Merge remote-tracking branch 'origin/hotfix/106_DSF_0.9.0_Backport' into

release/0.6.0.1

.gitignore

@@ -28,7 +28,6 @@ codex-processes-ap1-test-data-generator/rsa/*.pem
 ###
 codex-processes-ap1-docker-test-setup/**/bpe/log/*.log
 codex-processes-ap1-docker-test-setup/**/bpe/log/*.log.gz
-codex-processes-ap1-docker-test-setup/**/bpe/last_event/time.file
 codex-processes-ap1-docker-test-setup/**/bpe/plugin/*.jar
 codex-processes-ap1-docker-test-setup/**/bpe/process/*.jar
 

codex-process-data-transfer/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>de.netzwerk-universitaetsmedizin.codex</groupId>
 		<artifactId>codex-processes-ap1</artifactId>
-		<version>0.6.0</version>
+		<version>0.6.0.1</version>
 	</parent>
 
 	<properties>

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java

@@ -37,7 +37,7 @@ public class DataTransferProcessPluginDefinition implements ProcessPluginDefinit
 	private static final Logger logger = LoggerFactory.getLogger(DataTransferProcessPluginDefinition.class);
 
 	public static final String VERSION = "0.6.0";
-	public static final LocalDate DATE = LocalDate.of(2022, 7, 12);
+	public static final LocalDate DATE = LocalDate.of(2022, 10, 18);
 
 	@Override
 	public String getName()

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/GeccoFhirClientStub.java

@@ -33,7 +33,7 @@ public final class GeccoFhirClientStub implements GeccoFhirClient
 	private static final Logger logger = LoggerFactory.getLogger(GeccoFhirClientStub.class);
 
 	private static final String condition = "{\"resourceType\":\"Condition\",\"meta\":{\"profile\":[\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/chronic-lung-diseases\"]},\"clinicalStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-clinical\",\"code\":\"active\",\"display\":\"Active\"}]},\"verificationStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-ver-status\",\"code\":\"confirmed\",\"display\":\"Confirmed\"},{\"system\":\"http://snomed.info/sct\",\"code\":\"410605003\",\"display\":\"Confirmed present (qualifier value)\"}]},\"category\":[{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"418112009\",\"display\":\"Pulmonary medicine\"}]}],\"code\":{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"413839001\",\"display\":\"Chronic lung disease\"}]},\"recordedDate\":\"2020-11-10T15:50:41.000+01:00\"}";
-	private static final String patient = "{\"resourceType\":\"Patient\",\"meta\":{\"profile\":[\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/Patient\"]},\"extension\":[{\"url\":\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/ethnic-group\",\"valueCoding\":{\"system\":\"http://snomed.info/sct\",\"code\":\"186019001\",\"display\":\"Other ethnic, mixed origin\"}},{\"url\":\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/age\",\"extension\":[{\"url\":\"dateTimeOfDocumentation\",\"valueDateTime\":\"2020-10-01\"},{\"url\":\"age\",\"valueAge\":{\"value\":67,\"unit\":\"years\",\"system\":\"http://unitsofmeasure.org\",\"code\":\"a\"}}]}],\"birthDate\":\"1953-09-30\"}";
+	private static final String patient = "{\"resourceType\":\"Patient\",\"meta\":{\"profile\":[\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/Patient\"]},\"extension\":[{\"url\":\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/ethnic-group\",\"valueCoding\":{\"system\":\"http://snomed.info/sct\",\"code\":\"26242008\",\"display\":\"Mixed (qualifier value)\"}},{\"url\":\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/age\",\"extension\":[{\"url\":\"dateTimeOfDocumentation\",\"valueDateTime\":\"2020-10-01\"},{\"url\":\"age\",\"valueAge\":{\"value\":67,\"unit\":\"years\",\"system\":\"http://unitsofmeasure.org\",\"code\":\"a\"}}]}],\"birthDate\":\"1953-09-30\"}";
 	private static final String observation = "{\"resourceType\":\"Observation\",\"meta\":{\"profile\":[\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-rt-pcr\"]},\"identifier\":[{\"type\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/v2-0203\",\"code\":\"OBI\"}]}}],\"status\":\"final\",\"category\":[{\"coding\":[{\"system\":\"http://loinc.org\",\"code\":\"26436-6\"},{\"system\":\"http://terminology.hl7.org/CodeSystem/observation-category\",\"code\":\"laboratory\"}]}],\"code\":{\"coding\":[{\"system\":\"http://loinc.org\",\"code\":\"94500-6\",\"display\":\"SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by NAA with probe detection\"}],\"text\":\"SARS-CoV-2-RNA (PCR)\"},\"effectiveDateTime\":\"2020-11-10T15:50:41.000+01:00\",\"valueCodeableConcept\":{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"260373001\",\"display\":\"Detected (qualifier value)\"}],\"text\":\"SARS-CoV-2-RNA positiv\"}}";
 
