Merge branch 'release/0.3.0' into main

Conflicts: codex-process-data-transfer/pom.xml codex-processes-ap1-test-data-generator/pom.xml pom.xml
num-codex · Jun 2, 2021 · 9e561fd · 9e561fd
2 parents d1d5a65 + 77f3a95
commit 9e561fd
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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>0.2.2</version>
+		<version>0.3.0</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
@@ -4,47 +4,51 @@
 
 public interface ConstantsDataTransfer
 {
-	String BPMN_EXECUTION_VARIABLE_PSEUDONYMS_LIST = "pseudonyms";
+	String BPMN_EXECUTION_VARIABLE_PATIENT_REFERENCE_LIST = "patientReferenceList";
+	String BPMN_EXECUTION_VARIABLE_PATIENT_REFERENCE = "patientReference";
 	String BPMN_EXECUTION_VARIABLE_PSEUDONYM = "pseudonym";
 	String BPMN_EXECUTION_VARIABLE_STOP_TIMER = "stopTimer";
 	String BPMN_EXECUTION_VARIABLE_LAST_EXPORT_TO = "lastExportTo";
 	String BPMN_EXECUTION_VARIABLE_EXPORT_FROM = "exportFrom";
 	String BPMN_EXECUTION_VARIABLE_EXPORT_FROM_PRECISION = "exportFromPrecision";
 	String BPMN_EXECUTION_VARIABLE_EXPORT_TO = "exportTo";
 	String BPMN_EXECUTION_VARIABLE_BUNDLE = "bundle";
+	String BPMN_EXECUTION_VARIABLE_IDAT_MERGE_GRANTED = "idatMergeGranted";
 	String BPMN_EXECUTION_VARIABLE_USAGE_AND_TRANSFER_GRANTED = "usageAndTransferGranted";
 	String BPMN_EXECUTION_VARIABLE_BINARY_URL = "binaryUrl";
 
-	String NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM = "http://netzwerk-universitaetsmedizin.de/fhir/NamingSystem/dic-pseudonym";
-	String NAMING_SYSTEM_NUM_CODEX_CRR_PSEUDONYM = "http://netzwerk-universitaetsmedizin.de/fhir/NamingSystem/crr-pseudonym";
+	String NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM = "http://www.netzwerk-universitaetsmedizin.de/sid/dic-pseudonym";
+	String NAMING_SYSTEM_NUM_CODEX_CRR_PSEUDONYM = "http://www.netzwerk-universitaetsmedizin.de/sid/crr-pseudonym";
+	String NAMING_SYSTEM_NUM_CODEX_BLOOM_FILTER = "http://www.netzwerk-universitaetsmedizin.de/sid/bloom-filter";
 
-	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER = "http://netzwerk-universitaetsmedizin.de/fhir/CodeSystem/data-transfer";
+	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER = "http://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/data-transfer";
+	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_PATIENT = "patient";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_PSEUDONYM = "pseudonym";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_EXPORT_FROM = "export-from";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_EXPORT_TO = "export-to";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE = "data-reference";
 
-	String PROFILE_NUM_CODEX_TASK_START_DATA_TRIGGER = "http://netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/task-start-data-trigger";
-	String PROFILE_NUM_CODEX_TASK_STOP_DATA_TRIGGER = "http://netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/task-stop-data-trigger";
+	String PROFILE_NUM_CODEX_TASK_START_DATA_TRIGGER = "http://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/task-start-data-trigger";
+	String PROFILE_NUM_CODEX_TASK_STOP_DATA_TRIGGER = "http://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/task-stop-data-trigger";
 	String PROFILE_NUM_CODEX_TASK_DATA_TRIGGER_PROCESS_URI = "http://highmed.org/bpe/Process/dataTrigger/";
 	String PROFILE_NUM_CODEX_TASK_DATA_TRIGGER_PROCESS_URI_AND_LATEST_VERSION = PROFILE_NUM_CODEX_TASK_DATA_TRIGGER_PROCESS_URI
 			+ VERSION;
 	String PROFILE_NUM_CODEX_TASK_START_DATA_TRIGGER_MESSAGE_NAME = "startDataTrigger";
 	String PROFILE_NUM_CODEX_TASK_STOP_DATA_TRIGGER_MESSAGE_NAME = "stopDataTrigger";
 
