Merge remote-tracking branch 'origin/develop_2' into

issue/315_Reorganize_dsf-tools_Modules

Author: hhund

.gitignore

@@ -80,10 +80,10 @@ dsf-docker-test-setup-3dic-ttp/secrets/dic2.key
 dsf-docker-test-setup-3dic-ttp/secrets/dic3.crt
 dsf-docker-test-setup-3dic-ttp/secrets/dic3.key
 dsf-docker-test-setup-3dic-ttp/secrets/issuing_ca.crt
-dsf-docker-test-setup-3dic-ttp/secrets/keycloak.crt
+dsf-docker-test-setup-3dic-ttp/secrets/keycloak.chain.crt
 dsf-docker-test-setup-3dic-ttp/secrets/keycloak.key.plain
 dsf-docker-test-setup-3dic-ttp/secrets/keycloak_trust_store.jks
-dsf-docker-test-setup-3dic-ttp/secrets/localhost.crt
+dsf-docker-test-setup-3dic-ttp/secrets/localhost.chain.crt
 dsf-docker-test-setup-3dic-ttp/secrets/localhost.key.plain
 dsf-docker-test-setup-3dic-ttp/secrets/root_ca.crt
 dsf-docker-test-setup-3dic-ttp/secrets/ttp.crt

CITATION.cff

@@ -25,7 +25,7 @@ preferred-citation:
   type: proceedings
 title: "Data Sharing Framework (DSF)"
 version: 2.0.0
-date-released: 2025-01-22
+date-released: 2025-05-31
 url: https://dsf.dev
 repository-code: https://github.com/datasharingframework/dsf
 repository-artifact: https://github.com/datasharingframework/dsf/releases

README.md

@@ -1,4 +1,4 @@
-![Data Sharing Framework (DSF) logo.](dsf-fhir/dsf-fhir-server/src/main/resources/static/logo.svg)
+![Data Sharing Framework (DSF) logo.](dsf-fhir/dsf-fhir-server/src/main/resources/fhir/static/logo.svg)
 
 The Data Sharing Framework (DSF) implements a distributed process engine based on the BPMN 2.0 and FHIR R4 standards. The DSF is used to support biomedical research with real-world data. Every participating site runs a FHIR endpoint (dsf-fhir) accessible by other sites and a business process engine (dsf-bpe) in the local secured network. Authentication between sites is handled using X.509 client/server certificates. The process engines execute BPMN processes in order to coordinate local and remote steps necessary to enable cross-site data sharing and feasibility analyses. This includes access to local data repositories, use-and-access-committee decision support, consent filtering, and privacy preserving record-linkage and pseudonymization.  
 

dsf-bpe/dsf-bpe-process-api-v1-impl/pom.xml

@@ -9,6 +9,8 @@
 		<version>2.0.0-SNAPSHOT</version>
 	</parent>
 
+	<name>DSF BPE Process API v1 Implementation</name>
+
 	<dependencies>
 		<dependency>
 			<groupId>dev.dsf</groupId>
@@ -59,7 +61,7 @@
 			<scope>test</scope>
 		</dependency>
 	</dependencies>
-	
+
 	<build>
 		<plugins>
 			<plugin>
@@ -138,10 +140,10 @@
 									<artifactId>xpp3_xpath</artifactId>
 									<version>1.1.4c</version>
 								</artifactItem>-->
-								<artifactItem>
+								<!--<artifactItem>
 									<groupId>org.apache.commons</groupId>
 									<artifactId>commons-compress</artifactId>
-								</artifactItem>
+								</artifactItem>-->
 								<artifactItem>
 									<groupId>org.fhir</groupId>
 									<artifactId>ucum</artifactId>

dsf-bpe/dsf-bpe-process-api-v1-impl/src/main/java/dev/dsf/bpe/v1/plugin/ProcessPluginImpl.java

@@ -163,13 +163,19 @@ else if (filename.endsWith(XML_SUFFIX))
 						&& BpmnMessage.Codes.MESSAGE_NAME.equals(c.getCode())))
 				.count() == 1;
 
