Personal-Twin/hapi-fhir-jpaserver-starter
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Merge branch 'master' into rel_5_1_0

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jamesagnew
2020-08-13 15:57:38 -04:00
parent 2f28291681 a70fe5bfa0
commit 2805bb4683
9 changed files with 421 additions and 336 deletions
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3
.dockerignore Normal file
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@@ -0,0 +1,3 @@
target
.idea
.git

8
Dockerfile
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@@ -2,18 +2,16 @@ FROM hapiproject/hapi:base as build-hapi
ARG HAPI_FHIR_URL=https://github.com/jamesagnew/hapi-fhir/
ARG HAPI_FHIR_BRANCH=master
ARG HAPI_FHIR_STARTER_URL=https://github.com/hapifhir/hapi-fhir-jpaserver-starter/
ARG HAPI_FHIR_STARTER_BRANCH=master
RUN git clone --branch ${HAPI_FHIR_BRANCH} ${HAPI_FHIR_URL}
WORKDIR /tmp/hapi-fhir/
RUN /tmp/apache-maven-3.6.2/bin/mvn dependency:resolve
RUN /tmp/apache-maven-3.6.2/bin/mvn install -DskipTests
WORKDIR /tmp
RUN git clone --branch ${HAPI_FHIR_STARTER_BRANCH} ${HAPI_FHIR_STARTER_URL}
WORKDIR /tmp/hapi-fhir-jpaserver-starter
COPY . .
RUN /tmp/apache-maven-3.6.2/bin/mvn clean install -DskipTests
FROM tomcat:9-jre11

51
README.md
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@@ -12,6 +12,57 @@ In order to use this sample, you should have:
- Oracle Java (JDK) installed: Minimum JDK8 or newer.
- Apache Maven build tool (newest version)
## Running via [Docker Hub](https://hub.docker.com/repository/docker/hapiproject/hapi)
Each tagged/released version of `hapi-fhir-jpaserver` is built as a Docker image and published to Docker hub. To run the published Docker image from DockerHub:
```
docker pull hapiproject/hapi:latest
docker run -p 8080:8080 hapiproject/hapi:tagname
```
This will run the docker image with the default configuration, mapping port 8080 from the container to port 8080 in the host. Once running, you can access `http://localhost:8080/hapi-fhir-jpaserver/fhir` in the browser to access the HAPI FHIR server's UI.
If you change the mapped port, you need to change the configuration used by HAPI to have the correct `server_address` property/value.
### Configuration via environment variables
You can customize HAPI directly from the `run` command using environment variables. For example:
`docker run -p 8090:8080 -e server_address=http://localhost:8090/hapi-fhir-jpaserver/fhir hapiproject/hapi:tagname`
HAPI looks in the environment variables for properties in the [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties) file.
### Configuration via overridden hapi.properties file
You can customize HAPI by telling HAPI to look for the `hapi.properties` file in a different location:
`docker run -p 8090:8080 -e hapi.properties=/some/directory/with/hapi.properties hapiproject/hapi:tagname`
### Example docker-compose.yml
```
version: '3.7'
services:
web:
image: "hapiproject/hapi:tagname"
ports:
- "8090:8080"
configs:
- source: hapi
target: /data/hapi/hapi.properties
volumes:
- hapi-data:/data/hapi
environment:
JAVA_OPTS: '-Dhapi.properties=/data/hapi/hapi.properties'
configs:
hapi:
external: true
volumes:
hapi-data:
external: true
```
## Running locally
The easiest way to run this server is to run it directly in Maven using a built-in Jetty server. To do this, change `src/main/resources/hapi.properties` `server_address` and `server.base` with the values commented out as _For Jetty, use this_ and then execute the following command:

2
pom.xml
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@@ -48,7 +48,7 @@
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>8.0.11</version>
<version>8.0.16</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.postgresql/postgresql -->
<dependency>

