Merge remote-tracking branch 'origin/release/1.1.0.0' into main

num-codex · Mar 25, 2024 · ee36db8 · ee36db8
2 parents 4262d48 + 7710527
commit ee36db8
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diff --git a/codex-process-data-transfer/pom.xml b/codex-process-data-transfer/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>de.netzwerk-universitaetsmedizin.codex</groupId>
 		<artifactId>codex-processes-ap1</artifactId>
-		<version>1.0.0.0</version>
+		<version>1.1.0.0</version>
 	</parent>
 
 	<properties>

diff --git a/...de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/ConstantsDataTransfer.java b/...de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/ConstantsDataTransfer.java
@@ -91,6 +91,7 @@ public interface ConstantsDataTransfer
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_BAD_PATIENT_REFERENCE = "bad-patient-reference";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_FTTP_NOT_REACHABLE = "fttp-not-reachable";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_NO_DIC_PSEUDONYM_FOR_BLOOMFILTER = "no-dic-pseudonym-for-bloomfilter";
+	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_NO_DIC_PSEUDONYM_FOR_LOCAL_PSEUDONYM = "no-dic-pseudonym-for-local-pseudonym";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_VALIDATION_FAILED = "validation-failed";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_ECRYPTION_OF_DATA_FOR_CRR_FAILED = "ecryption-of-data-for-crr-failed";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_UNABLE_TO_STORE_ECRYPTED_DATA = "unable-to-store-ecrypted-data";

diff --git a/...iversitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java b/...iversitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java
@@ -17,8 +17,8 @@
 
 public class DataTransferProcessPluginDefinition implements ProcessPluginDefinition
 {
-	public static final String VERSION = "1.0.0.0";
-	public static final LocalDate DATE = LocalDate.of(2023, 10, 11);
+	public static final String VERSION = "1.1.0.0";
+	public static final LocalDate DATE = LocalDate.of(2024, 3, 25);
 
 	@Override
 	public String getName()

diff --git a/...erk_universitaetsmedizin/codex/processes/data_transfer/client/DataStoreClientFactory.java b/...erk_universitaetsmedizin/codex/processes/data_transfer/client/DataStoreClientFactory.java
@@ -155,11 +155,10 @@ public void testConnection()
 		{
 			logger.info(
 					"Testing connection to Data Store FHIR server with {trustStorePath: {}, certificatePath: {}, privateKeyPath: {}, privateKeyPassword: {},"
-							+ " basicAuthUsername {}, basicAuthPassword {}, bearerToken {}, serverBase: {}, proxyUrl {}, proxyUsername, proxyPassword {}}",
+							+ " basicAuthUsername: {}, basicAuthPassword: {}, bearerToken: {}, serverBase: {}, proxy: values from 'DEV_DSF_PROXY'... config}",
 					trustStorePath, certificatePath, privateKeyPath, privateKeyPassword != null ? "***" : "null",
 					dataStoreServerBasicAuthUsername, dataStoreServerBasicAuthPassword != null ? "***" : "null",
-					dataStoreServerBearerToken != null ? "***" : "null", dataStoreServerBase, proxyUrl, proxyUsername,
-					proxyPassword != null ? "***" : "null");
+					dataStoreServerBearerToken != null ? "***" : "null", dataStoreServerBase);
 
 			getDataStoreClient().testConnection();
 		}

diff --git a/...tzwerk_universitaetsmedizin/codex/processes/data_transfer/client/DataStoreClientImpl.java b/...tzwerk_universitaetsmedizin/codex/processes/data_transfer/client/DataStoreClientImpl.java
@@ -81,8 +81,7 @@ private void configureProxy(IRestfulClientFactory clientFactory, String proxyUrl
 				clientFactory.setProxy(url.getHost(), url.getPort());
 				clientFactory.setProxyCredentials(proxyUsername, proxyPassword);
 
-				logger.info("Using proxy for data FHIR server connection with {host: {}, port: {}, username: {}}",
-						url.getHost(), url.getPort(), proxyUsername);
+				logger.info("Using proxy for data FHIR server connection with values from 'DEV_DSF_PROXY'... config");
 			}
 			catch (MalformedURLException e)
 			{

diff --git a/...ava/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClient.java b/...ava/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClient.java
@@ -18,5 +18,7 @@ public interface FttpClient
 	 */
 	Optional<String> getDicPseudonym(String bloomFilter);
 
