASTIC_IMAGE = "docker.elastic.co/elasticsearch/elasticsearch:" + ELASTIC_VERSION;
|
||||
private static ElasticsearchContainer embeddedElastic;
|
||||
@Container
|
||||
public static ElasticsearchContainer embeddedElastic = TestElasticsearchContainerHelper.getEmbeddedElasticSearch();
|
||||
|
||||
@Autowired
|
||||
private ElasticsearchSvcImpl myElasticsearchSvc;
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeClass() {
|
||||
embeddedElastic = new ElasticsearchContainer(ELASTIC_IMAGE).withStartupTimeout(Duration.of(300, ChronoUnit.SECONDS));
|
||||
embeddedElastic.start();
|
||||
public static void beforeClass() throws IOException {
|
||||
//Given
|
||||
RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(
|
||||
"http", embeddedElastic.getHost() + ":" + embeddedElastic.getMappedPort(9200), "", "");
|
||||
|
||||
/* As of 2023-08-10, HAPI FHIR sets SubscriptionConstants.MAX_SUBSCRIPTION_RESULTS to 50000
|
||||
which is in excess of elastic's default max_result_window. If MAX_SUBSCRIPTION_RESULTS is changed
|
||||
to a value <= 10000, the following will no longer be necessary. - dotasek
|
||||
*/
|
||||
PutIndexTemplateRequest putIndexTemplateRequest = new PutIndexTemplateRequest("hapi_fhir_template");
|
||||
putIndexTemplateRequest.patterns(List.of("*"));
|
||||
Settings settings = Settings.builder().put("index.max_result_window", 50000).build();
|
||||
putIndexTemplateRequest.settings(settings);
|
||||
elasticsearchHighLevelRestClient.indices().putTemplate(putIndexTemplateRequest, RequestOptions.DEFAULT);
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
@PreDestroy
|
||||
public void stop() {
|
||||
embeddedElastic.stop();
|
||||
@@ -116,7 +139,7 @@ public class ElasticsearchLastNR4IT {
|
||||
}
|
||||
|
||||
@BeforeEach
|
||||
void beforeEach() {
|
||||
void beforeEach() throws IOException {
|
||||
|
||||
ourCtx = FhirContext.forR4();
|
||||
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
|
||||
@@ -124,6 +147,7 @@ public class ElasticsearchLastNR4IT {
|
||||
String ourServerBase = "http://localhost:" + port + "/fhir/";
|
||||
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
|
||||
ourClient.registerInterceptor(new LoggingInterceptor(true));
|
||||
|
||||
}
|
||||
|
||||
static class Initializer
|
||||
|
||||
@@ -23,7 +23,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
"spring.datasource.url=jdbc:h2:mem:dbr2",
|
||||
"hapi.fhir.cr_enabled=false",
|
||||
})
|
||||
public class ExampleServerDstu2IT {
|
||||
class ExampleServerDstu2IT {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
|
||||
private IGenericClient ourClient;
|
||||
|
||||
@@ -51,7 +51,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
})
|
||||
|
||||
|
||||
public class ExampleServerDstu3IT implements IServerSupport {
|
||||
class ExampleServerDstu3IT implements IServerSupport {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu3IT.class);
|
||||
private IGenericClient ourClient;
|
||||
@@ -73,8 +73,8 @@ public class ExampleServerDstu3IT implements IServerSupport {
|
||||
ourClient.registerInterceptor(new LoggingInterceptor(true));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreateAndRead() {
|
||||
@Test
|
||||
void testCreateAndRead() {
|
||||
|
||||
String methodName = "testCreateResourceConditional";
|
||||
|
||||
@@ -157,7 +157,7 @@ public class ExampleServerDstu3IT implements IServerSupport {
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testWebsocketSubscription() throws Exception {
|
||||
void testWebsocketSubscription() throws Exception {
|
||||
/*
|
||||
* Create subscription
|
||||
*/
|
||||
|
||||
@@ -55,7 +55,7 @@ class ExampleServerR4BIT {
|
||||
|
||||
|
||||
@Test
|
||||
public void testBatchPutWithIdenticalTags() {
|
||||
void testBatchPutWithIdenticalTags() {
|
||||
String batchPuts = "{\n" +
|
||||
"\t\"resourceType\": \"Bundle\",\n" +
|
||||
"\t\"id\": \"patients\",\n" +
|
||||
|
||||
@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.starter;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.model.primitive.IdDt;
|
||||
