just need to merge the email TLS

pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-        <version>5.0.0-SNAPSHOT</version>
+        <version>5.1.0-SNAPSHOT</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -255,7 +255,12 @@
             <scope>test</scope>
         </dependency>
 
-
+        <dependency>
+            <groupId>org.awaitility</groupId>
+            <artifactId>awaitility</artifactId>
+            <version>4.0.0-rc1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <packaging>war</packaging>

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

@@ -1,7 +1,7 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.empi.api.IEmpiSettings;
-import ca.uhn.fhir.empi.rules.config.EmpiSettingsImpl;
+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;
@@ -22,6 +22,6 @@ public class EmpiConfig {
     DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
     Resource resource = resourceLoader.getResource("empi-rules.json");
     String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
-    return new EmpiSettingsImpl().setEnabled(HapiProperties.getEmpiEnabled()).setScriptText(json);
+    return new EmpiSettings().setEnabled(HapiProperties.getEmpiEnabled()).setScriptText(json);
   }
 }

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

@@ -201,11 +201,10 @@ public class FhirServerConfigCommon {
       retVal.setSmtpServerPort(this.emailPort);
       retVal.setSmtpServerUsername(this.emailUsername);
       retVal.setSmtpServerPassword(this.emailPassword);
-      // FIXME KHS add these once this has merged in hapi
+      retVal.setAuth(this.emailAuth);
-//      retVal.setAuth(this.emailAuth);
+      retVal.setStartTlsEnable(this.emailStartTlsEnable);
-//      retVal.setStartTlsEnable(this.emailStartTlsEnable);
+      retVal.setStartTlsRequired(this.emailStartTlsRequired);
-//      retVal.setStartTlsRequired(this.emailStartTlsRequired);
+      retVal.setQuitWait(this.emailQuitWait);
-//      retVal.setQuitWait(this.emailQuitWait);
 
       Validate.notNull(mySubscriptionDeliveryHandlerFactory, "No subscription delivery handler");
       mySubscriptionDeliveryHandlerFactory.setEmailSender(retVal);

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

@@ -58,6 +58,10 @@ public class HapiProperties {
   static final String SUBSCRIPTION_RESTHOOK_ENABLED = "subscription.resthook.enabled";
   static final String SUBSCRIPTION_WEBSOCKET_ENABLED = "subscription.websocket.enabled";
   static final String EMPI_ENABLED = "empi.enabled";
+  static final String PARTITIONING_ENABLED = "partitioning.enabled";
+  static final String PARTITIONING_CROSS_PARTITION_REFERENCE_MODE = "partitioning.cross_partition_reference_mode";
+  private static final String PARTITIONING_INCLUDE_PARTITION_IN_SEARCH_HASHES = "partitioning.partitioning_include_in_search_hashes";
+
   static final String ALLOWED_BUNDLE_TYPES = "allowed_bundle_types";
   static final String TEST_PORT = "test.port";
   static final String TESTER_CONFIG_REFUSE_TO_FETCH_THIRD_PARTY_URLS = "tester.config.refuse_to_fetch_third_party_urls";
@@ -378,6 +382,18 @@ public class HapiProperties {
     return HapiProperties.getBooleanProperty(EMPI_ENABLED, false);
   }
 
+  public static Boolean getPartitioningEnabled() {
+    return HapiProperties.getBooleanProperty(PARTITIONING_ENABLED, false);
+  }
+
+  public static String getPartitioningCrossPartitionReferenceMode() {
+    return HapiProperties.getProperty(PARTITIONING_CROSS_PARTITION_REFERENCE_MODE, "NOT_ALLOWED");
+  }
+
+  public static Boolean getIncludePartitionInSearchHashes() {
+    return HapiProperties.getBooleanProperty(PARTITIONING_INCLUDE_PARTITION_IN_SEARCH_HASHES, true);
+  }
+
   public static Boolean getAllowContainsSearches() {
     return HapiProperties.getBooleanProperty(ALLOW_CONTAINS_SEARCHES, true);
   }

