Added support for FHIR version V4.

app/pom.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-  ~ Copyright (c) 2004-2018, University of Oslo
+  ~ Copyright (c) 2004-2019, University of Oslo
   ~ All rights reserved.
   ~
   ~ Redistribution and use in source and binary forms, with or without
@@ -74,6 +74,11 @@
       <artifactId>dhis2-fhir-adapter-fhir-dstu3</artifactId>
       <version>${project.version}</version>
     </dependency>
+    <dependency>
+      <groupId>org.dhis2.fhir.adapter</groupId>
+      <artifactId>dhis2-fhir-adapter-fhir-r4</artifactId>
+      <version>${project.version}</version>
+    </dependency>
 
     <dependency>
       <groupId>org.springframework.boot</groupId>

app/src/main/java/org/dhis2/fhir/adapter/DemoClient.java → app/src/main/java/org/dhis2/fhir/adapter/Dstu3DemoClient.java

@@ -62,7 +62,7 @@
  * This content LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the
  * LOINC Committee, and available at no cost under the license at http://loinc.org/terms-of-use
  */
-public class DemoClient
+public class Dstu3DemoClient
 {
     private static final String SERVER_BASE = "http://localhost:8082/hapi-fhir-jpaserver-example/baseDstu3";
 

app/src/main/java/org/dhis2/fhir/adapter/setup/SetupResult.java

@@ -1,7 +1,7 @@
 package org.dhis2.fhir.adapter.setup;
 
 /*
- * Copyright (c) 2004-2018, University of Oslo
+ * Copyright (c) 2004-2019, University of Oslo
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -29,6 +29,7 @@
  */
 
 import org.dhis2.fhir.adapter.fhir.metadata.model.FhirResourceType;
+import org.dhis2.fhir.adapter.fhir.metadata.model.System;
 
 import javax.annotation.Nonnull;
 import java.io.Serializable;
@@ -38,6 +39,8 @@
 
 /**
  * The result of the setup of the FHIR adapter.
+ *
+ * @author volsch
  */
 public class SetupResult implements Serializable
 {
@@ -47,10 +50,16 @@ public class SetupResult implements Serializable
 
     private final Map<FhirResourceType, UUID> fhirServerResourceIds;
 
-    public SetupResult( @Nonnull UUID fhirServerId, @Nonnull Map<FhirResourceType, UUID> fhirServerResourceIds )
+    private final System organizationSystem;
+
+    private final System patientSystem;
+
+    public SetupResult( @Nonnull UUID fhirServerId, @Nonnull Map<FhirResourceType, UUID> fhirServerResourceIds, @Nonnull System organizationSystem, @Nonnull System patientSystem )
     {
         this.fhirServerId = fhirServerId;
         this.fhirServerResourceIds = Collections.unmodifiableMap( fhirServerResourceIds );
+        this.organizationSystem = organizationSystem;
+        this.patientSystem = patientSystem;
     }
 
     @Nonnull
@@ -64,4 +73,14 @@ public Map<FhirResourceType, UUID> getFhirServerResourceIds()
     {
         return fhirServerResourceIds;
     }
+
+    public System getOrganizationSystem()
+    {
+        return organizationSystem;
+    }
+
+    public System getPatientSystem()
+    {
+        return patientSystem;
+    }
 }

app/src/main/java/org/dhis2/fhir/adapter/setup/SetupService.java

@@ -1,7 +1,7 @@
 package org.dhis2.fhir.adapter.setup;
 
 /*
- * Copyright (c) 2004-2018, University of Oslo
+ * Copyright (c) 2004-2019, University of Oslo
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -94,7 +94,7 @@ public class SetupService
     private final CodeCategoryRepository codeCategoryRepository;
 
     private final CodeRepository codeRepository;
-    
+
     private final SystemRepository systemRepository;
 
     private final SystemCodeRepository systemCodeRepository;
@@ -146,24 +146,25 @@ public SetupResult apply( @Nonnull Setup setup )
             setup.getFhirServerSetup().getSystemUriSetup().getPatientSystemUri(),
             "Default DHIS2 Patients", "DEFAULT_DHIS2_PATIENT", "National Patient ID", "Default DHIS2 patient system URI." );
 
-        final SetupResult setupResult = createFhirServer( setup.getFhirServerSetup(), organizationSystem, patientSystem );
+        final SetupResult setupResult = createFhirServer( setup.getFhirServerSetup(), FhirVersion.DSTU3, "", organizationSystem, patientSystem );
         createSystemCodes( setup.getOrganizationCodeSetup(), organizationSystem );
         updateTrackedEntity( setup.getTrackedEntitySetup() );
         return setupResult;
     }
 
