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Test fixes

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This commit is contained in:
jamesagnew
2020-05-14 08:08:52 -04:00
parent 1086e4cfb1
commit 3f43a91ed6
7 changed files with 117 additions and 96 deletions
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48
src/main/java/ca/uhn/fhir/jpa/starter/ApplicationContext.java
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@@ -1,28 +1,40 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirVersionEnum;
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(ca.uhn.fhir.jpa.config.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);
}
}
}

30
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
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@@ -1,14 +1,16 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.binstore.DatabaseBlobBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.subscription.module.channel.SubscriptionDeliveryHandlerFactory;
import ca.uhn.fhir.jpa.subscription.module.subscriber.email.IEmailSender;
import ca.uhn.fhir.jpa.subscription.module.subscriber.email.JavaMailEmailSender;
import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hl7.fhir.dstu2.model.Subscription;
import org.springframework.beans.factory.BeanFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@@ -50,9 +52,8 @@ 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");
@@ -116,15 +117,15 @@ public class FhirServerConfigCommon {
// Subscriptions are enabled by channel type
if (HapiProperties.getSubscriptionRestHookEnabled()) {
ourLog.info("Enabling REST-hook subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK);
}
if (HapiProperties.getSubscriptionEmailEnabled()) {
ourLog.info("Enabling email subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL);
}
if (HapiProperties.getSubscriptionWebsocketEnabled()) {
ourLog.info("Enabling websocket subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.WEBSOCKET);
retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET);
}
retVal.setFilterParameterEnabled(HapiProperties.getFilterSearchEnabled());
@@ -132,6 +133,12 @@ public class FhirServerConfigCommon {
return retVal;
}
@Bean
public PartitionSettings partitionSettings() {
return new PartitionSettings();
}
@Bean
public ModelConfig modelConfig() {
ModelConfig modelConfig = new ModelConfig();
@@ -197,8 +204,9 @@ 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;

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

@@ -485,5 +485,9 @@ 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);
}
}

109
src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java
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@@ -4,11 +4,12 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.rp.ResourceProviderFactory;
import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.DaoRegistry;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
@@ -22,25 +23,23 @@ import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
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.subscription.SubscriptionInterceptorLoader;
import ca.uhn.fhir.jpa.subscription.module.interceptor.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.jpa.util.ResourceProviderFactory;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
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;
import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import java.util.HashSet;
import java.util.TreeSet;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.springframework.context.ApplicationContext;
import org.springframework.http.HttpHeaders;
import org.springframework.web.cors.CorsConfiguration;
@@ -48,7 +47,9 @@ import org.springframework.web.cors.CorsConfiguration;
import javax.servlet.ServletException;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.Set;
import java.util.TreeSet;
public class JpaRestfulServer extends RestfulServer {
@@ -64,12 +65,12 @@ public class JpaRestfulServer extends RestfulServer {
* specified in the properties file.
*/
ApplicationContext appCtx = (ApplicationContext) getServletContext()
.getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
.getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
// Customize supported resource types
Set<String> supportedResourceTypes = HapiProperties.getSupportedResourceTypes();
if (!supportedResourceTypes.isEmpty() && !supportedResourceTypes.contains("SearchParameter")) {
supportedResourceTypes.add("SearchParameter");
supportedResourceTypes.add("SearchParameter");
}
if (!supportedResourceTypes.isEmpty()) {
@@ -112,36 +113,32 @@ 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));
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));
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));
confProvider.setImplementationDescription("HAPI FHIR R5 Server");
setServerConformanceProvider(confProvider);
} else {
throw new IllegalStateException();
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, 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, daoConfig, searchParamRegistry);
confProvider.setImplementationDescription("HAPI FHIR R5 Server");
setServerConformanceProvider(confProvider);
} else {
throw new IllegalStateException();
}
}
/*
@@ -179,9 +176,12 @@ 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
*/
@@ -218,7 +218,7 @@ public class JpaRestfulServer extends RestfulServer {
// manual triggering of a subscription delivery, enable this provider
if (false) { // <-- DISABLED RIGHT NOW
SubscriptionTriggeringProvider retriggeringProvider = appCtx
.getBean(SubscriptionTriggeringProvider.class);
.getBean(SubscriptionTriggeringProvider.class);
registerProvider(retriggeringProvider);
}
@@ -244,7 +244,7 @@ public class JpaRestfulServer extends RestfulServer {
config.addExposedHeader("Location");
config.addExposedHeader("Content-Location");
config.setAllowedMethods(
Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
config.setAllowCredentials(HapiProperties.getCorsAllowedCredentials());
// Create the interceptor and register it
@@ -255,14 +255,8 @@ public class JpaRestfulServer extends RestfulServer {
// If subscriptions are enabled, we want to register the interceptor that
// will activate them and match results against them
if (HapiProperties.getSubscriptionWebsocketEnabled() ||
HapiProperties.getSubscriptionEmailEnabled() ||
HapiProperties.getSubscriptionRestHookEnabled()) {
// Loads subscription interceptors (SubscriptionActivatingInterceptor, SubscriptionMatcherInterceptor)
// with activation of scheduled subscription
SubscriptionInterceptorLoader subscriptionInterceptorLoader = appCtx
.getBean(SubscriptionInterceptorLoader.class);
subscriptionInterceptorLoader.registerInterceptors();
HapiProperties.getSubscriptionEmailEnabled() ||
HapiProperties.getSubscriptionRestHookEnabled()) {
// Subscription debug logging
IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
@@ -272,15 +266,14 @@ public class JpaRestfulServer extends RestfulServer {
DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
if (HapiProperties.getAllowCascadingDeletes()) {
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(
daoRegistry, interceptorBroadcaster);
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster);
getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
}
// Binary Storage
if (HapiProperties.isBinaryStorageEnabled()) {
BinaryStorageInterceptor binaryStorageInterceptor = appCtx
.getBean(BinaryStorageInterceptor.class);
.getBean(BinaryStorageInterceptor.class);
getInterceptorService().registerInterceptor(binaryStorageInterceptor);
}
@@ -315,16 +308,16 @@ 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)));
Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
}
// Bulk Export
if (HapiProperties.getBulkExportEnabled()) {
registerProvider(appCtx.getBean(BulkDataExportProvider.class));
}
// Bulk Export
if (HapiProperties.getBulkExportEnabled()) {
registerProvider(appCtx.getBean(BulkDataExportProvider.class));
}
}
}

2
src/main/resources/hapi.properties
View File

@@ -61,6 +61,8 @@ validation.responses.enabled=false
###################################################
filter_search.enabled=true
graphql.enabled=true
# See FhirPathFilterInterceptor
fhirpath_interceptor.enabled=false
###################################################
# Supported Resources