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

@@ -2,6 +2,9 @@ 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;
@@ -10,6 +13,8 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 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.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;
@@ -37,11 +42,9 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
 import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
-import java.util.HashSet;
-import java.util.TreeSet;
 import org.hl7.fhir.dstu3.model.Bundle;
-import org.hl7.fhir.r4.model.Bundle.BundleType;
 import org.hl7.fhir.dstu3.model.Meta;
+import org.hl7.fhir.r4.model.Bundle.BundleType;
 import org.springframework.context.ApplicationContext;
 import org.springframework.http.HttpHeaders;
 import org.springframework.web.cors.CorsConfiguration;
@@ -49,7 +52,9 @@ import org.springframework.web.cors.CorsConfiguration;
 import javax.servlet.ServletException;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.HashSet;
 import java.util.Set;
+import java.util.TreeSet;
 
 public class JpaRestfulServer extends RestfulServer {
 
@@ -65,12 +70,12 @@ public class JpaRestfulServer extends RestfulServer {
      * specified in the properties file.
      */
     ApplicationContext appCtx = (ApplicationContext) getServletContext()
-        .getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
+      .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");
+      supportedResourceTypes.add("SearchParameter");
     }
 
     if (!supportedResourceTypes.isEmpty()) {
@@ -115,30 +120,30 @@ public class JpaRestfulServer extends RestfulServer {
      */
     if (fhirVersion == FhirVersionEnum.DSTU2) {
       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,
-          appCtx.getBean(DaoConfig.class));
+        appCtx.getBean(DaoConfig.class));
       confProvider.setImplementationDescription("HAPI FHIR DSTU2 Server");
       setServerConformanceProvider(confProvider);
     } else if (fhirVersion == FhirVersionEnum.DSTU3) {
       IFhirSystemDao<Bundle, Meta> systemDao = appCtx
-          .getBean("mySystemDaoDstu3", IFhirSystemDao.class);
+        .getBean("mySystemDaoDstu3", IFhirSystemDao.class);
       JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao,
-          appCtx.getBean(DaoConfig.class), appCtx.getBean(ISearchParamRegistry.class));
+        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
-          .getBean("mySystemDaoR4", IFhirSystemDao.class);
+        .getBean("mySystemDaoR4", IFhirSystemDao.class);
       JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao,
-          appCtx.getBean(DaoConfig.class), appCtx.getBean(ISearchParamRegistry.class));
+        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
-          .getBean("mySystemDaoR5", IFhirSystemDao.class);
+        .getBean("mySystemDaoR5", IFhirSystemDao.class);
       JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao,
-          appCtx.getBean(DaoConfig.class), appCtx.getBean(ISearchParamRegistry.class));
+        appCtx.getBean(DaoConfig.class), appCtx.getBean(ISearchParamRegistry.class));
       confProvider.setImplementationDescription("HAPI FHIR R5 Server");
       setServerConformanceProvider(confProvider);
     } else {
@@ -219,7 +224,7 @@ public class JpaRestfulServer extends RestfulServer {
     // manual triggering of a subscription delivery, enable this provider
     if (false) { // <-- DISABLED RIGHT NOW
       SubscriptionTriggeringProvider retriggeringProvider = appCtx
-          .getBean(SubscriptionTriggeringProvider.class);
+        .getBean(SubscriptionTriggeringProvider.class);
       registerProvider(retriggeringProvider);
     }
 
@@ -245,7 +250,7 @@ public class JpaRestfulServer extends RestfulServer {
       config.addExposedHeader("Location");
       config.addExposedHeader("Content-Location");
       config.setAllowedMethods(
-          Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
+        Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH", "HEAD"));
       config.setAllowCredentials(HapiProperties.getCorsAllowedCredentials());
 
       // Create the interceptor and register it
@@ -256,13 +261,13 @@ public class JpaRestfulServer extends RestfulServer {
     // 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.getSubscriptionEmailEnabled() ||
-        HapiProperties.getSubscriptionRestHookEnabled()) {
+      HapiProperties.getSubscriptionRestHookEnabled()) {
       // Loads subscription interceptors (SubscriptionActivatingInterceptor, SubscriptionMatcherInterceptor)
       // with activation of scheduled subscription
 
       SubscriptionSubmitInterceptorLoader subscriptionInterceptorLoader = appCtx
-          .getBean(SubscriptionSubmitInterceptorLoader.class);
+        .getBean(SubscriptionSubmitInterceptorLoader.class);
       subscriptionInterceptorLoader.start();
 
