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 {
 
@@ -287,31 +292,7 @@ public class JpaRestfulServer extends RestfulServer {
     }
 
     // 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();
@@ -351,11 +332,13 @@ public class JpaRestfulServer extends RestfulServer {
       registerProvider(appCtx.getBean(BulkDataExportProvider.class));
     }
 
-
+    if (HapiProperties.getPartitioningEnabled()) {
-    if (HapiProperties.getEmpiEnabled()) {
+      PartitionSettings partitionSettings = appCtx.getBean(PartitionSettings.class);
-      // FIXME KHS
+      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();
     }
 
@@ -57,6 +66,28 @@ 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());
+    }
+
+  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
@@ -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
@@ -117,6 +148,10 @@ public class ExampleServerR4IT {
         ourClient.delete().resourceById(mySubscriptionId).execute();
     }
 
+  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;
@@ -62,7 +68,7 @@ public class ExampleServerR5IT {
     /*
      * Create topic
      */
-        Topic topic = new Topic();
+    SubscriptionTopic topic = new SubscriptionTopic();
     topic.getResourceTrigger().getQueryCriteria().setCurrent("Observation?status=final");
 
     /*
@@ -71,14 +77,12 @@ public class ExampleServerR5IT {
     Subscription subscription = new Subscription();
     subscription.getTopic().setResource(topic);
     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();
     IIdType mySubscriptionId = methodOutcome.getId();