Moved more configuration values

.vscode/settings.json

@@ -0,0 +1,8 @@
+{
+    "files.exclude": {
+        "**/.classpath": true,
+        "**/.project": true,
+        "**/.settings": true,
+        "**/.factorypath": true
+    }
+}

pom.xml

@@ -19,7 +19,7 @@
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
 
     <prerequisites>
-        <maven>3.5.0</maven>
+        <maven>3.6.0</maven>
     </prerequisites>
 
     <packaging>war</packaging>
@@ -351,9 +351,9 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.8.1</version>
                 <configuration>
-                    <source>1.8</source>
+                    <release>11</release>
-                    <target>1.8</target>
                 </configuration>
             </plugin>
 

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

@@ -1,8 +1,11 @@
 package ca.uhn.fhir.jpa.starter;
 
+
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.api.config.DaoConfig.ClientIdStrategyEnum;
 import ca.uhn.fhir.rest.api.EncodingEnum;
+import java.util.ArrayList;
+import java.util.List;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.context.annotation.Configuration;
@@ -41,8 +44,17 @@ public class AppProperties {
   private ClientIdStrategyEnum client_id_strategy = ClientIdStrategyEnum.ALPHANUMERIC;
 
   private Validation validation = new Validation();
-  private Tester tester = new Tester();
+  private List<Tester> tester = new ArrayList<>();
   private Logger logger = new Logger();
+  private Subscription subscription = new Subscription();
+
+  public Subscription getSubscription() {
+    return subscription;
+  }
+
+  public void setSubscription(Subscription subscription) {
+    this.subscription = subscription;
+  }
 
   public Validation getValidation() {
     return validation;
@@ -52,13 +64,6 @@ public class AppProperties {
     this.validation = validation;
   }
 
-  public Tester getTester() {
-    return tester;
-  }
-
-  public void setTester(Tester tester) {
-    this.tester = tester;
-  }
 
   public Logger getLogger() {
     return logger;
@@ -273,6 +278,14 @@ public class AppProperties {
     this.reuse_cached_search_results_millis = reuse_cached_search_results_millis;
   }
 
+  public List<Tester> getTester() {
+    return tester;
+  }
+
+  public void setTester(List<Tester> tester) {
+    this.tester = tester;
+  }
+
   public static class Logger {
 
     private String name = "fhirtest.access";
@@ -318,8 +331,17 @@ public class AppProperties {
 
     private String id = "home";
     private String name = "Local Tester";
-    private String address = "http://localhost:8080/fhir";
+    private String server_address = "http://localhost:8080/fhir";
     private Boolean refuse_to_fetch_third_party_urls = true;
+    private FhirVersionEnum fhir_version = FhirVersionEnum.R4;
+
+    public FhirVersionEnum getFhir_version() {
+      return fhir_version;
+    }
+
+    public void setFhir_version(FhirVersionEnum fhir_version) {
+      this.fhir_version = fhir_version;
+    }
 
     public String getId() {
       return id;
@@ -337,12 +359,12 @@ public class AppProperties {
       this.name = name;
     }
 
-    public String getAddress() {
+    public String getServer_address() {
-      return address;
+      return server_address;
     }
 
-    public void setAddress(String address) {
+    public void setServer_address(String server_address) {
-      this.address = address;
+      this.server_address = server_address;
     }
 
     public Boolean getRefuse_to_fetch_third_party_urls() {
@@ -375,4 +397,35 @@ public class AppProperties {
       this.responses_enabled = responses_enabled;
     }
   }
+
+  public static class Subscription {
+
+    public Boolean getEmail_enabled() {
+      return email_enabled;
+    }
+
+    public void setEmail_enabled(Boolean email_enabled) {
+      this.email_enabled = email_enabled;
+    }
+
+    public Boolean getResthook_enabled() {
+      return resthook_enabled;
+    }
+
+    public void setResthook_enabled(Boolean resthook_enabled) {
+      this.resthook_enabled = resthook_enabled;
+    }
+
+    public Boolean getWebsocket_enabled() {
+      return websocket_enabled;
+    }
+
+    public void setWebsocket_enabled(Boolean websocket_enabled) {
+      this.websocket_enabled = websocket_enabled;
+    }
+
+    private Boolean email_enabled = false;
+    private Boolean resthook_enabled = false;
+    private Boolean websocket_enabled = false;
+  }
 }