       // Subscription debug logging
@@ -275,43 +280,19 @@ public class JpaRestfulServer extends RestfulServer {
     IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
     if (HapiProperties.getAllowCascadingDeletes()) {
       CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(getFhirContext(),
-          daoRegistry, interceptorBroadcaster);
+        daoRegistry, interceptorBroadcaster);
       getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
     }
 
     // Binary Storage
     if (HapiProperties.isBinaryStorageEnabled()) {
       BinaryStorageInterceptor binaryStorageInterceptor = appCtx
-          .getBean(BinaryStorageInterceptor.class);
+        .getBean(BinaryStorageInterceptor.class);
       getInterceptorService().registerInterceptor(binaryStorageInterceptor);
     }
 
     // Validation
-    IValidatorModule validatorModule;
+    IValidatorModule validatorModule = appCtx.getBean(IValidatorModule.class);
-    // FIXME KHS
-    /*
-    switch (fhirVersion) {
-            case DSTU2:
-                validatorModule = appCtx.getBean("myInstanceValidatorDstu2", IValidatorModule.class);
-                break;
-      case DSTU3:
-        validatorModule = appCtx.getBean("myInstanceValidatorDstu3", IValidatorModule.class);
-        break;
-      case R4:
-        validatorModule = appCtx.getBean("myInstanceValidatorR4", IValidatorModule.class);
-        break;
-      case R5:
-        validatorModule = appCtx.getBean("myInstanceValidatorR5", IValidatorModule.class);
-        break;
-            // These versions are not supported by HAPI FHIR JPA
-            case DSTU2_HL7ORG:
-            case DSTU2_1:
-      default:
-        validatorModule = null;
-        break;
-    }
-    */
-    validatorModule = appCtx.getBean(IValidatorModule.class);
     if (validatorModule != null) {
       if (HapiProperties.getValidateRequestsEnabled()) {
         RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
@@ -343,19 +324,21 @@ public class JpaRestfulServer extends RestfulServer {
       });
       DaoConfig config = appCtx.getBean(DaoConfig.class);
       config.setBundleTypesAllowedForStorage(
-          Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
+        Collections.unmodifiableSet(new TreeSet<>(allowedBundleTypes)));
-    }
-  
-        // Bulk Export
-        if (HapiProperties.getBulkExportEnabled()) {
-            registerProvider(appCtx.getBean(BulkDataExportProvider.class));
-        }
-
-
-    if (HapiProperties.getEmpiEnabled()) {
-      // FIXME KHS
     }
 
+    // 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));
+    }
   }
 }

src/main/resources/empi-rules.json

@@ -1,30 +1,33 @@
 {
-	"resourceSearchParams" : [ {
+	"candidateSearchParams" : [ {
 		"resourceType" : "Patient",
 		"searchParam" : "birthdate"
 	}, {
-		"resourceType" : "All",
+		"resourceType" : "*",
 		"searchParam" : "identifier"
+	},{
+		"resourceType" : "Patient",
+		"searchParam" : "general-practitioner"
 	} ],
-	"filterSearchParams" : [ {
+	"candidateFilterSearchParams" : [ {
-		"resourceType" : "All",
+		"resourceType" : "*",
 		"searchParam" : "active",
 		"fixedValue" : "true"
 	} ],
 	"matchFields" : [ {
 		"name" : "given-name",
-		"resourceType" : "All",
+		"resourceType" : "*",
 		"resourcePath" : "name.given",
 		"metric" : "COSINE",
 		"matchThreshold" : 0.8
 	}, {
 		"name" : "last-name",
-		"resourceType" : "All",
+		"resourceType" : "*",
 		"resourcePath" : "name.family",
 		"metric" : "JARO_WINKLER",
 		"matchThreshold" : 0.8
 	}],
-	"weightMap" : {
+	"matchResultMap" : {
 		"given-name" : "POSSIBLE_MATCH",
 		"given-name,last-name" : "MATCH"
 	},

src/main/resources/hapi.properties

@@ -148,7 +148,10 @@ email.password=
 # Enable Websocket Subscription Channel
 subscription.websocket.enabled=false
 
