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Improve multiversion support

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This commit is contained in:
James Agnew
2019-02-11 08:59:37 -05:00
parent e21e00cf09
commit c604d8be53
13 changed files with 458 additions and 159 deletions
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67
src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java → src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
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@@ -1,29 +1,16 @@
package ca.uhn.fhir.jpa.demo;
package ca.uhn.fhir.jpa.starter;
import java.lang.reflect.InvocationTargetException;
import java.sql.Driver;
import java.util.Properties;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
import org.apache.commons.dbcp2.BasicDataSource;
import org.apache.commons.lang3.time.DateUtils;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.hl7.fhir.instance.model.Subscription;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
@@ -35,7 +22,7 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
*/
@Configuration
@EnableTransactionManagement()
public class FhirServerConfig extends BaseJavaConfigDstu3 {
public class FhirServerConfigCommon {
/**
* Configure FHIR properties around the the JPA server via this bean
@@ -63,19 +50,6 @@ public class FhirServerConfig extends BaseJavaConfigDstu3 {
return new ModelConfig();
}
/**
* We override the paging provider definition so that we can customize
* the default/max page sizes for search results. You can set these however
* you want, although very large page sizes will require a lot of RAM.
*/
@Override
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
pagingProvider.setDefaultPageSize(HapiProperties.getDefaultPageSize());
pagingProvider.setMaximumPageSize(HapiProperties.getMaximumPageSize());
return pagingProvider;
}
/**
* The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
* directory called "jpaserver_derby_files".
@@ -93,31 +67,6 @@ public class FhirServerConfig extends BaseJavaConfigDstu3 {
return retVal;
}
@Override
@Bean()
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
retVal.setPersistenceUnitName(HapiProperties.getPersistenceUnitName());
try {
retVal.setDataSource(dataSource());
} catch (Exception e) {
throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
}
retVal.setJpaProperties(jpaProperties());
return retVal;
}
private Properties jpaProperties() {
Properties extraProperties = HapiProperties.getProperties();
if (extraProperties == null) {
extraProperties = new Properties();
}
return extraProperties;
}
/**
* Do some fancy logging to create a nice access log that has details about each incoming request.
@@ -140,16 +89,4 @@ public class FhirServerConfig extends BaseJavaConfigDstu3 {
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
public IServerInterceptor subscriptionSecurityInterceptor() {
SubscriptionsRequireManualActivationInterceptorDstu3 retVal = new SubscriptionsRequireManualActivationInterceptorDstu3();
return retVal;
}
@Bean()
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
}
}

57
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java Normal file
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@@ -0,0 +1,57 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
@Configuration
public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
@Autowired
private DataSource myDataSource;
/**
* We override the paging provider definition so that we can customize
* the default/max page sizes for search results. You can set these however
* you want, although very large page sizes will require a lot of RAM.
*/
@Override
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
pagingProvider.setDefaultPageSize(HapiProperties.getDefaultPageSize());
pagingProvider.setMaximumPageSize(HapiProperties.getMaximumPageSize());
return pagingProvider;
}
@Override
@Bean()
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
retVal.setPersistenceUnitName(HapiProperties.getPersistenceUnitName());
try {
retVal.setDataSource(myDataSource);
} catch (Exception e) {
throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
}
retVal.setJpaProperties(HapiProperties.getProperties());
return retVal;
}
@Bean()
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
}
}

57
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java Normal file
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@@ -0,0 +1,57 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
@Configuration
public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
@Autowired
private DataSource myDataSource;
/**
* We override the paging provider definition so that we can customize
* the default/max page sizes for search results. You can set these however
* you want, although very large page sizes will require a lot of RAM.
*/
@Override
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
pagingProvider.setDefaultPageSize(HapiProperties.getDefaultPageSize());
pagingProvider.setMaximumPageSize(HapiProperties.getMaximumPageSize());
return pagingProvider;
}
@Override
@Bean()
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
retVal.setPersistenceUnitName(HapiProperties.getPersistenceUnitName());
try {
retVal.setDataSource(myDataSource);
} catch (Exception e) {
throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
}
retVal.setJpaProperties(HapiProperties.getProperties());
return retVal;
}
@Bean()
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
}
}

57
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java Normal file
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@@ -0,0 +1,57 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
@Configuration
public class FhirServerConfigR4 extends BaseJavaConfigR4 {
@Autowired
private DataSource myDataSource;
/**
* We override the paging provider definition so that we can customize
* the default/max page sizes for search results. You can set these however
* you want, although very large page sizes will require a lot of RAM.
*/
@Override
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
pagingProvider.setDefaultPageSize(HapiProperties.getDefaultPageSize());
pagingProvider.setMaximumPageSize(HapiProperties.getMaximumPageSize());
return pagingProvider;
}
@Override
@Bean()
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
retVal.setPersistenceUnitName(HapiProperties.getPersistenceUnitName());
try {
retVal.setDataSource(myDataSource);
} catch (Exception e) {
throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
}
retVal.setJpaProperties(HapiProperties.getProperties());
return retVal;
}
@Bean()
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
}
}

