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Merge pull request #291 from hapifhir/5.6.0-upgrade

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5.6.0 upgrade
This commit is contained in:
Jens Kristian Villadsen
2021-11-18 20:23:59 +01:00
committed by GitHub
parent ea3f10ec86 96450874af
commit a58ef1cc7a
9 changed files with 48 additions and 47 deletions
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4
pom.xml
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@@ -14,13 +14,14 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.5.1</version> <version>5.6.0</version>
</parent> </parent>
<artifactId>hapi-fhir-jpaserver-starter</artifactId> <artifactId>hapi-fhir-jpaserver-starter</artifactId>
<properties> <properties>
<java.version>8</java.version> <java.version>8</java.version>
<spring_boot_version>2.5.6</spring_boot_version>
</properties> </properties>
<prerequisites> <prerequisites>
@@ -69,6 +70,7 @@
<dependency> <dependency>
<groupId>com.sun.mail</groupId> <groupId>com.sun.mail</groupId>
<artifactId>javax.mail</artifactId> <artifactId>javax.mail</artifactId>
<version>1.6.2</version>
<exclusions> <exclusions>
<exclusion> <exclusion>
<groupId>javax.activation</groupId> <groupId>javax.activation</groupId>

10
src/main/java/ca/uhn/fhir/jpa/starter/Application.java
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@@ -29,16 +29,6 @@ public class Application extends SpringBootServletInitializer {
public static void main(String[] args) { 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); SpringApplication.run(Application.class, args);
//Server is now accessible at eg. http://localhost:8080/fhir/metadata //Server is now accessible at eg. http://localhost:8080/fhir/metadata

8
src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java
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@@ -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.automaticindexing.session.AutomaticIndexingSynchronizationStrategyNames;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings; import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName; 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.SpringImplicitNamingStrategy;
import org.springframework.boot.orm.jpa.hibernate.SpringPhysicalNamingStrategy; import org.springframework.boot.orm.jpa.hibernate.SpringPhysicalNamingStrategy;
import org.springframework.core.env.CompositePropertySource; import org.springframework.core.env.CompositePropertySource;
@@ -25,7 +26,8 @@ import java.util.*;
public class EnvironmentHelper { public class EnvironmentHelper {
public static Properties getHibernateProperties(ConfigurableEnvironment environment) { public static Properties getHibernateProperties(ConfigurableEnvironment environment,
ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
Properties properties = new Properties(); Properties properties = new Properties();
Map<String, Object> jpaProps = getPropertiesStartingWith(environment, "spring.jpa.properties"); Map<String, Object> jpaProps = getPropertiesStartingWith(environment, "spring.jpa.properties");
for (Map.Entry<String, Object> entry : jpaProps.entrySet()) { for (Map.Entry<String, Object> entry : jpaProps.entrySet()) {
@@ -41,7 +43,7 @@ public class EnvironmentHelper {
//properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory)); //properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory));
//hapi-fhir-jpaserver-base "sensible defaults" //hapi-fhir-jpaserver-base "sensible defaults"
Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean().getJpaPropertyMap(); Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean(myConfigurableListableBeanFactory).getJpaPropertyMap();
hapiJpaPropertyMap.forEach(properties::putIfAbsent); hapiJpaPropertyMap.forEach(properties::putIfAbsent);
//hapi-fhir-jpaserver-starter defaults //hapi-fhir-jpaserver-starter defaults
@@ -73,7 +75,7 @@ public class EnvironmentHelper {
ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder(); ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder();
IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class); IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class);
builder.setRequiredIndexStatus(requireNonNullElse(requiredIndexStatus, IndexStatus.YELLOW)); builder.setRequiredIndexStatus(requireNonNullElse(requiredIndexStatus, IndexStatus.YELLOW));
builder.setRestUrl(getElasticsearchServerUrl(environment)); builder.setHosts(getElasticsearchServerUrl(environment));
builder.setUsername(getElasticsearchServerUsername(environment)); builder.setUsername(getElasticsearchServerUsername(environment));
builder.setPassword(getElasticsearchServerPassword(environment)); builder.setPassword(getElasticsearchServerPassword(environment));
builder.setProtocol(getElasticsearchServerProtocol(environment)); builder.setProtocol(getElasticsearchServerProtocol(environment));