337
src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java Normal file
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@@ -0,0 +1,337 @@
package ca.uhn.fhir.jpa.starter;
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.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
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.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.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import org.hl7.fhir.dstu3.model.Bundle;
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;
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 BaseJpaRestfulServer extends RestfulServer {
private static final long serialVersionUID = 1L;
@SuppressWarnings("unchecked")
@Override
protected void initialize() throws ServletException {
super.initialize();
/*
* Create a FhirContext object that uses the version of FHIR
* specified in the properties file.
*/
ApplicationContext appCtx = (ApplicationContext) getServletContext()
.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");
}
if (!supportedResourceTypes.isEmpty()) {
DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
daoRegistry.setSupportedResourceTypes(supportedResourceTypes);
}
/*
* ResourceProviders are fetched from the Spring context
*/
FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
ResourceProviderFactory resourceProviders;
Object systemProvider;
if (fhirVersion == FhirVersionEnum.DSTU2) {
resourceProviders = appCtx.getBean("myResourceProvidersDstu2", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
resourceProviders = appCtx.getBean("myResourceProvidersDstu3", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
} else if (fhirVersion == FhirVersionEnum.R4) {
resourceProviders = appCtx.getBean("myResourceProvidersR4", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class);
} else if (fhirVersion == FhirVersionEnum.R5) {
resourceProviders = appCtx.getBean("myResourceProvidersR5", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderR5", JpaSystemProviderR5.class);
} else {
throw new IllegalStateException();
}
setFhirContext(appCtx.getBean(FhirContext.class));
registerProviders(resourceProviders.createProviders());
registerProvider(systemProvider);
/*
* The conformance provider exports the supported resources, search parameters, etc for
* 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
*/
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, 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, 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();
}
}
/*
* ETag Support
*/
setETagSupport(HapiProperties.getEtagSupport());
/*
* This server tries to dynamically generate narratives
*/
FhirContext ctx = getFhirContext();
ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
/*
* Default to JSON and pretty printing
*/
setDefaultPrettyPrint(HapiProperties.getDefaultPrettyPrint());
/*
* Default encoding
*/
setDefaultResponseEncoding(HapiProperties.getDefaultEncoding());
/*
* 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(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 = new ResponseHighlighterInterceptor();
this.registerInterceptor(responseHighlighterInterceptor);
if (HapiProperties.isFhirPathFilterInterceptorEnabled()) {
registerInterceptor(new FhirPathFilterInterceptor());
}
/*
* Add some logging for each request
*/
LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
loggingInterceptor.setLoggerName(HapiProperties.getLoggerName());
loggingInterceptor.setMessageFormat(HapiProperties.getLoggerFormat());
loggingInterceptor.setErrorMessageFormat(HapiProperties.getLoggerErrorFormat());
loggingInterceptor.setLogExceptions(HapiProperties.getLoggerLogExceptions());
this.registerInterceptor(loggingInterceptor);
/*
* If you are hosting this server at a specific DNS name, the server will try to
* figure out the FHIR base URL based on what the web container tells it, but
* this doesn't always work. If you are setting links in your search bundles that
* just refer to "localhost", you might want to use a server address strategy:
*/
String serverAddress = HapiProperties.getServerAddress();
if (serverAddress != null && serverAddress.length() > 0) {
setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
}
/*
* If you are using DSTU3+, you may want to add a terminology uploader, which allows
* uploading of external terminologies such as Snomed CT. Note that this uploader
* does not have any security attached (any anonymous user may use it by default)
* so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
* with this feature.
*/
if (false) { // <-- DISABLED RIGHT NOW
registerProvider(appCtx.getBean(TerminologyUploaderProvider.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 = appCtx
.getBean(SubscriptionTriggeringProvider.class);
registerProvider(retriggeringProvider);
}
// Define your CORS configuration. This is an example
// showing a typical setup. You should customize this
// to your specific needs
if (HapiProperties.getCorsEnabled()) {
CorsConfiguration config = new CorsConfiguration();
config.addAllowedHeader(HttpHeaders.ORIGIN);
config.addAllowedHeader(HttpHeaders.ACCEPT);
config.addAllowedHeader(HttpHeaders.CONTENT_TYPE);
config.addAllowedHeader(HttpHeaders.AUTHORIZATION);
config.addAllowedHeader(HttpHeaders.CACHE_CONTROL);
config.addAllowedHeader("x-fhir-starter");
config.addAllowedHeader("X-Requested-With");
config.addAllowedHeader("Prefer");
String allAllowedCORSOrigins = HapiProperties.getCorsAllowedOrigin();
Arrays.stream(allAllowedCORSOrigins.split(",")).forEach(o -> {
config.addAllowedOrigin(o);
});
config.addAllowedOrigin(HapiProperties.getCorsAllowedOrigin());
config.addExposedHeader("Location");
config.addExposedHeader("Content-Location");
config.setAllowedMethods(
Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
config.setAllowCredentials(HapiProperties.getCorsAllowedCredentials());
// Create the interceptor and register it
CorsInterceptor interceptor = new CorsInterceptor(config);
registerInterceptor(interceptor);
}
// 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()) {
// Subscription debug logging
IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
}
// Cascading deletes
DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
if (HapiProperties.getAllowCascadingDeletes()) {
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster);
getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
}
// Binary Storage
if (HapiProperties.isBinaryStorageEnabled()) {
BinaryStorageInterceptor binaryStorageInterceptor = appCtx
.getBean(BinaryStorageInterceptor.class);
getInterceptorService().registerInterceptor(binaryStorageInterceptor);
}
// Validation
IValidatorModule validatorModule = appCtx.getBean(IValidatorModule.class);
if (validatorModule != null) {
if (HapiProperties.getValidateRequestsEnabled()) {
RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
registerInterceptor(interceptor);
}
if (HapiProperties.getValidateResponsesEnabled()) {
ResponseValidatingInterceptor interceptor = new ResponseValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
registerInterceptor(interceptor);
}
}
// GraphQL
if (HapiProperties.getGraphqlEnabled()) {
if (fhirVersion.isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
registerProvider(appCtx.getBean(GraphQLProvider.class));
}
}
if (!HapiProperties.getAllowedBundleTypes().isEmpty()) {
String allowedBundleTypesString = HapiProperties.getAllowedBundleTypes();
Set<String> allowedBundleTypes = new HashSet<>();
Arrays.stream(allowedBundleTypesString.split(",")).forEach(o -> {
BundleType type = BundleType.valueOf(o);
allowedBundleTypes.add(type.toCode());
});
DaoConfig config = daoConfig;
config.setBundleTypesAllowedForStorage(
Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
}
// Bulk Export
if (HapiProperties.getBulkExportEnabled()) {
registerProvider(appCtx.getBean(BulkDataExportProvider.class));
}
// Partitioning
if (HapiProperties.getPartitioningMultitenancyEnabled()) {
registerInterceptor(new RequestTenantPartitionInterceptor());
setTenantIdentificationStrategy(new UrlBaseTenantIdentificationStrategy());
registerProviders(appCtx.getBean(PartitionManagementProvider.class));
}
if (HapiProperties.getClientIdStrategy() == DaoConfig.ClientIdStrategyEnum.ANY) {
daoConfig.setResourceServerIdStrategy(DaoConfig.IdStrategyEnum.UUID);
daoConfig.setResourceClientIdStrategy(HapiProperties.getClientIdStrategy());
}
}
}

