pre-review cleanup

.travis.yml

@@ -29,7 +29,7 @@ before_script:
   - sudo chown -R travis:travis "$HOME/.m2/repository";
 
 script:
-  - mvn -U install
+  - mvn -B install
 
 
 

pom.xml

@@ -1,6 +1,5 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0"
-         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 
     <!--
@@ -12,7 +11,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-        <version>5.1.0-SNAPSHOT</version>
+        <version>5.0.0</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>

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

@@ -1,7 +1,12 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirVersionEnum;
+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;
 
 public class ApplicationContext extends AnnotationConfigWebApplicationContext {
@@ -24,6 +29,20 @@ public class ApplicationContext extends AnnotationConfigWebApplicationContext {
       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/EmpiConfig.java

@@ -2,23 +2,19 @@ package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.empi.api.IEmpiSettings;
 import ca.uhn.fhir.empi.rules.config.EmpiSettings;
-import ca.uhn.fhir.jpa.empi.config.EmpiConsumerConfig;
-import ca.uhn.fhir.jpa.empi.config.EmpiSubmitterConfig;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
 import org.springframework.core.io.DefaultResourceLoader;
 import org.springframework.core.io.Resource;
 
 import java.io.IOException;
 
 @Configuration
-@Import({EmpiSubmitterConfig.class, EmpiConsumerConfig.class})
 public class EmpiConfig {
   @Bean
-  IEmpiSettings empiProperties() throws IOException {
+  IEmpiSettings empiSettings() throws IOException {
     DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
     Resource resource = resourceLoader.getResource("empi-rules.json");
     String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);

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

@@ -5,18 +5,14 @@ import ca.uhn.fhir.jpa.binstore.DatabaseBlobBinaryStorageSvcImpl;
 import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
-import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
-import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
-import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Lazy;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 import org.thymeleaf.util.Validate;
@@ -29,11 +25,6 @@ import java.sql.Driver;
  */
 @Configuration
 @EnableTransactionManagement
-@Import({EmpiConfig.class,
-  SubscriptionSubmitterConfig.class,
-  SubscriptionProcessorConfig.class,
-  SubscriptionChannelConfig.class
-})
 public class FhirServerConfigCommon {
 
   private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
@@ -60,9 +51,8 @@ public class FhirServerConfigCommon {
   private Boolean emailStartTlsEnable = HapiProperties.getEmailStartTlsEnable();
   private Boolean emailStartTlsRequired = HapiProperties.getEmailStartTlsRequired();
   private Boolean emailQuitWait = HapiProperties.getEmailQuitWait();
-
   @Autowired
-  private SubscriptionDeliveryHandlerFactory mySubscriptionDeliveryHandlerFactory;
+  private ApplicationContext myAppCtx;
 
   public FhirServerConfigCommon() {
     ourLog.info("Server configured to " + (this.allowContainsSearches ? "allow" : "deny") + " contains searches");
@@ -142,6 +132,12 @@ public class FhirServerConfigCommon {
     return retVal;
   }
 
+  @Bean
+  public PartitionSettings partitionSettings() {
+    return new PartitionSettings();
+  }
+
+
   @Bean
   public ModelConfig modelConfig() {
     ModelConfig modelConfig = new ModelConfig();
@@ -206,8 +202,9 @@ public class FhirServerConfigCommon {
       retVal.setStartTlsRequired(this.emailStartTlsRequired);
       retVal.setQuitWait(this.emailQuitWait);
 
-      Validate.notNull(mySubscriptionDeliveryHandlerFactory, "No subscription delivery handler");
+      SubscriptionDeliveryHandlerFactory subscriptionDeliveryHandlerFactory = myAppCtx.getBean(SubscriptionDeliveryHandlerFactory.class);
-      mySubscriptionDeliveryHandlerFactory.setEmailSender(retVal);
+      Validate.notNull(subscriptionDeliveryHandlerFactory, "No subscription delivery handler");
+      subscriptionDeliveryHandlerFactory.setEmailSender(retVal);
 
 
       return retVal;
@@ -215,9 +212,4 @@ public class FhirServerConfigCommon {
 
     return null;
   }
-
-  @Bean
-  public PartitionSettings partitionSettings() {
-    return new PartitionSettings();
-  }
 }

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

@@ -506,5 +506,9 @@ public class HapiProperties {
   public static boolean getBulkExportEnabled() {
     return HapiProperties.getBooleanProperty(BULK_EXPORT_ENABLED, true);
   }
+
+  public static boolean isFhirPathFilterInterceptorEnabled() {
+    return HapiProperties.getBooleanProperty("fhirpath_interceptor.enabled", false);
+  }
 }
 