+	Optional<String> getDicPseudonymForLocalPseudonym(String localPseudonym);
+
 	void testConnection();
 }
diff --git a/...netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientFactory.java b/...netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientFactory.java
@@ -62,6 +62,18 @@ public Optional<String> getDicPseudonym(String bloomFilter)
 			return pseudonym;
 		}
 
+		@Override
+		public Optional<String> getDicPseudonymForLocalPseudonym(String localPseudonym)
+		{
+			Optional<String> pseudonym = sha256(localPseudonym).map(p -> "dic_test/" + p);
+
+			logger.warn(
+					"Returning simulated DIC pseudonym '{}' for local pseudonym '{}', fTTP connection not configured.",
+					pseudonym.orElseThrow(), localPseudonym);
+
+			return pseudonym;
+		}
+
 		private Optional<String> sha256(String original)
 		{
 			try
@@ -142,11 +154,10 @@ public void testConnection()
 		{
 			logger.info(
 					"Testing connection to fTTP with {trustStorePath: {}, certificatePath: {}, privateKeyPath: {}, privateKeyPassword: {},"
-							+ " basicAuthUsername {}, basicAuthPassword {}, serverBase: {}, apiKey: {}, study: {}, target: {}, proxyUrl {}, proxyUsername, proxyPassword {}}",
+							+ " basicAuthUsername: {}, basicAuthPassword: {}, serverBase: {}, apiKey: {}, study: {}, target: {}, proxy: values from 'DEV_DSF_PROXY'... config}",
 					trustStorePath, certificatePath, privateKeyPath, privateKeyPassword != null ? "***" : "null",
 					fttpBasicAuthUsername, fttpBasicAuthPassword != null ? "***" : "null", fttpServerBase,
-					fttpApiKey != null ? "***" : "null", fttpStudy, fttpTarget, proxyUrl, proxyUsername,
-					proxyPassword != null ? "***" : "null");
+					fttpApiKey != null ? "***" : "null", fttpStudy, fttpTarget);
 
 			getFttpClient().testConnection();
 		}

diff --git a/...de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientImpl.java b/...de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientImpl.java
@@ -101,8 +101,7 @@ private void configureProxy(IRestfulClientFactory clientFactory, String proxyUrl
 				clientFactory.setProxy(url.getHost(), url.getPort());
 				clientFactory.setProxyCredentials(proxyUsername, proxyPassword);
 
-				logger.info("Using proxy for fTTP connection with {host: {}, port: {}, username: {}}", url.getHost(),
-						url.getPort(), proxyUsername);
+				logger.info("Using proxy for fTTP connection with values from 'DEV_DSF_PROXY'... config");
 			}
 			catch (MalformedURLException e)
 			{
@@ -154,6 +153,18 @@ protected Parameters createParametersForPsnWorkflow(String dicSourceAndPseudonym
 		return p;
 	}
 
+	protected Parameters createParametersForPsnWorkflowLocalPseudonym(String localPseudonym)
+	{
+		Parameters p = new Parameters();
+		p.addParameter("study", fttpStudy);
+		p.addParameter("original", localPseudonym);
+		p.addParameter("source", "local");
+		p.addParameter("target", fttpTarget);
+		p.addParameter("apikey", fttpApiKey);
+
+		return p;
+	}
+
 	@Override
 	public Optional<String> getDicPseudonym(String bloomFilter)
 	{
@@ -178,6 +189,30 @@ public Optional<String> getDicPseudonym(String bloomFilter)
 		}
 	}
 