 	private final GeccoClient geccoClient;
@@ -82,15 +82,18 @@ public Stream<DomainResource> getNewData(String pseudonym, DateWithPrecision exp
 		logger.warn("Returning demo resources for {}", pseudonym);
 
 		Patient p = geccoClient.getFhirContext().newJsonParser().parseResource(Patient.class, patient);
+		p.setIdElement(new IdType(UUID.randomUUID().toString()));
 		p.addIdentifier().setSystem(NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM).setValue(pseudonym).getType()
 				.getCodingFirstRep().setSystem(IDENTIFIER_NUM_CODEX_DIC_PSEUDONYM_TYPE_SYSTEM)
 				.setCode(IDENTIFIER_NUM_CODEX_DIC_PSEUDONYM_TYPE_CODE);
 		p.setIdElement(new IdType("Patient", UUID.randomUUID().toString()));
 
 		Condition c = geccoClient.getFhirContext().newJsonParser().parseResource(Condition.class, condition);
+		c.setIdElement(new IdType(UUID.randomUUID().toString()));
 		c.setSubject(new Reference(p.getIdElement()));
 
 		Observation o = geccoClient.getFhirContext().newJsonParser().parseResource(Observation.class, observation);
+		o.setIdElement(new IdType(UUID.randomUUID().toString()));
 		o.setSubject(new Reference(p.getIdElement()));
 
 		return Stream.of(p, c, o);

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/crypto/CrrKeyProviderImpl.java

@@ -26,7 +26,7 @@ public class CrrKeyProviderImpl implements CrrKeyProvider
 
 	/**
 	 * One or both parameters should be <code>null</code>
-	 * 
+	 *
 	 * @param crrPrivateKeyFile
 	 * @param crrPublicKeyFile
 	 * @return

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/logging/ErrorLogger.java

@@ -1,41 +1,90 @@
 package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.logging;
 
+import java.util.Objects;
+
+import org.highmed.dsf.bpe.service.MailService;
 import org.hl7.fhir.r4.model.IdType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.InitializingBean;
 
-public class ErrorLogger
+public class ErrorLogger implements InitializingBean
 {
 	private static final Logger validationLogger = LoggerFactory.getLogger("validation-error-logger");
 	private static final Logger errorLogger = LoggerFactory.getLogger("error-logger");
 
+	private final MailService mailService;
+
+	private final boolean sendValidationFailedMail;
+	private final boolean sendProcessFailedMail;
+
+	public ErrorLogger(MailService mailService, boolean sendValidationFailedMail, boolean sendProcessFailedMail)
+	{
+		this.mailService = mailService;
+
+		this.sendValidationFailedMail = sendValidationFailedMail;
+		this.sendProcessFailedMail = sendProcessFailedMail;
+	}
+
+	@Override
+	public void afterPropertiesSet() throws Exception
+	{
+		Objects.requireNonNull(mailService, "mailService");
+	}
+
 	public void logValidationFailed(IdType taskId)
 	{
-		validationLogger.debug("Validation of FHIR resources failed, started by Task {}", taskId.getValue());
+		validationLogger.debug("Validation of FHIR resources failed in process started by {}",
+				taskId.toVersionless().getValue());
+
+		if (sendValidationFailedMail)
+			mailService.send("Validation Error",
+					"Validation of FHIR resources failed in process started by " + taskId.toVersionless().getValue());
 	}
 