import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
|
||||
import ca.uhn.fhir.rest.api.CacheControlDirective;
|
||||
import ca.uhn.fhir.rest.api.EncodingEnum;
|
||||
import ca.uhn.fhir.rest.api.MethodOutcome;
|
||||
@@ -16,11 +17,9 @@ import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Order;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.boot.test.context.SpringBootTest;
|
||||
import org.springframework.boot.web.server.LocalServerPort;
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension;
|
||||
|
||||
|
||||
import java.io.IOException;
|
||||
@@ -37,10 +36,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters;
|
||||
import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
|
||||
|
||||
@ExtendWith(SpringExtension.class)
|
||||
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
|
||||
classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class},
|
||||
properties = {
|
||||
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class, NicknameServiceConfig.class}, properties = {
|
||||
"spring.datasource.url=jdbc:h2:mem:dbr4",
|
||||
"hapi.fhir.enable_repository_validating_interceptor=true",
|
||||
"hapi.fhir.fhir_version=r4",
|
||||
@@ -147,7 +143,7 @@ class ExampleServerR4IT implements IServerSupport{
|
||||
return result.get(0);
|
||||
}
|
||||
@Test
|
||||
public void testBatchPutWithIdenticalTags() {
|
||||
void testBatchPutWithIdenticalTags() {
|
||||
String batchPuts = "{\n" +
|
||||
"\t\"resourceType\": \"Bundle\",\n" +
|
||||
"\t\"id\": \"patients\",\n" +
|
||||
|
||||
@@ -45,15 +45,15 @@ public class ExampleServerR5IT {
|
||||
private IGenericClient ourClient;
|
||||
private FhirContext ourCtx;
|
||||
|
||||
public static final String SUBSCRIPTION_TOPIC_TEST_URL = "http://example.com/topic/test";
|
||||
public static final String SUBSCRIPTION_TOPIC_TEST_URL = "http://example.com/topic/test";
|
||||
|
||||
|
||||
@LocalServerPort
|
||||
@LocalServerPort
|
||||
private int port;
|
||||
|
||||
|
||||
@Test
|
||||
public void testCreateAndRead() {
|
||||
void testCreateAndRead() {
|
||||
|
||||
String methodName = "testCreateResourceConditional";
|
||||
|
||||
@@ -66,7 +66,7 @@ public class ExampleServerR5IT {
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testWebsocketSubscription() throws Exception {
|
||||
void testWebsocketSubscription() throws Exception {
|
||||
String endpoint = "ws://localhost:" + port + "/websocket";
|
||||
/*
|
||||
* Create topic
|
||||
|
||||
@@ -27,7 +27,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
"hapi.fhir.partitioning.partitioning_include_in_search_hashes=false",
|
||||
|
||||
})
|
||||
public class MultitenantServerR4IT {
|
||||
class MultitenantServerR4IT {
|
||||
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
|
||||
@@ -41,7 +41,7 @@ public class MultitenantServerR4IT {
|
||||
|
||||
|
||||
@Test
|
||||
public void testCreateAndReadInTenantA() {
|
||||
void testCreateAndReadInTenantA() {
|
||||
|
||||
|
||||
// Create tenant A
|
||||
@@ -67,7 +67,7 @@ public class MultitenantServerR4IT {
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreateAndReadInTenantB() {
|
||||
void testCreateAndReadInTenantB() {
|
||||
|
||||
|
||||
// Create tenant A
|
||||
|
||||
@@ -18,7 +18,7 @@ public class SocketImplementation {
|
||||
private final String myCriteria;
|
||||
protected String myError;
|
||||
protected boolean myGotBound;
|
||||
private final List<String> myMessages = new ArrayList<String>();
|
||||
private final List<String> myMessages = new ArrayList<>();
|
||||
protected int myPingCount;
|
||||
protected String mySubsId;
|
||||
private Session session;
|
||||
|
||||
@@ -64,9 +64,10 @@ hapi:
|
||||
# swiss:
|
||||
# name: swiss.mednet.fhir
|
||||
# version: 0.8.0
|
||||
# reloadExisting : false
|
||||
# example not from registry
|
||||
# ips_1_0_0:
|
||||
# url: https://build.fhir.org/ig/HL7/fhir-ips/package.tgz
|
||||
# packageUrl: https://build.fhir.org/ig/HL7/fhir-ips/package.tgz
|
||||
# name: hl7.fhir.uv.ips
|
||||
# version: 1.0.0
|
||||
# supported_resource_types:
|
||||
|
||||
Reference in New Issue
Block a user