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Merge remote-tracking branch 'origin/master' into rel_8_1_tracking
2 parents fc70e52 + 6b5d24b commit 54c153a

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.github/workflows/spotless-check.yml

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- uses: mshick/add-pr-comment@v2
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if: always()
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with:
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proxy-url: https://slack-bots.azure.smilecdr.com/robogary/github
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message-success: |
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Formatting check succeeded!
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message-failure: |
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dependencies:
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- name: postgresql
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repository: oci://registry-1.docker.io/bitnamicharts
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version: 16.3.2
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version: 16.5.5
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- name: common
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repository: oci://registry-1.docker.io/bitnamicharts
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version: 2.28.0
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digest: sha256:99587bb3481cd94c1679d9dd23cb8c816701a1c6f0d458c77c71e7e541dd2f55
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generated: "2024-12-17T12:51:15.601470579+01:00"
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version: 2.30.0
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digest: sha256:c114b296b53007a7973260de8bad61917fe741c0ad9de15fdbeea5743c8f4910
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generated: "2025-03-21T21:44:22.334197366+01:00"

charts/hapi-fhir-jpaserver/Chart.yaml

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- https://github.com/hapifhir/hapi-fhir-jpaserver-starter
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dependencies:
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- name: postgresql
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version: 16.3.2
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version: 16.5.5
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repository: oci://registry-1.docker.io/bitnamicharts
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condition: postgresql.enabled
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- name: common
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repository: oci://registry-1.docker.io/bitnamicharts
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version: 2.28.0
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appVersion: 7.6.0
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version: 0.18.0
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version: 2.30.0
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appVersion: 8.0.0
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version: 0.19.0
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annotations:
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artifacthub.io/license: Apache-2.0
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artifacthub.io/containsSecurityUpdates: "false"
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# When using the list of objects option the valid supported kinds are
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# added, changed, deprecated, removed, fixed, and security.
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- kind: changed
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description: "updated postgresql sub-chart to 16.3.2"
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description: "updated postgresql sub-chart to 16.5.5"
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- kind: changed
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description: "updated curlimages/curl to 8.11.1"
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description: "updated curlimages/curl to 8.12.1"
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- kind: changed
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description: "updated hapiproject/hapi to 7.6.0"
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- kind: added
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description: "support for setting resource limits and requests from presets. With a default set for all containers"
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- kind: added
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description: "support for setting extra volumes and volume mounts"
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- kind: changed
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description: "set default pod security context for main and test pods"
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description: "updated hapiproject/hapi to v8.0.0-1"

charts/hapi-fhir-jpaserver/README.md

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# HAPI FHIR JPA Server Starter Helm Chart
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![Version: 0.18.0](https://img.shields.io/badge/Version-0.18.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 7.6.0](https://img.shields.io/badge/AppVersion-7.6.0-informational?style=flat-square)
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![Version: 0.19.0](https://img.shields.io/badge/Version-0.19.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 8.0.0](https://img.shields.io/badge/AppVersion-8.0.0-informational?style=flat-square)
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This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
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| Repository | Name | Version |
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|------------|------|---------|
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| oci://registry-1.docker.io/bitnamicharts | common | 2.28.0 |
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| oci://registry-1.docker.io/bitnamicharts | postgresql | 16.3.2 |
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| oci://registry-1.docker.io/bitnamicharts | common | 2.30.0 |
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| oci://registry-1.docker.io/bitnamicharts | postgresql | 16.5.5 |
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## Values
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| image.pullPolicy | string | `"IfNotPresent"` | image pullPolicy to use |
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| image.registry | string | `"docker.io"` | registry where the HAPI FHIR server image is hosted |
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| image.repository | string | `"hapiproject/hapi"` | the path inside the repository |
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| image.tag | string | `"v7.6.0@sha256:4771a178e764896c83881c1b3a52bd487e53d06e1acc3653ea0db0c6f6b2b8a1"` | the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image. |
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| image.tag | string | `"v8.0.0-1@sha256:9fbac7b012b4be91ba481e7008f1353ede4598bc99a36f3902b8abf873e70ed8"` | the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image. |
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| imagePullSecrets | list | `[]` | image pull secrets to use when pulling the image |
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| ingress.annotations | object | `{}` | provide any additional annotations which may be required. Evaluated as a template. |
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| ingress.enabled | bool | `false` | whether to create an Ingress to expose the FHIR server HTTP endpoint |

charts/hapi-fhir-jpaserver/templates/deployment.yaml

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{{- toYaml .Values.podSecurityContext | nindent 8 }}
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initContainers:
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- name: wait-for-db-to-be-ready
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image: docker.io/bitnami/postgresql:17.2.0-debian-12-r3@sha256:4de5c47eb98dd8fe09abdcbc2264984486ee8196e90902fb354f5d2ab97e8921
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image: docker.io/bitnami/postgresql:17.4.0-debian-12-r10@sha256:7b9af9dd759055265998bbf12368e6d7d6326e6fd23f8157be841fad0915c1a1
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imagePullPolicy: IfNotPresent
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{{- with .Values.restrictedContainerSecurityContext }}
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securityContext:

