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Merge remote-tracking branch 'origin/master' into rel_7_3_tracking
2 parents ab02bfe + 6b98988 commit cb6fa7d

27 files changed

+1729
-662
lines changed

‎.vscode/launch.json

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@@ -7,7 +7,18 @@
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"cwd": "${workspaceFolder}",
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"mainClass": "ca.uhn.fhir.jpa.starter.Application",
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"projectName": "hapi-fhir-jpaserver-starter",
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"args": "",
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"vmArgs": [
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"-XX:TieredStopAtLevel=1",
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// "-Ddebug=true",
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// "-Dloader.debug=true",
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"-Dhapi.fhir.bulk_export_enabled=false",
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"-Dspring.batch.job.enabled=false",
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"-Dspring.main.allow-bean-definition-overriding=true",
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"-Dhapi.fhir.cdshooks.enabled=true",
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"-Dhapi.fhir.cr.enabled=true",
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"-Dspring.main.allow-bean-definition-overriding=true"
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],
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"envFile": "${workspaceFolder}/.env"
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}
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]

‎.vscode/settings.json

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"**/.settings": true,
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"**/.factorypath": true
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},
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"java.compile.nullAnalysis.mode": "disabled"
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"java.compile.nullAnalysis.mode": "disabled",
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"java.configuration.updateBuildConfiguration": "automatic"
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}

‎README.md

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@@ -483,7 +483,11 @@ The server may be configured with subscription support by enabling properties in
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## Enabling Clinical Reasoning
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Set `hapi.fhir.cr_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [Clinical Quality Language](https://cql.hl7.org/) on this server.
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Set `hapi.fhir.cr_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [Clinical Quality Language](https://cql.hl7.org/) on this server. An alternate settings file, [cds.application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/cds.application.yaml), exists with the Clinical Reasoning module enabled and default settings that have been found to work with most CDS and dQM test cases.
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## Enabling CDS Hooks
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Set `hapi.fhir.cdshooks.enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable [CDS Hooks](https://cds-hooks.org/) on this server. The Clinical Reasoning module must also be enabled because this implementation of CDS Hooks includes [CDS on FHIR](https://build.fhir.org/clinicalreasoning-cds-on-fhir.html). An example CDS Service using CDS on FHIR is available in the CdsHooksServletIT test class.
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## Enabling MDM (EMPI)
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‎pom.xml

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@@ -42,6 +42,15 @@
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<dependencyManagement>
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<dependencies>
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<!-- Temporarily override CR depedencies for debugging -->
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<!-- <dependency>-->
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<!-- <groupId>org.opencds.cqf.fhir</groupId>-->
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<!-- <artifactId>cqf-fhir-bom</artifactId>-->
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<!-- <version>3.4.0</version>-->
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<!-- <type>pom</type>-->
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<!-- <scope>import</scope>-->
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<!-- </dependency>-->
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<dependency>
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<groupId>org.glassfish.jaxb</groupId>
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<artifactId>jaxb-runtime</artifactId>

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

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

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import ca.uhn.fhir.jpa.starter.cr.CrProperties;
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public class ProviderConfiguration {
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public static final ProviderConfiguration DEFAULT_PROVIDER_CONFIGURATION =
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new ProviderConfiguration(false, "client_id");
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private final String clientIdHeaderName;
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private final boolean cqlLoggingEnabled;
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}
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public ProviderConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
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this.clientIdHeaderName = cdsProperties.getClientIdHeaderName();
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this.cqlLoggingEnabled = crProperties.isCqlRuntimeDebugLoggingEnabled();
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this(crProperties.getCql().getRuntime().isDebugLoggingEnabled(), cdsProperties.getClientIdHeaderName());
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}
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public String getClientIdHeaderName() {

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

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package ca.uhn.fhir.jpa.starter.cdshooks;
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import ca.uhn.fhir.jpa.starter.cr.CrCommonConfig;
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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.CdsCrSettings;
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import ca.uhn.fhir.context.FhirVersionEnum;
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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.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 ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchDaoSvc;
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import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchFhirClientSvc;
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import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchSvc;
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import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsResolutionStrategySvc;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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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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@Configuration
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@Conditional({CdsHooksConfigCondition.class, CrConfigCondition.class})
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@Import(CdsHooksConfig.class)
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@Import({CdsHooksConfig.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, UpdatedCrDiscoveryServiceR4.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, UpdatedCdsCrServiceR4.class);
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return registry;
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}
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@Bean
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public CdsHooksProperties cdsHooksProperties() {
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return new CdsHooksProperties();

‎src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCdsCrServiceR4.java

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package ca.uhn.fhir.jpa.starter.cdshooks;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
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import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceR4;
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import org.hl7.fhir.r4.model.BooleanType;
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import org.hl7.fhir.r4.model.Parameters;
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import org.opencds.cqf.fhir.api.Repository;
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import java.util.stream.Collectors;
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import static ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrConstants.APPLY_PARAMETER_DATA;
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import static ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrConstants.APPLY_PARAMETER_DATA_ENDPOINT;
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import static org.opencds.cqf.fhir.utility.r4.Parameters.part;
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public class UpdatedCdsCrServiceR4 extends CdsCrServiceR4 {
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public UpdatedCdsCrServiceR4(RequestDetails theRequestDetails, Repository theRepository, ICdsConfigService theCdsConfigService) {
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super(theRequestDetails, theRepository, theCdsConfigService);
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}
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@Override
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public Parameters encodeParams(CdsServiceRequestJson theJson) {
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Parameters parameters = super.encodeParams(theJson);
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if (parameters.hasParameter(APPLY_PARAMETER_DATA)) {
26+
parameters.addParameter(part("useServerData", new BooleanType(false)));
27+
}
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return parameters;
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}
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}

‎src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCrDiscoveryServiceR4.java

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package ca.uhn.fhir.jpa.starter.cdshooks;
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import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CrDiscoveryServiceR4;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.opencds.cqf.fhir.api.Repository;
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public class UpdatedCrDiscoveryServiceR4 extends CrDiscoveryServiceR4 {
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public UpdatedCrDiscoveryServiceR4(IIdType thePlanDefinitionId, Repository theRepository) {
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super(thePlanDefinitionId, theRepository);
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myMaxUriLength = 6000;
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}
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}

‎src/main/java/ca/uhn/fhir/jpa/starter/cr/CareGapsProperties.java

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package ca.uhn.fhir.jpa.starter.cr;
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public class CareGapsProperties {
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private String reporter = "default";
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private String section_author = "default";
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public String getReporter() {
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return reporter;
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}
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public void setReporter(String reporter) {
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this.reporter = reporter;
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}
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public String getSection_author() {
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return section_author;
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}
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public void setSection_author(String section_author) {
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this.section_author = section_author;
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}
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}

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