diff --git a/.github/ct/config.yaml b/.github/ct/config.yaml index 484e994..9d1ae82 100644 --- a/.github/ct/config.yaml +++ b/.github/ct/config.yaml @@ -11,6 +11,4 @@ helm-extra-args: --timeout 300s upgrade: true skip-missing-values: true release-label: release -chart-repos: - - bitnami=https://charts.bitnami.com/bitnami release-name-template: "helm-v{{ .Version }}" diff --git a/.github/workflows/chart-release.yaml b/.github/workflows/chart-release.yaml index ae2045c..38c4fd2 100644 --- a/.github/workflows/chart-release.yaml +++ b/.github/workflows/chart-release.yaml @@ -9,10 +9,14 @@ on: jobs: release: - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 steps: + - name: Add workspace as safe directory + run: | + 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 @@ -21,14 +25,11 @@ jobs: git config user.name "$GITHUB_ACTOR" git config user.email "$GITHUB_ACTOR@users.noreply.github.com" - - name: Add bitnami repo - run: helm repo add bitnami https://charts.bitnami.com/bitnami - - name: Update dependencies run: find charts/ ! -path charts/ -maxdepth 1 -type d -exec helm dependency update {} \; - name: Run chart-releaser - uses: helm/chart-releaser-action@v1.2.0 + uses: helm/chart-releaser-action@be16258da8010256c6e82849661221415f031968 # v1.5.0 with: config: .github/ct/config.yaml env: diff --git a/.github/workflows/chart-test.yaml b/.github/workflows/chart-test.yaml index f4357fb..30d2932 100644 --- a/.github/workflows/chart-test.yaml +++ b/.github/workflows/chart-test.yaml @@ -9,8 +9,8 @@ on: jobs: lint: - runs-on: ubuntu-20.04 - container: quay.io/helmpack/chart-testing:v3.4.0 + runs-on: ubuntu-22.04 + container: quay.io/helmpack/chart-testing:v3.8.0@sha256:f058c660a28d99a9394ae081d98921efe068079531f247c86b8054e3c9d407aa steps: - name: Install helm-docs working-directory: /tmp @@ -22,11 +22,14 @@ jobs: chmod +x /usr/local/bin/helm-docs && \ helm-docs --version + - name: Add workspace as safe directory + run: | + 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 test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 strategy: matrix: - k8s-version: [1.22.9, 1.23.6, 1.24.1] + k8s-version: [1.25.9, 1.26.4, 1.27.2] needs: - lint 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' + if: ${{ steps.list-changed.outputs.changed == 'true' }} diff --git a/Dockerfile b/Dockerfile index 263fe9c..8e6c8b0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ -FROM maven:3.8-openjdk-17-slim as build-hapi +FROM docker.io/library/maven:3.9.2-eclipse-temurin-17 AS build-hapi WORKDIR /tmp/hapi-fhir-jpaserver-starter -ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.17.0 +ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.26.0 RUN curl -LSsO https://github.com/open-telemetry/opentelemetry-java-instrumentation/releases/download/v${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"] diff --git a/README.md b/README.md index dbb5740..0184cc5 100644 --- a/README.md +++ b/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/. diff --git a/charts/hapi-fhir-jpaserver/Chart.lock b/charts/hapi-fhir-jpaserver/Chart.lock index 5c8ec4a..98ba848 100644 --- a/charts/hapi-fhir-jpaserver/Chart.lock +++ b/charts/hapi-fhir-jpaserver/Chart.lock @@ -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" diff --git a/charts/hapi-fhir-jpaserver/Chart.yaml b/charts/hapi-fhir-jpaserver/Chart.yaml index 9158007..a81e108 100644 --- a/charts/hapi-fhir-jpaserver/Chart.yaml +++ b/charts/hapi-fhir-jpaserver/Chart.yaml @@ -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 diff --git a/charts/hapi-fhir-jpaserver/README.md b/charts/hapi-fhir-jpaserver/README.md index 8b4b461..7d4d338 100644 --- a/charts/hapi-fhir-jpaserver/README.md +++ b/charts/hapi-fhir-jpaserver/README.md @@ -1,6 +1,6 @@ # HAPI FHIR JPA Server Starter Helm Chart -![Version: 0.11.1](https://img.shields.io/badge/Version-0.11.1-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 6.2.2](https://img.shields.io/badge/AppVersion-6.2.2-informational?style=flat-square) +![Version: 0.13.0](https://img.shields.io/badge/Version-0.13.