Merge remote-tracking branch 'origin/develop_2' into issue/205_mimetype-service

* origin/develop_2: (111 commits)
  replace spaces with tab
  combine collapse-button css
  add Library.content html view
  API v1 dsf client config fix
  fixed log message
  abstract get name, version, release date impl using properties file
  removes dsf-fhir-validation from the excluded artifacts list
  removes dsf-common-documentation compile dependency
  added javadoc and source jar goals to publish-to-maven-central profile
  Added DocumentReference to default bookmarks
  removed not needed import
  add DocumentReference HTML view
  added maven project names for maven central deployment via sonatype
  adds missing not null check
  logo fix, current date
  org.hl7.fhir to 6.5.18 (version used by hapi 8.2.0)
  added "Binary" to default bookmarks
  removed not needed dependency from api v1, api v2 dependency upgrades
  empty cert directories for IDE dev-setup
  camunda version upgrade 7.22 -> 7.23
  ...

Author: wetret

.github/workflows/codeql.yml

@@ -1,10 +1,12 @@
-name: Java 21 CodeQL
+name: DSF 2.x CodeQL
 
 on:
   push:
-    branches: develop_2
+    branches: [ "develop_2", "hotfix/2*", "release/2*" ]
   pull_request:
-    branches: develop_2
+    branches: [ "develop_2", "hotfix/2*", "release/2*" ]
+  schedule:
+    - cron: '11 15 * * 0' # Sundays, 15:11
 
 jobs:
   analyze:
@@ -39,7 +41,7 @@ jobs:
 
     - name: Compile with Maven
       if: ${{ matrix.language == 'java-kotlin' }}
-      run: mvn --batch-mode --fail-at-end --threads 1C -Dmaven.javadoc.skip=true -Dimpsort.skip=true -Dformatter.skip=true -Dgpg.skip -Denforcer.skip -Dmaven.buildNumber.skip=true -Dexec.skip=true -DskipTests clean package
+      run: mvn --batch-mode --fail-at-end --threads 1C -Dimpsort.skip=true -Dformatter.skip=true -Denforcer.skip -Dmaven.buildNumber.skip=true -Dexec.skip=true -DskipTests -DskipShadePlugin=true -P!generate-source-and-javadoc-jars clean package
 
     - name: Perform CodeQL Analysis
       uses: github/codeql-action/analyze@v3

.github/workflows/maven-build.yml

@@ -1,6 +1,6 @@
-name: Java 21 CI Build with Maven
+name: DSF 2.x Java CI Build with Maven
 
-on: 
+on:
   pull_request:
     branches: develop_2
 
@@ -18,4 +18,4 @@ jobs:
         java-version: 21
         cache: 'maven'
     - name: Build with Maven
-      run: mvn --batch-mode --fail-at-end -DforkCount=2 -Dgpg.skip clean verify
+      run: mvn --batch-mode --fail-at-end -DforkCount=2 clean verify

.github/workflows/maven-publish.yml

@@ -1,4 +1,4 @@
-name: Java 21 CI Publish with Maven
+name: DSF 2.x Java CI Publish with Maven
 
 on:
   pull_request:
@@ -25,4 +25,4 @@ jobs:
       - name: Publish with Maven
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: mvn --batch-mode --fail-at-end -DforkCount=2 -Dgpg.skip clean deploy
+        run: mvn --batch-mode --fail-at-end -DforkCount=2 clean deploy

.gitignore

@@ -9,9 +9,15 @@
 
 **/*.iml
 
+## dev setup cert folder and files, folder and files generated by dsf-maven-plugin 
+cert
+cert/**
+
 ###
 # dsf-bpe ignores
 ###
+dsf-bpe/dsf-bpe-server-jetty/cert/*.crt
+dsf-bpe/dsf-bpe-server-jetty/cert/*.key
 dsf-bpe/dsf-bpe-server-jetty/conf/config.properties
 dsf-bpe/dsf-bpe-server-jetty/docker/api/v1/*.jar
 dsf-bpe/dsf-bpe-server-jetty/docker/api/v2/*.jar
@@ -74,10 +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
@@ -88,6 +94,8 @@ dsf-docker-test-setup-3dic-ttp/docker-compose.override.yml
 ###
 # dsf-fhir ignores
 ###
+dsf-fhir/dsf-fhir-server-jetty/cert/*.crt
+dsf-fhir/dsf-fhir-server-jetty/cert/*.key
 dsf-fhir/dsf-fhir-server-jetty/conf/bundle.xml
 dsf-fhir/dsf-fhir-server-jetty/conf/config.properties
 dsf-fhir/dsf-fhir-server-jetty/docker/ca/*.pem

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

@@ -44,6 +44,7 @@
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
 import dev.dsf.bpe.api.plugin.AbstractProcessPlugin;
+import dev.dsf.bpe.api.plugin.FhirResourceModifier;
 import dev.dsf.bpe.api.plugin.ProcessPlugin;
 import dev.dsf.bpe.api.plugin.ProcessPluginDeploymentListener;
 import dev.dsf.bpe.api.plugin.ProcessPluginFhirConfig;
@@ -162,13 +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()
@@ -328,4 +335,10 @@ public TaskListener getTaskListener(String className, List<FieldDeclaration> fie
 	{
 		return get(TaskListener.class, className, fieldDeclarations);
 	}
+
+	@Override
+	public FhirResourceModifier getFhirResourceModifier()
+	{
+		return FhirResourceModifier.identity();
+	}
 }

dsf-bpe/dsf-bpe-process-api-v1-impl/src/main/java/dev/dsf/bpe/v1/spring/ApiServiceConfig.java

@@ -101,8 +101,9 @@ public FhirWebserviceClientProvider clientProvider()
 				dsfClientConfig.getLocalConfig().getConnectTimeout(),
 				dsfClientConfig.getLocalConfig().isDebugLoggingEnabled(), dsfClientConfig.getTrustStore(),
 				dsfClientConfig.getKeyStore(), dsfClientConfig.getKeyStorePassword(),
-				dsfClientConfig.getLocalConfig().getReadTimeout(), dsfClientConfig.getLocalConfig().getConnectTimeout(),
-				dsfClientConfig.getLocalConfig().isDebugLoggingEnabled(), proxyConfig, buildInfoProvider);
+				dsfClientConfig.getRemoteConfig().getReadTimeout(),
+				dsfClientConfig.getRemoteConfig().getConnectTimeout(),
+				dsfClientConfig.getRemoteConfig().isDebugLoggingEnabled(), proxyConfig, buildInfoProvider);
 	}
 
 	@Bean

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

@@ -280,14 +280,7 @@ public void testInitializeAndValidateResourcesNotExistingFhirResources() throws
 		ProcessPluginImpl plugin = createPlugin(definition, false);
 
 		assertFalse(plugin.initializeAndValidateResources(null));
-		try
-		{
-			plugin.getApplicationContext();
-			fail("IllegalStateException expected");
-		}
-		catch (IllegalStateException e)
-		{
-		}
+		assertNotNull(plugin.getApplicationContext());
 
 		try
 		{
@@ -323,7 +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);