Merge remote-tracking branch 'origin/release/0.6.0' into main

.gitignore

@@ -35,6 +35,7 @@ dsf-docker-test-setup/bpe/log/*.log.gz
 dsf-docker-test-setup/bpe/plugin/*.jar
 dsf-docker-test-setup/bpe/process/*.jar
 dsf-docker-test-setup/bpe/psn/*.jceks
+dsf-docker-test-setup/bpe/psn/*.p12
 dsf-docker-test-setup/bpe/secrets/*.pem
 
 dsf-docker-test-setup/fhir/log/*.log
@@ -61,6 +62,7 @@ dsf-docker-test-setup-3medic-ttp-docker/**/bpe/log/*.log.gz
 dsf-docker-test-setup-3medic-ttp-docker/**/bpe/plugin/*.jar
 dsf-docker-test-setup-3medic-ttp-docker/**/bpe/process/*.jar
 dsf-docker-test-setup-3medic-ttp-docker/**/bpe/psn/*.jceks
+dsf-docker-test-setup-3medic-ttp-docker/**/bpe/psn/*.p12
 
 dsf-docker-test-setup-3medic-ttp-docker/**/fhir/log/*.log
 dsf-docker-test-setup-3medic-ttp-docker/**/fhir/log/*.log.gz

CITATION.cff

@@ -24,8 +24,8 @@ preferred-citation:
   doi: 10.3233/SHTI210060
   type: proceedings
 title: "HiGHmed Data Sharing Framework (HiGHmed DSF)"
-version: 0.5.5
-date-released: 2022-03-21
+version: 0.6.0
+date-released: 2022-03-10
 url: https://github.com/highmed/highmed-dsf/wiki
 repository-code: https://github.com/highmed/highmed-dsf
 repository-artifact: https://github.com/highmed/highmed-dsf/releases

dsf-bpe/dsf-bpe-process-base/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.5.5</version>
+		<version>0.6.0</version>
 	</parent>
 
 	<dependencies>
@@ -20,6 +20,10 @@
 			<artifactId>dsf-fhir-auth</artifactId>
 		</dependency>
 
+		<dependency>
+			<groupId>org.highmed.dsf</groupId>
+			<artifactId>dsf-pseudonymization-client</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>org.highmed.dsf</groupId>
 			<artifactId>dsf-pseudonymization-medic</artifactId>
@@ -34,6 +38,11 @@
 			<artifactId>dsf-mpi-client</artifactId>
 		</dependency>
 
+		<dependency>
+			<groupId>org.highmed.dsf</groupId>
+			<artifactId>dsf-consent-client</artifactId>
+		</dependency>
+
 		<dependency>
 			<groupId>org.highmed.dsf</groupId>
 			<artifactId>dsf-openehr-model</artifactId>

dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/bpe/ConstantsBase.java

@@ -37,14 +37,50 @@ public interface ConstantsBase
 	String CODESYSTEM_HIGHMED_BPMN_VALUE_CORRELATION_KEY = "correlation-key";
 	String CODESYSTEM_HIGHMED_BPMN_VALUE_ERROR = "error";
 
+	/**
+	 * @deprecated as of release 0.6.0, use {@link #CODESYSTEM_HIGHMED_ORGANIZATION_ROLE} instead
+	 */
+	@Deprecated
 	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE = "http://highmed.org/fhir/CodeSystem/organization-type";
+	/**
+	 * @deprecated as of release 0.6.0, use {@link #CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_TTP} instead
+	 */
+	@Deprecated
 	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_TTP = "TTP";
+	/**
+	 * @deprecated as of release 0.6.0, use {@link #CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_MEDIC} instead
+	 */
+	@Deprecated
 	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_MEDIC = "MeDIC";
+	/**
+	 * @deprecated as of release 0.6.0, use {@link #CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_DTS} instead
+	 */
+	@Deprecated
 	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_DTS = "DTS";
+	/**
+	 * @deprecated as of release 0.6.0, use {@link #CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_COS} instead
+	 */
+	@Deprecated
 	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_COS = "COS";
+	/**
+	 * @deprecated as of release 0.6.0, use {@link #CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_CRR} instead
+	 */
+	@Deprecated
 	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_CRR = "CRR";
+	/**
+	 * @deprecated as of release 0.6.0, use {@link #CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_HRP} instead
+	 */
+	@Deprecated
 	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_HRP = "HRP";
 
