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Merge pull request #89 from hapifhir/rel_5_0_0

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Start 5.0.0 release branch
This commit is contained in:
James Agnew
2020-05-14 08:40:42 -04:00
committed by GitHub
parent 7b5e0ae903 3f43a91ed6
commit f7fa572886
8 changed files with 119 additions and 118 deletions
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2
.travis.yml
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@@ -29,7 +29,7 @@ before_script:
- sudo chown -R travis:travis "$HOME/.m2/repository";
script:
- mvn -U install
- mvn -B install

2
pom.xml
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@@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>4.2.0</version>
<version>5.0.0</version>
</parent>
<artifactId>hapi-fhir-jpaserver-starter</artifactId>

14
src/main/java/ca/uhn/fhir/jpa/starter/ApplicationContext.java
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@@ -1,6 +1,10 @@
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 {
@@ -20,7 +24,15 @@ public class ApplicationContext extends AnnotationConfigWebApplicationContext {
}
if (HapiProperties.getSubscriptionWebsocketEnabled()) {
register(ca.uhn.fhir.jpa.config.WebsocketDispatcherConfig.class);
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
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@@ -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);
}
}

87
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 {
@@ -112,37 +113,33 @@ 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));
} 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));
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));
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
@@ -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
*/
@@ -257,12 +257,6 @@ public class JpaRestfulServer extends RestfulServer {
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();
// Subscription debug logging
IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
@@ -272,8 +266,7 @@ public class JpaRestfulServer extends RestfulServer {
DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
if (HapiProperties.getAllowCascadingDeletes()) {
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(
daoRegistry, interceptorBroadcaster);
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster);
getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
}
@@ -285,27 +278,7 @@ public class JpaRestfulServer extends RestfulServer {
}
// Validation
IValidatorModule validatorModule;
switch (fhirVersion) {
case DSTU2:
validatorModule = appCtx.getBean("myInstanceValidatorDstu2", IValidatorModule.class);
break;
case DSTU3:
validatorModule = appCtx.getBean("myInstanceValidatorDstu3", IValidatorModule.class);
break;
case R4:
validatorModule = appCtx.getBean("myInstanceValidatorR4", IValidatorModule.class);
break;
case R5:
validatorModule = appCtx.getBean("myInstanceValidatorR5", IValidatorModule.class);
break;
// These versions are not supported by HAPI FHIR JPA
case DSTU2_HL7ORG:
case DSTU2_1:
default:
validatorModule = null;
break;
}
IValidatorModule validatorModule = appCtx.getBean(IValidatorModule.class);
if (validatorModule != null) {
if (HapiProperties.getValidateRequestsEnabled()) {
RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
@@ -335,7 +308,7 @@ 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

18
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java
View File

@@ -14,7 +14,12 @@ import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
import org.eclipse.jetty.websocket.client.WebSocketClient;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Enumerations;
import org.hl7.fhir.r5.model.Observation;
import org.hl7.fhir.r5.model.Patient;
import org.hl7.fhir.r5.model.Subscription;
import org.hl7.fhir.r5.model.SubscriptionTopic;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
@@ -62,7 +67,7 @@ public class ExampleServerR5IT {
/*
* Create topic
*/
Topic topic = new Topic();
SubscriptionTopic topic = new SubscriptionTopic();
topic.getResourceTrigger().getQueryCriteria().setCurrent("Observation?status=final");
/*
@@ -71,14 +76,11 @@ public class ExampleServerR5IT {
Subscription subscription = new Subscription();
subscription.getTopic().setResource(topic);
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
channel.getType().addCoding()
subscription.setStatus(Enumerations.SubscriptionState.REQUESTED);
subscription.getChannelType()
.setSystem("http://terminology.hl7.org/CodeSystem/subscription-channel-type")
.setCode("websocket");
channel.getPayload().setContentType("application/json");
subscription.setChannel(channel);
subscription.setContentType("application/json");
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
IIdType mySubscriptionId = methodOutcome.getId();