Merge pull request #102 from hapifhir/rel_5_1_0

Start Release branch for 5.1.0

Author: jamesagnew

README.md

@@ -209,6 +209,10 @@ The server may be configured with subscription support by enabling properties in
 
 - `subscription.websocket.enabled` - Enables websocket subscriptions. With this enabled, your server will accept incoming websocket connections on the following URL (this example uses the default context path and port, you may need to tweak depending on your deployment environment): [ws://localhost:8080/hapi-fhir-jpaserver/websocket](ws://localhost:8080/hapi-fhir-jpaserver/websocket)
 
+## Enabling EMPI
+
+Set `empi.enabled=true` in the [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties) file to enable EMPI on this server.  The EMPI matching rules are configured in [empi-rules.json](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/empi-rules.json).  The rules in this example file should be replaced with actual matching rules appropriate to your data. Note that EMPI relies on subscriptions, so for EMPI to work, subscriptions must be enabled. 
+
 ## Using Elasticsearch
 
 By default, the server will use embedded lucene indexes for terminology and fulltext indexing purposes. You can switch this to using lucene by editing the properties in [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties)

pom.xml

@@ -1,4 +1,4 @@
-<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">
     <modelVersion>4.0.0</modelVersion>
 
@@ -11,7 +11,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-        <version>5.0.2</version>
+        <version>5.1.0</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -20,6 +20,20 @@
         <maven>3.5.0</maven>
     </prerequisites>
 
+    <packaging>war</packaging>
+
+    <name>HAPI FHIR JPA Server - Starter Project</name>
+
+    <repositories>
+        <repository>
+            <id>oss-snapshots</id>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+            <url>https://oss.sonatype.org/content/repositories/snapshots/</url>
+        </repository>
+    </repositories>
+
     <dependencies>
         <dependency>
             <groupId>org.eclipse.jetty.websocket</groupId>
@@ -84,7 +98,12 @@
                 </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>
@@ -249,22 +268,22 @@
             <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>
-
-    <name>HAPI FHIR JPA Server - Starter Project</name>
+        <!-- TODO: remove this and migrate to JU5 -->
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.12</version>
+            <scope>test</scope>
+        </dependency>
 
-    <repositories>
-        <repository>
-            <id>oss-snapshots</id>
-            <snapshots>
-                <enabled>false</enabled>
-            </snapshots>
-            <url>https://oss.sonatype.org/content/repositories/snapshots/</url>
-        </repository>
-    </repositories>
+    </dependencies>
 
     <build>
 
@@ -276,7 +295,7 @@
             <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>
@@ -421,6 +440,7 @@
                     <ignoredResourcePatterns>
                         <ignoredResourcePattern>.*\.txt$</ignoredResourcePattern>
                         <ignoredResourcePattern>.*\.html$</ignoredResourcePattern>
+                        <ignoredResourcePattern>config/favicon.ico</ignoredResourcePattern>
                     </ignoredResourcePatterns>
                 </configuration>
             </plugin>

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

@@ -1,6 +1,8 @@
 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;
@@ -28,13 +30,19 @@ public ApplicationContext() {
     }
 
     if (HapiProperties.getSubscriptionEmailEnabled()
-    || HapiProperties.getSubscriptionRestHookEnabled()
-    || HapiProperties.getSubscriptionWebsocketEnabled()) {
+      || 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

@@ -7,9 +7,8 @@
 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.api.rp.ResourceProviderFactory;
 import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
-import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider;
+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;
@@ -37,6 +36,7 @@
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
+import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
 import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
 import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;

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

@@ -0,0 +1,31 @@
+package ca.uhn.fhir.jpa.starter;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.empi.api.IEmpiSettings;
+import ca.uhn.fhir.empi.rules.config.EmpiRuleValidator;
+import ca.uhn.fhir.empi.rules.config.EmpiSettings;
+import ca.uhn.fhir.jpa.empi.svc.EmpiSearchParamSvc;
+import ca.uhn.fhir.jpa.subscription.channel.subscription.IChannelNamer;
+import ca.uhn.fhir.rest.server.util.ISearchParamRetriever;
+import com.google.common.base.Charsets;
+import org.apache.commons.io.IOUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.core.io.DefaultResourceLoader;
+import org.springframework.core.io.Resource;
+
+import java.io.IOException;
+
+@Configuration
+public class EmpiConfig {
+
+  @Bean
+  IEmpiSettings empiSettings(EmpiRuleValidator theEmpiRuleValidator) throws IOException {
+    DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
+    Resource resource = resourceLoader.getResource("empi-rules.json");
+    String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
+    return new EmpiSettings(theEmpiRuleValidator).setEnabled(HapiProperties.getEmpiEnabled()).setScriptText(json);
+  }
+
+}

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

@@ -10,7 +10,6 @@
 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.BeanFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -25,7 +24,7 @@
  * This is the primary configuration file for the example server
  */
 @Configuration
-@EnableTransactionManagement()
+@EnableTransactionManagement
 public class FhirServerConfigCommon {
 
   private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
@@ -205,11 +204,10 @@ public IEmailSender emailSender() {
       retVal.setSmtpServerPort(this.emailPort);
       retVal.setSmtpServerUsername(this.emailUsername);
       retVal.setSmtpServerPassword(this.emailPassword);
-      // TODO KHS add these when HAPI 4.2.0 is released
-//      retVal.setAuth(this.emailAuth);
-//      retVal.setStartTlsEnable(this.emailStartTlsEnable);
-//      retVal.setStartTlsRequired(this.emailStartTlsRequired);
-//      retVal.setQuitWait(this.emailQuitWait);
+      retVal.setAuth(this.emailAuth);
+      retVal.setStartTlsEnable(this.emailStartTlsEnable);
+      retVal.setStartTlsRequired(this.emailStartTlsRequired);
+      retVal.setQuitWait(this.emailQuitWait);
 
       SubscriptionDeliveryHandlerFactory subscriptionDeliveryHandlerFactory = myAppCtx.getBean(SubscriptionDeliveryHandlerFactory.class);
       Validate.notNull(subscriptionDeliveryHandlerFactory, "No subscription delivery handler");

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java

@@ -6,6 +6,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -47,8 +48,9 @@ public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
         return retVal;
     }
 
-    @Bean()
-    public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+  @Bean
+  @Primary
+  public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
         JpaTransactionManager retVal = new JpaTransactionManager();
         retVal.setEntityManagerFactory(entityManagerFactory);
         return retVal;

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java

@@ -6,6 +6,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -32,7 +33,7 @@ public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
     }
 
     @Override
-    @Bean()
+    @Bean
     public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
         LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
         retVal.setPersistenceUnitName("HAPI_PU");
@@ -47,8 +48,9 @@ public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
         return retVal;
     }
 
-    @Bean()
-    public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+    @Bean
+    @Primary
+    public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
         JpaTransactionManager retVal = new JpaTransactionManager();
         retVal.setEntityManagerFactory(entityManagerFactory);
         return retVal;

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

@@ -6,6 +6,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -47,8 +48,9 @@ public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
         return retVal;
     }
 
-    @Bean()
-    public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+  @Bean
+  @Primary
+  public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
         JpaTransactionManager retVal = new JpaTransactionManager();
         retVal.setEntityManagerFactory(entityManagerFactory);
         return retVal;

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java

@@ -6,6 +6,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -47,8 +48,9 @@ public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
         return retVal;
     }
 
-    @Bean()
-    public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+  @Bean
+  @Primary
+  public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
         JpaTransactionManager retVal = new JpaTransactionManager();
         retVal.setEntityManagerFactory(entityManagerFactory);
         return retVal;