2
src/main/java/ca/uhn/fhir/jpa/demo/FhirTesterConfig.java → src/main/java/ca/uhn/fhir/jpa/starter/FhirTesterConfig.java
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@@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.demo;
package ca.uhn.fhir.jpa.starter;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;

34
src/main/java/ca/uhn/fhir/jpa/demo/HapiProperties.java → src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java
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@@ -1,12 +1,11 @@
package ca.uhn.fhir.jpa.demo;
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import com.google.common.annotations.VisibleForTesting;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.util.Properties;
@@ -30,22 +29,35 @@ public class HapiProperties {
public static final String TEST_PORT = "test.port";
public static final String SERVER_NAME = "server.name";
public static final String SERVER_ID = "server.id";
private static Properties properties;
private static final String HAPI_PROPERTIES = "hapi.properties";
private static final String FHIR_VERSION = "fhir_version";
static final String FHIR_VERSION = "fhir_version";
private static final String DEFAULT_ENCODING = "default_encoding";
private static final String ETAG_SUPPORT = "etag_support";
private static Properties properties;
/**
* Force the configuration to be reloaded
*/
public static void forceReload() {
properties = null;
getProperties();
}
/**
* This is mostly here for unit tests. Use the actual properties file
* to set values
*/
@VisibleForTesting
public static void setProperty(String theKey, String theValue) {
getProperties().setProperty(theKey, theValue);
}
public static Properties getProperties() {
if (properties == null) {
// Load the configurable properties file
InputStream in = null;
try {
in = HapiProperties.class.getClassLoader().getResourceAsStream(HAPI_PROPERTIES);
try (InputStream in = HapiProperties.class.getClassLoader().getResourceAsStream(HAPI_PROPERTIES)){
HapiProperties.properties = new Properties();
HapiProperties.properties.load(in);
in.close();
} catch (Exception e) {
throw new ConfigurationException("Could not load HAPI properties", e);
}
@@ -197,7 +209,7 @@ public class HapiProperties {
}
public static String getServerBase() {
return HapiProperties.getProperty(SERVER_BASE, "/baseDstu3");
return HapiProperties.getProperty(SERVER_BASE, "/fhir");
}
public static String getServerName() {

95
src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java → src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java
View File