 	public void logValidationFailedLocal(IdType taskId)
 	{
-		validationLogger.debug("Local validation of FHIR resources failed, started by Task {}", taskId.getValue());
+		validationLogger.debug("Local validation of FHIR resources failed in process started by {}",
+				taskId.toVersionless().getValue());
+
+		if (sendValidationFailedMail)
+			mailService.send("Validation Error", "Local validation of FHIR resources failed in process started by "
+					+ taskId.toVersionless().getValue());
 	}
 
 	public void logValidationFailedRemote(IdType taskId)
 	{
-		validationLogger.debug("Remote validation of FHIR resources failed, started by Task {}", taskId.getValue());
+		validationLogger.debug("Remote validation of FHIR resources failed in process started by {}",
+				taskId.toVersionless().getValue());
+
+		if (sendValidationFailedMail)
+			mailService.send("Validation Error", "Remote validation of FHIR resources failed in process started by "
+					+ taskId.toVersionless().getValue());
 	}
 
 	public void logDataSendFailed(IdType taskId)
 	{
-		errorLogger.debug("Send process failed, started by Task {}", taskId.getValue());
+		errorLogger.debug("Send process failed started by {}", taskId.toVersionless().getValue());
+
+		if (sendProcessFailedMail)
+			mailService.send("Proccess Failed", "Send process failed started by " + taskId.toVersionless().getValue());
 	}
 
 	public void logDataTranslateFailed(IdType taskId)
 	{
-		errorLogger.debug("Translate process failed, started by Task {}", taskId.getValue());
+		errorLogger.debug("Translate process failed started by {}", taskId.toVersionless().getValue());
+
+		if (sendProcessFailedMail)
+			mailService.send("Proccess Failed",
+					"Translate process failed started by " + taskId.toVersionless().getValue());
 	}
 
 	public void logDataReceiveFailed(IdType taskId)
 	{
-		errorLogger.debug("Receive process failed, started by Task {}", taskId.getValue());
+		errorLogger.debug("Receive process failed started by {}", taskId.toVersionless().getValue());
+
+		if (sendProcessFailedMail)
+			mailService.send("Proccess Failed",
+					"Receive process failed started by " + taskId.toVersionless().getValue());
 	}
 }

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/message/ContinueSendProcess.java

@@ -2,43 +2,27 @@
 
 import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_RETURN_TARGET;
 
-import java.util.stream.Stream;
-
+import org.camunda.bpm.engine.delegate.DelegateExecution;
 import org.highmed.dsf.fhir.authorization.read.ReadAccessHelper;
 import org.highmed.dsf.fhir.client.FhirWebserviceClientProvider;
 import org.highmed.dsf.fhir.organization.OrganizationProvider;
 import org.highmed.dsf.fhir.task.AbstractTaskMessageSend;
 import org.highmed.dsf.fhir.task.TaskHelper;
 import org.highmed.dsf.fhir.variables.Target;
-import org.hl7.fhir.r4.model.Task.ParameterComponent;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import ca.uhn.fhir.context.FhirContext;
 
 public class ContinueSendProcess extends AbstractTaskMessageSend
 {
-	private static final Logger logger = LoggerFactory.getLogger(ContinueSendProcess.class);
-
 	public ContinueSendProcess(FhirWebserviceClientProvider clientProvider, TaskHelper taskHelper,
 			ReadAccessHelper readAccessHelper, OrganizationProvider organizationProvider, FhirContext fhirContext)
 	{
 		super(clientProvider, taskHelper, readAccessHelper, organizationProvider, fhirContext);
 	}
 
 	@Override
-	protected Target getTarget()
+	protected Target getTarget(DelegateExecution execution)
 	{
 		return (Target) execution.getVariable(BPMN_EXECUTION_VARIABLE_RETURN_TARGET);
 	}
-
-	@Override
-	protected void sendTask(Target target, String instantiatesUri, String messageName, String businessKey,
-			String profile, Stream<ParameterComponent> additionalInputParameters)
-	{
-		// TODO implement continue send
-		logger.debug("implement continue send");
-
-		super.sendTask(target, instantiatesUri, messageName, businessKey, profile, additionalInputParameters);
-	}
 }