-########
 # EMPI
-########
 empi.enabled=false
+
+# Partitioning
+partitioning.enabled=false
+partitioning.cross_partition_reference_mode=NOT_ALLOWED
+partitioning.partitioning_include_in_search_hashes=true

src/main/resources/logback.xml

@@ -9,6 +9,25 @@
 		</encoder>
 	</appender>
 
+	<appender name="EMPI_TROUBLESHOOTING" class="ch.qos.logback.core.rolling.RollingFileAppender">
+		<filter class="ch.qos.logback.classic.filter.ThresholdFilter"><level>DEBUG</level></filter>
+		<file>${smile.basedir}/log/empi-troubleshooting.log</file>
+		<rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
+			<fileNamePattern>${smile.basedir}/log/empi-troubleshooting.log.%i.gz</fileNamePattern>
+			<minIndex>1</minIndex>
+			<maxIndex>9</maxIndex>
+		</rollingPolicy>
+		<triggeringPolicy class="ch.qos.logback.core.rolling.SizeBasedTriggeringPolicy">
+			<maxFileSize>5MB</maxFileSize>
+		</triggeringPolicy>
+		<encoder>
+			<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n${log.stackfilter.pattern}</pattern>
+		</encoder>
+	</appender>
+	<logger name="ca.uhn.fhir.log.empi_troubleshooting" level="TRACE">
+		<appender-ref ref="EMPI_TROUBLESHOOTING"/>
+	</logger>
+
 	<root level="INFO">
 		<appender-ref ref="STDOUT" />
 	</root>

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

@@ -8,6 +8,7 @@ import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.test.utilities.JettyUtil;
+import ca.uhn.fhir.util.BundleUtil;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.webapp.WebAppContext;
 import org.eclipse.jetty.websocket.api.Session;
@@ -17,6 +18,8 @@ import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Person;
+import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Subscription;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
@@ -24,11 +27,16 @@ import org.junit.Test;
 
 import java.net.URI;
 import java.nio.file.Paths;
+import java.util.Collection;
+import java.util.List;
+import java.util.Optional;
 import java.util.concurrent.Future;
 import java.util.concurrent.TimeUnit;
 
 import static ca.uhn.fhir.util.TestUtil.waitForSize;
+import static org.awaitility.Awaitility.await;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 public class ExampleServerR4IT {
 
@@ -43,6 +51,7 @@ public class ExampleServerR4IT {
         HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr4");
         HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R4");
         HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
+        HapiProperties.setProperty(HapiProperties.EMPI_ENABLED, "true");
         ourCtx = FhirContext.forR4();
     }
 
@@ -57,9 +66,31 @@ 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
+        await().until(() -> getPeople().size() > 0);
+        List<Person> persons = getPeople();
+
+        // Verify a Person was created that links to our Patient
+        Optional<String> personLinkToCreatedPatient = persons.stream()
+          .map(Person::getLink)
+          .flatMap(Collection::stream)
+          .map(Person.PersonLinkComponent::getTarget)
+          .map(Reference::getReference)
+          .filter(pid -> id.toUnqualifiedVersionless().getValue().equals(pid))
+          .findAny();
+        assertTrue(personLinkToCreatedPatient.isPresent());
     }
 
-    @Test
+  private List<Person> getPeople() {
+    Bundle bundle = ourClient.search().forResource(Person.class).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
+    return BundleUtil.toListOfResourcesOfType(ourCtx, bundle, Person.class);
+  }
+
+  @Test
     public void testWebsocketSubscription() throws Exception {
         /*
          * Create subscription
@@ -78,7 +109,7 @@ public class ExampleServerR4IT {
         IIdType mySubscriptionId = methodOutcome.getId();
 
         // Wait for the subscription to be activated
-        waitForSize(1, () -> ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size());
+        await().until(() -> activeSubscriptionCount() == 3);
 
         /*
          * Attach websocket
@@ -117,7 +148,11 @@ public class ExampleServerR4IT {
         ourClient.delete().resourceById(mySubscriptionId).execute();
     }
 
