Merge remote-tracking branch 'origin/release/1.0.3.0'

* origin/release/1.0.3.0:
  release 1.0.3.0
  update dependencies
  added missing try-catch and harmonized error messages
  local_role before remote_role
  allow dic and dms to be same organization for dataset status message
  add TORCH export demo data
  sort method parameters
  search for exisiting DocumentReferences and update if exists
  add demo bundle for evaluation report
  start development cycle 1.0.3.0

pom.xml

@@ -6,14 +6,14 @@
 
 	<groupId>de.medizininformatik-initiative</groupId>
 	<artifactId>mii-process-data-transfer</artifactId>
-	<version>1.0.2.1</version>
+	<version>1.0.3.0</version>
 
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<compileSource>17</compileSource>
 		<compileTarget>17</compileTarget>
 
-		<dsf.version>1.5.2</dsf.version>
+		<dsf.version>1.6.0</dsf.version>
 		<testSetup.location>../mii-processes-test-setup</testSetup.location>
 	</properties>
 
@@ -45,13 +45,13 @@
 		<dependency>
 			<groupId>de.medizininformatik-initiative</groupId>
 			<artifactId>mii-processes-common</artifactId>
-			<version>1.0.2.1</version>
+			<version>1.0.3.0</version>
 		</dependency>
 
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-api</artifactId>
-			<version>2.0.13</version>
+			<version>2.0.16</version>
 			<scope>provided</scope>
 		</dependency>
 
@@ -91,7 +91,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
-				<version>3.3.1</version>
+				<version>3.5.2</version>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
@@ -141,7 +141,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-dependency-plugin</artifactId>
-				<version>3.7.1</version>
+				<version>3.8.1</version>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
@@ -177,7 +177,7 @@
 			<plugin>
 				<groupId>net.revelc.code</groupId>
 				<artifactId>impsort-maven-plugin</artifactId>
-				<version>1.11.0</version>
+				<version>1.12.0</version>
 				<configuration>
 					<compliance>17</compliance>
 					<groups>java.,javax.,org.,com.</groups>
@@ -204,22 +204,22 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-site-plugin</artifactId>
-				<version>3.12.1</version>
+				<version>3.21.0</version>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-project-info-reports-plugin</artifactId>
-				<version>3.6.2</version>
+				<version>3.8.0</version>
 			</plugin>
 			<plugin>
 				<groupId>com.github.spotbugs</groupId>
 				<artifactId>spotbugs-maven-plugin</artifactId>
-				<version>4.8.6.2</version>
+				<version>4.8.6.5</version>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-pmd-plugin</artifactId>
-				<version>3.24.0</version>
+				<version>3.26.0</version>
 			</plugin>
 		</plugins>
 	</build>

src/main/java/de/medizininformatik_initiative/process/data_transfer/DataTransferProcessPluginDefinition.java

@@ -11,8 +11,8 @@
 
 public class DataTransferProcessPluginDefinition implements ProcessPluginDefinition
 {
-	public static final String VERSION = "1.0.2.1";
-	public static final LocalDate RELEASE_DATE = LocalDate.of(2024, 8, 1);
+	public static final String VERSION = "1.0.3.0";
+	public static final LocalDate RELEASE_DATE = LocalDate.of(2024, 11, 8);
 
 	@Override
 	public String getName()

src/main/java/de/medizininformatik_initiative/process/data_transfer/service/CreateBundle.java

@@ -15,6 +15,7 @@
 import org.hl7.fhir.r4.model.DocumentReference;
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.ResourceType;
+import org.hl7.fhir.r4.model.Task;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.InitializingBean;
@@ -48,6 +49,7 @@ public void afterPropertiesSet() throws Exception
 	@Override
 	protected void doExecute(DelegateExecution execution, Variables variables)
 	{
+		Task task = variables.getStartTask();
 		String projectIdentifier = variables
 				.getString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_PROJECT_IDENTIFIER);
 		String dmsIdentifier = variables.getString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DMS_IDENTIFIER);
@@ -56,14 +58,26 @@ protected void doExecute(DelegateExecution execution, Variables variables)
 				"Creating transferable data-set for DMS '{}' and project-identifier '{}' referenced in Task with id '{}'",
 				dmsIdentifier, projectIdentifier, variables.getStartTask().getId());
 