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 6.6.0](https://img.shields.io/badge/AppVersion-6.6.0-informational?style=flat-square) This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment. @@ -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 diff --git a/charts/hapi-fhir-jpaserver/README.md.gotmpl b/charts/hapi-fhir-jpaserver/README.md.gotmpl index bfea032..4647395 100644 --- a/charts/hapi-fhir-jpaserver/README.md.gotmpl +++ b/charts/hapi-fhir-jpaserver/README.md.gotmpl @@ -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 diff --git a/charts/hapi-fhir-jpaserver/ci/extra-config-values.yaml b/charts/hapi-fhir-jpaserver/ci/extra-config-values.yaml new file mode 100644 index 0000000..d2406ac --- /dev/null +++ b/charts/hapi-fhir-jpaserver/ci/extra-config-values.yaml @@ -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: ["/"] diff --git a/charts/hapi-fhir-jpaserver/templates/application-config.yaml b/charts/hapi-fhir-jpaserver/templates/application-config.yaml new file mode 100644 index 0000000..e4df9ce --- /dev/null +++ b/charts/hapi-fhir-jpaserver/templates/application-config.yaml @@ -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 }} diff --git a/charts/hapi-fhir-jpaserver/templates/deployment.yaml b/charts/hapi-fhir-jpaserver/templates/deployment.yaml index 8f3c65e..c15609f 100644 --- a/charts/hapi-fhir-jpaserver/templates/deployment.yaml +++ b/charts/hapi-fhir-jpaserver/templates/deployment.yaml @@ -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 }} diff --git a/charts/hapi-fhir-jpaserver/templates/tests/test-endpoints.yaml b/charts/hapi-fhir-jpaserver/templates/tests/test-endpoints.yaml index 034efb1..bd81c4a 100644 --- a/charts/hapi-fhir-jpaserver/templates/tests/test-endpoints.yaml +++ b/charts/hapi-fhir-jpaserver/templates/tests/test-endpoints.yaml @@ -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"] diff --git a/charts/hapi-fhir-jpaserver/values.yaml b/charts/hapi-fhir-jpaserver/values.yaml index be02b18..9e9c187 100644 --- a/charts/hapi-fhir-jpaserver/values.yaml +++ b/charts/hapi-fhir-jpaserver/values.yaml @@ -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 diff --git a/pom.xml b/pom.xml index e38c38c..5b1ef93 100644 --- a/pom.xml +++ b/pom.xml @@ -247,6 +247,12 @@ + + ca.uhn.hapi.fhir + hapi-fhir-jpaserver-test-utilities + ${project.version} + test + org.eclipse.jetty jetty-servlets diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java b/src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java index 22696a9..f83d80f 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java @@ -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 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 supported_resource_types = new ArrayList<>(); private List allowed_bundle_types = null; private Boolean narrative_enabled = true; + private Validation validation = new Validation(); - private Map tester = new HashMap<>(); + private Map 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 implementationGuides = null; + private Map 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 local_base_urls = new ArrayList<>(); + private final Set local_base_urls = new HashSet<>(); private final List custom_interceptor_classes = new ArrayList<>(); + public String getStaticLocationPrefix() { + return staticLocationPrefix; + } + + public void setStaticLocationPrefix(String staticLocationPrefix) { + this.staticLocationPrefix = staticLocationPrefix; + } + + public List 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 getImplementationGuides() { + public Map getImplementationGuides() { return implementationGuides; } - public void setImplementationGuides(Map implementationGuides) { + public void setImplementationGuides(Map 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 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 getLocal_base_urls() { + public Set getLocal_base_urls() { return local_base_urls; } public static class Cors { private Boolean allow_Credentials = true; - private List allowed_origin = ImmutableList.of("*"); + private List allowed_origin = List.of("*"); public List 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; } -} +} \ No newline at end of file diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/ExtraStaticFilesConfigurer.java b/src/main/java/ca/uhn/fhir/jpa/starter/ExtraStaticFilesConfigurer.java index d875ec6..a3b528c 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/ExtraStaticFilesConfigurer.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/ExtraStaticFilesConfigurer.java @@ -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); } diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java b/src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java index b9473f9..2f673ed 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java @@ -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()); diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfig.java b/src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfig.java index cb28659..c8c8925 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfig.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfig.java @@ -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. - * + *