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

@@ -2,9 +2,6 @@ package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.empi.provider.EmpiProviderDstu3;
-import ca.uhn.fhir.empi.provider.EmpiProviderR4;
-import ca.uhn.fhir.empi.rules.config.EmpiSettings;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
@@ -28,13 +25,13 @@ 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.submit.interceptor.SubscriptionSubmitInterceptorLoader;
 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;
@@ -118,37 +115,33 @@ public class JpaRestfulServer extends RestfulServer {
      * You can also create your own subclass of the conformance provider if you need to
      * provide further customization of your server's CapabilityStatement
      */
+    DaoConfig daoConfig = appCtx.getBean(DaoConfig.class);
+    ISearchParamRegistry searchParamRegistry = appCtx.getBean(ISearchParamRegistry.class);
     if (fhirVersion == FhirVersionEnum.DSTU2) {
-      IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = appCtx
+      IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = appCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
-        .getBean("mySystemDaoDstu2", IFhirSystemDao.class);
+      JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao, daoConfig);
-      JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao,
-        appCtx.getBean(DaoConfig.class));
       confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
       setServerConformanceProvider(confProvider);
-    } else if (fhirVersion == FhirVersionEnum.DSTU3) {
+    } else {
-      IFhirSystemDao<Bundle, Meta> systemDao = appCtx
+      if (fhirVersion == FhirVersionEnum.DSTU3) {
-        .getBean("mySystemDaoDstu3", IFhirSystemDao.class);
+        IFhirSystemDao<Bundle, Meta> systemDao = appCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
-      JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao,
+        JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, daoConfig, searchParamRegistry);
-        appCtx.getBean(DaoConfig.class), appCtx.getBean(ISearchParamRegistry.class));
       confProvider.setImplementationDescription("HAPI FHIR DSTU3 Server");
       setServerConformanceProvider(confProvider);
     } else if (fhirVersion == FhirVersionEnum.R4) {
-      IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = appCtx
+        IFhirSystemDao<org.hl7.fhir.r4.model.Bundle, org.hl7.fhir.r4.model.Meta> systemDao = appCtx.getBean("mySystemDaoR4", IFhirSystemDao.class);
-        .getBean("mySystemDaoR4", IFhirSystemDao.class);
+        JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao, daoConfig, searchParamRegistry);
-      JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao,
-        appCtx.getBean(DaoConfig.class), appCtx.getBean(ISearchParamRegistry.class));
       confProvider.setImplementationDescription("HAPI FHIR R4 Server");
       setServerConformanceProvider(confProvider);
     } else if (fhirVersion == FhirVersionEnum.R5) {
-      IFhirSystemDao<org.hl7.fhir.r5.model.Bundle, org.hl7.fhir.r5.model.Meta> systemDao = appCtx
+        IFhirSystemDao<org.hl7.fhir.r5.model.Bundle, org.hl7.fhir.r5.model.Meta> systemDao = appCtx.getBean("mySystemDaoR5", IFhirSystemDao.class);
-        .getBean("mySystemDaoR5", IFhirSystemDao.class);
+        JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao, daoConfig, searchParamRegistry);
-      JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao,
-        appCtx.getBean(DaoConfig.class), appCtx.getBean(ISearchParamRegistry.class));
       confProvider.setImplementationDescription("HAPI FHIR R5 Server");
       setServerConformanceProvider(confProvider);
     } else {
       throw new IllegalStateException();
     }
+    }
 
     /*
      * ETag Support
@@ -185,9 +178,12 @@ public class JpaRestfulServer extends RestfulServer {
      * browser.
      */
     ResponseHighlighterInterceptor responseHighlighterInterceptor = new ResponseHighlighterInterceptor();
-    ;
     this.registerInterceptor(responseHighlighterInterceptor);
 
+    if (HapiProperties.isFhirPathFilterInterceptorEnabled()) {
+      registerInterceptor(new FhirPathFilterInterceptor());
+    }
+
     /*
      * Add some logging for each request
      */
@@ -263,13 +259,6 @@ public class JpaRestfulServer extends RestfulServer {
     if (HapiProperties.getSubscriptionWebsocketEnabled() ||
       HapiProperties.getSubscriptionEmailEnabled() ||
       HapiProperties.getSubscriptionRestHookEnabled()) {
-      // Loads subscription interceptors (SubscriptionActivatingInterceptor, SubscriptionMatcherInterceptor)
-      // with activation of scheduled subscription
-
-      SubscriptionSubmitInterceptorLoader subscriptionInterceptorLoader = appCtx
-        .getBean(SubscriptionSubmitInterceptorLoader.class);
-      subscriptionInterceptorLoader.start();
-
       // Subscription debug logging
       IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
       interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
@@ -279,8 +268,7 @@ public class JpaRestfulServer extends RestfulServer {
     DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
     IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
     if (HapiProperties.getAllowCascadingDeletes()) {
-      CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(getFhirContext(),
+      CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(ctx, daoRegistry, interceptorBroadcaster);
-        daoRegistry, interceptorBroadcaster);
       getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
     }
 
@@ -322,7 +310,7 @@ public class JpaRestfulServer extends RestfulServer {
         BundleType type = BundleType.valueOf(o);
         allowedBundleTypes.add(type.toCode());
       });
-      DaoConfig config = appCtx.getBean(DaoConfig.class);
+      DaoConfig config = (DaoConfig) daoConfig;
       config.setBundleTypesAllowedForStorage(
         Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
     }

src/main/resources/hapi.properties

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

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java

@@ -67,7 +67,6 @@ public class ExampleServerR4IT {
         Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
         assertEquals(methodName, pt2.getName().get(0).getFamily());
 
-
         // Test EMPI
 
         // Wait until the EMPI message has been processed

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java

@@ -15,7 +15,6 @@ import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
 import org.eclipse.jetty.websocket.client.WebSocketClient;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r5.model.Bundle;
-import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.Enumerations;
 import org.hl7.fhir.r5.model.Observation;
 import org.hl7.fhir.r5.model.Patient;
@@ -78,11 +77,10 @@ public class ExampleServerR5IT {
     subscription.getTopic().setResource(topic);
     subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
     subscription.setStatus(Enumerations.SubscriptionState.REQUESTED);
-
+        subscription.getChannelType()
+                .setSystem("http://terminology.hl7.org/CodeSystem/subscription-channel-type")
+                .setCode("websocket");
     subscription.setContentType("application/json");
-    Coding channelType = new Coding().setSystem("http://terminology.hl7.org/CodeSystem/subscription-channel-type")
-      .setCode("websocket");;
-    subscription.setChannelType(channelType);
 
     MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
     IIdType mySubscriptionId = methodOutcome.getId();