-	String PROFILE_NUM_CODEX_TASK_START_DATA_SEND = "http://netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/task-start-data-send";
+	String PROFILE_NUM_CODEX_TASK_START_DATA_SEND = "http://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/task-start-data-send";
 	String PROFILE_NUM_CODEX_TASK_DATA_SEND_PROCESS_URI = "http://highmed.org/bpe/Process/dataSend/";
 	String PROFILE_NUM_CODEX_TASK_DATA_SEND_PROCESS_URI_AND_LATEST_VERSION = PROFILE_NUM_CODEX_TASK_DATA_SEND_PROCESS_URI
 			+ VERSION;
 	String PROFILE_NUM_CODEX_TASK_START_DATA_SEND_MESSAGE_NAME = "startDataSend";
 
-	String PROFILE_NUM_CODEX_TASK_START_DATA_TRANSLATE = "http://netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/task-start-data-translate";
+	String PROFILE_NUM_CODEX_TASK_START_DATA_TRANSLATE = "http://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/task-start-data-translate";
 	String PROFILE_NUM_CODEX_TASK_DATA_TRANSLATE_PROCESS_URI = "http://highmed.org/bpe/Process/dataTranslate/";
 	String PROFILE_NUM_CODEX_TASK_DATA_TRANSLATE_PROCESS_URI_AND_LATEST_VERSION = PROFILE_NUM_CODEX_TASK_DATA_TRANSLATE_PROCESS_URI
 			+ VERSION;
 	String PROFILE_NUM_CODEX_TASK_START_DATA_TRANSLATE_MESSAGE_NAME = "startDataTranslate";
 
-	String PROFILE_NUM_CODEX_TASK_START_DATA_RECEIVE = "http://netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/task-start-data-receive";
+	String PROFILE_NUM_CODEX_TASK_START_DATA_RECEIVE = "http://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/task-start-data-receive";
 	String PROFILE_NUM_CODEX_TASK_DATA_RECEIVE_PROCESS_URI = "http://highmed.org/bpe/Process/dataReceive/";
 	String PROFILE_NUM_CODEX_TASK_DATA_RECEIVE_PROCESS_URI_AND_LATEST_VERSION = PROFILE_NUM_CODEX_TASK_DATA_RECEIVE_PROCESS_URI
 			+ VERSION;

diff --git a/...iversitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java b/...iversitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java
@@ -20,7 +20,7 @@
 
 public class DataTransferProcessPluginDefinition implements ProcessPluginDefinition
 {
-	public static final String VERSION = "0.2.2";
+	public static final String VERSION = "0.3.0";
 
 	@Override
 	public String getName()
@@ -58,6 +58,7 @@ public ResourceProvider getResourceProvider(FhirContext fhirContext, ClassLoader
 
 		var nD = NamingSystemResource.file("fhir/NamingSystem/num-codex-dic-pseudonym-identifier.xml");
 		var nC = NamingSystemResource.file("fhir/NamingSystem/num-codex-crr-pseudonym-identifier.xml");
+		var nB = NamingSystemResource.file("fhir/NamingSystem/num-codex-bloom-filter-identifier.xml");
 
 		var sTstaDtri = StructureDefinitionResource
 				.file("fhir/StructureDefinition/num-codex-task-start-data-trigger.xml");
@@ -73,7 +74,7 @@ public ResourceProvider getResourceProvider(FhirContext fhirContext, ClassLoader
 
 		Map<String, List<AbstractResource>> resourcesByProcessKeyAndVersion = Map.of( //
 				"dataTrigger/" + VERSION, Arrays.asList(aTri, cD, nD, sTstaDtri, sTstoDtri, vD), //
-				"dataSend/" + VERSION, Arrays.asList(aSen, cD, nD, sTstaDsen, vD), //
+				"dataSend/" + VERSION, Arrays.asList(aSen, cD, nD, nB, sTstaDsen, vD), //
 				"dataTranslate/" + VERSION, Arrays.asList(aTra, cD, nD, nC, sTstaDtra, vD), //
 				"dataReceive/" + VERSION, Arrays.asList(aRec, cD, nC, sTstaDrec, vD));
 

diff --git a/...medizin/codex/processes/data_transfer/client/ApacheRestfulClientFactoryWithTlsConfig.java b/...medizin/codex/processes/data_transfer/client/ApacheRestfulClientFactoryWithTlsConfig.java
@@ -63,7 +63,7 @@ public ApacheRestfulClientFactoryWithTlsConfig(FhirContext fhirContext, KeyStore
 	@Override
 	protected synchronized ApacheHttpClient getHttpClient(String theServerBase)
 	{
-		logger.info("Returning new ApacheHttpClient for ServerNase {}", theServerBase);
+		logger.info("Returning new ApacheHttpClient for ServerBase {}", theServerBase);
 
 		return new ApacheHttpClient(getNativeHttpClient(), new StringBuilder(theServerBase), null, null, null, null);
 	}
@@ -136,7 +136,7 @@ protected void resetHttpClient()
 