     @Nonnull
-    private SetupResult createFhirServer( @Nonnull FhirServerSetup setup, @Nonnull System organizationSystem, @Nonnull System patientSystem )
+    @Transactional
+    public SetupResult createFhirServer( @Nonnull FhirServerSetup setup, @Nonnull FhirVersion fhirVersion, @Nonnull String suffix, @Nonnull System organizationSystem, @Nonnull System patientSystem )
     {
         final Set<FhirResourceType> autoCreatedSubscriptionResources = new HashSet<>();
         autoCreatedSubscriptionResources.add( FhirResourceType.PATIENT );
 
         final FhirServer fhirServer = new FhirServer();
         fhirServer.setSystems( new ArrayList<>() );
-        fhirServer.setName( "Default Remote Subscription" );
-        fhirServer.setCode( "DEFAULT" );
+        fhirServer.setName( "Default Remote Subscription" + suffix );
+        fhirServer.setCode( "DEFAULT" + suffix );
         fhirServer.setDescription( "Default FHIR server." );
-        fhirServer.setFhirVersion( FhirVersion.DSTU3 );
+        fhirServer.setFhirVersion( fhirVersion );
         fhirServer.setEnabled( true );
         fhirServer.setToleranceMillis( setup.getFhirSetup().getToleranceMillis() );
 
@@ -227,7 +228,8 @@ private SetupResult createFhirServer( @Nonnull FhirServerSetup setup, @Nonnull S
 
         fhirServerRepository.saveAndFlush( fhirServer );
         return new SetupResult( fhirServer.getId(), fhirServer.getResources().stream()
-            .collect( Collectors.toMap( FhirServerResource::getFhirResourceType, VersionedBaseMetadata::getId ) ) );
+            .collect( Collectors.toMap( FhirServerResource::getFhirResourceType, VersionedBaseMetadata::getId ) ),
+            organizationSystem, patientSystem );
     }
 
     private void createSystemCodes( @Nonnull OrganizationCodeSetup setup, @Nonnull System organizationSystem )

app/src/test/java/org/dhis2/fhir/adapter/AbstractAppTest.java

@@ -1,7 +1,7 @@
 package org.dhis2.fhir.adapter;
 
 /*
- * Copyright (c) 2004-2018, University of Oslo
+ * Copyright (c) 2004-2019, University of Oslo
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -40,6 +40,7 @@
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.dhis2.fhir.adapter.fhir.metadata.model.FhirResourceType;
+import org.dhis2.fhir.adapter.fhir.model.FhirVersion;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.runner.RunWith;
@@ -153,6 +154,37 @@ public abstract class AbstractAppTest
 
     private long resourceDlQueueCount;
 
