diff --git a/pom.xml b/pom.xml index a7d67e5..6b677e8 100644 --- a/pom.xml +++ b/pom.xml @@ -14,7 +14,7 @@ ca.uhn.hapi.fhir hapi-fhir - 5.5.1 + 5.6.0 hapi-fhir-jpaserver-starter diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/Application.java b/src/main/java/ca/uhn/fhir/jpa/starter/Application.java index e823d5f..2cf60f5 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/Application.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/Application.java @@ -29,16 +29,6 @@ public class Application extends SpringBootServletInitializer { public static void main(String[] args) { - /* - * https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/246 - * This will be allowed for a short period until we know how MDM should be configured - * or don't have multiple equal bean instantiations. - * - * This will require changes in the main project as stated in the Github comment - * */ - System.setProperty("spring.main.allow-bean-definition-overriding","true"); - - System.setProperty("spring.batch.job.enabled", "false"); SpringApplication.run(Application.class, args); //Server is now accessible at eg. http://localhost:8080/fhir/metadata diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java b/src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java index 75db0f8..96a958f 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java @@ -14,6 +14,7 @@ import org.hibernate.search.engine.cfg.BackendSettings; import org.hibernate.search.mapper.orm.automaticindexing.session.AutomaticIndexingSynchronizationStrategyNames; 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; @@ -25,7 +26,8 @@ import java.util.*; public class EnvironmentHelper { - public static Properties getHibernateProperties(ConfigurableEnvironment environment) { + public static Properties getHibernateProperties(ConfigurableEnvironment environment, + ConfigurableListableBeanFactory myConfigurableListableBeanFactory) { Properties properties = new Properties(); Map jpaProps = getPropertiesStartingWith(environment, "spring.jpa.properties"); for (Map.Entry entry : jpaProps.entrySet()) { @@ -41,7 +43,7 @@ public class EnvironmentHelper { //properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory)); //hapi-fhir-jpaserver-base "sensible defaults" - Map hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean().getJpaPropertyMap(); + Map hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean(myConfigurableListableBeanFactory).getJpaPropertyMap(); hapiJpaPropertyMap.forEach(properties::putIfAbsent); //hapi-fhir-jpaserver-starter defaults @@ -73,7 +75,7 @@ public class EnvironmentHelper { ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder(); IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class); builder.setRequiredIndexStatus(requireNonNullElse(requiredIndexStatus, IndexStatus.YELLOW)); - builder.setRestUrl(getElasticsearchServerUrl(environment)); + builder.setHosts(getElasticsearchServerUrl(environment)); builder.setUsername(getElasticsearchServerUsername(environment)); builder.setPassword(getElasticsearchServerPassword(environment)); builder.setProtocol(getElasticsearchServerProtocol(environment)); diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java index 4ec5912..1e296d9 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java @@ -8,8 +8,9 @@ import ca.uhn.fhir.jpa.model.config.PartitionSettings; import ca.uhn.fhir.jpa.model.config.PartitionSettings.CrossPartitionReferenceMode; import ca.uhn.fhir.jpa.model.entity.ModelConfig; import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory; +import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl; import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender; -import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender; +import ca.uhn.fhir.rest.server.mail.MailConfig; import com.google.common.base.Strings; import org.hl7.fhir.dstu2.model.Subscription; import org.springframework.boot.env.YamlPropertySourceLoader; @@ -207,22 +208,21 @@ public class FhirServerConfigCommon { @Bean() public IEmailSender emailSender(AppProperties appProperties, Optional subscriptionDeliveryHandlerFactory) { if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) { - JavaMailEmailSender retVal = new JavaMailEmailSender(); + MailConfig mailConfig = new MailConfig(); AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail(); - retVal.setSmtpServerHostname(email.getHost()); - retVal.setSmtpServerPort(email.getPort()); - retVal.setSmtpServerUsername(email.getUsername()); - retVal.setSmtpServerPassword(email.getPassword()); - retVal.setAuth(email.getAuth()); - retVal.setStartTlsEnable(email.getStartTlsEnable()); - retVal.setStartTlsRequired(email.getStartTlsRequired()); - retVal.setQuitWait(email.getQuitWait()); + mailConfig.setSmtpHostname(email.getHost()); + mailConfig.setSmtpPort(email.getPort()); + mailConfig.setSmtpUsername(email.getUsername()); + mailConfig.setSmtpPassword(email.getPassword()); + mailConfig.setSmtpUseStartTLS(email.getStartTlsEnable()); + + IEmailSender emailSender = new EmailSenderImpl(mailConfig); if(subscriptionDeliveryHandlerFactory.isPresent()) - subscriptionDeliveryHandlerFactory.get().setEmailSender(retVal); + subscriptionDeliveryHandlerFactory.get().setEmailSender(emailSender); - return retVal; + return emailSender; } return null; diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java index 6e26d41..25548bf 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java @@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; import ca.uhn.fhir.jpa.starter.annotations.OnDSTU2Condition; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.config.ConfigurableListableBeanFactory; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Configuration; @@ -58,8 +59,9 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 { @Override @Bean() - public LocalContainerEntityManagerFactoryBean entityManagerFactory() { - LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(); + public LocalContainerEntityManagerFactoryBean entityManagerFactory( + ConfigurableListableBeanFactory myConfigurableListableBeanFactory) { + LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory); retVal.setPersistenceUnitName("HAPI_PU"); try { @@ -67,7 +69,7 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 { } catch (Exception e) { throw new ConfigurationException("Could not set the data source due to a configuration issue", e); } - retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment)); + retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory)); return retVal; } diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java index 367c0ec..84822dd 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java @@ -10,6 +10,7 @@ import javax.annotation.PostConstruct; import javax.persistence.EntityManagerFactory; import javax.sql.DataSource; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.config.ConfigurableListableBeanFactory; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Configuration; @@ -62,8 +63,9 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 { @Override @Bean - public LocalContainerEntityManagerFactoryBean entityManagerFactory() { - LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(); + public LocalContainerEntityManagerFactoryBean entityManagerFactory( + ConfigurableListableBeanFactory myConfigurableListableBeanFactory) { + LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory); retVal.setPersistenceUnitName("HAPI_PU"); try { @@ -72,7 +74,8 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 { throw new ConfigurationException("Could not set the data source due to a configuration issue", e); } - retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment)); + retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, + myConfigurableListableBeanFactory)); return retVal; } @@ -96,8 +99,7 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 { } String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment); String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment); - int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1)); - return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword); + return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword); } else { return null; } diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java index a53b057..842256a 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java @@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl; import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition; import ca.uhn.fhir.jpa.starter.cql.StarterCqlR4Config; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.config.ConfigurableListableBeanFactory; import org.springframework.context.annotation.*; import org.springframework.core.env.ConfigurableEnvironment; import org.springframework.orm.jpa.JpaTransactionManager; @@ -58,8 +59,9 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 { @Override @Bean() - public LocalContainerEntityManagerFactoryBean entityManagerFactory() { - LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(); + public LocalContainerEntityManagerFactoryBean entityManagerFactory( + ConfigurableListableBeanFactory myConfigurableListableBeanFactory) { + LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory); retVal.setPersistenceUnitName("HAPI_PU"); try { @@ -68,7 +70,8 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 { throw new ConfigurationException("Could not set the data source due to a configuration issue", e); } - retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment)); + retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, + myConfigurableListableBeanFactory)); return retVal; } @@ -93,8 +96,7 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 { String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment); String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment); - int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1)); - return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword); + return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword); } else { return null; } diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java index 2c6d72e..3cb6968 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java @@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl; import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.config.ConfigurableListableBeanFactory; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Configuration; @@ -59,8 +60,9 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 { @Override @Bean() - public LocalContainerEntityManagerFactoryBean entityManagerFactory() { - LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(); + public LocalContainerEntityManagerFactoryBean entityManagerFactory( + ConfigurableListableBeanFactory myConfigurableListableBeanFactory) { + LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory); retVal.setPersistenceUnitName("HAPI_PU"); try { @@ -69,7 +71,8 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 { throw new ConfigurationException("Could not set the data source due to a configuration issue", e); } - retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment)); + retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, + myConfigurableListableBeanFactory)); return retVal; } @@ -93,8 +96,7 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 { } String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment); String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment); - int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1)); - return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword); + return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword); } else { return null; } diff --git a/src/main/resources/application.yaml b/src/main/resources/application.yaml index 1c51699..7dd9ece 100644 --- a/src/main/resources/application.yaml +++ b/src/main/resources/application.yaml @@ -10,6 +10,8 @@ spring: # database connection pool size hikari: maximum-pool-size: 10 + flyway: + check-location: false jpa: properties: hibernate.format_sql: false @@ -31,9 +33,6 @@ spring: batch: job: enabled: false - main: -# TODO 5.6.0 -> Prevent duplicate bean definitions in the Spring batch config in HAPI: see: - allow-bean-definition-overriding: true 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)