20
src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java
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@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
@@ -17,6 +18,7 @@ import java.util.Arrays;
import java.util.Locale;
import java.util.Properties;
import java.util.Set;
import java.util.Map;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.defaultString;
@@ -78,6 +80,7 @@ public class HapiProperties {
static final String MAX_BINARY_SIZE = "max_binary_size";
static final String PARTITIONING_MULTITENANCY_ENABLED = "partitioning.multitenancy.enabled";
private static final String PARTITIONING_INCLUDE_PARTITION_IN_SEARCH_HASHES = "partitioning.partitioning_include_in_search_hashes";
static final String CLIENT_ID_STRATEGY = "daoconfig.client_id_strategy";
private static Properties ourProperties;
public static boolean isElasticSearchEnabled() {
@@ -143,6 +146,10 @@ public class HapiProperties {
if (overrideProps != null) {
properties.putAll(overrideProps);
}
properties.putAll(System.getenv().entrySet()
.stream()
.filter(e -> e.getValue() != null && properties.containsKey(e.getKey()))
.collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue)));
return properties;
}
@@ -243,6 +250,16 @@ public class HapiProperties {
return ETagSupportEnum.ENABLED;
}
public static DaoConfig.ClientIdStrategyEnum getClientIdStrategy() {
String idStrategy = HapiProperties.getProperty(CLIENT_ID_STRATEGY);
if (idStrategy != null && idStrategy.length() > 0) {
return DaoConfig.ClientIdStrategyEnum.valueOf(idStrategy);
}
return DaoConfig.ClientIdStrategyEnum.ALPHANUMERIC;
}
public static EncodingEnum getDefaultEncoding() {
String defaultEncodingString = HapiProperties.getProperty(DEFAULT_ENCODING);
@@ -515,5 +532,8 @@ public class HapiProperties {
return HapiProperties.getBooleanProperty("fhirpath_interceptor.enabled", false);
}
public static boolean getPartitioningMultitenancyEnabled() {
return HapiProperties.getBooleanProperty(PARTITIONING_MULTITENANCY_ENABLED, false);
}
}

