Personal-Twin/hapi-fhir-jpaserver-starter
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pre-review cleanup

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This commit is contained in:
Ken Stevens
2020-05-27 17:54:07 -04:00
parent 0c9b9f7f77
commit e9fa2f2b8a
10 changed files with 80 additions and 83 deletions
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55
src/main/java/ca/uhn/fhir/jpa/starter/ApplicationContext.java
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@@ -1,29 +1,48 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.empi.config.EmpiConsumerConfig;
import ca.uhn.fhir.jpa.empi.config.EmpiSubmitterConfig;
import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
public class ApplicationContext extends AnnotationConfigWebApplicationContext {
public ApplicationContext() {
FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
if (fhirVersion == FhirVersionEnum.DSTU2) {
register(FhirServerConfigDstu2.class, FhirServerConfigCommon.class);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
register(FhirServerConfigDstu3.class, FhirServerConfigCommon.class);
} else if (fhirVersion == FhirVersionEnum.R4) {
register(FhirServerConfigR4.class, FhirServerConfigCommon.class);
} else if (fhirVersion == FhirVersionEnum.R5) {
register(FhirServerConfigR5.class, FhirServerConfigCommon.class);
} else {
throw new IllegalStateException();
}
if (HapiProperties.getSubscriptionWebsocketEnabled()) {
register(WebsocketDispatcherConfig.class);
}
public ApplicationContext() {
FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
if (fhirVersion == FhirVersionEnum.DSTU2) {
register(FhirServerConfigDstu2.class, FhirServerConfigCommon.class);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
register(FhirServerConfigDstu3.class, FhirServerConfigCommon.class);
} else if (fhirVersion == FhirVersionEnum.R4) {
register(FhirServerConfigR4.class, FhirServerConfigCommon.class);
} else if (fhirVersion == FhirVersionEnum.R5) {
register(FhirServerConfigR5.class, FhirServerConfigCommon.class);
} else {
throw new IllegalStateException();
}
if (HapiProperties.getSubscriptionWebsocketEnabled()) {
register(WebsocketDispatcherConfig.class);
}
if (HapiProperties.getSubscriptionEmailEnabled()
|| HapiProperties.getSubscriptionRestHookEnabled()
|| HapiProperties.getSubscriptionWebsocketEnabled()) {
register(SubscriptionSubmitterConfig.class);
register(SubscriptionProcessorConfig.class);
register(SubscriptionChannelConfig.class);
}
if (HapiProperties.getEmpiEnabled()) {
register(EmpiSubmitterConfig.class);
register(EmpiConsumerConfig.class);
register(EmpiConfig.class);
}
}
}

6
src/main/java/ca/uhn/fhir/jpa/starter/EmpiConfig.java
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@@ -2,23 +2,19 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.empi.api.IEmpiSettings;
import ca.uhn.fhir.empi.rules.config.EmpiSettings;
import ca.uhn.fhir.jpa.empi.config.EmpiConsumerConfig;
import ca.uhn.fhir.jpa.empi.config.EmpiSubmitterConfig;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.core.io.DefaultResourceLoader;
import org.springframework.core.io.Resource;
import java.io.IOException;
@Configuration
@Import({EmpiSubmitterConfig.class, EmpiConsumerConfig.class})
public class EmpiConfig {
@Bean
IEmpiSettings empiProperties() throws IOException {
IEmpiSettings empiSettings() throws IOException {
DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
Resource resource = resourceLoader.getResource("empi-rules.json");
String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);

28
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
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@@ -5,18 +5,14 @@ import ca.uhn.fhir.jpa.binstore.DatabaseBlobBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hl7.fhir.dstu2.model.Subscription;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import org.thymeleaf.util.Validate;
@@ -29,11 +25,6 @@ import java.sql.Driver;
*/
@Configuration
@EnableTransactionManagement
@Import({EmpiConfig.class,
SubscriptionSubmitterConfig.class,
SubscriptionProcessorConfig.class,
SubscriptionChannelConfig.class
})
public class FhirServerConfigCommon {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
@@ -60,9 +51,8 @@ public class FhirServerConfigCommon {
private Boolean emailStartTlsEnable = HapiProperties.getEmailStartTlsEnable();
private Boolean emailStartTlsRequired = HapiProperties.getEmailStartTlsRequired();
private Boolean emailQuitWait = HapiProperties.getEmailQuitWait();
@Autowired
private SubscriptionDeliveryHandlerFactory mySubscriptionDeliveryHandlerFactory;
private ApplicationContext myAppCtx;
public FhirServerConfigCommon() {
ourLog.info("Server configured to " + (this.allowContainsSearches ? "allow" : "deny") + " contains searches");
@@ -142,6 +132,12 @@ public class FhirServerConfigCommon {
return retVal;
}
@Bean
public PartitionSettings partitionSettings() {
return new PartitionSettings();
}
@Bean
public ModelConfig modelConfig() {
ModelConfig modelConfig = new ModelConfig();
@@ -206,8 +202,9 @@ public class FhirServerConfigCommon {
retVal.setStartTlsRequired(this.emailStartTlsRequired);
retVal.setQuitWait(this.emailQuitWait);
Validate.notNull(mySubscriptionDeliveryHandlerFactory, "No subscription delivery handler");
mySubscriptionDeliveryHandlerFactory.setEmailSender(retVal);
SubscriptionDeliveryHandlerFactory subscriptionDeliveryHandlerFactory = myAppCtx.getBean(SubscriptionDeliveryHandlerFactory.class);
Validate.notNull(subscriptionDeliveryHandlerFactory, "No subscription delivery handler");
subscriptionDeliveryHandlerFactory.setEmailSender(retVal);
return retVal;
@@ -215,9 +212,4 @@ public class FhirServerConfigCommon {
return null;
}
@Bean
public PartitionSettings partitionSettings() {
return new PartitionSettings();
}
}

