Personal-Twin/hapi-fhir-jpaserver-starter
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Merge remote-tracking branch 'origin/master' into rel_8_1_tracking

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dotasek
2025-04-08 10:29:23 -04:00
parent fc70e529c9 6b5d24b3d6
commit 54c153a5c1
22 changed files with 120 additions and 117 deletions
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1
.github/workflows/spotless-check.yml vendored
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@@ -22,6 +22,7 @@ jobs:
- uses: mshick/add-pr-comment@v2 - uses: mshick/add-pr-comment@v2
if: always() if: always()
with: with:
proxy-url: https://slack-bots.azure.smilecdr.com/robogary/github
message-success: | message-success: |
Formatting check succeeded! Formatting check succeeded!
message-failure: | message-failure: |

8
charts/hapi-fhir-jpaserver/Chart.lock
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@@ -1,9 +1,9 @@
dependencies: dependencies:
- name: postgresql - name: postgresql
repository: oci://registry-1.docker.io/bitnamicharts repository: oci://registry-1.docker.io/bitnamicharts
version: 16.3.2 version: 16.5.5
- name: common - name: common
repository: oci://registry-1.docker.io/bitnamicharts repository: oci://registry-1.docker.io/bitnamicharts
version: 2.28.0 version: 2.30.0
digest: sha256:99587bb3481cd94c1679d9dd23cb8c816701a1c6f0d458c77c71e7e541dd2f55 digest: sha256:c114b296b53007a7973260de8bad61917fe741c0ad9de15fdbeea5743c8f4910
generated: "2024-12-17T12:51:15.601470579+01:00" generated: "2025-03-21T21:44:22.334197366+01:00"

20
charts/hapi-fhir-jpaserver/Chart.yaml
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@@ -7,14 +7,14 @@ sources:
- https://github.com/hapifhir/hapi-fhir-jpaserver-starter - https://github.com/hapifhir/hapi-fhir-jpaserver-starter
dependencies: dependencies:
- name: postgresql - name: postgresql
version: 16.3.2 version: 16.5.5
repository: oci://registry-1.docker.io/bitnamicharts repository: oci://registry-1.docker.io/bitnamicharts
condition: postgresql.enabled condition: postgresql.enabled
- name: common - name: common
repository: oci://registry-1.docker.io/bitnamicharts repository: oci://registry-1.docker.io/bitnamicharts
version: 2.28.0 version: 2.30.0
appVersion: 7.6.0 appVersion: 8.0.0
version: 0.18.0 version: 0.19.0
annotations: annotations:
artifacthub.io/license: Apache-2.0 artifacthub.io/license: Apache-2.0
artifacthub.io/containsSecurityUpdates: "false" artifacthub.io/containsSecurityUpdates: "false"
@@ -27,14 +27,8 @@ annotations:
# When using the list of objects option the valid supported kinds are # When using the list of objects option the valid supported kinds are
# added, changed, deprecated, removed, fixed, and security. # added, changed, deprecated, removed, fixed, and security.
- kind: changed - kind: changed
description: "updated postgresql sub-chart to 16.3.2" description: "updated postgresql sub-chart to 16.5.5"
- kind: changed - kind: changed
description: "updated curlimages/curl to 8.11.1" description: "updated curlimages/curl to 8.12.1"
- kind: changed - kind: changed
description: "updated hapiproject/hapi to 7.6.0" description: "updated hapiproject/hapi to v8.0.0-1"
- kind: added
description: "support for setting resource limits and requests from presets. With a default set for all containers"
- kind: added
description: "support for setting extra volumes and volume mounts"
- kind: changed
description: "set default pod security context for main and test pods"