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

@@ -16,7 +16,6 @@ public class Application {
 
   public static void main(String[] args) {
 
-    System.setProperty("spring.profiles.active", "r4");
     System.setProperty("spring.batch.job.enabled", "false");
     SpringApplication.run(Application.class, args);
 

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

@@ -1,56 +0,0 @@
-package ca.uhn.fhir.jpa.starter;
-
-import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.jpa.empi.EmpiConfig;
-import ca.uhn.fhir.jpa.empi.config.EmpiConsumerConfig;
-import ca.uhn.fhir.jpa.empi.config.EmpiSubmitterConfig;
-import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
-import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
-import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
-import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
-import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
-
-/**
- * The class is unused for Spring Boot
- */
-public class ApplicationContext extends AnnotationConfigWebApplicationContext {
-
-
-  public ApplicationContext() {
-    FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
-    this.getEnvironment().setActiveProfiles(fhirVersion.toString().toLowerCase());
-
-
-    if (fhirVersion == FhirVersionEnum.DSTU2) {
-      register(FhirServerConfigDstu2.class, FhirServerConfigCommon.class);
-    } else if (fhirVersion == FhirVersionEnum.DSTU3) {
-      register(FhirServerConfigDstu3.class, FhirServerConfigCommon.class);
-    } else if (fhirVersion == FhirVersionEnum.R4) {
-      register(FhirServerConfigR4.class, FhirServerConfigCommon.class);
-    } else if (fhirVersion == FhirVersionEnum.R5) {
-      register(FhirServerConfigR5.class, FhirServerConfigCommon.class);
-    } else {
-      throw new IllegalStateException();
-    }
-
-    if (HapiProperties.getSubscriptionWebsocketEnabled()) {
-      register(WebsocketDispatcherConfig.class);
-    }
-
-    if (HapiProperties.getSubscriptionEmailEnabled()
-      || HapiProperties.getSubscriptionRestHookEnabled()
-      || HapiProperties.getSubscriptionWebsocketEnabled()) {
-      register(SubscriptionSubmitterConfig.class);
-      register(SubscriptionProcessorConfig.class);
-      register(SubscriptionChannelConfig.class);
-    }
-
-    if (HapiProperties.getEmpiEnabled()) {
-      register(EmpiSubmitterConfig.class);
-      register(EmpiConsumerConfig.class);
-      register(EmpiConfig.class);
-    }
-
-  }
-
-}

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

@@ -4,6 +4,7 @@ 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.IDaoRegistry;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
@@ -12,6 +13,7 @@ import ca.uhn.fhir.jpa.bulk.provider.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.IJpaSystemProvider;
 import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
 import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
 import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
@@ -49,6 +51,9 @@ import javax.servlet.ServletException;
 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.aop.framework.Advised;
+import org.springframework.aop.support.AopUtils;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
 import org.springframework.http.HttpHeaders;
 import org.springframework.web.cors.CorsConfiguration;
@@ -58,6 +63,24 @@ public class BaseJpaRestfulServer extends RestfulServer {
 
   AppProperties hapiProperties;
 
+  @Autowired
+  DaoRegistry daoRegistry;
+
+  @Autowired
+  DaoConfig daoConfig;
+
+  @Autowired
+  ISearchParamRegistry searchParamRegistry;
+
+  @Autowired
+  IFhirSystemDao fhirSystemDao;
+
+  @Autowired
+  ResourceProviderFactory resourceProviders;
+
+  @Autowired
+  IJpaSystemProvider jpaSystemProvider;
+
   public BaseJpaRestfulServer(AppProperties appProperties) {
     this.hapiProperties = appProperties;
   }
@@ -69,12 +92,13 @@ public class BaseJpaRestfulServer extends RestfulServer {
   protected void initialize() throws ServletException {
     super.initialize();
 
+    ApplicationContext appCtx = (ApplicationContext) getServletContext()
+      .getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
+
     /*
      * 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();
 
@@ -83,37 +107,16 @@ public class BaseJpaRestfulServer extends RestfulServer {
     }
 