4
src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java
View File

@@ -506,5 +506,9 @@ public class HapiProperties {
public static boolean getBulkExportEnabled() {
return HapiProperties.getBooleanProperty(BULK_EXPORT_ENABLED, true);
}
public static boolean isFhirPathFilterInterceptorEnabled() {
return HapiProperties.getBooleanProperty("fhirpath_interceptor.enabled", false);
}
}

52
src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java
View File

@@ -2,9 +2,6 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.empi.provider.EmpiProviderDstu3;
import ca.uhn.fhir.empi.provider.EmpiProviderR4;
import ca.uhn.fhir.empi.rules.config.EmpiSettings;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
@@ -28,13 +25,13 @@ import ca.uhn.fhir.jpa.provider.r5.JpaConformanceProviderR5;
import ca.uhn.fhir.jpa.provider.r5.JpaSystemProviderR5;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionSubmitInterceptorLoader;
import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
import ca.uhn.fhir.rest.server.interceptor.FhirPathFilterInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
@@ -118,37 +115,33 @@ public class JpaRestfulServer extends RestfulServer {
* You can also create your own subclass of the conformance provider if you need to
* provide further customization of your server's CapabilityStatement
*/
DaoConfig daoConfig = appCtx.getBean(DaoConfig.class);
ISearchParamRegistry searchParamRegistry = appCtx.getBean(ISearchParamRegistry.class);
if (fhirVersion == FhirVersionEnum.DSTU2) {
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));
IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = appCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao, daoConfig);
confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
IFhirSystemDao<Bundle, Meta> systemDao = appCtx
.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao,
appCtx.getBean(DaoConfig.class), appCtx.getBean(ISearchParamRegistry.class));
} else {
if (fhirVersion == FhirVersionEnum.DSTU3) {
IFhirSystemDao<Bundle, Meta> systemDao = appCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, daoConfig, searchParamRegistry);
confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.R4) {
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), appCtx.getBean(ISearchParamRegistry.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, daoConfig, searchParamRegistry);
confProvider.setImplementationDescription("HAPI FHIR R4 Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.R5) {
IFhirSystemDao<org.hl7.fhir.r5.model.Bundle, org.hl7.fhir.r5.model.Meta> systemDao = appCtx
.getBean("mySystemDaoR5", IFhirSystemDao.class);
JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao,
appCtx.getBean(DaoConfig.class), appCtx.getBean(ISearchParamRegistry.class));
IFhirSystemDao<org.hl7.fhir.r5.model.Bundle, org.hl7.fhir.r5.model.Meta> systemDao = appCtx.getBean("mySystemDaoR5", IFhirSystemDao.class);
JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao, daoConfig, searchParamRegistry);
confProvider.setImplementationDescription("HAPI FHIR R5 Server");
setServerConformanceProvider(confProvider);
} else {
throw new IllegalStateException();
}
}
/*
* ETag Support
@@ -185,9 +178,12 @@ public class JpaRestfulServer extends RestfulServer {
* browser.
*/
ResponseHighlighterInterceptor responseHighlighterInterceptor = new ResponseHighlighterInterceptor();
;
this.registerInterceptor(responseHighlighterInterceptor);
if (HapiProperties.isFhirPathFilterInterceptorEnabled()) {
registerInterceptor(new FhirPathFilterInterceptor());
}
/*
* Add some logging for each request
*/
@@ -263,13 +259,6 @@ public class JpaRestfulServer extends RestfulServer {
if (HapiProperties.getSubscriptionWebsocketEnabled() ||
HapiProperties.getSubscriptionEmailEnabled() ||
HapiProperties.getSubscriptionRestHookEnabled()) {
// Loads subscription interceptors (SubscriptionActivatingInterceptor, SubscriptionMatcherInterceptor)
// with activation of scheduled subscription
SubscriptionSubmitInterceptorLoader subscriptionInterceptorLoader = appCtx
.getBean(SubscriptionSubmitInterceptorLoader.class);
subscriptionInterceptorLoader.start();
// Subscription debug logging
IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
@@ -279,8 +268,7 @@ public class JpaRestfulServer extends RestfulServer {
DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
if (HapiProperties.getAllowCascadingDeletes()) {
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(getFhirContext(),
daoRegistry, interceptorBroadcaster);
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster);
getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
}
@@ -322,7 +310,7 @@ public class JpaRestfulServer extends RestfulServer {
BundleType type = BundleType.valueOf(o);
allowedBundleTypes.add(type.toCode());
});
DaoConfig config = appCtx.getBean(DaoConfig.class);
DaoConfig config = (DaoConfig) daoConfig;
config.setBundleTypesAllowedForStorage(
Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
}

2
src/main/resources/hapi.properties
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@@ -61,6 +61,8 @@ validation.responses.enabled=false
###################################################
filter_search.enabled=true
graphql.enabled=true
# See FhirPathFilterInterceptor
fhirpath_interceptor.enabled=false
###################################################
# Supported Resources