8
charts/hapi-fhir-jpaserver/README.md
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@@ -1,6 +1,6 @@
# HAPI FHIR JPA Server Starter Helm Chart # HAPI FHIR JPA Server Starter Helm Chart
![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) ![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)
This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment. This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
@@ -15,8 +15,8 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| Repository | Name | Version | | Repository | Name | Version |
|------------|------|---------| |------------|------|---------|
| oci://registry-1.docker.io/bitnamicharts | common | 2.28.0 | | oci://registry-1.docker.io/bitnamicharts | common | 2.30.0 |
| oci://registry-1.docker.io/bitnamicharts | postgresql | 16.3.2 | | oci://registry-1.docker.io/bitnamicharts | postgresql | 16.5.5 |
## Values ## Values
@@ -39,7 +39,7 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
| image.pullPolicy | string | `"IfNotPresent"` | image pullPolicy to use | | image.pullPolicy | string | `"IfNotPresent"` | image pullPolicy to use |
| image.registry | string | `"docker.io"` | registry where the HAPI FHIR server image is hosted | | 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.repository | string | `"hapiproject/hapi"` | the path inside the repository |
| 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. | | 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. |
| imagePullSecrets | list | `[]` | image pull secrets to use when pulling the 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.annotations | object | `{}` | provide any additional annotations which may be required. Evaluated as a template. |
| ingress.enabled | bool | `false` | whether to create an Ingress to expose the FHIR server HTTP endpoint | | ingress.enabled | bool | `false` | whether to create an Ingress to expose the FHIR server HTTP endpoint |

2
charts/hapi-fhir-jpaserver/templates/deployment.yaml
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@@ -31,7 +31,7 @@ spec:
{{- toYaml .Values.podSecurityContext | nindent 8 }} {{- toYaml .Values.podSecurityContext | nindent 8 }}
initContainers: initContainers:
- name: wait-for-db-to-be-ready - name: wait-for-db-to-be-ready
image: docker.io/bitnami/postgresql:17.2.0-debian-12-r3@sha256:4de5c47eb98dd8fe09abdcbc2264984486ee8196e90902fb354f5d2ab97e8921 image: docker.io/bitnami/postgresql:17.4.0-debian-12-r10@sha256:7b9af9dd759055265998bbf12368e6d7d6326e6fd23f8157be841fad0915c1a1
imagePullPolicy: IfNotPresent imagePullPolicy: IfNotPresent
{{- with .Values.restrictedContainerSecurityContext }} {{- with .Values.restrictedContainerSecurityContext }}
securityContext: securityContext:

4
charts/hapi-fhir-jpaserver/values.yaml
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@@ -7,7 +7,7 @@ image:
# -- the path inside the repository # -- the path inside the repository
repository: hapiproject/hapi 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. # -- the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image.
tag: "v7.6.0@sha256:4771a178e764896c83881c1b3a52bd487e53d06e1acc3653ea0db0c6f6b2b8a1" tag: "v8.0.0-1@sha256:9fbac7b012b4be91ba481e7008f1353ede4598bc99a36f3902b8abf873e70ed8"
# -- image pullPolicy to use # -- image pullPolicy to use
pullPolicy: IfNotPresent pullPolicy: IfNotPresent
@@ -241,7 +241,7 @@ curl:
image: image:
registry: docker.io registry: docker.io
repository: curlimages/curl repository: curlimages/curl
tag: 8.11.1@sha256:c1fe1679c34d9784c1b0d1e5f62ac0a79fca01fb6377cdd33e90473c6f9f9a69 tag: 8.12.1@sha256:94e9e444bcba979c2ea12e27ae39bee4cd10bc7041a472c4727a558e213744e6
tests: tests:
# -- whether the service account token should be auto-mounted for the test pods # -- whether the service account token should be auto-mounted for the test pods