+    @Nonnull
+    protected abstract FhirVersion getFhirVersion();
+
+    @Nonnull
+    protected String getBaseFhirContext()
+    {
+        switch ( getFhirVersion() )
+        {
+            case DSTU3:
+                return TestConfiguration.BASE_DSTU3_CONTEXT;
+            case R4:
+                return TestConfiguration.BASE_R4_CONTEXT;
+            default:
+                throw new AssertionError( "Unhandled FHIR version: " + getFhirVersion() );
+        }
+    }
+
+    @Nonnull
+    protected String getResourceDir()
+    {
+        switch ( getFhirVersion() )
+        {
+            case DSTU3:
+                return "dstu3";
+            case R4:
+                return "r4";
+            default:
+                throw new AssertionError( "Unhandled FHIR version: " + getFhirVersion() );
+        }
+    }
+
     @Nonnull
     protected HttpHeaders createDefaultHeaders()
     {
@@ -171,7 +203,7 @@ protected void notifyResource( @Nonnull FhirResourceType resourceType, @Nullable
         }
         if ( StringUtils.isNotBlank( resourceSearchResponse ) )
         {
-            final UrlPattern urlPattern = urlMatching( TestConfiguration.BASE_DSTU3_CONTEXT +
+            final UrlPattern urlPattern = urlMatching( getBaseFhirContext() +
                 "/" + resourceType.getResourceTypeName() +
                 "\\?_sort=_lastUpdated&_count=10000&_lastUpdated=ge[^&]+&_elements=meta\\%2[cC]id" );
             previousResourceSearchStubMapping = fhirMockServer.stubFor(
@@ -181,7 +213,7 @@ protected void notifyResource( @Nonnull FhirResourceType resourceType, @Nullable
         }
         if ( StringUtils.isNotBlank( resourceId ) && StringUtils.isNotBlank( resourceResponse ) )
         {
-            fhirMockServer.stubFor( WireMock.get( urlEqualTo( TestConfiguration.BASE_DSTU3_CONTEXT +
+            fhirMockServer.stubFor( WireMock.get( urlEqualTo( getBaseFhirContext() +
                 "/" + resourceType.getResourceTypeName() + "/" + resourceId ) ).willReturn( aResponse()
                 .withHeader( "Content-Type", "application/fhir+json" )
                 .withBody( resourceResponse ) ) );
@@ -192,15 +224,15 @@ protected void notifyResource( @Nonnull FhirResourceType resourceType, @Nullable
             Assert.assertNotNull( resourceId );
             Assert.assertNotNull( resourceResponse );
             mockMvc.perform( MockMvcRequestBuilders.put( "/remote-fhir-rest-hook/{subscriptionId}/{fhirServerResourceId}/{resourceType}/{resourceId}",
-                testConfiguration.getFhirServerId(), testConfiguration.getFhirServerResourceId( resourceType ),
+                testConfiguration.getFhirServerId( getFhirVersion() ), testConfiguration.getFhirServerResourceId( getFhirVersion(), resourceType ),
                 resourceType.getResourceTypeName(), resourceId ).content( resourceResponse ).contentType( FHIR_JSON_MEDIA_TYPE )
                 .header( "Authorization", TestConfiguration.ADAPTER_AUTHORIZATION ) )
                 .andExpect( status().isOk() );
         }
         else
         {
             mockMvc.perform( MockMvcRequestBuilders.post( "/remote-fhir-rest-hook/{subscriptionId}/{fhirServerResourceId}",
-                testConfiguration.getFhirServerId(), testConfiguration.getFhirServerResourceId( resourceType ) )
+                testConfiguration.getFhirServerId( getFhirVersion() ), testConfiguration.getFhirServerResourceId( getFhirVersion(), resourceType ) )
                 .header( "Authorization", TestConfiguration.ADAPTER_AUTHORIZATION ) )
                 .andExpect( status().isOk() );
         }
@@ -267,9 +299,9 @@ public void beforeAbstractAppTest() throws Exception
         userDhis2Server = MockRestServiceServer.bindTo( userDhis2RestTemplate ).build();
 
         fhirMockServer.stubFor(
-            WireMock.get( urlPathEqualTo( TestConfiguration.BASE_DSTU3_CONTEXT + "/metadata" ) ).willReturn( aResponse()
+            WireMock.get( urlPathEqualTo( getBaseFhirContext() + "/metadata" ) ).willReturn( aResponse()
                 .withHeader( "Content-Type", "application/fhir+json" )
-                .withBody( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/fhir/test/dstu3/metadata.json", StandardCharsets.UTF_8 ) ) ) );
+                .withBody( IOUtils.resourceToString( "/org/dhis2/fhir/adapter/fhir/test/" + getResourceDir() + "/metadata.json", StandardCharsets.UTF_8 ) ) ) );
 
         clearCache( metadataCacheManager );
         clearCache( dhisCacheManager );

app/src/test/java/org/dhis2/fhir/adapter/StaticResourcesAppTest.java

@@ -28,8 +28,11 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
+import org.dhis2.fhir.adapter.fhir.model.FhirVersion;
 import org.junit.Test;
 
+import javax.annotation.Nonnull;
+
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
 
@@ -40,6 +43,13 @@
  */
 public class StaticResourcesAppTest extends AbstractAppTest
 {
+    @Nonnull
+    @Override
+    protected FhirVersion getFhirVersion()
+    {
+        return FhirVersion.DSTU3;
+    }
+
     @Test
     public void apiGuide() throws Exception
     {

app/src/test/java/org/dhis2/fhir/adapter/TestConfiguration.java

@@ -1,7 +1,7 @@
 package org.dhis2.fhir.adapter;
 
 /*
- * Copyright (c) 2004-2018, University of Oslo
+ * Copyright (c) 2004-2019, University of Oslo
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -33,6 +33,7 @@
 import org.dhis2.fhir.adapter.dhis.security.SecurityConfig;
 import org.dhis2.fhir.adapter.fhir.metadata.model.FhirResourceType;
 import org.dhis2.fhir.adapter.fhir.metadata.model.SubscriptionType;
+import org.dhis2.fhir.adapter.fhir.model.FhirVersion;
 import org.dhis2.fhir.adapter.fhir.security.AdapterSystemAuthenticationToken;
 import org.dhis2.fhir.adapter.lock.LockManager;
 import org.dhis2.fhir.adapter.lock.impl.EmbeddedLockManagerImpl;
@@ -88,6 +89,8 @@ public class TestConfiguration
 
     public static final String BASE_DSTU3_CONTEXT = "/baseDstu3";
 