     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));
 
+    setFhirContext(fhirSystemDao.getContext());
     registerProviders(resourceProviders.createProviders());
-    registerProvider(systemProvider);
+    registerProvider(jpaSystemProvider);
 
+    FhirVersionEnum fhirVersion = fhirSystemDao.getContext().getVersion().getVersion();
     /*
      * 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
@@ -122,34 +125,30 @@ public class BaseJpaRestfulServer 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, fhirSystemDao,
-      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, fhirSystemDao,
-        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, fhirSystemDao,
-        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, fhirSystemDao,
-        JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao,
           daoConfig, searchParamRegistry);
         confProvider.setImplementationDescription("HAPI FHIR R5 Server");
         setServerConformanceProvider(confProvider);
@@ -185,6 +184,7 @@ public class BaseJpaRestfulServer extends RestfulServer {
      * a performance hit when performing searches that return lots of results,
      * but makes the server much more scalable.
      */
+
     setPagingProvider(appCtx.getBean(DatabaseBackedPagingProvider.class));
 
     /*
@@ -349,4 +349,16 @@ public class BaseJpaRestfulServer extends RestfulServer {
     }
   }
 
+  protected <T> T getBeanWithoutProxy(Object bean) {
+
+    if (AopUtils.isAopProxy(bean) && bean instanceof Advised) {
+      try {
+        return (T) ((Advised) bean).getTargetSource().getTarget();
+      } catch (Exception e) {
+        throw new RuntimeException(e);
+      }
+    }
+    return (T)bean;
+  }
+
 }

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

@@ -31,18 +31,10 @@ public class FhirServerConfigCommon {
   private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
 
 
-  private Boolean enableIndexMissingFields = HapiProperties.getEnableIndexMissingFields();
+
-  private Boolean autoCreatePlaceholderReferenceTargets = HapiProperties.getAutoCreatePlaceholderReferenceTargets();
-  private Boolean enforceReferentialIntegrityOnWrite = HapiProperties.getEnforceReferentialIntegrityOnWrite();
-  private Boolean enforceReferentialIntegrityOnDelete = HapiProperties.getEnforceReferentialIntegrityOnDelete();
-  private Boolean allowContainsSearches = HapiProperties.getAllowContainsSearches();
-  private Boolean allowMultipleDelete = HapiProperties.getAllowMultipleDelete();
-  private Boolean allowExternalReferences = HapiProperties.getAllowExternalReferences();
-  private Boolean expungeEnabled = HapiProperties.getExpungeEnabled();
-  private Boolean allowPlaceholderReferences = HapiProperties.getAllowPlaceholderReferences();
   private Boolean subscriptionRestHookEnabled = HapiProperties.getSubscriptionRestHookEnabled();
   private Boolean subscriptionEmailEnabled = HapiProperties.getSubscriptionEmailEnabled();
-  private Boolean allowOverrideDefaultSearchParams = HapiProperties.getAllowOverrideDefaultSearchParams();
+
   private String emailFrom = HapiProperties.getEmailFrom();
   private Boolean emailEnabled = HapiProperties.getEmailEnabled();
   private String emailHost = HapiProperties.getEmailHost();
@@ -118,26 +110,26 @@ public class FhirServerConfigCommon {
     retVal.setExpireSearchResultsAfterMillis(retainCachedSearchesMinutes * 60 * 1000);
 
     // Subscriptions are enabled by channel type
-    if (HapiProperties.getSubscriptionRestHookEnabled()) {
+    if (appProperties.getSubscription().getResthook_enabled()) {
       ourLog.info("Enabling REST-hook subscriptions");
       retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.RESTHOOK);
     }
-    if (HapiProperties.getSubscriptionEmailEnabled()) {
+    if (appProperties.getSubscription().getEmail_enabled()) {
       ourLog.info("Enabling email subscriptions");
       retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.EMAIL);
     }
-    if (HapiProperties.getSubscriptionWebsocketEnabled()) {
+    if (appProperties.getSubscription().getWebsocket_enabled()) {
       ourLog.info("Enabling websocket subscriptions");
       retVal.addSupportedSubscriptionType(org.hl7.fhir.dstu2.model.Subscription.SubscriptionChannelType.WEBSOCKET);
     }
 