 	/**
 	 * Only allows to set an instance of type org.apache.http.client.HttpClient
-	 * 
+	 *
 	 * @see ca.uhn.fhir.rest.client.api.IRestfulClientFactory#setHttpClient(Object)
 	 */
 	@Override

diff --git a/.../de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/ConsentClient.java b/.../de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/ConsentClient.java
@@ -4,5 +4,7 @@
 
 public interface ConsentClient
 {
-	List<String> getConsentOidsFor(String dicSourceAndPseudonym);
+	List<String> getConsentOidsForIdentifierReference(String dicSourceAndPseudonym);
+
+	List<String> getConsentOidsForAbsoluteReference(String reference);
 }
diff --git a/...zwerk_universitaetsmedizin/codex/processes/data_transfer/client/ConsentClientFactory.java b/...zwerk_universitaetsmedizin/codex/processes/data_transfer/client/ConsentClientFactory.java
@@ -1,7 +1,8 @@
 package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client;
 
-import java.util.Arrays;
 import java.util.List;
+import java.util.stream.Collectors;
+import java.util.stream.IntStream;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -10,18 +11,26 @@ public class ConsentClientFactory
 {
 	private static final Logger logger = LoggerFactory.getLogger(ConsentClientFactory.class);
 
-	private static final String BASE_OID = "2.16.840.1.113883.3.1937.777";
+	private static final String BASE_OID = "2.16.840.1.113883.3.1937.777.24.5.3";
+	private static final List<String> ALL_POLICIES = IntStream.of(1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 34, 35, 36)
+			.mapToObj(i -> BASE_OID + "." + i).collect(Collectors.toList());
 
 	public ConsentClient getConsentClient()
 	{
 		return new ConsentClient()
 		{
 			@Override
-			public List<String> getConsentOidsFor(String dicSourceAndPseudonym)
+			public List<String> getConsentOidsForIdentifierReference(String dicSourceAndPseudonym)
 			{
 				logger.warn("Returning 'all allowed' OIDs for DIC pseudonym {}", dicSourceAndPseudonym);
+				return ALL_POLICIES;
+			}
 
-				return Arrays.asList(BASE_OID + ".24.5.1.1", BASE_OID + ".24.5.1.34", BASE_OID + ".24.5.1.37");
+			@Override
+			public List<String> getConsentOidsForAbsoluteReference(String reference)
+			{
+				logger.warn("Returning 'all allowed' OIDs for absolute patient reference {}", reference);
+				return ALL_POLICIES;
 			}
 		};
 	}

diff --git a/...ava/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FhirClient.java b/...ava/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FhirClient.java
@@ -1,13 +1,15 @@
 package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client;
 
 import java.util.Date;
+import java.util.Optional;
 import java.util.stream.Stream;
 
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.DomainResource;
+import org.hl7.fhir.r4.model.Patient;
 
 import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.domain.DateWithPrecision;
-import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.variables.PseudonymList;
+import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.variables.PatientReferenceList;
 
 public interface FhirClient
 {
@@ -18,7 +20,7 @@ public interface FhirClient
 	 *            not <code>null</code>
 	 * @return
 	 */
-	PseudonymList getPseudonymsWithNewData(DateWithPrecision exportFrom, Date exportTo);
+	PatientReferenceList getPatientReferencesWithNewData(DateWithPrecision exportFrom, Date exportTo);
 