+		Function<StructureDefinition, Optional<String>> getStructureDefinitionBaseDefinition = s -> s
+				.hasBaseDefinitionElement() && s.getBaseDefinitionElement().hasValue()
+						? Optional.of(s.getBaseDefinitionElement().getValue())
+						: Optional.empty();
+
 		return new ProcessPluginFhirConfig<>(ActivityDefinition.class, CodeSystem.class, Library.class, Measure.class,
 				NamingSystem.class, Questionnaire.class, StructureDefinition.class, Task.class, ValueSet.class,
 				OrganizationIdentifier.SID, TaskIdentifier.SID, TaskStatus.DRAFT.toCode(), BpmnMessage.URL,
 				BpmnMessage.Codes.MESSAGE_NAME, parseResource, encodeResource, getResourceName, hasMetadataResourceUrl,
 				hasMetadataResourceVersion, getMetadataResourceVersion, getActivityDefinitionUrl, NamingSystem::hasName,
 				getTaskInstantiatesCanonical, getTaskIdentifierValue, isTaskStatusDraft, getRequester, getRecipient,
-				Task::hasInput, hasTaskInputMessageName, Task::hasOutput);
+				Task::hasInput, hasTaskInputMessageName, Task::hasOutput, getStructureDefinitionBaseDefinition,
+				StructureDefinition::setBaseDefinition);
 	}
 
 	private IParser newXmlParser()

dsf-bpe/dsf-bpe-process-api-v1-impl/src/test/java/dev/dsf/bpe/v1/plugin/ProcessPluginImplTest.java

@@ -316,7 +316,7 @@ public void testInitializeAndValidateResources() throws Exception
 		List<BpmnFileAndModel> models = plugin.getProcessModels();
 		assertEquals(1, models.size());
 		BpmnFileAndModel bpmnFileAndModel = models.get(0);
-		BpmnModelInstance model = bpmnFileAndModel.getModel();
+		BpmnModelInstance model = bpmnFileAndModel.model();
 		assertNotNull(model);
 
 		Collection<Process> processes = model.getModelElementsByType(Process.class);

dsf-bpe/dsf-bpe-process-api-v1/pom.xml

@@ -9,6 +9,8 @@
 		<version>2.0.0-SNAPSHOT</version>
 	</parent>
 
+	<name>DSF BPE Process API v1</name>
+
 	<dependencies>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>

dsf-bpe/dsf-bpe-process-api-v2-impl/pom.xml

@@ -9,6 +9,8 @@
 		<version>2.0.0-SNAPSHOT</version>
 	</parent>
 
+	<name>DSF BPE Process API v2 Implementation</name>
+
 	<dependencies>
 		<dependency>
 			<groupId>dev.dsf</groupId>
@@ -182,7 +184,7 @@
 								<artifactItem>
 									<groupId>net.sf.saxon</groupId>
 									<artifactId>Saxon-HE</artifactId>
-									<version>9.8.0-15</version>
+									<version>11.6</version>
 								</artifactItem>
 								<!--<artifactItem>
 									<groupId>org.ogce</groupId>
@@ -194,23 +196,23 @@
 									<artifactId>jakarta-regexp</artifactId>
 									<version>1.4</version>
 								</artifactItem>
-								<artifactItem>
+								<!--<artifactItem>
 									<groupId>org.apache.commons</groupId>
 									<artifactId>commons-compress</artifactId>
-								</artifactItem>
+								</artifactItem>-->
 								<artifactItem>
 									<groupId>org.fhir</groupId>
 									<artifactId>ucum</artifactId>
-									<version>1.0.8</version>
+									<version>1.0.9</version>
 								</artifactItem>
-								<artifactItem>
+								<!--<artifactItem>
 									<groupId>com.google.code.gson</groupId>
 									<artifactId>gson</artifactId>
-								</artifactItem>
+								</artifactItem>-->
 								<artifactItem>
 									<groupId>com.google.errorprone</groupId>
 									<artifactId>error_prone_annotations</artifactId>
-									<version>2.27.0</version>
+									<version>2.38.0</version>
 								</artifactItem>
 								<artifactItem>
 									<groupId>ca.uhn.hapi.fhir</groupId>
@@ -234,7 +236,7 @@
 								<artifactItem>
 									<groupId>org.checkerframework</groupId>
 									<artifactId>checker-qual</artifactId>
-									<version>3.43.0</version>
+									<version>3.49.3</version>
 								</artifactItem>
 								<artifactItem>
 									<groupId>com.google.j2objc</groupId>
@@ -244,17 +246,17 @@
 								<artifactItem>
 									<groupId>io.opentelemetry</groupId>
 									<artifactId>opentelemetry-api</artifactId>
-									<version>1.38.0</version>
+									<version>1.44.1</version>
 								</artifactItem>
 								<artifactItem>
 									<groupId>io.opentelemetry</groupId>
 									<artifactId>opentelemetry-context</artifactId>
-									<version>1.38.0</version>
+									<version>1.44.1</version>
 								</artifactItem>
 								<artifactItem>
 									<groupId>io.opentelemetry.instrumentation</groupId>
 									<artifactId>opentelemetry-instrumentation-annotations</artifactId>
-									<version>2.4.0</version>
+									<version>2.10.0</version>
 								</artifactItem>
 								<artifactItem>
 									<groupId>org.apache.tika</groupId>

dsf-bpe/dsf-bpe-process-api-v2-impl/src/main/java/dev/dsf/bpe/v2/ProcessPluginApiImpl.java