-    retVal.setFilterParameterEnabled(HapiProperties.getFilterSearchEnabled());
+    retVal.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
 
     return retVal;
   }
 
   @Bean
-  public PartitionSettings partitionSettings() {
+  public PartitionSettings partitionSettings(AppProperties appProperties) {
     PartitionSettings retVal = new PartitionSettings();
 
     // Partitioning

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java

@@ -17,7 +17,6 @@ import javax.sql.DataSource;
 
 @Configuration
 @Profile("r4")
-@ConditionalOnClass(DataSource.class)
 public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 
     @Autowired

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

@@ -33,18 +33,22 @@ public class FhirTesterConfig {
 	 * deploying your server to a place with a fully qualified domain name,
 	 * you might want to use that instead of using the variable.
 	 */
-	@Bean
+  @Bean
-	public TesterConfig testerConfig(AppProperties appProperties) {
+  public TesterConfig testerConfig(AppProperties appProperties) {
-		TesterConfig retVal = new TesterConfig();
+    TesterConfig retVal = new TesterConfig();
-		retVal
+    appProperties.getTester().stream().forEach(t -> {
-			.addServer()
+      retVal
-				.withId(appProperties.getTester().getId())
+        .addServer()
-				.withFhirVersion(appProperties.getFhir_version())
+        .withId(t.getId())
-				.withBaseUrl(appProperties.getTester().getAddress())
+        .withFhirVersion(t.getFhir_version())
-				.withName(appProperties.getTester().getName());
+        .withBaseUrl(t.getServer_address())
-		retVal.setRefuseToFetchThirdPartyUrls(appProperties.getTester().getRefuse_to_fetch_third_party_urls());
+        .withName(t.getName());
-		return retVal;
+      retVal.setRefuseToFetchThirdPartyUrls(
-	}
+        t.getRefuse_to_fetch_third_party_urls());
+
+    });
+    return retVal;
+  }
 
 }
 //@formatter:on

src/main/resources/application.yaml

@@ -2,9 +2,12 @@ spring:
   datasource:
     url: 'jdbc:h2:file:./target/database/h2dflkjglkj'
     username: sa
-    password:
+    password: null
     driverClassName: org.h2.Driver
     max-active: 15
+  profiles:
+    ### This is the FHIR version. Choose between, dstu2, dstu3, r4 or r5
+    active: r4
 hapi:
   fhir:
     allow_cascading_deletes: true
@@ -21,8 +24,7 @@ hapi:
     enforce_referential_integrity_on_write: false
     etag_support_enabled: true
     expunge_enabled: true
-    fhir_version: DSTU3
+    daoconfig_client_id_strategy: null
-    daoconfig_client_id_strategy:
     fhirpath_interceptor_enabled: false
     filter_search_enabled: true
     graphql_enabled: true
@@ -40,16 +42,28 @@ hapi:
     retain_cached_searches_mins: 60
     reuse_cached_search_results_millis: 60000
     tester:
-      id: home
+      -
-      name: Local Tester
+          id: home
-      server_address: 'http://localhost:8080/fhir'
+          name: Local Tester
-      refuse_to_fetch_third_party_urls: false
+          server_address: 'http://localhost:8080/fhir'
+          refuse_to_fetch_third_party_urls: false
+          fhir_version: R4
+      -
+          id: global
+          name: Global Tester
+          server_address: "http://hapi.fhir.org/baseR4"
+          refuse_to_fetch_third_party_urls: false
+          fhir_version: R4
     validation:
       requests_enabled: true
       responses_enabled: true
-
     binary_storage_enabled: true
     bulk_export_enabled: true
+    partitioning_multitenancy_enabled:
+    subscription:
+      email_enabled: false
+      resthook_enabled: false
+      websocket_enabled: false
 elasticsearch:
   debug:
     pretty_print_json_log: false
@@ -59,4 +73,4 @@ elasticsearch:
   required_index_status: YELLOW
   rest_url: 'http://localhost:9200'
   schema_management_strategy: CREATE
-  username: SomeUsername
+  username: SomeUsername