+	@Override
+	public Optional<String> getDicPseudonymForLocalPseudonym(String localPseudonym)
+	{
+		Objects.requireNonNull(localPseudonym, "localPseudonym");
+
+		logger.info("Requesting DIC Pseudonym for local Pseudonym {} ...", localPseudonym);
+
+		try
+		{
+			IGenericClient client = createGenericClient();
+
+			Parameters parameters = client.operation().onServer().named("requestPsnWorkflow")
+					.withParameters(createParametersForPsnWorkflowLocalPseudonym(localPseudonym))
+					.accept(Constants.CT_FHIR_XML_NEW).encoded(EncodingEnum.XML).execute();
+
+			return getPseudonym(parameters).map(p -> fttpTarget + "/" + p);
+		}
+		catch (Exception e)
+		{
+			logger.error("Error while retrieving DIC pseudonym: {} - {}", e.getClass().getName(), e.getMessage());
+			throw new BpmnError(CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_FTTP_NOT_REACHABLE, e.getMessage());
+		}
+	}
+
 	protected Parameters createParametersForBfWorkflow(String bloomFilter)
 	{
 		Parameters p = new Parameters();

diff --git a/...ersitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractComplexFhirClient.java b/...ersitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractComplexFhirClient.java
@@ -66,7 +66,7 @@ else if (resource instanceof Encounter e)
 			e.setSubject(patientRef);
 		else if (resource instanceof Immunization i)
 			i.setPatient(patientRef);
-		else if (resource instanceof Medication m)
+		else if (resource instanceof Medication)
 			; // nothing to do
 		else if (resource instanceof MedicationAdministration ma)
 			ma.setSubject(patientRef);
@@ -94,7 +94,7 @@ else if (resource instanceof Encounter e)
 			return Optional.of(e.getSubject());
 		else if (resource instanceof Immunization i)
 			return Optional.of(i.getPatient());
-		else if (resource instanceof Medication m)
+		else if (resource instanceof Medication)
 			return Optional.empty();
 		else if (resource instanceof MedicationAdministration ma)
 			return Optional.of(ma.getSubject());
@@ -198,8 +198,8 @@ protected Optional<Patient> findPatientInLocalFhirStore(String pseudonym)
 		}
 		catch (Exception e)
 		{
-			logger.warn("Error while searching for Patient with pseudonym " + NAMING_SYSTEM_NUM_CODEX_CRR_PSEUDONYM
-					+ "|" + pseudonym, e);
+			logger.warn("Error while searching for Patient with pseudonym {}|{}", NAMING_SYSTEM_NUM_CODEX_CRR_PSEUDONYM,
+					pseudonym, e);
 			throw e;
 		}
 	}

diff --git a/...rk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClient.java b/...rk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClient.java
@@ -636,7 +636,7 @@ public Optional<Patient> getPatient(String reference)
 				logger.warn("Patient {} not found: {} - {}", reference, e.getClass().getName(), e.getMessage());
 
 				if (logger.isDebugEnabled())
-					logger.debug("Error while reading patient " + reference, e);
+					logger.debug("Error while reading patient {}", reference, e);
 
 				return Optional.empty();
 			}
@@ -653,6 +653,8 @@ public void updatePatient(Patient patient)
 		Objects.requireNonNull(patient, "patient");
 
 		String id = patient.getIdElement().toVersionless().getValue();
+		// set the patient id to versionless id to workaround a `If-Match`-header bug in hapi fhir client
+		patient.setId(id);
 		logger.info("Updating patient {}", id);
 
 		try
@@ -682,7 +684,7 @@ public void updatePatient(Patient patient)
 		}
 		catch (Exception e)
 		{
-			logger.warn("Could not update patient " + id, e);
+			logger.warn("Could not update patient {}", id, e);
 			throw e;
 		}
 	}