 	/**
 	 * @param pseudonym
@@ -32,4 +34,19 @@ public interface FhirClient
 	Stream<DomainResource> getNewData(String pseudonym, DateWithPrecision exportFrom, Date exportTo);
 
 	void storeBundle(Bundle bundle);
+
+	/**
+	 * @param reference
+	 *            Absolute reference, not <code>null</code>
+	 * @return
+	 */
+	Optional<Patient> getPatient(String reference);
+
+	/**
+	 * @param patient
+	 *            containing an identifier with system
+	 *            {@link de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer#NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM}
+	 *            not <code>null</code>
+	 */
+	void updatePatient(Patient patient);
 }
diff --git a/...netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FhirClientFactory.java b/...netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FhirClientFactory.java
@@ -1,15 +1,19 @@
 package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client;
 
+import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM;
+
 import java.nio.file.Path;
-import java.util.Arrays;
 import java.util.Date;
+import java.util.List;
+import java.util.Optional;
 import java.util.UUID;
 import java.util.stream.Stream;
 
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Condition;
 import org.hl7.fhir.r4.model.DomainResource;
 import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Reference;
@@ -19,7 +23,8 @@
 import ca.uhn.fhir.context.FhirContext;
 import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer;
 import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.domain.DateWithPrecision;
-import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.variables.PseudonymList;
+import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.variables.PatientReference;
+import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.variables.PatientReferenceList;
 
 public class FhirClientFactory
 {
@@ -66,10 +71,16 @@ public void storeBundle(Bundle bundle)
 			}
 
 			@Override
-			public PseudonymList getPseudonymsWithNewData(DateWithPrecision exportFrom, Date exportTo)
+			public PatientReferenceList getPatientReferencesWithNewData(DateWithPrecision exportFrom, Date exportTo)
 			{
 				logger.warn("Returning demo pseudonyms for {}", localIdentifierValue);
-				return new PseudonymList(Arrays.asList("dic_foo/bar", "dic_foo/baz"));
+				return new PatientReferenceList(List.of(
+						PatientReference.from(new Identifier().setSystem(NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM)
+								.setValue("dic_foo/bar")),
+						PatientReference.from(new Identifier().setSystem(NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM)
+								.setValue("dic_foo/baz")),
+						PatientReference.from("http://dic-foo/fhir/Patient/3"),
+						PatientReference.from("http://dic-foo/fhir/Patient/4")));
 			}
 
 			@Override
@@ -78,8 +89,7 @@ public Stream<DomainResource> getNewData(String pseudonym, DateWithPrecision exp
 				logger.warn("Returning demo resources for {}", pseudonym);
 
 				Patient p = fhirContext.newJsonParser().parseResource(Patient.class, patient);
-				p.addIdentifier().setSystem(ConstantsDataTransfer.NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM)
-						.setValue(pseudonym);
+				p.addIdentifier().setSystem(NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM).setValue(pseudonym);
 				p.setIdElement(new IdType("Patient", UUID.randomUUID().toString()));
 
 				Condition c = fhirContext.newJsonParser().parseResource(Condition.class, condition);
@@ -90,6 +100,22 @@ public Stream<DomainResource> getNewData(String pseudonym, DateWithPrecision exp
 
 				return Stream.of(p, c, o);
 			}
+
+			@Override
+			public Optional<Patient> getPatient(String reference)
+			{
+				Patient patient = fhirContext.newJsonParser().parseResource(Patient.class, FhirClientFactory.patient);
+				patient.addIdentifier().setSystem(ConstantsDataTransfer.NAMING_SYSTEM_NUM_CODEX_BLOOM_FILTER).setValue(
+						"J75gYl+RiKSsxeu33tixBEEtFGCZwIEsWIKgvESaluvpSGBte/SBNZilz+sLSZdHSDKTL2J2d1yZsakqjtV5U2SMMJZ5IF3gEk1MT3sCRkxXEo1aJWKpnqndUTR+fvtSeMFj0y/O5yqrLV9zU79CNiTfZN5t1/6XGxZUXq2DovfCRrrpRxWjFwjKIDo0OkRANf7Mqp+Fsu0Un53JF57p/p1RLpWcJkC3xO+UslGbDo3mjgczdvxz0aLmWNA7/NIhk+Q50gxCX3B4QrntPfLLlBkrmIpsKRcLFVuYZik7pYZ9prd0qCLQ9tc8qiw1ry5kMfIvLnIS/FV36w==");
+				patient.setIdElement(new IdType("Patient", UUID.randomUUID().toString()));
+				return Optional.of(patient);
+			}
+
+			@Override
+			public void updatePatient(Patient patient)
+			{
+				// Nothing to do in stub client
+			}
 		};
 	}
 }