+	String CODESYSTEM_HIGHMED_ORGANIZATION_ROLE = "http://highmed.org/fhir/CodeSystem/organization-role";
+	String CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_TTP = "TTP";
+	String CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_MEDIC = "MeDIC";
+	String CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_DTS = "DTS";
+	String CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_COS = "COS";
+	String CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_CRR = "CRR";
+	String CODESYSTEM_HIGHMED_ORGANIZATION_ROLE_VALUE_HRP = "HRP";
+
 	String CODESYSTEM_HIGHMED_QUERY_TYPE = "http://highmed.org/fhir/CodeSystem/query-type";
 	String CODESYSTEM_HIGMED_QUERY_TYPE_VALUE_AQL = "application/x-aql-query";
 

dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/bpe/ProcessPluginDefinition.java

@@ -1,12 +1,19 @@
 package org.highmed.dsf.bpe;
 
+import java.time.LocalDate;
 import java.util.Collections;
 import java.util.List;
 import java.util.ServiceLoader;
 import java.util.stream.Stream;
 
 import org.camunda.bpm.engine.impl.variable.serializer.TypedValueSerializer;
+import org.highmed.dsf.fhir.resources.ActivityDefinitionResource;
+import org.highmed.dsf.fhir.resources.CodeSystemResource;
+import org.highmed.dsf.fhir.resources.NamingSystemResource;
 import org.highmed.dsf.fhir.resources.ResourceProvider;
+import org.highmed.dsf.fhir.resources.StructureDefinitionResource;
+import org.highmed.dsf.fhir.resources.ValueSetResource;
+import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.core.env.PropertyResolver;
@@ -44,6 +51,18 @@ default String getNameAndVersion()
 		return getName() + "-" + getVersion();
 	}
 
+	/**
+	 * <i>Override this method to replace <code>#{date}</code> in FHIR and BPMN files with the returned value.</i>
+	 *
+	 * @return the release date of the process plugin, if not overridden {@link LocalDate#MIN}
+	 * @see ResourceProvider#read(String, LocalDate, java.util.function.Supplier, ClassLoader, PropertyResolver,
+	 *      java.util.Map)
+	 */
+	default LocalDate getReleaseDate()
+	{
+		return LocalDate.MIN;
+	}
+
 	/**
 	 * Return <code>Stream.of("foo.bpmn");</code> for a foo.bpmn file located in the root folder of the process plugin
 	 * jar. The returned files will be read via {@link ClassLoader#getResourceAsStream(String)}.
@@ -60,14 +79,31 @@ default String getNameAndVersion()
 	Stream<Class<?>> getSpringConfigClasses();
 