diff --git a/...werk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/FhirBridgeClient.java b/...werk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/FhirBridgeClient.java
@@ -167,7 +167,7 @@ private Optional<Patient> update(Patient existingPatient, Patient newPatient, St
 		}
 		catch (Exception e)
 		{
-			logger.warn("Could not update patient " + newPatient.getIdElement().toString(), e);
+			logger.warn("Could not update patient {}", newPatient.getIdElement().toString(), e);
 			throw e;
 		}
 	}
@@ -230,7 +230,7 @@ private Optional<Patient> create(Patient newPatient, String pseudonym, String bu
 		}
 		catch (Exception e)
 		{
-			logger.warn("Could not create patient " + newPatient.getIdElement().toString(), e);
+			logger.warn("Could not create patient {}", newPatient.getIdElement().toString(), e);
 			throw e;
 		}
 	}
@@ -318,7 +318,7 @@ private Optional<Resource> findResourceInLocalFhirStore(String url, Class<? exte
 		}
 		catch (Exception e)
 		{
-			logger.warn("Error while searching for Resource with url " + url, e);
+			logger.warn("Error while searching for Resource with url {}", url, e);
 			throw e;
 		}
 	}
@@ -426,8 +426,8 @@ else if (outcome.getOperationOutcome() != null && outcome.getOperationOutcome()
 		}
 		catch (Exception e)
 		{
-			logger.warn("Count not update " + newResource.getResourceType().name() + " "
-					+ newResource.getIdElement().toString(), e);
+			logger.warn("Count not update {} {}", newResource.getResourceType().name(),
+					newResource.getIdElement().toString(), e);
 			throw e;
 		}
 	}
@@ -497,8 +497,8 @@ else if (outcome.getOperationOutcome() != null && outcome.getOperationOutcome()
 		}
 		catch (Exception e)
 		{
-			logger.warn("Could not create " + newResource.getResourceType().name() + " "
-					+ newResource.getIdElement().toString(), e);
+			logger.warn("Could not create {} {}", newResource.getResourceType().name(),
+					newResource.getIdElement().toString(), e);
 			throw e;
 		}
 	}

diff --git a/...zwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/DecryptData.java b/...zwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/DecryptData.java
@@ -67,7 +67,7 @@ protected void doExecute(DelegateExecution execution, Variables variables) throw
 		catch (InvalidKeyException | BadPaddingException | IllegalBlockSizeException | NoSuchPaddingException
 				| NoSuchAlgorithmException | InvalidAlgorithmParameterException | IOException e)
 		{
-			logger.warn("Unable to decrypt data from DIC: " + e.getMessage(), e);
+			logger.warn("Unable to decrypt data from DIC: {}", e.getMessage(), e);
 			throw new BpmnError(CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_DECRYPTION_OF_DATA_FROM_DIC_FAILED,
 					"Error while decrypting data from DIC");
 		}

diff --git a/...iversitaetsmedizin/codex/processes/data_transfer/service/receive/DownloadDataFromDts.java b/...iversitaetsmedizin/codex/processes/data_transfer/service/receive/DownloadDataFromDts.java
@@ -44,7 +44,7 @@ protected void doExecute(DelegateExecution execution, Variables variables) throw
 		}
 		catch (Exception e)
 		{
-			logger.warn("Error while reading Binary resoruce: " + e.getMessage(), e);
+			logger.warn("Error while reading Binary resoruce: {}", e.getMessage(), e);
 
 			throw new BpmnError(
 					CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_DOWNLOAD_OF_ENCRYPTED_DATA_FROM_DTS_FAILED,

diff --git a/...rsitaetsmedizin/codex/processes/data_transfer/service/receive/EncryptValidationError.java b/...rsitaetsmedizin/codex/processes/data_transfer/service/receive/EncryptValidationError.java
@@ -58,7 +58,7 @@ protected void doExecute(DelegateExecution execution, Variables variables) throw
 				| InvalidAlgorithmParameterException | IllegalBlockSizeException | BadPaddingException
 				| ShortBufferException e)
 		{
-			logger.warn("Unable to encrypt validation error for DIC: " + e.getMessage(), e);
+			logger.warn("Unable to encrypt validation error for DIC: {}", e.getMessage(), e);
 			throw new BpmnError(
 					CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_ECRYPTION_OF_VALIDATION_ERROR_FOR_DIC_FAILED,
 					"Unable to encrypt validation error for DIC");

diff --git a/...aetsmedizin/codex/processes/data_transfer/service/receive/StoreValidationErrorForDts.java b/...aetsmedizin/codex/processes/data_transfer/service/receive/StoreValidationErrorForDts.java
@@ -15,7 +15,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import ca.uhn.fhir.context.FhirContext;
+import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.logging.DataLogger;
 import dev.dsf.bpe.v1.ProcessPluginApi;
 import dev.dsf.bpe.v1.activity.AbstractServiceDelegate;
 import dev.dsf.bpe.v1.constants.NamingSystems;
@@ -26,12 +26,14 @@ public class StoreValidationErrorForDts extends AbstractServiceDelegate
 	private static final Logger logger = LoggerFactory.getLogger(StoreValidationErrorForDts.class);
 
 	private final String dtsIdentifierValue;
+	private final DataLogger dataLogger;
 