7
pom.xml
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@@ -6,6 +6,7 @@
<properties> <properties>
<java.version>17</java.version> <java.version>17</java.version>
<hapi.fhir.jpa.server.starter.revision>1</hapi.fhir.jpa.server.starter.revision> <hapi.fhir.jpa.server.starter.revision>1</hapi.fhir.jpa.server.starter.revision>
<clinical-reasoning.version>3.19.0</clinical-reasoning.version>
</properties> </properties>
<!-- one-liner to take you to the cloud with settings form the application.yaml file: --> <!-- one-liner to take you to the cloud with settings form the application.yaml file: -->
@@ -113,9 +114,9 @@
</dependency> </dependency>
<!-- This dependency includes the JPA CQL Server --> <!-- This dependency includes the JPA CQL Server -->
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>org.opencds.cqf.fhir</groupId>
<artifactId>hapi-fhir-storage-cr</artifactId> <artifactId>cqf-fhir-cr-hapi</artifactId>
<version>${project.parent.version}</version> <version>${clinical-reasoning.version}</version>
</dependency> </dependency>
<!-- This dependency includes the JPA MDM Server --> <!-- This dependency includes the JPA MDM Server -->
<dependency> <dependency>

2
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -695,7 +695,7 @@ public class AppProperties {
return this.enable_task_pre_expand_value_sets; return this.enable_task_pre_expand_value_sets;
} }
public void setEnable_task_pre_expand_value_setss(Boolean enable_task_pre_expand_value_sets) { public void setEnable_task_pre_expand_value_sets(Boolean enable_task_pre_expand_value_sets) {
this.enable_task_pre_expand_value_sets = enable_task_pre_expand_value_sets; this.enable_task_pre_expand_value_sets = enable_task_pre_expand_value_sets;
} }

2
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksServlet.java
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@@ -24,7 +24,7 @@ import org.springframework.beans.factory.annotation.Qualifier;
import java.io.IOException; import java.io.IOException;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import static ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY; import static org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY;
@Configurable @Configurable
public class CdsHooksServlet extends HttpServlet { public class CdsHooksServlet extends HttpServlet {

33
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/StarterCdsHooksConfig.java
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@@ -5,14 +5,16 @@ import ca.uhn.fhir.jpa.starter.cr.CrCommonConfig;
import ca.uhn.fhir.jpa.starter.cr.CrConfigCondition; import ca.uhn.fhir.jpa.starter.cr.CrConfigCondition;
import ca.uhn.fhir.jpa.starter.cr.CrProperties; import ca.uhn.fhir.jpa.starter.cr.CrProperties;
import ca.uhn.hapi.fhir.cdshooks.api.ICdsHooksDaoAuthorizationSvc; import ca.uhn.hapi.fhir.cdshooks.api.ICdsHooksDaoAuthorizationSvc;
import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter; import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter;
import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceRegistry;
import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrSettings;
import ca.uhn.hapi.fhir.cdshooks.svc.cr.ICdsCrServiceRegistry;
import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CdsCrDiscoveryServiceRegistry;
import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.ICdsCrDiscoveryServiceRegistry;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrServiceRegistry;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrSettings;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.ICdsCrServiceRegistry;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.CdsCrDiscoveryServiceRegistry;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.ICdsCrDiscoveryServiceRegistry;
import org.opencds.cqf.fhir.cr.hapi.config.CrCdsHooksConfig;
import org.opencds.cqf.fhir.cr.hapi.config.RepositoryConfig;
import org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig;
import org.springframework.beans.factory.config.AutowireCapableBeanFactory; import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
import org.springframework.boot.web.servlet.ServletRegistrationBean; import org.springframework.boot.web.servlet.ServletRegistrationBean;
import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Bean;
@@ -22,27 +24,14 @@ import org.springframework.context.annotation.Import;
@Configuration @Configuration
@Conditional({CdsHooksConfigCondition.class, CrConfigCondition.class}) @Conditional({CdsHooksConfigCondition.class, CrConfigCondition.class})
@Import({CdsHooksConfig.class, CrCommonConfig.class}) @Import({RepositoryConfig.class, TestCdsHooksConfig.class, CrCdsHooksConfig.class, CrCommonConfig.class})
public class StarterCdsHooksConfig { public class StarterCdsHooksConfig {
// @Bean
// CdsPrefetchSvc cdsPrefetchSvc(
// CdsResolutionStrategySvc theCdsResolutionStrategySvc,
// CdsPrefetchDaoSvc theResourcePrefetchDao,
// CdsPrefetchFhirClientSvc theResourcePrefetchFhirClient,
// ICdsHooksDaoAuthorizationSvc theCdsHooksDaoAuthorizationSvc) {
// return new ModuleConfigurationPrefetchSvc(
// theCdsResolutionStrategySvc,
// theResourcePrefetchDao,
// theResourcePrefetchFhirClient,
// theCdsHooksDaoAuthorizationSvc);
// }
@Bean @Bean
public ICdsCrDiscoveryServiceRegistry cdsCrDiscoveryServiceRegistry() { public ICdsCrDiscoveryServiceRegistry cdsCrDiscoveryServiceRegistry() {
CdsCrDiscoveryServiceRegistry registry = new CdsCrDiscoveryServiceRegistry(); CdsCrDiscoveryServiceRegistry registry = new CdsCrDiscoveryServiceRegistry();
registry.unregister(FhirVersionEnum.R4); registry.unregister(FhirVersionEnum.R4);
registry.register(FhirVersionEnum.R4, UpdatedCrDiscoveryServiceR4.class); registry.register(FhirVersionEnum.R4, UpdatedCrDiscoveryService.class);
return registry; return registry;
} }
@@ -50,7 +39,7 @@ public class StarterCdsHooksConfig {
public ICdsCrServiceRegistry cdsCrServiceRegistry() { public ICdsCrServiceRegistry cdsCrServiceRegistry() {
CdsCrServiceRegistry registry = new CdsCrServiceRegistry(); CdsCrServiceRegistry registry = new CdsCrServiceRegistry();
registry.unregister(FhirVersionEnum.R4); registry.unregister(FhirVersionEnum.R4);
registry.register(FhirVersionEnum.R4, UpdatedCdsCrServiceR4.class); registry.register(FhirVersionEnum.R4, UpdatedCdsCrService.class);
return registry; return registry;
} }