-		DocumentReference documentReference = variables
-				.getResource(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DOCUMENT_REFERENCE);
-		Resource resource = variables.getResource(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RESOURCE);
-		Bundle bundle = createTransactionBundle(variables, projectIdentifier, documentReference, resource);
-
-		dataLogger.logResource("Created Transfer Bundle", bundle);
-
-		variables.setResource(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_SET, bundle);
+		try
+		{
+			DocumentReference documentReference = variables
+					.getResource(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DOCUMENT_REFERENCE);
+			Resource resource = variables.getResource(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RESOURCE);
+
+			Bundle bundle = createTransactionBundle(variables, projectIdentifier, documentReference, resource);
+			dataLogger.logResource("Created Transfer Bundle", bundle);
+
+			variables.setResource(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_SET, bundle);
+		}
+		catch (Exception exception)
+		{
+			logger.warn(
+					"Could not create transferable data-set for DMS '{}' and project-identifier '{}' referenced in Task with id '{}' - {}",
+					dmsIdentifier, projectIdentifier, task.getId(), exception.getMessage());
+
+			String error = "Create transferable data-set failed - " + exception.getMessage();
+			throw new RuntimeException(error, exception);
+		}
 	}
 
 	private Bundle createTransactionBundle(Variables variables, String projectIdentifier,

src/main/java/de/medizininformatik_initiative/process/data_transfer/service/DecryptData.java

@@ -84,17 +84,16 @@ protected void doExecute(DelegateExecution execution, Variables variables)
 					ConstantsDataTransfer.CODESYSTEM_DATA_TRANSFER_VALUE_DATA_SET_STATUS, "Decrypt data-set failed"));
 			variables.updateTask(task);
 
-			variables.setString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR_MESSAGE,
-					"Decrypt data-set failed");
-
 			logger.warn(
 					"Could not decrypt data-set with id '{}' from organization '{}' and project-identifier '{}' referenced in Task with id '{}' - {}",
 					variables.getString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_SET_REFERENCE),
 					task.getRequester().getIdentifier().getValue(),
 					variables.getString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_PROJECT_IDENTIFIER), task.getId(),
 					exception.getMessage());
-			throw new BpmnError(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR,
-					"Decrypt data-set - " + exception.getMessage());
+
+			String error = "Decrypt data-set failed - " + exception.getMessage();
+			variables.setString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR_MESSAGE, error);
+			throw new BpmnError(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR, error, exception);
 		}
 	}
 

src/main/java/de/medizininformatik_initiative/process/data_transfer/service/DeleteData.java

@@ -47,9 +47,9 @@ protected void doExecute(DelegateExecution execution, Variables variables)
 			logger.warn(
 					"Could not permanently delete data-set for DMS '{}' and project-identifier '{}' referenced in Task with id '{}' - {}",
 					dmsIdentifier, projectIdentifier, task.getId(), exception.getMessage());
-			throw new RuntimeException("Could not permanently delete data-set for DMS '" + dmsIdentifier
-					+ "' and project-identifier '" + projectIdentifier + "' referenced in Task with id '" + task.getId()
-					+ "' - " + exception.getMessage(), exception);
+
+			String error = "Permanently deleting encrypted transferable data-set failed - " + exception.getMessage();
+			throw new RuntimeException(error, exception);
 		}
 	}
 

src/main/java/de/medizininformatik_initiative/process/data_transfer/service/DownloadData.java

@@ -75,15 +75,14 @@ protected void doExecute(DelegateExecution execution, Variables variables)
 					ConstantsDataTransfer.CODESYSTEM_DATA_TRANSFER_VALUE_DATA_SET_STATUS, "Download data-set failed"));
 			variables.updateTask(task);
 
-			variables.setString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR_MESSAGE,
-					"Download data-set failed");
-
 			logger.warn(
 					"Could not download data-set with id '{}' from organization '{}' and project-identifier '{}' referenced in Task with id '{}' - {}",
 					dataSetReference.getValue(), sendingOrganization, projectIdentifier, task.getId(),
 					exception.getMessage());
-			throw new BpmnError(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR,
-					"Download data-set - " + exception.getMessage());
+
+			String error = "Download data-set failed - " + exception.getMessage();
+			variables.setString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR_MESSAGE, error);
+			throw new BpmnError(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR, error, exception);
 		}
 	}
 

src/main/java/de/medizininformatik_initiative/process/data_transfer/service/EncryptData.java

@@ -56,16 +56,17 @@ protected void doExecute(DelegateExecution execution, Variables variables)
 		String projectIdentifier = variables
 				.getString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_PROJECT_IDENTIFIER);
 		String dmsIdentifier = variables.getString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DMS_IDENTIFIER);
-		Bundle toEncrypt = variables.getResource(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_SET);
-		String localOrganizationIdentifier = api.getOrganizationProvider().getLocalOrganizationIdentifierValue()
-				.orElseThrow(() -> new RuntimeException("LocalOrganizationIdentifierValue is null"));
 
 		logger.info(
 				"Encrypting transferable data-set for DMS '{}' and project-identifier '{}' referenced in Task with id '{}'",
 				dmsIdentifier, projectIdentifier, task.getId());
 
 		try
 		{
+			Bundle toEncrypt = variables.getResource(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_SET);
+			String localOrganizationIdentifier = api.getOrganizationProvider().getLocalOrganizationIdentifierValue()
+					.orElseThrow(() -> new RuntimeException("LocalOrganizationIdentifierValue is null"));
+
 			PublicKey publicKey = readPublicKey(dmsIdentifier);
 			byte[] encrypted = encrypt(publicKey, toEncrypt, localOrganizationIdentifier, dmsIdentifier);
 