charts/hapi-fhir-jpaserver/values.yaml

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# -- the path inside the repository
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repository: hapiproject/hapi
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# -- the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image.
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tag: "v7.6.0@sha256:4771a178e764896c83881c1b3a52bd487e53d06e1acc3653ea0db0c6f6b2b8a1"
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tag: "v8.0.0-1@sha256:9fbac7b012b4be91ba481e7008f1353ede4598bc99a36f3902b8abf873e70ed8"
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# -- image pullPolicy to use
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pullPolicy: IfNotPresent
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image:
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registry: docker.io
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repository: curlimages/curl
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tag: 8.11.1@sha256:c1fe1679c34d9784c1b0d1e5f62ac0a79fca01fb6377cdd33e90473c6f9f9a69
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tag: 8.12.1@sha256:94e9e444bcba979c2ea12e27ae39bee4cd10bc7041a472c4727a558e213744e6
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tests:
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# -- whether the service account token should be auto-mounted for the test pods

pom.xml

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<properties>
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<java.version>17</java.version>
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<hapi.fhir.jpa.server.starter.revision>1</hapi.fhir.jpa.server.starter.revision>
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<clinical-reasoning.version>3.19.0</clinical-reasoning.version>
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</properties>
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<!-- one-liner to take you to the cloud with settings form the application.yaml file: -->
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</dependency>
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<!-- This dependency includes the JPA CQL Server -->
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-storage-cr</artifactId>
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<version>${project.parent.version}</version>
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<groupId>org.opencds.cqf.fhir</groupId>
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<artifactId>cqf-fhir-cr-hapi</artifactId>
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<version>${clinical-reasoning.version}</version>
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</dependency>
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<!-- This dependency includes the JPA MDM Server -->
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<dependency>

src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java

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return this.enable_task_pre_expand_value_sets;
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}
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public void setEnable_task_pre_expand_value_setss(Boolean enable_task_pre_expand_value_sets) {
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public void setEnable_task_pre_expand_value_sets(Boolean enable_task_pre_expand_value_sets) {
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this.enable_task_pre_expand_value_sets = enable_task_pre_expand_value_sets;
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}
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src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksServlet.java

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import java.io.IOException;
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import java.util.stream.Collectors;
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import static ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY;
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import static org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY;
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@Configurable
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public class CdsHooksServlet extends HttpServlet {

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/StarterCdsHooksConfig.java

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import ca.uhn.fhir.jpa.starter.cr.CrConfigCondition;
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import ca.uhn.fhir.jpa.starter.cr.CrProperties;
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import ca.uhn.hapi.fhir.cdshooks.api.ICdsHooksDaoAuthorizationSvc;
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import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
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import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceRegistry;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrSettings;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.ICdsCrServiceRegistry;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CdsCrDiscoveryServiceRegistry;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.ICdsCrDiscoveryServiceRegistry;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrServiceRegistry;
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import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrSettings;
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import org.opencds.cqf.fhir.cr.hapi.cdshooks.ICdsCrServiceRegistry;
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import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.CdsCrDiscoveryServiceRegistry;
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import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.ICdsCrDiscoveryServiceRegistry;
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import org.opencds.cqf.fhir.cr.hapi.config.CrCdsHooksConfig;
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import org.opencds.cqf.fhir.cr.hapi.config.RepositoryConfig;
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import org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig;
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import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
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import org.springframework.boot.web.servlet.ServletRegistrationBean;
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import org.springframework.context.annotation.Bean;
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@Configuration
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@Conditional({CdsHooksConfigCondition.class, CrConfigCondition.class})
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@Import({CdsHooksConfig.class, CrCommonConfig.class})
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@Import({RepositoryConfig.class, TestCdsHooksConfig.class, CrCdsHooksConfig.class, CrCommonConfig.class})
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public class StarterCdsHooksConfig {
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// @Bean
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// CdsPrefetchSvc cdsPrefetchSvc(
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// CdsResolutionStrategySvc theCdsResolutionStrategySvc,
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// CdsPrefetchDaoSvc theResourcePrefetchDao,
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// CdsPrefetchFhirClientSvc theResourcePrefetchFhirClient,
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// ICdsHooksDaoAuthorizationSvc theCdsHooksDaoAuthorizationSvc) {
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// return new ModuleConfigurationPrefetchSvc(
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// theCdsResolutionStrategySvc,
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// theResourcePrefetchDao,
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// theResourcePrefetchFhirClient,
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// theCdsHooksDaoAuthorizationSvc);
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// }
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@Bean
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public ICdsCrDiscoveryServiceRegistry cdsCrDiscoveryServiceRegistry() {
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CdsCrDiscoveryServiceRegistry registry = new CdsCrDiscoveryServiceRegistry();
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registry.unregister(FhirVersionEnum.R4);
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registry.register(FhirVersionEnum.R4, UpdatedCrDiscoveryService.class);
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return registry;
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}
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@Bean
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public ICdsCrServiceRegistry cdsCrServiceRegistry() {
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CdsCrServiceRegistry registry = new CdsCrServiceRegistry();
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registry.unregister(FhirVersionEnum.R4);
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registry.register(FhirVersionEnum.R4, UpdatedCdsCrService.class);
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return registry;
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}
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