Merge remote-tracking branch 'origin/develop_2' into

issue/296_Optimize_Binary_Resource_Handling

Author: hhund

.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

@@ -9,13 +9,20 @@
 
 **/*.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
-dsf-bpe/dsf-bpe-server-jetty/docker/ca/*.pem
+dsf-bpe/dsf-bpe-server-jetty/docker/ca/client_ca_chains/*.crt
+dsf-bpe/dsf-bpe-server-jetty/docker/ca/server_root_cas/*.crt
 dsf-bpe/dsf-bpe-server-jetty/docker/dsf_bpe.jar
 dsf-bpe/dsf-bpe-server-jetty/docker/dsf_status_client.jar
 dsf-bpe/dsf-bpe-server-jetty/docker/lib/*.jar
@@ -26,8 +33,10 @@ dsf-bpe/dsf-bpe-server-jetty/ui
 ###
 # dsf-docker ignore
 ###
-dsf-docker/bpe_proxy/ca/*.pem
-dsf-docker/fhir_proxy/ca/*.pem
+dsf-docker/bpe_proxy/ca/client_ca_chains/*.crt
+dsf-docker/bpe_proxy/ca/client_issuing_cas/*.crt
+dsf-docker/fhir_proxy/ca/client_ca_chains/*.crt
+dsf-docker/fhir_proxy/ca/client_issuing_cas/*.crt
 
 ###
 # dsf-docker-test-setup ignores
@@ -74,10 +83,10 @@ 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
@@ -88,27 +97,14 @@ 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
+dsf-fhir/dsf-fhir-server-jetty/docker/ca/client_ca_chains/*.crt
+dsf-fhir/dsf-fhir-server-jetty/docker/ca/server_root_cas/*.crt
 dsf-fhir/dsf-fhir-server-jetty/docker/dsf_fhir.jar
 dsf-fhir/dsf-fhir-server-jetty/docker/dsf_status_client.jar
 dsf-fhir/dsf-fhir-server-jetty/docker/lib/*.jar
 dsf-fhir/dsf-fhir-server-jetty/ui
-dsf-fhir/dsf-fhir-validation/src/main/resources/fhir/bundle.xml
-
-###
-# dsf-tools ignores
-###
-dsf-tools/dsf-tools-default-ca-files-generator/cert/*.pem
-
-dsf-tools/dsf-tools-test-data-generator/bundle/*.xml
-
-dsf-tools/dsf-tools-test-data-generator/cert/**/*.pem
-dsf-tools/dsf-tools-test-data-generator/cert/**/*.key
-dsf-tools/dsf-tools-test-data-generator/cert/**/*.crt
-dsf-tools/dsf-tools-test-data-generator/cert/**/*.csr
-dsf-tools/dsf-tools-test-data-generator/cert/**/*.p12
-dsf-tools/dsf-tools-test-data-generator/cert/thumbprints.txt
-
-dsf-tools/dsf-tools-test-data-generator/config/*.properties
+dsf-fhir/dsf-fhir-validation/src/main/resources/fhir/bundle.xml

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>
@@ -59,13 +61,25 @@
 			<scope>test</scope>
 		</dependency>
 	</dependencies>
-	
+
 	<build>
 		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<configuration>
+					<testCompilerArgument>-proc:none</testCompilerArgument>
+				</configuration>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-dependency-plugin</artifactId>
 				<executions>
+					<execution>
+						<goals>
+							<goal>properties</goal>
+						</goals>
+					</execution>
 					<execution>
 						<id>copy-api-v1-dependencies-to-docker</id>
 						<phase>pre-integration-test</phase>
@@ -138,10 +152,10 @@
 									<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>
@@ -185,6 +199,13 @@
 					</execution>
 				</executions>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<configuration>
+					<argLine>-javaagent:${org.mockito:mockito-core:jar}</argLine>
+				</configuration>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-clean-plugin</artifactId>

dsf-bpe/dsf-bpe-process-api-v1-impl/src/main/java/dev/dsf/bpe/v1/logging/PluginMdcImpl.java