@@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.demo;
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
@@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
import ca.uhn.fhir.jpa.provider.r4.TerminologyUploaderProviderR4;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
@@ -21,21 +22,20 @@ import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.instance.model.Subscription;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
import org.springframework.context.annotation.AnnotationConfigApplicationContext;
import javax.servlet.ServletException;
import java.util.List;
public class JpaServerDemo extends RestfulServer {
public class JpaRestfulServer extends RestfulServer {
private static final long serialVersionUID = 1L;
private static final Logger ourLog = LoggerFactory.getLogger(JpaServerDemo.class);
private AnnotationConfigApplicationContext appCtx;
private WebApplicationContext myAppCtx;
@Override
public void destroy() {
appCtx.close();
}
@SuppressWarnings("unchecked")
@Override
@@ -43,69 +43,61 @@ public class JpaServerDemo extends RestfulServer {
super.initialize();
/*
* We want to support FHIR DSTU2 format. This means that the server
* will use the DSTU2 bundle format and other DSTU2 encoding changes.
*
* If you want to use DSTU1 instead, change the following line, and change the 2 occurrences of dstu2 in web.xml to dstu1
* Create a FhirContext object that uses the version of FHIR
* specified in the properties file.
*/
FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
setFhirContext(new FhirContext(fhirVersion));
// Get the spring context from the web container (it's declared in web.xml)
myAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
appCtx = new AnnotationConfigApplicationContext();
/*
* The BaseJavaConfigDstu2.java class is a spring configuration
* file which is automatically generated as a part of hapi-fhir-jpaserver-base and
* contains bean definitions for a resource provider for each resource type
*/
String resourceProviderBeanName;
if (fhirVersion == FhirVersionEnum.DSTU2) {
resourceProviderBeanName = "myResourceProvidersDstu2";
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
resourceProviderBeanName = "myResourceProvidersDstu3";
} else if (fhirVersion == FhirVersionEnum.R4) {
resourceProviderBeanName = "myResourceProviderR4";
} else {
throw new IllegalStateException();
}
List<IResourceProvider> beans = myAppCtx.getBean(resourceProviderBeanName, List.class);
setResourceProviders(beans);
/*
* The system provider implements non-resource-type methods, such as
* transaction, and global history.
* ResourceProviders are fetched from the Spring context
*/
List<IResourceProvider> resourceProviders;
Object systemProvider;
if (fhirVersion == FhirVersionEnum.DSTU2) {
systemProvider = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
appCtx.register(FhirServerConfigDstu2.class, FhirServerConfigCommon.class);
appCtx.refresh();
resourceProviders = appCtx.getBean("myResourceProvidersDstu2", List.class);
systemProvider = appCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
systemProvider = myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
appCtx.register(FhirServerConfigDstu3.class, FhirServerConfigCommon.class);
appCtx.refresh();
resourceProviders = appCtx.getBean("myResourceProvidersDstu3", List.class);
systemProvider = appCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
} else if (fhirVersion == FhirVersionEnum.R4) {
systemProvider = myAppCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class);
appCtx.register(FhirServerConfigR4.class, FhirServerConfigCommon.class);
appCtx.refresh();
resourceProviders = appCtx.getBean("myResourceProvidersR4", List.class);
systemProvider = appCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class);
} else {
throw new IllegalStateException();
}
setPlainProviders(systemProvider);
registerProviders(resourceProviders);
registerProvider(systemProvider);
/*
* The conformance provider exports the supported resources, search parameters, etc for
* this server. The JPA version adds resource counts to the exported statement, so it
* this server. The JPA version adds resourceProviders counts to the exported statement, so it
* is a nice addition.
*
* You can also create your own subclass of the conformance provider if you need to
* provide further customization of your server's CapabilityStatement
*/
if (fhirVersion == FhirVersionEnum.DSTU2) {
IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = myAppCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao, myAppCtx.getBean(DaoConfig.class));
IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = appCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao, appCtx.getBean(DaoConfig.class));
confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
IFhirSystemDao<Bundle, Meta> systemDao = myAppCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, myAppCtx.getBean(DaoConfig.class));
IFhirSystemDao<Bundle, Meta> systemDao = appCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, appCtx.getBean(DaoConfig.class));
confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.R4) {
IFhirSystemDao<Bundle, Meta> systemDao = myAppCtx.getBean("mySystemDaoR4", IFhirSystemDao.class);
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, myAppCtx.getBean(DaoConfig.class));
IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = appCtx.getBean("mySystemDaoR4", IFhirSystemDao.class);
JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao, appCtx.getBean(DaoConfig.class));
confProvider.setImplementationDescription("HAPI FHIR R4 Server");
setServerConformanceProvider(confProvider);
} else {
@@ -134,20 +126,19 @@ public class JpaServerDemo extends RestfulServer {
setDefaultResponseEncoding(HapiProperties.getDefaultEncoding());
/*
* -- New in HAPI FHIR 1.5 --
* This configures the server to page search results to and from
* the database, instead of only paging them to memory. This may mean
* a performance hit when performing searches that return lots of results,
* but makes the server much more scalable.
*/
setPagingProvider(myAppCtx.getBean(DatabaseBackedPagingProvider.class));
setPagingProvider(appCtx.getBean(DatabaseBackedPagingProvider.class));
/*
* This interceptor formats the output using nice colourful
* HTML output when the request is detected to come from a
* browser.
*/
ResponseHighlighterInterceptor responseHighlighterInterceptor = myAppCtx.getBean(ResponseHighlighterInterceptor.class);
ResponseHighlighterInterceptor responseHighlighterInterceptor = appCtx.getBean(ResponseHighlighterInterceptor.class);
this.registerInterceptor(responseHighlighterInterceptor);
/*
@@ -170,16 +161,16 @@ public class JpaServerDemo extends RestfulServer {
*/
if (false) { // <-- DISABLED RIGHT NOW
if (fhirVersion == FhirVersionEnum.DSTU3) {
registerProvider(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
registerProvider(appCtx.getBean(TerminologyUploaderProviderDstu3.class));
} else if (fhirVersion == FhirVersionEnum.R4) {
registerProvider(myAppCtx.getBean(TerminologyUploaderProviderR4.class));
registerProvider(appCtx.getBean(TerminologyUploaderProviderR4.class));
}
}
// If you want to enable the $trigger-subscription operation to allow
// manual triggering of a subscription delivery, enable this provider
if (false) { // <-- DISABLED RIGHT NOW
SubscriptionTriggeringProvider retriggeringProvider = myAppCtx.getBean(SubscriptionTriggeringProvider.class);
SubscriptionTriggeringProvider retriggeringProvider = appCtx.getBean(SubscriptionTriggeringProvider.class);
registerProvider(retriggeringProvider);
}
}