329
src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java
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@@ -1,341 +1,16 @@
package ca.uhn.fhir.jpa.starter;
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.binstore.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.bulk.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
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.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.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import org.hl7.fhir.dstu3.model.Bundle;
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;
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 {
public class JpaRestfulServer extends BaseJpaRestfulServer {
private static final long serialVersionUID = 1L;
@SuppressWarnings("unchecked")
@Override
protected void initialize() throws ServletException {
super.initialize();
/*
* Create a FhirContext object that uses the version of FHIR
* specified in the properties file.
*/
ApplicationContext appCtx = (ApplicationContext) getServletContext()
.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");
}
if (!supportedResourceTypes.isEmpty()) {
DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
daoRegistry.setSupportedResourceTypes(supportedResourceTypes);
}
/*
* ResourceProviders are fetched from the Spring context
*/
FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
ResourceProviderFactory resourceProviders;
Object systemProvider;
if (fhirVersion == FhirVersionEnum.DSTU2) {
resourceProviders = appCtx.getBean("myResourceProvidersDstu2", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
resourceProviders = appCtx.getBean("myResourceProvidersDstu3", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
} else if (fhirVersion == FhirVersionEnum.R4) {
resourceProviders = appCtx.getBean("myResourceProvidersR4", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class);
} else if (fhirVersion == FhirVersionEnum.R5) {
resourceProviders = appCtx.getBean("myResourceProvidersR5", ResourceProviderFactory.class);
systemProvider = appCtx.getBean("mySystemProviderR5", JpaSystemProviderR5.class);
} else {
throw new IllegalStateException();
}
setFhirContext(appCtx.getBean(FhirContext.class));
registerProviders(resourceProviders.createProviders());
registerProvider(systemProvider);
/*
* The conformance provider exports the supported resources, search parameters, etc for
* 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
*/
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, 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, 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();
}
}
/*
* ETag Support
*/
setETagSupport(HapiProperties.getEtagSupport());
/*
* This server tries to dynamically generate narratives
*/
FhirContext ctx = getFhirContext();
ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
/*
* Default to JSON and pretty printing
*/
setDefaultPrettyPrint(HapiProperties.getDefaultPrettyPrint());
/*
* Default encoding
*/
setDefaultResponseEncoding(HapiProperties.getDefaultEncoding());
/*
* 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(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 = new ResponseHighlighterInterceptor();
this.registerInterceptor(responseHighlighterInterceptor);
if (HapiProperties.isFhirPathFilterInterceptorEnabled()) {
registerInterceptor(new FhirPathFilterInterceptor());
}
/*
* Add some logging for each request
*/
LoggingInterceptor loggingInterceptor = new LoggingInterceptor();
loggingInterceptor.setLoggerName(HapiProperties.getLoggerName());
loggingInterceptor.setMessageFormat(HapiProperties.getLoggerFormat());
loggingInterceptor.setErrorMessageFormat(HapiProperties.getLoggerErrorFormat());
loggingInterceptor.setLogExceptions(HapiProperties.getLoggerLogExceptions());
this.registerInterceptor(loggingInterceptor);
/*
* If you are hosting this server at a specific DNS name, the server will try to
* figure out the FHIR base URL based on what the web container tells it, but
* this doesn't always work. If you are setting links in your search bundles that
* just refer to "localhost", you might want to use a server address strategy:
*/
String serverAddress = HapiProperties.getServerAddress();
if (serverAddress != null && serverAddress.length() > 0) {
setServerAddressStrategy(new HardcodedServerAddressStrategy(serverAddress));
}
/*
* If you are using DSTU3+, you may want to add a terminology uploader, which allows
* uploading of external terminologies such as Snomed CT. Note that this uploader
* does not have any security attached (any anonymous user may use it by default)
* so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
* with this feature.
*/
if (false) { // <-- DISABLED RIGHT NOW
registerProvider(appCtx.getBean(TerminologyUploaderProvider.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 = appCtx
.getBean(SubscriptionTriggeringProvider.class);