44
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCdsCrService.java Normal file
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@@ -0,0 +1,44 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.cdshooks.CdsServiceRequestJson;
import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrService;
import org.opencds.cqf.fhir.utility.adapter.IAdapterFactory;
import static org.opencds.cqf.fhir.utility.Constants.APPLY_PARAMETER_DATA;
public class UpdatedCdsCrService extends CdsCrService {
private final IAdapterFactory adapterFactory;
public UpdatedCdsCrService(
RequestDetails theRequestDetails, Repository theRepository, ICdsConfigService theCdsConfigService) {
super(theRequestDetails, theRepository, theCdsConfigService);
adapterFactory = IAdapterFactory.forFhirContext(theRepository.fhirContext());
}
@Override
public IBaseParameters encodeParams(CdsServiceRequestJson theJson) {
var parameters = adapterFactory.createParameters(super.encodeParams(theJson));
if (parameters.hasParameter(APPLY_PARAMETER_DATA)) {
parameters.addParameter(
"useServerData",
booleanTypeForVersion(parameters.fhirContext().getVersion().getVersion(), false));
}
return (IBaseParameters) parameters.get();
}
private IPrimitiveType<Boolean> booleanTypeForVersion(FhirVersionEnum fhirVersion, boolean value) {
return switch (fhirVersion) {
case DSTU2 -> new org.hl7.fhir.dstu2.model.BooleanType(value);
case DSTU3 -> new org.hl7.fhir.dstu3.model.BooleanType(value);
case R4 -> new org.hl7.fhir.r4.model.BooleanType(value);
case R5 -> new org.hl7.fhir.r5.model.BooleanType(value);
default -> throw new IllegalArgumentException("unknown or unsupported FHIR version");
};
}
}

