Merge remote-tracking branch 'origin/release/0.2.1'

highmed · Jul 6, 2020 · 76ecdc5 · 76ecdc5
2 parents c31ff40 + 603c9f6
commit 76ecdc5
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diff --git a/dsf-bpe/dsf-bpe-process-base/pom.xml b/dsf-bpe/dsf-bpe-process-base/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-process-feasibility/pom.xml b/dsf-bpe/dsf-bpe-process-feasibility/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<artifactId>dsf-bpe-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-process-ping/pom.xml b/dsf-bpe/dsf-bpe-process-ping/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-process-plugin-example/dsf-bpe-process-child/pom.xml b/dsf-bpe/dsf-bpe-process-plugin-example/dsf-bpe-process-child/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<artifactId>dsf-bpe-process-plugin-example</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-process-plugin-example/dsf-bpe-process-parent/pom.xml b/dsf-bpe/dsf-bpe-process-plugin-example/dsf-bpe-process-parent/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<artifactId>dsf-bpe-process-plugin-example</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-process-plugin-example/dsf-bpe-process-service-overwrite/pom.xml b/dsf-bpe/dsf-bpe-process-plugin-example/dsf-bpe-process-service-overwrite/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<artifactId>dsf-bpe-process-plugin-example</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-process-plugin-example/pom.xml b/dsf-bpe/dsf-bpe-process-plugin-example/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<artifactId>dsf-bpe-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<artifactId>dsf-bpe-process-plugin-example</artifactId>

diff --git a/dsf-bpe/dsf-bpe-process-update-resources/pom.xml b/dsf-bpe/dsf-bpe-process-update-resources/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-process-update-whitelist/pom.xml b/dsf-bpe/dsf-bpe-process-update-whitelist/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-server-jetty/docker/dsf_bpe_start.sh b/dsf-bpe/dsf-bpe-server-jetty/docker/dsf_bpe_start.sh
@@ -4,7 +4,7 @@ echo "Executing DSF BPE with"
 java --version
 
 trap 'kill -TERM $PID' TERM INT
-java -cp lib/*:plugin/*:dsf_bpe.jar org.highmed.dsf.bpe.BpeJettyServer &
+java $EXTRA_JVM_ARGS -Djdk.tls.acknowledgeCloseNotify=true -cp lib/*:plugin/*:dsf_bpe.jar org.highmed.dsf.bpe.BpeJettyServer &
 PID=$!
 wait $PID
 trap - TERM INT

diff --git a/dsf-bpe/dsf-bpe-server-jetty/pom.xml b/dsf-bpe/dsf-bpe-server-jetty/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-server/pom.xml b/dsf-bpe/dsf-bpe-server/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-webservice-client/pom.xml b/dsf-bpe/dsf-bpe-webservice-client/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/pom.xml b/dsf-bpe/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<modules>

diff --git a/dsf-docker-test-setup-3medic-ttp/highmed.yml b/dsf-docker-test-setup-3medic-ttp/highmed.yml
@@ -67,9 +67,9 @@
          append: true
    -  name: Download docker-compose
       get_url:
-         url: https://github.com/docker/compose/releases/download/1.26.0/docker-compose-Linux-x86_64
+         url: https://github.com/docker/compose/releases/download/1.26.2/docker-compose-Linux-x86_64
          dest: /usr/local/bin/docker-compose
-         checksum: sha256:ff6816932a57eab448798105926adbe4363b82f217802b105ade2edad95706cb
+         checksum: sha256:13e50875393decdb047993c3c0192b0a3825613e6dfc0fa271efed4f5dbdd6eb
          mode: '777'
    -  name: update /etc/hosts file
       blockinfile:

diff --git a/dsf-docker-test-setup/bpe/docker-compose.yml b/dsf-docker-test-setup/bpe/docker-compose.yml
@@ -21,6 +21,10 @@ services:
    app:
       image: highmed/bpe
       restart: on-failure
+# Ports for jmx debug connections
+#      ports:
+#      - 9020:9020
+#      - 9021:9021
       volumes:
       -  type: bind
          source: ./app/conf
@@ -38,6 +42,8 @@ services:
          target: /opt/bpe/last_event
       environment:
          TZ: Europe/Berlin
+# Use EXTRA_JVM_ARGS to specify special jvm parameters, e.g. jmx connection config below
+#         EXTRA_JVM_ARGS: -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false -Dcom.sun.management.jmxremote.port=9020 -Dcom.sun.management.jmxremote.rmi.port=9021 -Djava.rmi.server.hostname=localhost -Dcom.sun.management.jmxremote.local.only=false
       networks:
          frontend:
             ipv4_address: 172.28.3.3

