Merge branch 'master' into rel_5_1_0

.dockerignore

@@ -0,0 +1,3 @@
+target
+.idea
+.git

Dockerfile

@@ -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

README.md

@@ -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:

pom.xml

@@ -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>

src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java

@@ -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());
+    }
+  }
+
+}

src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java

@@ -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);
+  }
 }
 

src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java

@@ -1,342 +1,17 @@
 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();
 
-    /*
+    // Add your own customization here
-     * 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());
-      }
-
-    }
 
   }
 
-}
+}

src/main/resources/hapi.properties

@@ -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
+

src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java

@@ -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;