@@ -76,9 +77,9 @@ protected void doExecute(DelegateExecution execution, Variables variables)
 			logger.warn(
 					"Could not encrypt data-set for DMS '{}' and project-identifier '{}' referenced in Task with id '{}' - {}",
 					dmsIdentifier, projectIdentifier, task.getId(), exception.getMessage());
-			throw new RuntimeException("Could not encrypt data-set for DMS '" + dmsIdentifier
-					+ "' and project-identifier '" + projectIdentifier + "' referenced in Task with id '" + task.getId()
-					+ "' - " + exception.getMessage(), exception);
+
+			String error = "Encrypt transferable data-set failed - " + exception.getMessage();
+			throw new RuntimeException(error, exception);
 		}
 	}
 

src/main/java/de/medizininformatik_initiative/process/data_transfer/service/HandleErrorReceive.java

@@ -25,9 +25,12 @@ protected void doExecute(DelegateExecution delegateExecution, Variables variable
 		String error = variables.getString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR_MESSAGE);
 
 		sendMail(task, projectIdentifier, error);
+
+		task.setStatus(Task.TaskStatus.FAILED);
 		api.getFhirWebserviceClientProvider().getLocalWebserviceClient()
 				.withRetry(ConstantsBase.DSF_CLIENT_RETRY_6_TIMES, ConstantsBase.DSF_CLIENT_RETRY_INTERVAL_5MIN)
 				.update(task);
+		variables.updateTask(task);
 	}
 
 	private void sendMail(Task task, String projectIdentifier, String error)

src/main/java/de/medizininformatik_initiative/process/data_transfer/service/InsertData.java

@@ -8,7 +8,9 @@
 import org.camunda.bpm.engine.delegate.BpmnError;
 import org.camunda.bpm.engine.delegate.DelegateExecution;
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.DocumentReference;
 import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.ResourceType;
 import org.hl7.fhir.r4.model.Task;
@@ -23,6 +25,7 @@
 import de.medizininformatik_initiative.processes.common.util.DataSetStatusGenerator;
 import dev.dsf.bpe.v1.ProcessPluginApi;
 import dev.dsf.bpe.v1.activity.AbstractServiceDelegate;
+import dev.dsf.bpe.v1.constants.NamingSystems;
 import dev.dsf.bpe.v1.variables.Variables;
 
 public class InsertData extends AbstractServiceDelegate implements InitializingBean
@@ -66,7 +69,7 @@ protected void doExecute(DelegateExecution execution, Variables variables)
 
 		try
 		{
-			List<IdType> createdIds = storeData(variables, fhirClient, bundle, sendingOrganization, projectIdentifier);
+			List<IdType> createdIds = storeData(fhirClient, bundle, sendingOrganization, projectIdentifier, variables);
 
 			task.addOutput(
 					statusGenerator.createDataSetStatusOutput(ConstantsBase.CODESYSTEM_DATA_SET_STATUS_VALUE_RECEIVE_OK,
@@ -85,24 +88,25 @@ protected void doExecute(DelegateExecution execution, Variables variables)
 					ConstantsDataTransfer.CODESYSTEM_DATA_TRANSFER_VALUE_DATA_SET_STATUS, "Insert data-set failed"));
 			variables.updateTask(task);
 
-			variables.setString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR_MESSAGE,
-					"Insert data-set failed");
-
 			logger.warn(
 					"Could not insert data-set with id '{}' from organization '{}' and project-identifier '{}' referenced in Task with id '{}' - {}",
 					variables.getString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_SET_REFERENCE),
 					task.getRequester().getIdentifier().getValue(),
 					variables.getString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_PROJECT_IDENTIFIER), task.getId(),
 					exception.getMessage());
-			throw new BpmnError(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR,
-					"Insert data-set - " + exception.getMessage());
+
+			String error = "Insert data-set failed - " + exception.getMessage();
+			variables.setString(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR_MESSAGE, error);
+			throw new BpmnError(ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_DATA_RECEIVE_ERROR, error, exception);
 		}
 	}
 