28
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCdsCrServiceR4.java
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@@ -1,28 +0,0 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.cdshooks.CdsServiceRequestJson;
import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceR4;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.Parameters;
import org.opencds.cqf.fhir.api.Repository;
import static ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrConstants.APPLY_PARAMETER_DATA;
import static org.opencds.cqf.fhir.utility.r4.Parameters.part;
public class UpdatedCdsCrServiceR4 extends CdsCrServiceR4 {
public UpdatedCdsCrServiceR4(
RequestDetails theRequestDetails, Repository theRepository, ICdsConfigService theCdsConfigService) {
super(theRequestDetails, theRepository, theCdsConfigService);
}
@Override
public Parameters encodeParams(CdsServiceRequestJson theJson) {
Parameters parameters = super.encodeParams(theJson);
if (parameters.hasParameter(APPLY_PARAMETER_DATA)) {
parameters.addParameter(part("useServerData", new BooleanType(false)));
}
return parameters;
}
}

12
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCrDiscoveryService.java Normal file
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@@ -0,0 +1,12 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import org.hl7.fhir.instance.model.api.IIdType;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.CrDiscoveryService;
public class UpdatedCrDiscoveryService extends CrDiscoveryService {
public UpdatedCrDiscoveryService(IIdType thePlanDefinitionId, Repository theRepository) {
super(thePlanDefinitionId, theRepository);
maxUriLength = 6000;
}
}

12
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCrDiscoveryServiceR4.java
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@@ -1,12 +0,0 @@
package ca.uhn.fhir.jpa.starter.cdshooks;
import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CrDiscoveryServiceR4;
import org.hl7.fhir.instance.model.api.IIdType;
import org.opencds.cqf.fhir.api.Repository;
public class UpdatedCrDiscoveryServiceR4 extends CrDiscoveryServiceR4 {
public UpdatedCrDiscoveryServiceR4(IIdType thePlanDefinitionId, Repository theRepository) {
super(thePlanDefinitionId, theRepository);
myMaxUriLength = 6000;
}
}

4
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java
View File

@@ -97,9 +97,9 @@ public class FhirServerConfigCommon {
ourLog.info("Server configured for pre-expand value set default count of " ourLog.info("Server configured for pre-expand value set default count of "
+ (appProperties.getPre_expand_value_sets_default_count().toString())); + (appProperties.getPre_expand_value_sets_default_count().toString()));
ourLog.info("Server configured for pre-expand value set max count of " ourLog.info("Server configured for pre-expand value set max count of "
+ (appProperties.getPre_expand_value_sets_default_count().toString())); + (appProperties.getPre_expand_value_sets_max_count().toString()));
ourLog.info("Server configured for maximum expansion size of " ourLog.info("Server configured for maximum expansion size of "
+ (appProperties.getPre_expand_value_sets_default_count().toString())); + (appProperties.getMaximum_expansion_size().toString()));
} }
@Bean @Bean

6
src/main/java/ca/uhn/fhir/jpa/starter/cr/CrCommonConfig.java
View File

@@ -1,8 +1,5 @@
package ca.uhn.fhir.jpa.starter.cr; package ca.uhn.fhir.jpa.starter.cr;
import ca.uhn.fhir.cr.common.CodeCacheResourceChangeListener;
import ca.uhn.fhir.cr.common.CqlThreadFactory;
import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry; import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry; import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor; import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor;
@@ -19,6 +16,9 @@ import org.opencds.cqf.cql.engine.runtime.Code;
import org.opencds.cqf.fhir.cql.EvaluationSettings; import org.opencds.cqf.fhir.cql.EvaluationSettings;
import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings; import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings;
import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings; import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings;
import org.opencds.cqf.fhir.cr.hapi.common.CodeCacheResourceChangeListener;
import org.opencds.cqf.fhir.cr.hapi.common.CqlThreadFactory;
import org.opencds.cqf.fhir.cr.hapi.common.ElmCacheResourceChangeListener;
import org.opencds.cqf.fhir.cr.measure.CareGapsProperties; import org.opencds.cqf.fhir.cr.measure.CareGapsProperties;
import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions; import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
import org.opencds.cqf.fhir.utility.ValidationProfile; import org.opencds.cqf.fhir.utility.ValidationProfile;