24
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
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@@ -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.config.PartitionSettings.CrossPartitionReferenceMode;
import ca.uhn.fhir.jpa.model.entity.ModelConfig; import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory; 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.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 com.google.common.base.Strings;
import org.hl7.fhir.dstu2.model.Subscription; import org.hl7.fhir.dstu2.model.Subscription;
import org.springframework.boot.env.YamlPropertySourceLoader; import org.springframework.boot.env.YamlPropertySourceLoader;
@@ -207,22 +208,21 @@ public class FhirServerConfigCommon {
@Bean() @Bean()
public IEmailSender emailSender(AppProperties appProperties, Optional<SubscriptionDeliveryHandlerFactory> subscriptionDeliveryHandlerFactory) { public IEmailSender emailSender(AppProperties appProperties, Optional<SubscriptionDeliveryHandlerFactory> subscriptionDeliveryHandlerFactory) {
if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) { if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
JavaMailEmailSender retVal = new JavaMailEmailSender(); MailConfig mailConfig = new MailConfig();
AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail(); AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
retVal.setSmtpServerHostname(email.getHost()); mailConfig.setSmtpHostname(email.getHost());
retVal.setSmtpServerPort(email.getPort()); mailConfig.setSmtpPort(email.getPort());
retVal.setSmtpServerUsername(email.getUsername()); mailConfig.setSmtpUsername(email.getUsername());
retVal.setSmtpServerPassword(email.getPassword()); mailConfig.setSmtpPassword(email.getPassword());
retVal.setAuth(email.getAuth()); mailConfig.setSmtpUseStartTLS(email.getStartTlsEnable());
retVal.setStartTlsEnable(email.getStartTlsEnable());
retVal.setStartTlsRequired(email.getStartTlsRequired()); IEmailSender emailSender = new EmailSenderImpl(mailConfig);
retVal.setQuitWait(email.getQuitWait());
if(subscriptionDeliveryHandlerFactory.isPresent()) if(subscriptionDeliveryHandlerFactory.isPresent())
subscriptionDeliveryHandlerFactory.get().setEmailSender(retVal); subscriptionDeliveryHandlerFactory.get().setEmailSender(emailSender);
return retVal; return emailSender;
} }
return null; return null;

8
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java
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@@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.starter.annotations.OnDSTU2Condition; import ca.uhn.fhir.jpa.starter.annotations.OnDSTU2Condition;
import org.springframework.beans.factory.annotation.Autowired; 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.Bean;
import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Configuration;
@@ -58,8 +59,9 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
@Override @Override
@Bean() @Bean()
public LocalContainerEntityManagerFactoryBean entityManagerFactory() { public LocalContainerEntityManagerFactoryBean entityManagerFactory(
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(); ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
retVal.setPersistenceUnitName("HAPI_PU"); retVal.setPersistenceUnitName("HAPI_PU");
try { try {
@@ -67,7 +69,7 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
} catch (Exception e) { } catch (Exception e) {
throw new ConfigurationException("Could not set the data source due to a configuration issue", 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; return retVal;
} }

12
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java
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@@ -10,6 +10,7 @@ import javax.annotation.PostConstruct;
import javax.persistence.EntityManagerFactory; import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource; import javax.sql.DataSource;
import org.springframework.beans.factory.annotation.Autowired; 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.Bean;
import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Configuration;
@@ -62,8 +63,9 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
@Override @Override
@Bean @Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() { public LocalContainerEntityManagerFactoryBean entityManagerFactory(
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(); ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
retVal.setPersistenceUnitName("HAPI_PU"); retVal.setPersistenceUnitName("HAPI_PU");
try { 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); 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; return retVal;
} }
@@ -96,8 +99,7 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
} }
String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment); String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment); String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1)); return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword);
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword);
} else { } else {
return null; return null;
} }

12
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java
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@@ -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.annotations.OnR4Condition;
import ca.uhn.fhir.jpa.starter.cql.StarterCqlR4Config; import ca.uhn.fhir.jpa.starter.cql.StarterCqlR4Config;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.*; import org.springframework.context.annotation.*;
import org.springframework.core.env.ConfigurableEnvironment; import org.springframework.core.env.ConfigurableEnvironment;
import org.springframework.orm.jpa.JpaTransactionManager; import org.springframework.orm.jpa.JpaTransactionManager;
@@ -58,8 +59,9 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
@Override @Override
@Bean() @Bean()
public LocalContainerEntityManagerFactoryBean entityManagerFactory() { public LocalContainerEntityManagerFactoryBean entityManagerFactory(
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(); ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
retVal.setPersistenceUnitName("HAPI_PU"); retVal.setPersistenceUnitName("HAPI_PU");
try { 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); 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; return retVal;
} }
@@ -93,8 +96,7 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment); String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment); String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1)); return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword);
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword);
} else { } else {
return null; return null;
} }

12
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java
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@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl; import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition; import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition;
import org.springframework.beans.factory.annotation.Autowired; 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.Bean;
import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Configuration;
@@ -59,8 +60,9 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
@Override @Override
@Bean() @Bean()
public LocalContainerEntityManagerFactoryBean entityManagerFactory() { public LocalContainerEntityManagerFactoryBean entityManagerFactory(
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(); ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
retVal.setPersistenceUnitName("HAPI_PU"); retVal.setPersistenceUnitName("HAPI_PU");
try { 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); 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; return retVal;
} }
@@ -93,8 +96,7 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
} }
String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment); String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment); String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1)); return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword);
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword);
} else { } else {
return null; return null;
} }

5
src/main/resources/application.yaml
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@@ -10,6 +10,8 @@ spring:
# database connection pool size # database connection pool size
hikari: hikari:
maximum-pool-size: 10 maximum-pool-size: 10
flyway:
check-location: false
jpa: jpa:
properties: properties:
hibernate.format_sql: false hibernate.format_sql: false
@@ -31,9 +33,6 @@ spring:
batch: batch:
job: job:
enabled: false 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: hapi:
fhir: 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) ### 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)