-    @AfterClass
+  private int activeSubscriptionCount() {
+    return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size();
+  }
+
+  @AfterClass
     public static void afterClass() throws Exception {
         ourServer.stop();
     }

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

@@ -14,7 +14,13 @@ import org.eclipse.jetty.websocket.api.Session;
 import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
 import org.eclipse.jetty.websocket.client.WebSocketClient;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r5.model.*;
+import org.hl7.fhir.r5.model.Bundle;
+import org.hl7.fhir.r5.model.Coding;
+import org.hl7.fhir.r5.model.Enumerations;
+import org.hl7.fhir.r5.model.Observation;
+import org.hl7.fhir.r5.model.Patient;
+import org.hl7.fhir.r5.model.Subscription;
+import org.hl7.fhir.r5.model.SubscriptionTopic;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -29,135 +35,133 @@ import static org.junit.Assert.assertEquals;
 
 public class ExampleServerR5IT {
 
-    private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR5IT.class);
+  private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR5IT.class);
-    private static IGenericClient ourClient;
+  private static IGenericClient ourClient;
-    private static FhirContext ourCtx;
+  private static FhirContext ourCtx;
-    private static int ourPort;
+  private static int ourPort;
-    private static Server ourServer;
+  private static Server ourServer;
 
-    static {
+  static {
-        HapiProperties.forceReload();
+    HapiProperties.forceReload();
-        HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr5");
+    HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr5");
-        HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R5");
+    HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R5");
-        HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
+    HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
-        ourCtx = FhirContext.forR5();
+    ourCtx = FhirContext.forR5();
-    }
+  }
 
-    @Test
+  @Test
-    public void testCreateAndRead() {
+  public void testCreateAndRead() {
-        ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
+    ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
-        String methodName = "testCreateResourceConditional";
+    String methodName = "testCreateResourceConditional";
 
-        Patient pt = new Patient();
+    Patient pt = new Patient();
-        pt.addName().setFamily(methodName);
+    pt.addName().setFamily(methodName);
-        IIdType id = ourClient.create().resource(pt).execute().getId();
+    IIdType id = ourClient.create().resource(pt).execute().getId();
 
-        Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
+    Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
-        assertEquals(methodName, pt2.getName().get(0).getFamily());
+    assertEquals(methodName, pt2.getName().get(0).getFamily());
-    }
+  }
 
-    @Test
+  @Test
-    public void testWebsocketSubscription() throws Exception {
+  public void testWebsocketSubscription() throws Exception {
 
-        /*
+    /*
-         * Create topic
+     * Create topic
-         */
+     */
-        Topic topic = new Topic();
+    SubscriptionTopic topic = new SubscriptionTopic();
-        topic.getResourceTrigger().getQueryCriteria().setCurrent("Observation?status=final");
+    topic.getResourceTrigger().getQueryCriteria().setCurrent("Observation?status=final");
 
-        /*
+    /*
-         * Create subscription
+     * Create subscription
-         */
+     */
-        Subscription subscription = new Subscription();
+    Subscription subscription = new Subscription();
-        subscription.getTopic().setResource(topic);
+    subscription.getTopic().setResource(topic);
-        subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
+    subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
-        subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
+    subscription.setStatus(Enumerations.SubscriptionState.REQUESTED);
 
-        Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
+    subscription.setContentType("application/json");
-        channel.getType().addCoding()
+    Coding channelType = new Coding().setSystem("http://terminology.hl7.org/CodeSystem/subscription-channel-type")
-                .setSystem("http://terminology.hl7.org/CodeSystem/subscription-channel-type")
+      .setCode("websocket");;
-                .setCode("websocket");
+    subscription.setChannelType(channelType);
-        channel.getPayload().setContentType("application/json");
-        subscription.setChannel(channel);
 
-        MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
+    MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
-        IIdType mySubscriptionId = methodOutcome.getId();
+    IIdType mySubscriptionId = methodOutcome.getId();
 
-        // Wait for the subscription to be activated
+    // Wait for the subscription to be activated
-        waitForSize(1, () -> ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size());
+    waitForSize(1, () -> ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size());
 
-        /*
+    /*
-         * Attach websocket
+     * Attach websocket
-         */
+     */
 