diff --git a/dsf-docker-test-setup/fhir/docker-compose.yml b/dsf-docker-test-setup/fhir/docker-compose.yml
@@ -25,6 +25,10 @@ services:
    app:
       image: highmed/fhir
       restart: on-failure
+ # Ports for jmx debug connections
+ #     ports:
+ #     - 9010:9010
+ #     - 9011:9011
       volumes:
       -  type: bind
          source: ./app/conf
@@ -34,6 +38,8 @@ services:
          target: /opt/fhir/log
       environment:
          TZ: Europe/Berlin
+# Use EXTRA_JVM_ARGS to specify special jvm parameters, e.g. jmx connection config below
+#         EXTRA_JVM_ARGS: -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false -Dcom.sun.management.jmxremote.port=9010 -Dcom.sun.management.jmxremote.rmi.port=9011 -Djava.rmi.server.hostname=localhost -Dcom.sun.management.jmxremote.local.only=false
       networks:
          frontend:
             ipv4_address: 172.28.1.3

diff --git a/dsf-fhir/dsf-fhir-rest-adapter/pom.xml b/dsf-fhir/dsf-fhir-rest-adapter/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-fhir/dsf-fhir-server-jetty/docker/dsf_fhir_start.sh b/dsf-fhir/dsf-fhir-server-jetty/docker/dsf_fhir_start.sh
@@ -4,7 +4,7 @@ echo "Executing DSF FHIR with"
 java --version
 
 trap 'kill -TERM $PID' TERM INT
-java -cp lib/*:dsf_fhir.jar org.highmed.dsf.fhir.FhirJettyServer &
+java $EXTRA_JVM_ARGS -Djdk.tls.acknowledgeCloseNotify=true -cp lib/*:dsf_fhir.jar org.highmed.dsf.fhir.FhirJettyServer &
 PID=$!
 wait $PID
 trap - TERM INT

diff --git a/dsf-fhir/dsf-fhir-server-jetty/pom.xml b/dsf-fhir/dsf-fhir-server-jetty/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-fhir/dsf-fhir-server/pom.xml b/dsf-fhir/dsf-fhir-server/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>
@@ -225,7 +225,7 @@
 				</configuration>
 				<!-- Workaround for exec maven plugin issue -->
 				<!-- https://github.com/mojohaus/exec-maven-plugin/issues/76 -->
-				<!-- <dependencies> <dependency> <groupId>org.highmed.dsf</groupId> <artifactId>dsf-tools-bundle-generator</artifactId> <version>0.2.0</version> </dependency> 
+				<!-- <dependencies> <dependency> <groupId>org.highmed.dsf</groupId> <artifactId>dsf-tools-bundle-generator</artifactId> <version>0.2.1</version> </dependency> 
 					</dependencies> -->
 			</plugin>
 			<plugin>

diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/history/HistoryServiceImpl.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/history/HistoryServiceImpl.java
@@ -7,9 +7,9 @@
 import javax.ws.rs.WebApplicationException;
 import javax.ws.rs.core.HttpHeaders;
 import javax.ws.rs.core.MultivaluedMap;
+import javax.ws.rs.core.Response.Status;
 import javax.ws.rs.core.UriBuilder;
 import javax.ws.rs.core.UriInfo;
-import javax.ws.rs.core.Response.Status;
 
 import org.highmed.dsf.fhir.authentication.User;
 import org.highmed.dsf.fhir.dao.HistoryDao;
@@ -21,7 +21,9 @@
 import org.highmed.dsf.fhir.search.PageAndCount;
 import org.highmed.dsf.fhir.search.SearchQuery;
 import org.highmed.dsf.fhir.search.SearchQueryParameterError;
+import org.highmed.dsf.fhir.service.ReferenceCleaner;
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r4.model.Resource;
 import org.springframework.beans.factory.InitializingBean;
 
@@ -34,18 +36,20 @@ public class HistoryServiceImpl implements HistoryService, InitializingBean
 	private final ParameterConverter parameterConverter;
 	private final ExceptionHandler exceptionHandler;
 	private final ResponseGenerator responseGenerator;
+	private final ReferenceCleaner referenceCleaner;
 	private final HistoryDao historyDao;
 	private final HistoryUserFilterFactory historyUserFilterFactory;
 