-	private List<IdType> storeData(Variables variables, FhirClient fhirClient, Bundle bundle,
-			String sendingOrganization, String projectIdentifier)
+	private List<IdType> storeData(FhirClient fhirClient, Bundle bundle, String sendingOrganization,
+			String projectIdentifier, Variables variables)
 	{
-		Bundle stored = fhirClient.executeTransaction(bundle);
+		Bundle transactionBundle = checkAndAdaptBundleForExistingData(fhirClient, bundle, sendingOrganization,
+				projectIdentifier, variables.getStartTask());
+		Bundle stored = fhirClient.executeTransaction(transactionBundle);
 
 		List<IdType> idsOfCreatedResources = stored.getEntry().stream().filter(Bundle.BundleEntryComponent::hasResponse)
 				.map(Bundle.BundleEntryComponent::getResponse).map(Bundle.BundleEntryResponseComponent::getLocation)
@@ -116,6 +120,48 @@ private List<IdType> storeData(Variables variables, FhirClient fhirClient, Bundl
 		return idsOfCreatedResources;
 	}
 
+	private Bundle checkAndAdaptBundleForExistingData(FhirClient fhirClient, Bundle bundle, String sendingOrganization,
+			String projectIdentifier, Task task)
+	{
+		Bundle searchResult = fhirClient.getGenericFhirClient().search().forResource(DocumentReference.class)
+				.where(DocumentReference.IDENTIFIER.exactly()
+						.systemAndCode(ConstantsBase.NAMINGSYSTEM_MII_PROJECT_IDENTIFIER, projectIdentifier))
+				.and(DocumentReference.AUTHOR.hasChainedProperty(Organization.IDENTIFIER.exactly()
+						.systemAndCode(NamingSystems.OrganizationIdentifier.SID, sendingOrganization)))
+				.returnBundle(Bundle.class).execute();
+
+		List<DocumentReference> existingDocumentReferences = searchResult.getEntry().stream()
+				.filter(Bundle.BundleEntryComponent::hasResource).map(Bundle.BundleEntryComponent::getResource)
+				.filter(r -> r instanceof DocumentReference).map(r -> (DocumentReference) r).toList();
+
+		if (existingDocumentReferences.size() < 1)
+			return bundle;
+
+		if (existingDocumentReferences.size() > 1)
+			logger.warn(
+					"Found more than one DocumentReference for project-identifier '{}' authored by '{}', using the first",
+					projectIdentifier, sendingOrganization);
+
+		DocumentReference existingDocumentReference = existingDocumentReferences.get(0);
+		String existingDocumentReferenceId = existingDocumentReference.getIdElement().getIdPart();
+
+		logger.info(
+				"DocumentReference for project-identifier '{}' authored by '{}' already exists, updating data-set on FHIR server with baseUrl '{}' in Task with id '{}'",
+				projectIdentifier, sendingOrganization, fhirClient.getFhirBaseUrl(), task.getId());
+
+		bundle.getEntry().stream().filter(Bundle.BundleEntryComponent::hasResource)
+				.filter(e -> e.getResource() instanceof DocumentReference)
+				.filter(Bundle.BundleEntryComponent::hasRequest).filter(Bundle.BundleEntryComponent::hasResource)
+				.forEach(e ->
+				{
+					e.getRequest().setMethod(Bundle.HTTPVerb.PUT)
+							.setUrl(ResourceType.DocumentReference.name() + "/" + existingDocumentReferenceId);
+					e.getResource().setId(existingDocumentReferenceId);
+				});
+
+		return bundle;
+	}
+
 	private void sendMail(Task task, List<IdType> createdIds, String sendingOrganization, String projectIdentifier)
 	{
 		String subject = "New data-set received in process '" + ConstantsDataTransfer.PROCESS_NAME_FULL_DATA_RECEIVE

src/main/java/de/medizininformatik_initiative/process/data_transfer/service/ReadData.java

@@ -72,10 +72,9 @@ protected void doExecute(DelegateExecution execution, Variables variables)
 					"Could not read data-set on FHIR server with baseUrl '{}' for DMS '{}' and project-identifier '{}' referenced in Task with id '{}' - {}",
 					fhirClient.getFhirBaseUrl(), dmsIdentifier, projectIdentifier, task.getId(),
 					exception.getMessage());
-			throw new RuntimeException(
-					"Could not read data-set on FHIR server with baseUrl '" + fhirClient.getFhirBaseUrl()
-							+ "' for DMS '" + dmsIdentifier + "' and project-identifier '" + projectIdentifier
-							+ "' referenced in Task with id '" + task.getId() + "' - " + exception.getMessage());
+
+			String error = "Read data-set failed - " + exception.getMessage();
+			throw new RuntimeException(error, exception);
 		}
 	}