updated to match 5.0.0

pom.xml

@@ -1,5 +1,6 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" 
+<project xmlns="http://maven.apache.org/POM/4.0.0"
-    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">
+         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">
     <modelVersion>4.0.0</modelVersion>
 
     <!--
@@ -11,7 +12,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-        <version>4.2.0</version>
+        <version>5.0.0-SNAPSHOT</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -84,7 +85,12 @@
                 </exclusion>
             </exclusions>
         </dependency>
-
+        <!-- This dependency includes the JPA EMPI Server -->
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>hapi-fhir-jpaserver-empi</artifactId>
+            <version>${project.version}</version>
+        </dependency>
         <!-- This dependency is used for the "FHIR Tester" web app overlay -->
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
@@ -276,7 +282,7 @@
             <plugin>
                 <groupId>org.eclipse.jetty</groupId>
                 <artifactId>jetty-maven-plugin</artifactId>
-					 <version>${jetty_version}</version>
+                <version>${jetty_version}</version>
                 <configuration>
                     <webApp>
                         <contextPath>/hapi-fhir-jpaserver</contextPath>

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

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
 import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
 
 public class ApplicationContext extends AnnotationConfigWebApplicationContext {
@@ -20,7 +21,7 @@ public class ApplicationContext extends AnnotationConfigWebApplicationContext {
         }
 
         if (HapiProperties.getSubscriptionWebsocketEnabled()) {
-            register(ca.uhn.fhir.jpa.config.WebsocketDispatcherConfig.class);
+            register(WebsocketDispatcherConfig.class);
         }
 
     }

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

@@ -0,0 +1,27 @@
+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.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 {
+    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);
+  }
+}

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

@@ -1,17 +1,18 @@
 package ca.uhn.fhir.jpa.starter;
 
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.binstore.DatabaseBlobBinaryStorageSvcImpl;
 import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
-import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
-import ca.uhn.fhir.jpa.subscription.module.channel.SubscriptionDeliveryHandlerFactory;
+import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
-import ca.uhn.fhir.jpa.subscription.module.subscriber.email.IEmailSender;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
-import ca.uhn.fhir.jpa.subscription.module.subscriber.email.JavaMailEmailSender;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
 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;
@@ -23,7 +24,8 @@ import java.sql.Driver;
  * This is the primary configuration file for the example server
  */
 @Configuration
-@EnableTransactionManagement()
+@EnableTransactionManagement
+@Import(EmpiConfig.class)
 public class FhirServerConfigCommon {
 
   private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
@@ -191,7 +193,7 @@ public class FhirServerConfigCommon {
       retVal.setSmtpServerPort(this.emailPort);
       retVal.setSmtpServerUsername(this.emailUsername);
       retVal.setSmtpServerPassword(this.emailPassword);
-      // TODO KHS add these when HAPI 4.2.0 is released
+      // FIXME KHS add these once this has merged in hapi
 //      retVal.setAuth(this.emailAuth);
 //      retVal.setStartTlsEnable(this.emailStartTlsEnable);
 //      retVal.setStartTlsRequired(this.emailStartTlsRequired);

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

@@ -57,6 +57,7 @@ public class HapiProperties {
   static final String SUBSCRIPTION_EMAIL_ENABLED = "subscription.email.enabled";
   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 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";
@@ -373,6 +374,10 @@ public class HapiProperties {
     return HapiProperties.getBooleanProperty(SUBSCRIPTION_WEBSOCKET_ENABLED, false);
   }
 
+  public static Boolean getEmpiEnabled() {
+    return HapiProperties.getBooleanProperty(EMPI_ENABLED, false);
+  }
+
   public static Boolean getAllowContainsSearches() {
     return HapiProperties.getBooleanProperty(ALLOW_CONTAINS_SEARCHES, true);
   }