10
src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrDstu3Config.java
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@@ -1,11 +1,11 @@
package ca.uhn.fhir.jpa.starter.cr; package ca.uhn.fhir.jpa.starter.cr;
import ca.uhn.fhir.cr.config.dstu3.ApplyOperationConfig;
import ca.uhn.fhir.cr.config.dstu3.CrDstu3Config;
import ca.uhn.fhir.cr.config.dstu3.DataRequirementsOperationConfig;
import ca.uhn.fhir.cr.config.dstu3.EvaluateOperationConfig;
import ca.uhn.fhir.cr.config.dstu3.PackageOperationConfig;
import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition; import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
import org.opencds.cqf.fhir.cr.hapi.config.dstu3.ApplyOperationConfig;
import org.opencds.cqf.fhir.cr.hapi.config.dstu3.CrDstu3Config;
import org.opencds.cqf.fhir.cr.hapi.config.dstu3.DataRequirementsOperationConfig;
import org.opencds.cqf.fhir.cr.hapi.config.dstu3.EvaluateOperationConfig;
import org.opencds.cqf.fhir.cr.hapi.config.dstu3.PackageOperationConfig;
import org.springframework.context.annotation.*; import org.springframework.context.annotation.*;
@Configuration @Configuration

16
src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrR4Config.java
View File

@@ -1,14 +1,14 @@
package ca.uhn.fhir.jpa.starter.cr; package ca.uhn.fhir.jpa.starter.cr;
import ca.uhn.fhir.cr.config.r4.ApplyOperationConfig;
import ca.uhn.fhir.cr.config.r4.CrR4Config;
import ca.uhn.fhir.cr.config.r4.DataRequirementsOperationConfig;
import ca.uhn.fhir.cr.config.r4.EvaluateOperationConfig;
import ca.uhn.fhir.cr.config.r4.ExtractOperationConfig;
import ca.uhn.fhir.cr.config.r4.PackageOperationConfig;
import ca.uhn.fhir.cr.config.r4.PopulateOperationConfig;
import ca.uhn.fhir.cr.config.r4.QuestionnaireOperationConfig;
import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition; import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
import org.opencds.cqf.fhir.cr.hapi.config.r4.ApplyOperationConfig;
import org.opencds.cqf.fhir.cr.hapi.config.r4.CrR4Config;
import org.opencds.cqf.fhir.cr.hapi.config.r4.DataRequirementsOperationConfig;
import org.opencds.cqf.fhir.cr.hapi.config.r4.EvaluateOperationConfig;
import org.opencds.cqf.fhir.cr.hapi.config.r4.ExtractOperationConfig;
import org.opencds.cqf.fhir.cr.hapi.config.r4.PackageOperationConfig;
import org.opencds.cqf.fhir.cr.hapi.config.r4.PopulateOperationConfig;
import org.opencds.cqf.fhir.cr.hapi.config.r4.QuestionnaireOperationConfig;
import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import; import org.springframework.context.annotation.Import;

4
src/main/resources/cds.application.yaml
View File

@@ -124,7 +124,7 @@ hapi:
data: data:
search_parameter_mode: USE_SEARCH_PARAMETERS # AUTO, USE_SEARCH_PARAMETERS, FILTER_IN_MEMORY search_parameter_mode: USE_SEARCH_PARAMETERS # AUTO, USE_SEARCH_PARAMETERS, FILTER_IN_MEMORY
terminology_parameter_mode: FILTER_IN_MEMORY # AUTO, USE_VALUE_SET_URL, USE_INLINE_CODES, FILTER_IN_MEMORY terminology_parameter_mode: FILTER_IN_MEMORY # AUTO, USE_VALUE_SET_URL, USE_INLINE_CODES, FILTER_IN_MEMORY
profile_mode: OFF # ENFORCED, DECLARED, OPTIONAL, TRUST, OFF profile_mode: DECLARED # ENFORCED, DECLARED, OPTIONAL, TRUST, OFF
cdshooks: cdshooks:
enabled: true enabled: true
@@ -217,7 +217,7 @@ hapi:
# - https://hapi.fhir.org/baseR4 # - https://hapi.fhir.org/baseR4
# pre_expand_value_sets: true # pre_expand_value_sets: true
# enable_task_pre_expand_value_sets: true # enable_task_pre_expand_value_sets: true
# pre_expand_value_sets_default_count: 1000 # pre_expand_value_sets_default_count: 1000
# pre_expand_value_sets_max_count: 1000 # pre_expand_value_sets_max_count: 1000
# maximum_expansion_size: 1000 # maximum_expansion_size: 1000