* 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 diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfigCondition.java b/src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfigCondition.java new file mode 100644 index 0000000..f5670d9 --- /dev/null +++ b/src/main/java/ca/uhn/fhir/jpa/starter/common/FhirTesterConfigCondition.java @@ -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(); + } +} diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java b/src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java index 442b811..766870a 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java @@ -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 reindexJobParametersJobDefinition, - JobDefinitionRegistry jobDefinitionRegistry, IPackageInstallerSvc packageInstallerSvc) { + public IPackageInstallerSvc packageInstaller(AppProperties appProperties, JobDefinition reindexJobParametersJobDefinition, JobDefinitionRegistry jobDefinitionRegistry, IPackageInstallerSvc packageInstallerSvc) + { jobDefinitionRegistry.addJobDefinitionIfNotRegistered(reindexJobParametersJobDefinition); if (appProperties.getImplementationGuides() != null) { - Map guides = appProperties.getImplementationGuides(); - for (Map.Entry 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 guides = appProperties.getImplementationGuides(); + for (Map.Entry 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 mdmProviderProvider, IJpaSystemProvider jpaSystemProvider, - ResourceProviderFactory resourceProviderFactory, JpaStorageSettings jpaStorageSettings, - ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport, - DatabaseBackedPagingProvider databaseBackedPagingProvider, LoggingInterceptor loggingInterceptor, - Optional terminologyUploaderProvider, - Optional subscriptionTriggeringProvider, - Optional corsInterceptor, IInterceptorBroadcaster interceptorBroadcaster, - Optional binaryAccessProvider, BinaryStorageInterceptor binaryStorageInterceptor, - IValidatorModule validatorModule, Optional graphQLProvider, - BulkDataExportProvider bulkDataExportProvider, BulkDataImportProvider bulkDataImportProvider, - ValueSetOperationProvider theValueSetOperationProvider, ReindexProvider reindexProvider, - PartitionManagementProvider partitionManagementProvider, - Optional repositoryValidatingInterceptor, - IPackageInstallerSvc packageInstallerSvc, ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc, - ApplicationContext appContext, - Optional theIpsOperationProvider) { + public RestfulServer restfulServer(IFhirSystemDao fhirSystemDao, AppProperties appProperties, DaoRegistry daoRegistry, Optional mdmProviderProvider, IJpaSystemProvider jpaSystemProvider, ResourceProviderFactory resourceProviderFactory, JpaStorageSettings jpaStorageSettings, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport, DatabaseBackedPagingProvider databaseBackedPagingProvider, LoggingInterceptor loggingInterceptor, Optional terminologyUploaderProvider, Optional subscriptionTriggeringProvider, Optional corsInterceptor, IInterceptorBroadcaster interceptorBroadcaster, Optional binaryAccessProvider, BinaryStorageInterceptor binaryStorageInterceptor, IValidatorModule validatorModule, Optional graphQLProvider, BulkDataExportProvider bulkDataExportProvider, BulkDataImportProvider bulkDataImportProvider, ValueSetOperationProvider theValueSetOperationProvider, ReindexProvider reindexProvider, PartitionManagementProvider partitionManagementProvider, Optional repositoryValidatingInterceptor, IPackageInstallerSvc packageInstallerSvc, ThreadSafeResourceDeleterSvc theThreadSafeResourceDeleterSvc, ApplicationContext appContext, Optional theIpsOperationProvider) { RestfulServer fhirServer = new RestfulServer(fhirSystemDao.getContext()); List 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 customInterceptorClasses) { + private void registerCustomInterceptors(RestfulServer fhirServer, ApplicationContext theAppContext, List 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 { diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryDstu3.java b/src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryDstu3.java index f8874b3..edaade7 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryDstu3.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryDstu3.java @@ -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> structureDefintions = results.getResources(0, results.size()) + Map> 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(); }); diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrR4Config.java b/src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrR4Config.java index 190f534..74578ef 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrR4Config.