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

@@ -4,11 +4,11 @@ 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.BulkDataExportProvider;
-import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.jpa.dao.DaoRegistry;
-import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
 import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
@@ -22,9 +22,9 @@ 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.subscription.SubscriptionInterceptorLoader;
+import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
-import ca.uhn.fhir.jpa.subscription.module.interceptor.SubscriptionDebugLogInterceptor;
+import ca.uhn.fhir.jpa.subscription.submit.interceptor.SubscriptionSubmitInterceptorLoader;
-import ca.uhn.fhir.jpa.util.ResourceProviderFactory;
+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;
@@ -34,6 +34,7 @@ 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.provider.ResourceProviderFactory;
 import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import java.util.HashSet;
@@ -123,21 +124,21 @@ public class JpaRestfulServer extends RestfulServer {
       IFhirSystemDao<Bundle, Meta> systemDao = appCtx
           .getBean("mySystemDaoDstu3", IFhirSystemDao.class);
       JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao,
-          appCtx.getBean(DaoConfig.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);
       JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, systemDao,
-          appCtx.getBean(DaoConfig.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);
       JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, systemDao,
-          appCtx.getBean(DaoConfig.class));
+          appCtx.getBean(DaoConfig.class), appCtx.getBean(ISearchParamRegistry.class));
       confProvider.setImplementationDescription("HAPI FHIR R5 Server");
       setServerConformanceProvider(confProvider);
     } else {
@@ -259,9 +260,10 @@ public class JpaRestfulServer extends RestfulServer {
         HapiProperties.getSubscriptionRestHookEnabled()) {
       // Loads subscription interceptors (SubscriptionActivatingInterceptor, SubscriptionMatcherInterceptor)
       // with activation of scheduled subscription
-      SubscriptionInterceptorLoader subscriptionInterceptorLoader = appCtx
+
-          .getBean(SubscriptionInterceptorLoader.class);
+      SubscriptionSubmitInterceptorLoader subscriptionInterceptorLoader = appCtx
-      subscriptionInterceptorLoader.registerInterceptors();
+          .getBean(SubscriptionSubmitInterceptorLoader.class);
+      subscriptionInterceptorLoader.start();
 
       // Subscription debug logging
       IInterceptorService interceptorService = appCtx.getBean(IInterceptorService.class);
@@ -272,7 +274,7 @@ public class JpaRestfulServer extends RestfulServer {
     DaoRegistry daoRegistry = appCtx.getBean(DaoRegistry.class);
     IInterceptorBroadcaster interceptorBroadcaster = appCtx.getBean(IInterceptorBroadcaster.class);
     if (HapiProperties.getAllowCascadingDeletes()) {
-      CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(
+      CascadingDeleteInterceptor cascadingDeleteInterceptor = new CascadingDeleteInterceptor(getFhirContext(),
           daoRegistry, interceptorBroadcaster);
       getInterceptorService().registerInterceptor(cascadingDeleteInterceptor);
     }
@@ -345,6 +347,11 @@ public class JpaRestfulServer extends RestfulServer {
             registerProvider(appCtx.getBean(BulkDataExportProvider.class));
         }
 
+
+    if (HapiProperties.getEmpiEnabled()) {
+      // FIXME KHS
     }
 
+
+  }
 }

src/main/resources/empi-rules.json

@@ -0,0 +1,32 @@
+{
+	"resourceSearchParams" : [ {
+		"resourceType" : "Patient",
+		"searchParam" : "birthdate"
+	}, {
+		"resourceType" : "All",
+		"searchParam" : "identifier"
+	} ],
+	"filterSearchParams" : [ {
+		"resourceType" : "All",
+		"searchParam" : "active",
+		"fixedValue" : "true"
+	} ],
+	"matchFields" : [ {
+		"name" : "given-name",
+		"resourceType" : "All",
+		"resourcePath" : "name.given",
+		"metric" : "COSINE",
+		"matchThreshold" : 0.8
+	}, {
+		"name" : "last-name",
+		"resourceType" : "All",
+		"resourcePath" : "name.family",
+		"metric" : "JARO_WINKLER",
+		"matchThreshold" : 0.8
+	}],
+	"weightMap" : {
+		"given-name" : "POSSIBLE_MATCH",
+		"given-name,last-name" : "MATCH"
+	},
+	"eidSystem": "http://company.io/fhir/NamingSystem/custom-eid-system"
+}