@@ -18,6 +18,7 @@
 import dev.dsf.bpe.v2.service.OrganizationProvider;
 import dev.dsf.bpe.v2.service.QuestionnaireResponseHelper;
 import dev.dsf.bpe.v2.service.ReadAccessHelper;
+import dev.dsf.bpe.v2.service.TargetProvider;
 import dev.dsf.bpe.v2.service.TaskHelper;
 import dev.dsf.bpe.v2.service.process.ProcessAuthorizationHelper;
 
@@ -39,14 +40,15 @@ public class ProcessPluginApiImpl implements ProcessPluginApi, InitializingBean
 	private final ReadAccessHelper readAccessHelper;
 	private final TaskHelper taskHelper;
 	private final CryptoService cryptoService;
+	private final TargetProvider targetProvider;
 
 	public ProcessPluginApiImpl(ProxyConfig proxyConfig, EndpointProvider endpointProvider, FhirContext fhirContext,
 			DsfClientProvider dsfClientProvider, FhirClientProvider fhirClientProvider,
 			OidcClientProvider oidcClientProvider, MailService mailService, MimetypeService mimetypeService,
 			ObjectMapper objectMapper, OrganizationProvider organizationProvider,
 			ProcessAuthorizationHelper processAuthorizationHelper,
 			QuestionnaireResponseHelper questionnaireResponseHelper, ReadAccessHelper readAccessHelper,
-			TaskHelper taskHelper, CryptoService cryptoService)
+			TaskHelper taskHelper, CryptoService cryptoService, TargetProvider targetProvider)
 	{
 		this.proxyConfig = proxyConfig;
 		this.endpointProvider = endpointProvider;
@@ -63,6 +65,7 @@ public ProcessPluginApiImpl(ProxyConfig proxyConfig, EndpointProvider endpointPr
 		this.readAccessHelper = readAccessHelper;
 		this.taskHelper = taskHelper;
 		this.cryptoService = cryptoService;
+		this.targetProvider = targetProvider;
 	}
 
 	@Override
@@ -82,6 +85,7 @@ public void afterPropertiesSet() throws Exception
 		Objects.requireNonNull(readAccessHelper, "readAccessHelper");
 		Objects.requireNonNull(taskHelper, "taskHelper");
 		Objects.requireNonNull(cryptoService, "cryptoService");
+		Objects.requireNonNull(targetProvider, "targetProvider");
 	}
 
 	@Override
@@ -173,4 +177,10 @@ public CryptoService getCryptoService()
 	{
 		return cryptoService;
 	}
+
+	@Override
+	public TargetProvider getTargetProvider()
+	{
+		return targetProvider;
+	}
 }

dsf-bpe/dsf-bpe-process-api-v2-impl/src/main/java/dev/dsf/bpe/v2/plugin/ProcessPluginImpl.java

@@ -185,13 +185,19 @@ else if (filename.endsWith(XML_SUFFIX))
 		Predicate<Task> hasTaskInputMessageName = t -> t.getInput().stream()
 				.filter(i -> i.getType().getCoding().stream().anyMatch(BpmnMessage::isMessageName)).count() == 1;
 
+		Function<StructureDefinition, Optional<String>> getStructureDefinitionBaseDefinition = s -> s
+				.hasBaseDefinitionElement() && s.getBaseDefinitionElement().hasValue()
+						? Optional.of(s.getBaseDefinitionElement().getValue())
+						: Optional.empty();
+
 		return new ProcessPluginFhirConfig<>(ActivityDefinition.class, CodeSystem.class, Library.class, Measure.class,
 				NamingSystem.class, Questionnaire.class, StructureDefinition.class, Task.class, ValueSet.class,
 				OrganizationIdentifier.SID, TaskIdentifier.SID, TaskStatus.DRAFT.toCode(), BpmnMessage.SYSTEM,
 				BpmnMessage.Codes.MESSAGE_NAME, parseResource, encodeResource, getResourceName, hasMetadataResourceUrl,
 				hasMetadataResourceVersion, getMetadataResourceVersion, getActivityDefinitionUrl, NamingSystem::hasName,
 				getTaskInstantiatesCanonical, getTaskIdentifierValue, isTaskStatusDraft, getRequester, getRecipient,
-				Task::hasInput, hasTaskInputMessageName, Task::hasOutput);
+				Task::hasInput, hasTaskInputMessageName, Task::hasOutput, getStructureDefinitionBaseDefinition,
+				StructureDefinition::setBaseDefinition);
 	}
 
 	private IParser newXmlParser()