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/message/ContinueSendProcessWithError.java

@@ -43,7 +43,7 @@ public void afterPropertiesSet() throws Exception
 	}
 
 	@Override
-	protected Target getTarget()
+	protected Target getTarget(DelegateExecution execution)
 	{
 		return (Target) execution.getVariable(BPMN_EXECUTION_VARIABLE_RETURN_TARGET);
 	}

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/message/ContinueSendProcessWithValidationError.java

@@ -29,7 +29,7 @@ public ContinueSendProcessWithValidationError(FhirWebserviceClientProvider clien
 	}
 
 	@Override
-	protected Target getTarget()
+	protected Target getTarget(DelegateExecution execution)
 	{
 		return (Target) execution.getVariable(BPMN_EXECUTION_VARIABLE_RETURN_TARGET);
 	}

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/message/ContinueTranslateProcess.java

@@ -2,44 +2,27 @@
 
 import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_RETURN_TARGET;
 
-import java.util.stream.Stream;
-
+import org.camunda.bpm.engine.delegate.DelegateExecution;
 import org.highmed.dsf.fhir.authorization.read.ReadAccessHelper;
 import org.highmed.dsf.fhir.client.FhirWebserviceClientProvider;
 import org.highmed.dsf.fhir.organization.OrganizationProvider;
 import org.highmed.dsf.fhir.task.AbstractTaskMessageSend;
 import org.highmed.dsf.fhir.task.TaskHelper;
 import org.highmed.dsf.fhir.variables.Target;
-import org.hl7.fhir.r4.model.Task.ParameterComponent;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import ca.uhn.fhir.context.FhirContext;
 
 public class ContinueTranslateProcess extends AbstractTaskMessageSend
 {
-	private static final Logger logger = LoggerFactory.getLogger(ContinueTranslateProcess.class);
-
 	public ContinueTranslateProcess(FhirWebserviceClientProvider clientProvider, TaskHelper taskHelper,
 			ReadAccessHelper readAccessHelper, OrganizationProvider organizationProvider, FhirContext fhirContext)
 	{
 		super(clientProvider, taskHelper, readAccessHelper, organizationProvider, fhirContext);
 	}
 
 	@Override
-	protected Target getTarget()
+	protected Target getTarget(DelegateExecution execution)
 	{
 		return (Target) execution.getVariable(BPMN_EXECUTION_VARIABLE_RETURN_TARGET);
 	}
-
-	@Override
-	protected void sendTask(Target target, String instantiatesUri, String messageName, String businessKey,
-			String profile, Stream<ParameterComponent> additionalInputParameters)
-	{
-
-		// TODO implement continue translate
-		logger.debug("implement continue translate");
-
-		super.sendTask(target, instantiatesUri, messageName, businessKey, profile, additionalInputParameters);
-	}
 }

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/message/ContinueTranslateProcessWithError.java

@@ -43,7 +43,7 @@ public void afterPropertiesSet() throws Exception
 	}
 
 	@Override
-	protected Target getTarget()
+	protected Target getTarget(DelegateExecution execution)
 	{
 		return (Target) execution.getVariable(BPMN_EXECUTION_VARIABLE_RETURN_TARGET);
 	}

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/message/ContinueTranslateProcessWithValidationError.java

@@ -30,7 +30,7 @@ public ContinueTranslateProcessWithValidationError(FhirWebserviceClientProvider
 	}
 
 	@Override
-	protected Target getTarget()
+	protected Target getTarget(DelegateExecution execution)
 	{
 		return (Target) execution.getVariable(BPMN_EXECUTION_VARIABLE_RETURN_TARGET);
 	}

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/message/StartReceiveProcess.java

@@ -44,14 +44,15 @@ protected Stream<ParameterComponent> getAdditionalInputParameters(DelegateExecut
 	}
 
 	@Override
-	protected void sendTask(Target target, String instantiatesUri, String messageName, String businessKey,
-			String profile, Stream<ParameterComponent> additionalInputParameters)
+	protected void sendTask(DelegateExecution execution, Target target, String instantiatesUri, String messageName,
+			String businessKey, String profile, Stream<ParameterComponent> additionalInputParameters)
 	{
-		String crrBusinessKey = createAndSaveAlternativeBusinessKey();
+		String crrBusinessKey = createAndSaveAlternativeBusinessKey(execution);
 
 		logger.debug("DIC businessKey {}, CRR businessKey {}", businessKey, crrBusinessKey);
 