-        WebSocketClient myWebSocketClient = new WebSocketClient();
+    WebSocketClient myWebSocketClient = new WebSocketClient();
-        SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
+    SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
 
-        myWebSocketClient.start();
+    myWebSocketClient.start();
-        URI echoUri = new URI("ws://localhost:" + ourPort + "/hapi-fhir-jpaserver/websocket");
+    URI echoUri = new URI("ws://localhost:" + ourPort + "/hapi-fhir-jpaserver/websocket");
-        ClientUpgradeRequest request = new ClientUpgradeRequest();
+    ClientUpgradeRequest request = new ClientUpgradeRequest();
-        ourLog.info("Connecting to : {}", echoUri);
+    ourLog.info("Connecting to : {}", echoUri);
-        Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
+    Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
-        Session session = connection.get(2, TimeUnit.SECONDS);
+    Session session = connection.get(2, TimeUnit.SECONDS);
 
-        ourLog.info("Connected to WS: {}", session.isOpen());
+    ourLog.info("Connected to WS: {}", session.isOpen());
 
-        /*
+    /*
-         * Create a matching resource
+     * Create a matching resource
-         */
+     */
-        Observation obs = new Observation();
+    Observation obs = new Observation();
-        obs.setStatus(Enumerations.ObservationStatus.FINAL);
+    obs.setStatus(Enumerations.ObservationStatus.FINAL);
-        ourClient.create().resource(obs).execute();
+    ourClient.create().resource(obs).execute();
 
-        // Give some time for the subscription to deliver
+    // Give some time for the subscription to deliver
-        Thread.sleep(2000);
+    Thread.sleep(2000);
 
-        /*
+    /*
-         * Ensure that we receive a ping on the websocket
+     * Ensure that we receive a ping on the websocket
-         */
+     */
-        waitForSize(1, () -> mySocketImplementation.myPingCount);
+    waitForSize(1, () -> mySocketImplementation.myPingCount);
 
-        /*
+    /*
-         * Clean up
+     * Clean up
-         */
+     */
-        ourClient.delete().resourceById(mySubscriptionId).execute();
+    ourClient.delete().resourceById(mySubscriptionId).execute();
-    }
+  }
 
-    @AfterClass
+  @AfterClass
-    public static void afterClass() throws Exception {
+  public static void afterClass() throws Exception {
-        ourServer.stop();
+    ourServer.stop();
-    }
+  }
 
-    @BeforeClass
+  @BeforeClass
-    public static void beforeClass() throws Exception {
+  public static void beforeClass() throws Exception {
-        String path = Paths.get("").toAbsolutePath().toString();
+    String path = Paths.get("").toAbsolutePath().toString();
 
-        ourLog.info("Project base path is: {}", path);
+    ourLog.info("Project base path is: {}", path);
 
-        ourServer = new Server(0);
+    ourServer = new Server(0);
 
-        WebAppContext webAppContext = new WebAppContext();
+    WebAppContext webAppContext = new WebAppContext();
-        webAppContext.setContextPath("/hapi-fhir-jpaserver");
+    webAppContext.setContextPath("/hapi-fhir-jpaserver");
-        webAppContext.setDisplayName("HAPI FHIR");
+    webAppContext.setDisplayName("HAPI FHIR");
-        webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
+    webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
-        webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
+    webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
-        webAppContext.setParentLoaderPriority(true);
+    webAppContext.setParentLoaderPriority(true);
 
-        ourServer.setHandler(webAppContext);
+    ourServer.setHandler(webAppContext);
-        ourServer.start();
+    ourServer.start();
 
-        ourPort = JettyUtil.getPortForStartedServer(ourServer);
+    ourPort = JettyUtil.getPortForStartedServer(ourServer);
 
-        ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+    ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
-        ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
+    ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
-        String ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver/fhir/";
+    String ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver/fhir/";
 
-        ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
+    ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
-        ourClient.registerInterceptor(new LoggingInterceptor(true));
+    ourClient.registerInterceptor(new LoggingInterceptor(true));
-    }
+  }
 
-    public static void main(String[] theArgs) throws Exception {
+  public static void main(String[] theArgs) throws Exception {
-        ourPort = 8080;
+    ourPort = 8080;
-        beforeClass();
+    beforeClass();
-    }
+  }
 }