 	public HistoryServiceImpl(String serverBase, int defaultPageCount, ParameterConverter parameterConverter,
-			ExceptionHandler exceptionHandler, ResponseGenerator responseGenerator, HistoryDao historyDao,
-			HistoryUserFilterFactory historyUserFilterFactory)
+			ExceptionHandler exceptionHandler, ResponseGenerator responseGenerator, ReferenceCleaner referenceCleaner,
+			HistoryDao historyDao, HistoryUserFilterFactory historyUserFilterFactory)
 	{
 		this.serverBase = serverBase;
 		this.defaultPageCount = defaultPageCount;
 		this.parameterConverter = parameterConverter;
 		this.exceptionHandler = exceptionHandler;
 		this.responseGenerator = responseGenerator;
+		this.referenceCleaner = referenceCleaner;
 		this.historyDao = historyDao;
 		this.historyUserFilterFactory = historyUserFilterFactory;
 	}
@@ -57,6 +61,7 @@ public void afterPropertiesSet() throws Exception
 		Objects.requireNonNull(parameterConverter, "parameterConverter");
 		Objects.requireNonNull(exceptionHandler, "exceptionHandler");
 		Objects.requireNonNull(responseGenerator, "responseGenerator");
+		Objects.requireNonNull(referenceCleaner, "referenceCleaner");
 		Objects.requireNonNull(historyDao, "historyDao");
 		Objects.requireNonNull(historyUserFilterFactory, "historyUserFilterFactory");
 	}
@@ -136,7 +141,11 @@ else if (resource != null)
 		atParameter.modifyBundleUri(bundleUri);
 		sinceParameter.modifyBundleUri(bundleUri);
 
-		return responseGenerator.createHistoryBundle(history, errors, bundleUri, format, pretty);
+		Bundle bundle = responseGenerator.createHistoryBundle(history, errors, bundleUri, format, pretty);
+		// clean literal references from bundle entries
+		bundle.getEntry().stream().filter(BundleEntryComponent::hasResource).map(BundleEntryComponent::getResource)
+				.forEach(referenceCleaner::cleanLiteralReferences);
+		return bundle;
 	}
 
 	private String getResourceTypeName(Class<? extends Resource> resource)

diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/spring/config/HistoryConfig.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/spring/config/HistoryConfig.java
@@ -21,6 +21,9 @@ public class HistoryConfig
 	@Autowired
 	private HelperConfig helperConfig;
 
+	@Autowired
+	private ReferenceConfig referenceConfig;
+
 	@Autowired
 	private DaoConfig daoConfig;
 
@@ -34,7 +37,7 @@ public HistoryUserFilterFactory historyUserFilterFactory()
 	public HistoryService historyService()
 	{
 		return new HistoryServiceImpl(serverBase, defaultPageCount, helperConfig.parameterConverter(),
-				helperConfig.exceptionHandler(), helperConfig.responseGenerator(), daoConfig.historyDao(),
-				historyUserFilterFactory());
+				helperConfig.exceptionHandler(), helperConfig.responseGenerator(), referenceConfig.referenceCleaner(),
+				daoConfig.historyDao(), historyUserFilterFactory());
 	}
 }
diff --git a/dsf-fhir/dsf-fhir-webservice-client/pom.xml b/dsf-fhir/dsf-fhir-webservice-client/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-fhir/dsf-fhir-websocket-client/pom.xml b/dsf-fhir/dsf-fhir-websocket-client/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-fhir/pom.xml b/dsf-fhir/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-pom</artifactId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<modules>

diff --git a/dsf-mpi/dsf-mpi-client-pdq/pom.xml b/dsf-mpi/dsf-mpi-client-pdq/pom.xml
@@ -9,7 +9,7 @@
 	<parent>
 		<artifactId>dsf-mpi-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-mpi/dsf-mpi-client-stub/pom.xml b/dsf-mpi/dsf-mpi-client-stub/pom.xml
@@ -9,7 +9,7 @@
 	<parent>
 		<artifactId>dsf-mpi-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-mpi/dsf-mpi-client/pom.xml b/dsf-mpi/dsf-mpi-client/pom.xml
@@ -9,6 +9,6 @@
 	<parent>
 		<artifactId>dsf-mpi-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 </project>
diff --git a/dsf-mpi/pom.xml b/dsf-mpi/pom.xml
@@ -10,7 +10,7 @@
 	<parent>
 		<artifactId>dsf-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<modules>

diff --git a/dsf-openehr/dsf-openehr-model/pom.xml b/dsf-openehr/dsf-openehr-model/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<artifactId>dsf-openehr-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-openehr/dsf-openehr-webservice-client/pom.xml b/dsf-openehr/dsf-openehr-webservice-client/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<artifactId>dsf-openehr-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-openehr/pom.xml b/dsf-openehr/pom.xml
@@ -9,7 +9,7 @@
 	<parent>
 		<artifactId>dsf-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.2.0</version>
+		<version>0.2.1</version>
 	</parent>
 
 	<modules>