registerProvider(retriggeringProvider);
}
// Define your CORS configuration. This is an example
// showing a typical setup. You should customize this
// to your specific needs
if (HapiProperties.getCorsEnabled()) {
CorsConfiguration config = new CorsConfiguration();
config.addAllowedHeader(HttpHeaders.ORIGIN);
config.addAllowedHeader(HttpHeaders.ACCEPT);
config.addAllowedHeader(HttpHeaders.CONTENT_TYPE);
config.addAllowedHeader(HttpHeaders.AUTHORIZATION);
config.addAllowedHeader(HttpHeaders.CACHE_CONTROL);
config.addAllowedHeader("x-fhir-starter");
config.addAllowedHeader("X-Requested-With");
config.addAllowedHeader("Prefer");
String allAllowedCORSOrigins = HapiProperties.getCorsAllowedOrigin();
Arrays.stream(allAllowedCORSOrigins.split(",")).forEach(o -> {
config.addAllowedOrigin(o);
});
config.addAllowedOrigin(HapiProperties.getCorsAllowedOrigin());
config.addExposedHeader("Location");
config.addExposedHeader("Content-Location");
config.setAllowedMethods(
Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
config.setAllowCredentials(HapiProperties.getCorsAllowedCredentials());
// Create the interceptor and register it
CorsInterceptor interceptor = new CorsInterceptor(config);
registerInterceptor(interceptor);
}
// 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()) {
// Subscription debug logging
IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
}
// Cascading deletes
DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
if (HapiProperties.getAllowCascadingDeletes()) {
CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster);
getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
}
// Binary Storage
if (HapiProperties.isBinaryStorageEnabled()) {
BinaryStorageInterceptor binaryStorageInterceptor = appCtx
.getBean(BinaryStorageInterceptor.class);
getInterceptorService().registerInterceptor(binaryStorageInterceptor);
}
// Validation
IValidatorModule validatorModule = appCtx.getBean(IValidatorModule.class);
if (validatorModule != null) {
if (HapiProperties.getValidateRequestsEnabled()) {
RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
registerInterceptor(interceptor);
}
if (HapiProperties.getValidateResponsesEnabled()) {
ResponseValidatingInterceptor interceptor = new ResponseValidatingInterceptor();
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setValidatorModules(Collections.singletonList(validatorModule));
registerInterceptor(interceptor);
}
}
// GraphQL
if (HapiProperties.getGraphqlEnabled()) {
if (fhirVersion.isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
registerProvider(appCtx.getBean(GraphQLProvider.class));
}
}
if (!HapiProperties.getAllowedBundleTypes().isEmpty()) {
String allowedBundleTypesString = HapiProperties.getAllowedBundleTypes();
Set<String> allowedBundleTypes = new HashSet<>();
Arrays.stream(allowedBundleTypesString.split(",")).forEach(o -> {
BundleType type = BundleType.valueOf(o);
allowedBundleTypes.add(type.toCode());
});
DaoConfig config = daoConfig;
config.setBundleTypesAllowedForStorage(
Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
}
// Bulk Export
if (HapiProperties.getBulkExportEnabled()) {
registerProvider(appCtx.getBean(BulkDataExportProvider.class));
}
if (HapiProperties.getPartitioningEnabled()) {
PartitionSettings partitionSettings = appCtx.getBean(PartitionSettings.class);
partitionSettings.setPartitioningEnabled(true);
PartitionSettings.CrossPartitionReferenceMode mode = PartitionSettings.CrossPartitionReferenceMode.valueOf(HapiProperties.getPartitioningCrossPartitionReferenceMode());
partitionSettings.setAllowReferencesAcrossPartitions(mode);
partitionSettings.setIncludePartitionInSearchHashes(HapiProperties.getIncludePartitionInSearchHashes());
registerProvider(appCtx.getBean(PartitionManagementProvider.class));
if (HapiProperties.getPartitioningMultitenancyEnabled()) {
registerInterceptor(new RequestTenantPartitionInterceptor());
setTenantIdentificationStrategy(new UrlBaseTenantIdentificationStrategy());
}
}
// Add your own customization here
}

4
src/main/resources/hapi.properties
View File

@@ -124,7 +124,7 @@ cors.enabled=true
cors.allowCredentials=true
# Supports multiple, comma separated allowed origin entries
# cors.allowed_origin=http://localhost:8080,https://localhost:8080,https://fhirtest.uhn.ca
cors.allow_origin=*
cors.allowed_origin=*
##################################################
# Allowed Bundle Types for persistence (defaults are: COLLECTION,DOCUMENT,MESSAGE)
@@ -163,3 +163,5 @@ partitioning.cross_partition_reference_mode=NOT_ALLOWED
partitioning.partitioning_include_in_search_hashes=true
partitioning.multitenancy.enabled=false
#daoconfig.client_id_strategy=ANY

1
src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java
View File

@@ -17,7 +17,6 @@ import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Ignore;
import org.junit.Test;
import java.nio.file.Paths;