 	/**
+	 * <i>Override this method to return a {@link ResourceProvider} with fhir metadata resources (ActivityDefinition,
+	 * CodeSystem, NamingSystem, StructureDefinition, ValueSet) needed by this process plugin.</i>
+	 *
 	 * @param fhirContext
-	 *            the applications fhir context, never <code>null</code>
+	 *            applications fhir context, never <code>null</code>
 	 * @param classLoader
-	 *            the classLoader that was used to initialize the process plugin, never <code>null</code>
+	 *            class loader that was used to initialize the process plugin, never <code>null</code>
 	 * @param resolver
-	 *            the property resolver used to access config properties and to replace place holders in fhir resources,
+	 *            property resolver used to access config properties and to replace place holders in fhir resources,
 	 *            never <code>null</code>
-	 * @return {@link ResourceProvider} with FHIR resources needed to enable the included processes
+	 * @return {@link ResourceProvider} with FHIR resources needed to enable the included processes, if not overridden
+	 *         {@link ResourceProvider#empty()}
+	 *
+	 * @see ActivityDefinitionResource#file(String)
+	 * @see CodeSystemResource#file(String)
+	 * @see NamingSystemResource#file(String)
+	 * @see StructureDefinitionResource#file(String)
+	 * @see ValueSetResource#file(String)
+	 *
+	 * @see FhirContext#newJsonParser()
+	 * @see FhirContext#newXmlParser()
+	 *
+	 * @see ResourceProvider#read(String, java.util.function.Supplier, ClassLoader, PropertyResolver, java.util.Map)
+	 * @see ResourceProvider#read(String, LocalDate, java.util.function.Supplier, ClassLoader, PropertyResolver,
+	 *      java.util.Map)
 	 */
 	default ResourceProvider getResourceProvider(FhirContext fhirContext, ClassLoader classLoader,
 			PropertyResolver resolver)
@@ -83,4 +119,17 @@ default List<String> getDependencyNamesAndVersions()
 	{
 		return Collections.emptyList();
 	}
+
+	/**
+	 * <i>Override this method to implement custom logic after a process has been deployed and is active, e.g. test the
+	 * connection to an external server needed by a process.</i>
+	 *
+	 * @param pluginApplicationContext
+	 *            the process plugin spring application context, never <code>null</code>
+	 * @param activeProcesses
+	 *            active processes from this plugin by process key
+	 */
+	default void onProcessesDeployed(ApplicationContext pluginApplicationContext, List<String> activeProcesses)
+	{
+	}
 }

dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/bpe/delegate/AbstractServiceDelegate.java

@@ -14,6 +14,7 @@
 import org.highmed.dsf.fhir.authorization.read.ReadAccessHelper;
 import org.highmed.dsf.fhir.client.FhirWebserviceClientProvider;
 import org.highmed.dsf.fhir.task.TaskHelper;
+import org.highmed.dsf.fhir.variables.FhirResourceValues;
 import org.hl7.fhir.r4.model.Task;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -27,7 +28,7 @@ public abstract class AbstractServiceDelegate implements JavaDelegate, Initializ
 	private final TaskHelper taskHelper;
 	private final ReadAccessHelper readAccessHelper;
 
-	private DelegateExecution execution;
+	protected DelegateExecution execution;
 
 	public AbstractServiceDelegate(FhirWebserviceClientProvider clientProvider, TaskHelper taskHelper,
 			ReadAccessHelper readAccessHelper)
@@ -158,4 +159,49 @@ protected final Task getLeadingTaskFromExecutionVariables()
 		Task leadingTask = (Task) execution.getVariable(BPMN_EXECUTION_VARIABLE_LEADING_TASK);
 		return leadingTask != null ? leadingTask : getCurrentTaskFromExecutionVariables();
 	}
+
+	/**
+	 * <i>Uses this method to update the process engine variable {@link ConstantsBase#BPMN_EXECUTION_VARIABLE_TASK},
+	 * after modifying the {@link Task}.</i>
+	 *
+	 * @param task
+	 *            not <code>null</code>
+	 * @throws IllegalStateException
+	 *             if execution of this service delegate has not been started
+	 * @see ConstantsBase#BPMN_EXECUTION_VARIABLE_TASK
+	 */
+	protected final void updateCurrentTaskInExecutionVariables(Task task)
+	{
+		if (execution == null)
+			throw new IllegalStateException("execution not started");
+
+		Objects.requireNonNull(task, "task");
+		execution.setVariable(BPMN_EXECUTION_VARIABLE_TASK, FhirResourceValues.create(task));
+	}
+
+	/**
+	 * <i>Uses this method to update the process engine variable
+	 * {@link ConstantsBase#BPMN_EXECUTION_VARIABLE_LEADING_TASK}, after modifying the {@link Task}.</i>
+	 *
+	 * Updates the current task if no leading task is set.
+	 *
+	 * @param task
+	 *            not <code>null</code>
+	 * @throws IllegalStateException
+	 *             if execution of this service delegate has not been started
+	 * @see ConstantsBase#BPMN_EXECUTION_VARIABLE_LEADING_TASK
+	 */
+	protected final void updateLeadingTaskInExecutionVariables(Task task)
+	{
+		if (execution == null)
+			throw new IllegalStateException("execution not started");
+
+		Objects.requireNonNull(task, "task");
+		Task leadingTask = (Task) execution.getVariable(BPMN_EXECUTION_VARIABLE_LEADING_TASK);
+
+		if (leadingTask != null)
+			execution.setVariable(BPMN_EXECUTION_VARIABLE_LEADING_TASK, FhirResourceValues.create(task));
+		else
+			updateCurrentTaskInExecutionVariables(task);
+	}
 }

dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/fhir/json/ObjectMapperFactory.java