@@ -0,0 +1,92 @@
+package dev.dsf.bpe.v1.logging;
+
+import java.util.Objects;
+import java.util.function.Function;
+
+import org.camunda.bpm.engine.delegate.DelegateExecution;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.ResourceType;
+import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.model.Task;
+import org.hl7.fhir.r4.model.Task.ParameterComponent;
+
+import dev.dsf.bpe.api.Constants;
+import dev.dsf.bpe.api.logging.AbstractPluginMdc;
+import dev.dsf.bpe.v1.constants.CodeSystems.BpmnMessage;
+import dev.dsf.bpe.v1.variables.Variables;
+
+public class PluginMdcImpl extends AbstractPluginMdc
+{
+	private final String serverBaseUrl;
+	private final Function<DelegateExecution, Variables> variablesFactory;
+
+	/**
+	 * @param apiVersion
+	 * @param name
+	 *            not <code>null</code>
+	 * @param version
+	 *            not <code>null</code>
+	 * @param jar
+	 *            not <code>null</code>
+	 * @param serverBaseUrl
+	 *            not <code>null</code>
+	 * @param variablesFactory
+	 *            not <code>null</code>
+	 */
+	public PluginMdcImpl(int apiVersion, String name, String version, String jar, String serverBaseUrl,
+			Function<DelegateExecution, Variables> variablesFactory)
+	{
+		super(apiVersion, name, version, jar);
+
+		this.serverBaseUrl = Objects.requireNonNull(serverBaseUrl, "serverBaseUrl");
+		this.variablesFactory = Objects.requireNonNull(variablesFactory, "variablesFactory");
+	}
+
+	@Override
+	protected ProcessValues getProcessValues(DelegateExecution delegateExecution)
+	{
+		Variables variables = variablesFactory.apply(delegateExecution);
+
+		Task startTask = variables.getStartTask();
+		if (startTask == null)
+			startTask = variables.getResource(Constants.TASK_VARIABLE);
+
+		Task latestTask = variables.getLatestTask();
+		if (startTask == latestTask)
+			latestTask = null;
+
+		return new ProcessValues(startTask == null ? null : startTask.getInstantiatesCanonical(),
+				getLocalVersionlessAbsoluteUrl(startTask), getRequesterIdentifierValue(startTask),
+				getFirstInputParameter(latestTask, BpmnMessage.correlationKey()),
+				getLocalVersionlessAbsoluteUrl(latestTask), getRequesterIdentifierValue(latestTask));
+	}
+
+	private String getLocalVersionlessAbsoluteUrl(Task task)
+	{
+		return task == null ? null
+				: task.getIdElement().toVersionless().withServerBase(serverBaseUrl, ResourceType.Task.name())
+						.getValue();
+	}
+
+	private String getRequesterIdentifierValue(Task task)
+	{
+		if (task == null)
+			return null;
+
+		return task.getRequester().getIdentifier().getValue();
+	}
+
+	private String getFirstInputParameter(Task task, Coding code)
+	{
+		if (task == null || code == null)
+			return null;
+
+		return task.getInput().stream().filter(ParameterComponent::hasType)
+				.filter(c -> c.getType().getCoding().stream()
+						.anyMatch(co -> co != null && Objects.equals(code.getSystem(), co.getSystem())
+								&& Objects.equals(code.getCode(), co.getCode())))
+				.filter(ParameterComponent::hasValue).map(ParameterComponent::getValue)
+				.filter(v -> v instanceof StringType).map(v -> (StringType) v).map(StringType::getValue).findFirst()
+				.orElse(null);
+	}
+}

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

@@ -11,9 +11,9 @@ public class ProcessPluginApiBuilderImpl implements ProcessPluginApiBuilder
 {
 	@Override
 	public ProcessPluginFactory build(ClassLoader apiClassLoader, ApplicationContext apiApplicationContext,
-			ConfigurableEnvironment environment)
+			ConfigurableEnvironment environment, String serverBaseUrl)
 	{
-		return new ProcessPluginFactoryImpl(apiClassLoader, apiApplicationContext, environment);
+		return new ProcessPluginFactoryImpl(apiClassLoader, apiApplicationContext, environment, serverBaseUrl);
 	}
 
 	@Override

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

@@ -19,17 +19,18 @@ public class ProcessPluginFactoryImpl extends AbstractProcessPluginFactory imple
 	public static final int API_VERSION = 1;
 
 	public ProcessPluginFactoryImpl(ClassLoader apiClassLoader, ApplicationContext apiApplicationContext,
-			ConfigurableEnvironment environment)
+			ConfigurableEnvironment environment, String serverBaseUrl)
 	{
-		super(API_VERSION, apiClassLoader, apiApplicationContext, environment, ProcessPluginDefinition.class);
+		super(API_VERSION, apiClassLoader, apiApplicationContext, environment, serverBaseUrl,
+				ProcessPluginDefinition.class);
 	}
 
 	@Override
 	protected ProcessPlugin createProcessPlugin(Object processPluginDefinition, boolean draft, Path jarFile,
 			URLClassLoader pluginClassLoader)
 	{
 		return new ProcessPluginImpl((ProcessPluginDefinition) processPluginDefinition, API_VERSION, draft, jarFile,
-				pluginClassLoader, environment, apiApplicationContext);
+				pluginClassLoader, environment, apiApplicationContext, serverBaseUrl);
 	}
 
 	@Override