10
src/test/java/ca/uhn/fhir/jpa/starter/CdsHooksServletIT.java
View File

@@ -1,7 +1,6 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.cr.config.RepositoryConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry; import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig; import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
import ca.uhn.fhir.jpa.starter.cdshooks.StarterCdsHooksConfig; import ca.uhn.fhir.jpa.starter.cdshooks.StarterCdsHooksConfig;
@@ -9,7 +8,6 @@ import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.client.api.IGenericClient; import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum; import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry; import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
import com.google.gson.Gson; import com.google.gson.Gson;
import com.google.gson.JsonArray; import com.google.gson.JsonArray;
import com.google.gson.JsonObject; import com.google.gson.JsonObject;
@@ -22,6 +20,9 @@ import org.apache.http.impl.client.HttpClients;
import org.apache.http.util.EntityUtils; import org.apache.http.util.EntityUtils;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.opencds.cqf.fhir.cr.hapi.config.CrCdsHooksConfig;
import org.opencds.cqf.fhir.cr.hapi.config.RepositoryConfig;
import org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest; import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.test.web.server.LocalServerPort; import org.springframework.boot.test.web.server.LocalServerPort;
@@ -39,7 +40,8 @@ import static org.junit.jupiter.api.Assertions.fail;
Application.class, Application.class,
NicknameServiceConfig.class, NicknameServiceConfig.class,
RepositoryConfig.class, RepositoryConfig.class,
CdsHooksConfig.class, TestCdsHooksConfig.class,
CrCdsHooksConfig.class,
StarterCdsHooksConfig.class StarterCdsHooksConfig.class
}, properties = { }, properties = {
"spring.profiles.include=storageSettingsTest", "spring.profiles.include=storageSettingsTest",
@@ -116,7 +118,7 @@ class CdsHooksServletIT implements IServerSupport {
} }
@Test @Test
void testCdsHooks() throws IOException, InterruptedException { void testCdsHooks() throws IOException {
loadBundle("r4/HelloWorld-Bundle.json", ourCtx, ourClient); loadBundle("r4/HelloWorld-Bundle.json", ourCtx, ourClient);
await().atMost(10000, TimeUnit.MILLISECONDS).until(() -> hasCdsServices()); await().atMost(10000, TimeUnit.MILLISECONDS).until(() -> hasCdsServices());
var cdsRequest = "{\n" + var cdsRequest = "{\n" +

2
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java
View File

@@ -1,7 +1,6 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.cr.config.RepositoryConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry; import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.model.primitive.IdDt; import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.CacheControlDirective; import ca.uhn.fhir.rest.api.CacheControlDirective;
@@ -19,6 +18,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.opencds.cqf.fhir.cr.hapi.config.RepositoryConfig;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest; import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.test.web.server.LocalServerPort; import org.springframework.boot.test.web.server.LocalServerPort;

2
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
View File

@@ -1,7 +1,6 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.cr.config.RepositoryConfig;
import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig; import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
import ca.uhn.fhir.jpa.starter.cr.CrProperties; import ca.uhn.fhir.jpa.starter.cr.CrProperties;
import ca.uhn.fhir.model.primitive.IdDt; import ca.uhn.fhir.model.primitive.IdDt;
@@ -35,6 +34,7 @@ import org.junit.jupiter.api.Order;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest; import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource; import org.junit.jupiter.params.provider.ValueSource;
import org.opencds.cqf.fhir.cr.hapi.config.RepositoryConfig;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest; import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.test.web.server.LocalServerPort; import org.springframework.boot.test.web.server.LocalServerPort;