+    public static final String BASE_R4_CONTEXT = "/baseR4";
+
     @Value( "${dhis2.fhir-adapter.endpoint.system-authentication.username}" )
     private String dhis2SystemAuthenticationUsername;
 
@@ -103,16 +106,39 @@ public class TestConfiguration
 
     private Map<FhirResourceType, UUID> fhirServerResourceIds;
 
+    private UUID fhirServerIdR4;
+
+    private Map<FhirResourceType, UUID> fhirServerResourceIdsR4;
+
     @Nonnull
-    public UUID getFhirServerId()
+    public UUID getFhirServerId( @Nonnull FhirVersion fhirVersion )
     {
-        return fhirServerId;
+        switch ( fhirVersion )
+        {
+            case DSTU3:
+                return fhirServerId;
+            case R4:
+                return fhirServerIdR4;
+            default:
+                throw new AssertionError( "Unhandled FHIR version: " + fhirVersion );
+        }
     }
 
     @Nonnull
-    public UUID getFhirServerResourceId( @Nonnull FhirResourceType resourceType )
+    public UUID getFhirServerResourceId( @Nonnull FhirVersion fhirVersion, @Nonnull FhirResourceType resourceType )
     {
-        final UUID resourceId = fhirServerResourceIds.get( resourceType );
+        final UUID resourceId;
+        switch ( fhirVersion )
+        {
+            case DSTU3:
+                resourceId = fhirServerResourceIds.get( resourceType );
+                break;
+            case R4:
+                resourceId = fhirServerResourceIdsR4.get( resourceType );
+                break;
+            default:
+                throw new AssertionError( "Unhandled FHIR version: " + fhirVersion );
+        }
         Assert.assertNotNull( "FHIR server resource for " + resourceType + " could not be found.", resourceId );
         return resourceId;
     }
@@ -196,12 +222,34 @@ protected void postConstruct()
         setup.getTrackedEntitySetup().getLastName().setReferenceType( ReferenceType.NAME );
         setup.getTrackedEntitySetup().getLastName().setReferenceValue( "Last Name" );
 
+        final Setup setupR4 = new Setup();
+
+        setupR4.getFhirServerSetup().getAdapterSetup().setBaseUrl( "http://localhost:8081" );
+        setupR4.getFhirServerSetup().getAdapterSetup().setAuthorizationHeaderValue( ADAPTER_AUTHORIZATION );
+
+        setupR4.getFhirServerSetup().getDhisSetup().setUsername( DHIS2_USERNAME );
+        setupR4.getFhirServerSetup().getDhisSetup().setPassword( DHIS2_PASSWORD );
+
+        setupR4.getFhirServerSetup().getFhirSetup().setBaseUrl( fhirMockServer.baseUrl() + BASE_R4_CONTEXT );
+        setupR4.getFhirServerSetup().getFhirSetup().setHeaderName( FHIR_SERVICE_HEADER_NAME );
+        setupR4.getFhirServerSetup().getFhirSetup().setHeaderValue( FHIR_SERVICE_HEADER_VALUE );
+        setupR4.getFhirServerSetup().getFhirSetup().setSubscriptionType( SubscriptionType.REST_HOOK );
+        setupR4.getFhirServerSetup().getFhirSetup().setSupportsRelatedPerson( true );
+
+        setupR4.getFhirServerSetup().getSystemUriSetup().setOrganizationSystemUri( "http://example.sl/organizations" );
+        setupR4.getFhirServerSetup().getSystemUriSetup().setOrganizationCodePrefix( "OU_" );
+        setupR4.getFhirServerSetup().getSystemUriSetup().setPatientSystemUri( "http://example.sl/patients" );
+        setupR4.getFhirServerSetup().getSystemUriSetup().setPatientCodePrefix( "PT_" );
+
         final SetupResult setupResult;
+        final SetupResult setupResultR4;
         SecurityContextHolder.getContext().setAuthentication( new AdapterSystemAuthenticationToken() );
         try
         {
             Assert.assertFalse( setupService.hasCompletedSetup() );
             setupResult = setupService.apply( setup );
+            setupResultR4 = setupService.createFhirServer( setupR4.getFhirServerSetup(), FhirVersion.R4, "_R4",
+                setupResult.getOrganizationSystem(), setupResult.getPatientSystem() );
             Assert.assertTrue( setupService.hasCompletedSetup() );
         }
         finally
@@ -211,6 +259,8 @@ protected void postConstruct()
 
         this.fhirServerId = setupResult.getFhirServerId();
         this.fhirServerResourceIds = setupResult.getFhirServerResourceIds();
+        this.fhirServerIdR4 = setupResultR4.getFhirServerId();
+        this.fhirServerResourceIdsR4 = setupResultR4.getFhirServerResourceIds();
     }
 
     @PreDestroy