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrR4Config.java @@ -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 }) diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/ips/StarterIpsConfig.java b/src/main/java/ca/uhn/fhir/jpa/starter/ips/StarterIpsConfig.java index e777879..308a3aa 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/ips/StarterIpsConfig.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/ips/StarterIpsConfig.java @@ -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); } diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/mdm/MdmConfig.java b/src/main/java/ca/uhn/fhir/jpa/starter/mdm/MdmConfig.java index 50dfe9e..7f0ee4c 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/mdm/MdmConfig.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/mdm/MdmConfig.java @@ -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); } } diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/util/EnvironmentHelper.java b/src/main/java/ca/uhn/fhir/jpa/starter/util/EnvironmentHelper.java index 41bb556..71d947a 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/util/EnvironmentHelper.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/util/EnvironmentHelper.java @@ -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; diff --git a/src/main/resources/application.yaml b/src/main/resources/application.yaml index 09dbe8d..a0755d4 100644 --- a/src/main/resources/application.yaml +++ b/src/main/resources/application.yaml @@ -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 diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/CustomBeanTest.java b/src/test/java/ca/uhn/fhir/jpa/starter/CustomBeanTest.java index 2e3ae07..d5a3d18 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/CustomBeanTest.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/CustomBeanTest.java @@ -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; diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/CustomInterceptorTest.java b/src/test/java/ca/uhn/fhir/jpa/starter/CustomInterceptorTest.java index 02176d9..859752a 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/CustomInterceptorTest.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/CustomInterceptorTest.java @@ -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; diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java index 24b5ac0..2365120 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java @@ -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 diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java index 2f0e71c..bc88d47 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java @@ -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; diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java index c239dba..a9d7e1d 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java @@ -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 */ diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4BIT.java b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4BIT.java index 5c36bb2..82e48a3 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4BIT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4BIT.java @@ -55,7 +55,7 @@ class ExampleServerR4BIT { @Test - public void testBatchPutWithIdenticalTags() { + void testBatchPutWithIdenticalTags() { String batchPuts = "{\n" + "\t\"resourceType\": \"Bundle\",\n" + "\t\"id\": \"patients\",\n" + diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java index be3473f..e058a61 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java @@ -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" + diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java index fdd3f0f..76d90e0 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java @@ -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 diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java index f2c6203..6729fa6 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java @@ -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 diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/SocketImplementation.java b/src/test/java/ca/uhn/fhir/jpa/starter/SocketImplementation.java index 7734a23..4a536f0 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/SocketImplementation.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/SocketImplementation.java @@ -18,7 +18,7 @@ public class SocketImplementation { private final String myCriteria; protected String myError; protected boolean myGotBound; - private final List myMessages = new ArrayList(); + private final List myMessages = new ArrayList<>(); protected int myPingCount; protected String mySubsId; private Session session; diff --git a/src/test/resources/application.yaml b/src/test/resources/application.yaml index 89229c9..9f473c5 100644 --- a/src/test/resources/application.yaml +++ b/src/test/resources/application.yaml @@ -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: