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fixes for support of R4B / 6.2.0 (#455)

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This commit is contained in:
Jens Kristian Villadsen
2022-11-12 18:39:38 +01:00
committed by GitHub
parent 64aeb9b2fe
commit 2e1f5f5276
8 changed files with 252 additions and 6 deletions
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11
pom.xml
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@@ -14,7 +14,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.2.0-PRE18-SNAPSHOT</version>
<version>6.2.0</version>
</parent>
<artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -316,11 +316,18 @@
<version>${spring_boot_version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-core -->
<dependency>
<groupId>io.micrometer</groupId>
<artifactId>micrometer-core</artifactId>
<version>1.9.4</version>
</dependency>
<!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-registry-prometheus -->
<dependency>
<groupId>io.micrometer</groupId>
<artifactId>micrometer-registry-prometheus</artifactId>
<version>1.8.5</version>
<version>1.9.4</version>
</dependency>
<dependency>

4
src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnEitherVersion.java
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@@ -28,6 +28,10 @@ public class OnEitherVersion extends AnyNestedCondition {
static class OnR4 {
}
@Conditional(OnR4BCondition.class)
static class OnR4B {
}
@Conditional(OnR5Condition.class)
static class OnR5 {
}

18
src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR4BCondition.java Normal file
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@@ -0,0 +1,18 @@
package ca.uhn.fhir.jpa.starter.annotations;
import ca.uhn.fhir.context.FhirVersionEnum;
import org.springframework.context.annotation.Condition;
import org.springframework.context.annotation.ConditionContext;
import org.springframework.core.type.AnnotatedTypeMetadata;
public class OnR4BCondition implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
String version = conditionContext.
getEnvironment()
.getProperty("hapi.fhir.fhir_version")
.toUpperCase();
return FhirVersionEnum.R4B.name().equals(version);
}
}

17
src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigR4B.java Normal file
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@@ -0,0 +1,17 @@
package ca.uhn.fhir.jpa.starter.common;
import ca.uhn.fhir.jpa.config.r4b.JpaR4BConfig;
import ca.uhn.fhir.jpa.starter.annotations.OnR4BCondition;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@Configuration
@Conditional(OnR4BCondition.class)
@Import({
JpaR4BConfig.class,
StarterJpaConfig.class,
ElasticsearchConfig.class
})
public class FhirServerConfigR4B {
}

7
src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java
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@@ -26,7 +26,6 @@ import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.mdm.MdmLinkDaoJpaImpl;
import ca.uhn.fhir.jpa.dao.search.HSearchSortHelperImpl;
import ca.uhn.fhir.jpa.dao.search.IHSearchSortHelper;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.ThreadSafeResourceDeleterSvc;
import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
@@ -423,7 +422,6 @@ public class StarterJpaConfig {
public static IServerConformanceProvider<?> calculateConformanceProvider(IFhirSystemDao fhirSystemDao, RestfulServer fhirServer, DaoConfig daoConfig, ISearchParamRegistry searchParamRegistry, IValidationSupport theValidationSupport) {
FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
if (fhirVersion == FhirVersionEnum.DSTU2) {
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(fhirServer, fhirSystemDao, daoConfig);
confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
return confProvider;
@@ -437,6 +435,11 @@ public class StarterJpaConfig {
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, daoConfig, searchParamRegistry, theValidationSupport);
confProvider.setImplementationDescription("HAPI FHIR R4 Server");
return confProvider;
} else if (fhirVersion == FhirVersionEnum.R4B) {
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, daoConfig, searchParamRegistry, theValidationSupport);
confProvider.setImplementationDescription("HAPI FHIR R4B Server");
return confProvider;
} else if (fhirVersion == FhirVersionEnum.R5) {
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(fhirServer, fhirSystemDao, daoConfig, searchParamRegistry, theValidationSupport);

77
src/main/java/ca/uhn/fhir/jpa/starter/common/validation/RepositoryValidationInterceptorFactoryR4B.java Normal file
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@@ -0,0 +1,77 @@
package ca.uhn.fhir.jpa.starter.common.validation;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.interceptor.validation.IRepositoryValidatingRule;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingRuleBuilder;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.starter.annotations.OnR4BCondition;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.TokenParam;
import org.hl7.fhir.r4b.model.StructureDefinition;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
/**
* This class can be customized to enable the {@link RepositoryValidatingInterceptor}
* on this server.
* <p>
* The <code>enable_repository_validating_interceptor</code> property must be enabled in <code>application.yaml</code>
* in order to use this class.
*/
@ConditionalOnProperty(prefix = "hapi.fhir", name = ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR, havingValue = "true")
@Configuration
@Conditional(OnR4BCondition.class)
public class RepositoryValidationInterceptorFactoryR4B implements IRepositoryValidationInterceptorFactory {
private final FhirContext fhirContext;
private final RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder;
private final IFhirResourceDao structureDefinitionResourceProvider;
public RepositoryValidationInterceptorFactoryR4B(RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder, DaoRegistry daoRegistry) {
this.repositoryValidatingRuleBuilder = repositoryValidatingRuleBuilder;
this.fhirContext = daoRegistry.getSystemDao().getContext();
structureDefinitionResourceProvider = daoRegistry.getResourceDao("StructureDefinition");
}
@Override
public RepositoryValidatingInterceptor buildUsingStoredStructureDefinitions() {
IBundleProvider results = structureDefinitionResourceProvider.search(new SearchParameterMap().add(StructureDefinition.SP_KIND, new TokenParam("resource")));
Map<String, List<StructureDefinition>> structureDefintions = results.getResources(0, results.size())
.stream()
.map(StructureDefinition.class::cast)
.collect(Collectors.groupingBy(StructureDefinition::getType));
structureDefintions.forEach((key, value) -> {
String[] urls = value.stream().map(StructureDefinition::getUrl).toArray(String[]::new);
repositoryValidatingRuleBuilder.forResourcesOfType(key).requireAtLeastOneProfileOf(urls).and().requireValidationToDeclaredProfiles();
});
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
return new RepositoryValidatingInterceptor(fhirContext, rules);
}
@Override
public RepositoryValidatingInterceptor build() {
// Customize the ruleBuilder here to have the rules you want! We will give a simple example
// of enabling validation for all Patient resources
repositoryValidatingRuleBuilder.forResourcesOfType("Patient").requireAtLeastProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient").and().requireValidationToDeclaredProfiles();
// Do not customize below this line
List<IRepositoryValidatingRule> rules = repositoryValidatingRuleBuilder.build();
return new RepositoryValidatingInterceptor(fhirContext, rules);
}
}

4
src/main/resources/application.yaml
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@@ -48,8 +48,8 @@ spring:
# hibernate.search.backend.directory.root: target/lucenefiles
# hibernate.search.backend.lucene_version: lucene_current
### elastic parameters ===> see also elasticsearch section below <===
hibernate.search.backend.type: elasticsearch
hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
# hibernate.search.backend.type: elasticsearch
# hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
hapi:
fhir:
### This enables the swagger-ui at /fhir/swagger-ui/index.html as well as the /fhir/api-docs (see https://hapifhir.io/hapi-fhir/docs/server_plain/openapi.html)

120
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4BIT.java Normal file
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@@ -0,0 +1,120 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4b.model.Bundle;
import org.hl7.fhir.r4b.model.Patient;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Order;
import org.junit.jupiter.api.Test;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.web.server.LocalServerPort;
import static org.junit.jupiter.api.Assertions.assertEquals;
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties = {
"spring.datasource.url=jdbc:h2:mem:dbr4b",
"hapi.fhir.enable_repository_validating_interceptor=true",
"hapi.fhir.fhir_version=r4b",
"hapi.fhir.subscription.websocket_enabled=false",
"hapi.fhir.mdm_enabled=false",
"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
"hapi.fhir.implementationguides.dk-core.version=1.1.0",
// Override is currently required when using MDM as the construction of the MDM
// beans are ambiguous as they are constructed multiple places. This is evident
// when running in a spring boot environment
"spring.main.allow-bean-definition-overriding=true"})
class ExampleServerR4BIT {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4BIT.class);
private IGenericClient ourClient;
private FhirContext ourCtx;
@LocalServerPort
private int port;
@Test
@Order(0)
void testCreateAndRead() {
String methodName = "testCreateAndRead";
ourLog.info("Entering " + methodName + "()...");
Patient pt = new Patient();
pt.setActive(true);
pt.getBirthDateElement().setValueAsString("2020-01-01");
pt.addIdentifier().setSystem("http://foo").setValue("12345");
pt.addName().setFamily(methodName);
IIdType id = ourClient.create().resource(pt).execute().getId();
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
assertEquals(methodName, pt2.getName().get(0).getFamily());
}
@Test
public void testBatchPutWithIdenticalTags() {
String batchPuts = "{\n" +
"\t\"resourceType\": \"Bundle\",\n" +
"\t\"id\": \"patients\",\n" +
"\t\"type\": \"batch\",\n" +
"\t\"entry\": [\n" +
"\t\t{\n" +
"\t\t\t\"request\": {\n" +
"\t\t\t\t\"method\": \"PUT\",\n" +
"\t\t\t\t\"url\": \"Patient/pat-1\"\n" +
"\t\t\t},\n" +
"\t\t\t\"resource\": {\n" +
"\t\t\t\t\"resourceType\": \"Patient\",\n" +
"\t\t\t\t\"id\": \"pat-1\",\n" +
"\t\t\t\t\"meta\": {\n" +
"\t\t\t\t\t\"tag\": [\n" +
"\t\t\t\t\t\t{\n" +
"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
"\t\t\t\t\t\t}\n" +
"\t\t\t\t\t]\n" +
"\t\t\t\t}\n" +
"\t\t\t},\n" +
"\t\t\t\"fullUrl\": \"/Patient/pat-1\"\n" +
"\t\t},\n" +
"\t\t{\n" +
"\t\t\t\"request\": {\n" +
"\t\t\t\t\"method\": \"PUT\",\n" +
"\t\t\t\t\"url\": \"Patient/pat-2\"\n" +
"\t\t\t},\n" +
"\t\t\t\"resource\": {\n" +
"\t\t\t\t\"resourceType\": \"Patient\",\n" +
"\t\t\t\t\"id\": \"pat-2\",\n" +
"\t\t\t\t\"meta\": {\n" +
"\t\t\t\t\t\"tag\": [\n" +
"\t\t\t\t\t\t{\n" +
"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
"\t\t\t\t\t\t}\n" +
"\t\t\t\t\t]\n" +
"\t\t\t\t}\n" +
"\t\t\t},\n" +
"\t\t\t\"fullUrl\": \"/Patient/pat-2\"\n" +
"\t\t}\n" +
"\t]\n" +
"}";
Bundle bundle = FhirContext.forR4B().newJsonParser().parseResource(Bundle.class, batchPuts);
ourClient.transaction().withBundle(bundle).execute();
}
@BeforeEach
void beforeEach() {
ourCtx = FhirContext.forR4B();
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
String ourServerBase = "http://localhost:" + port + "/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
}
}