-		super.sendTask(target, instantiatesUri, messageName, crrBusinessKey, profile, additionalInputParameters);
+		super.sendTask(execution, target, instantiatesUri, messageName, crrBusinessKey, profile,
+				additionalInputParameters);
 	}
 
 	private ParameterComponent pseudonymParameter(DelegateExecution execution)
@@ -82,7 +83,7 @@ private ParameterComponent dataReferenceParameter(DelegateExecution execution)
 	}
 
 	@Override
-	protected void handleSendTaskError(Exception exception, String errorMessage)
+	protected void handleSendTaskError(DelegateExecution execution, Exception exception, String errorMessage)
 	{
 		throw new BpmnError(CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_CRR_NOT_REACHABLE,
 				"Error while sending Task to CRR: " + exception.getMessage());

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/message/StartSendProcess.java

@@ -46,11 +46,11 @@ public StartSendProcess(FhirWebserviceClientProvider clientProvider, TaskHelper
 	}
 
 	@Override
-	protected void sendTask(Target target, String instantiatesUri, String messageName, String businessKey,
-			String profile, Stream<ParameterComponent> additionalInputParameters)
+	protected void sendTask(DelegateExecution execution, Target target, String instantiatesUri, String messageName,
+			String businessKey, String profile, Stream<ParameterComponent> additionalInputParameters)
 	{
 		// can't use same business key as trigger process
-		super.sendTask(target, instantiatesUri, messageName, UUID.randomUUID().toString(), profile,
+		super.sendTask(execution, target, instantiatesUri, messageName, UUID.randomUUID().toString(), profile,
 				additionalInputParameters);
 	}
 

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/message/StartTranslateProcess.java

@@ -68,7 +68,7 @@ private ParameterComponent dataReferenceParameter(DelegateExecution execution)
 	}
 
 	@Override
-	protected void handleSendTaskError(Exception exception, String errorMessage)
+	protected void handleSendTaskError(DelegateExecution execution, Exception exception, String errorMessage)
 	{
 		throw new BpmnError(CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_GTH_NOT_REACHABLE,
 				"Error while sending Task to GTH: " + exception.getMessage());

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/DecryptData.java

@@ -85,7 +85,7 @@ private void decryptGeccoData(DelegateExecution execution)
 			throws InvalidKeyException, BadPaddingException, IllegalBlockSizeException, NoSuchPaddingException,
 			NoSuchAlgorithmException, InvalidAlgorithmParameterException, IOException
 	{
-		Task task = getCurrentTaskFromExecutionVariables();
+		Task task = getCurrentTaskFromExecutionVariables(execution);
 		Optional<String> pseudonym = getPseudonym(task);
 
 		byte[] encrypted = (byte[]) execution.getVariable(BPMN_EXECUTION_VARIABLE_BUNDLE);
@@ -108,7 +108,7 @@ private Optional<String> getPseudonym(Task task)
 	{
 		return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,
 				CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_PSEUDONYM, Identifier.class).findFirst()
-						.map(Identifier::getValue);
+				.map(Identifier::getValue);
 	}
 
 	private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/DownloadDataFromGth.java

@@ -70,7 +70,7 @@ protected void doExecute(DelegateExecution execution) throws BpmnError, Exceptio
 				TargetValues.create(Target.createUniDirectionalTarget(gthIdentifierValue,
 						getEndpointIdentifier(targetEndpoint), targetEndpoint.getAddress())));
 
-		Task task = getCurrentTaskFromExecutionVariables();
+		Task task = getCurrentTaskFromExecutionVariables(execution);
 
 		IdType id = getDataReference(task).map(ref -> new IdType(ref)).get();
 
@@ -93,7 +93,7 @@ private Optional<String> getDataReference(Task task)
 	{
 		return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,
 				CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE, Reference.class).findFirst()
-						.map(Reference::getReference);
+				.map(Reference::getReference);
 	}
 
 	private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)