-	public StoreValidationErrorForDts(ProcessPluginApi api, String dtsIdentifierValue)
+	public StoreValidationErrorForDts(ProcessPluginApi api, String dtsIdentifierValue, DataLogger dataLogger)
 	{
 		super(api);
 
 		this.dtsIdentifierValue = dtsIdentifierValue;
+		this.dataLogger = dataLogger;
 	}
 
 	@Override
@@ -40,6 +42,7 @@ public void afterPropertiesSet() throws Exception
 		super.afterPropertiesSet();
 
 		Objects.requireNonNull(dtsIdentifierValue, "dtsIdentifierValue");
+		Objects.requireNonNull(dataLogger, "dataLogger");
 	}
 
 	@Override
@@ -72,8 +75,8 @@ private IdType createBinaryResource(Binary binary)
 		}
 		catch (Exception e)
 		{
-			logger.debug("Binary to create {}", FhirContext.forR4().newJsonParser().encodeResourceToString(binary));
-			logger.warn("Error while creating Binary resource: " + e.getMessage(), e);
+			dataLogger.logData("Binary to create", binary);
+			logger.warn("Error while creating Binary resource: {}", e.getMessage(), e);
 
 			throw new BpmnError(
 					CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_UNABLE_TO_STORE_ECRYPTED_VALIDATION_ERROR,

diff --git a/...aetsmedizin/codex/processes/data_transfer/service/send/DecryptValidationErrorFromDts.java b/...aetsmedizin/codex/processes/data_transfer/service/send/DecryptValidationErrorFromDts.java
@@ -49,7 +49,7 @@ protected void doExecute(DelegateExecution execution, Variables variables) throw
 		catch (InvalidKeyException | NoSuchAlgorithmException | NoSuchPaddingException
 				| InvalidAlgorithmParameterException | IllegalBlockSizeException | BadPaddingException | IOException e)
 		{
-			logger.warn("Unable to decrypt validation error from CRR: " + e.getMessage(), e);
+			logger.warn("Unable to decrypt validation error from CRR: {}", e.getMessage(), e);
 			throw new BpmnError(
 					CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_DECRYPTION_OF_VALIDATION_ERROR_FROM_CRR_FAILED,
 					"Error while decrypting validation error from CRR");

diff --git a/...etsmedizin/codex/processes/data_transfer/service/send/DownloadValidationErrorFromDts.java b/...etsmedizin/codex/processes/data_transfer/service/send/DownloadValidationErrorFromDts.java
@@ -57,7 +57,7 @@ protected void doExecute(DelegateExecution execution, Variables variables) throw
 		}
 		catch (Exception e)
 		{
-			logger.warn("Error while reading Binary resoruce: " + e.getMessage(), e);
+			logger.warn("Error while reading Binary resoruce: {}", e.getMessage(), e);
 
 			throw new BpmnError(
 					CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_DOWNLOAD_OF_ENCRYPTED_VALIDATION_ERROR_FROM_DTS_FAILED,

diff --git a/...netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/EncryptData.java b/...netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/EncryptData.java
@@ -88,7 +88,7 @@ protected void doExecute(DelegateExecution execution, dev.dsf.bpe.v1.variables.V
 				| InvalidAlgorithmParameterException | IllegalBlockSizeException | BadPaddingException
 				| ShortBufferException | IOException e)
 		{
-			logger.warn("Unable to encrypt data for CRR: " + e.getMessage(), e);
+			logger.warn("Unable to encrypt data for CRR: {}", e.getMessage(), e);
 			throw new BpmnError(CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_ECRYPTION_OF_DATA_FOR_CRR_FAILED,
 					"Unable to encrypt data for CRR");
 		}