@@ -0,0 +1,36 @@
+package org.highmed.dsf.fhir.json;
+
+import org.highmed.dsf.fhir.variables.FhirResourceJacksonDeserializer;
+import org.highmed.dsf.fhir.variables.FhirResourceJacksonSerializer;
+import org.highmed.openehr.json.OpenEhrObjectMapperFactory;
+import org.hl7.fhir.r4.model.Resource;
+
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
+import com.fasterxml.jackson.databind.MapperFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.json.JsonMapper;
+import com.fasterxml.jackson.databind.module.SimpleModule;
+
+import ca.uhn.fhir.context.FhirContext;
+
+public class ObjectMapperFactory
+{
+	private ObjectMapperFactory()
+	{
+	}
+
+	public static ObjectMapper createObjectMapper(FhirContext fhirContext)
+	{
+		return JsonMapper.builder().serializationInclusion(Include.NON_NULL).serializationInclusion(Include.NON_EMPTY)
+				.addModule(fhirModule(fhirContext)).addModule(OpenEhrObjectMapperFactory.openEhrModule())
+				.disable(MapperFeature.AUTO_DETECT_CREATORS).disable(MapperFeature.AUTO_DETECT_FIELDS)
+				// .disable(MapperFeature.AUTO_DETECT_GETTERS).disable(MapperFeature.AUTO_DETECT_IS_GETTERS)
+				.disable(MapperFeature.AUTO_DETECT_SETTERS).build();
+	}
+
+	public static SimpleModule fhirModule(FhirContext fhirContext)
+	{
+		return new SimpleModule().addSerializer(Resource.class, new FhirResourceJacksonSerializer(fhirContext))
+				.addDeserializer(Resource.class, new FhirResourceJacksonDeserializer(fhirContext));
+	}
+}

dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/fhir/organization/EndpointProvider.java

@@ -1,11 +1,14 @@
 package org.highmed.dsf.fhir.organization;
 
+import static org.highmed.dsf.bpe.ConstantsBase.NAMINGSYSTEM_HIGHMED_ENDPOINT_IDENTIFIER;
+
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
 import org.hl7.fhir.r4.model.Endpoint;
+import org.hl7.fhir.r4.model.Identifier;
 
 public interface EndpointProvider
 {
@@ -16,6 +19,12 @@ default String getLocalEndpointAddress()
 		return getLocalEndpoint().getAddress();
 	}
 
+	default Identifier getLocalEndpointIdentifier()
+	{
+		return getLocalEndpoint().getIdentifier().stream()
+				.filter(i -> NAMINGSYSTEM_HIGHMED_ENDPOINT_IDENTIFIER.equals(i.getSystem())).findFirst().get();
+	}
+
 	Map<String, Endpoint> getDefaultEndpointsByOrganizationIdentifier();
 
 	default Map<String, String> getDefaultEndpointAdressesByOrganizationIdentifier()
@@ -58,4 +67,11 @@ default Optional<String> getFirstConsortiumEndpointAdress(String consortiumIdent
 		return getFirstConsortiumEndpoint(consortiumIdentifierValue, roleSystem, roleCode, organizationIdentifierValue)
 				.map(Endpoint::getAddress);
 	}
+
+	Optional<Endpoint> getEndpoint(String endpointIdentifierValue);
+
+	default Optional<String> getEndpointAddress(String endpointIdentifierValue)
+	{
+		return getEndpoint(endpointIdentifierValue).map(Endpoint::getAddress);
+	}
 }