Merge remote-tracking branch 'origin/release/0.5.1' into main

highmed · Sep 2, 2021 · 769747a · 769747a
2 parents d9daa3c + ad2b00b
commit 769747a
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diff --git a/CITATION.cff b/CITATION.cff
@@ -6,8 +6,8 @@ authors:
   - family-names: Wettstein
     given-names: Reto
 title: "HiGHmed Data Sharing Framework (HiGHmed DSF)"
-version: 0.5.0
-date-released: 2021-08-24
+version: 0.5.1
+date-released: 2021-09-03
 url: https://github.com/highmed/highmed-dsf/wiki
 repository-code: https://github.com/highmed/highmed-dsf
 repository-artifact: https://github.com/highmed/highmed-dsf/releases

diff --git a/dsf-bpe/dsf-bpe-process-base/pom.xml b/dsf-bpe/dsf-bpe-process-base/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/...f-bpe-process-base/src/main/java/org/highmed/dsf/fhir/resources/ResourceProviderImpl.java b/...f-bpe-process-base/src/main/java/org/highmed/dsf/fhir/resources/ResourceProviderImpl.java
@@ -279,7 +279,7 @@ private static <T extends MetadataResource> T parseResourceAndSetVersion(String
 			Supplier<IParser> parserSupplier, ClassLoader classLoader, PropertyResolver resolver, String fileName,
 			Class<T> type)
 	{
-		logger.debug("Reading {} from {} and replacing all occurrence of {} with {}", type.getSimpleName(), fileName,
+		logger.debug("Reading {} from {} and replacing all occurrences of {} with {}", type.getSimpleName(), fileName,
 				VERSION_PATTERN_STRING, processPluginVersion);
 
 		try (InputStream in = classLoader.getResourceAsStream(fileName))

diff --git a/dsf-bpe/dsf-bpe-server-jetty/pom.xml b/dsf-bpe/dsf-bpe-server-jetty/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-server/pom.xml b/dsf-bpe/dsf-bpe-server/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/fhir/task/TaskHandler.java b/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/fhir/task/TaskHandler.java
@@ -190,7 +190,7 @@ private ProcessDefinition getProcessDefinition(String processDomain, String proc
 		if (processVersion != null && !processVersion.isBlank())
 			return repositoryService.createProcessDefinitionQuery()
 					.processDefinitionKey(processDomain + "_" + processDefinitionKey).versionTag(processVersion)
-					.latestVersion().singleResult();
+					.singleResult();
 		else
 			return repositoryService.createProcessDefinitionQuery()
 					.processDefinitionKey(processDomain + "_" + processDefinitionKey).latestVersion().singleResult();

diff --git a/dsf-bpe/dsf-bpe-webservice-client/pom.xml b/dsf-bpe/dsf-bpe-webservice-client/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<dependencies>

diff --git a/dsf-bpe/pom.xml b/dsf-bpe/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<modules>

diff --git a/dsf-fhir/dsf-fhir-auth/pom.xml b/dsf-fhir/dsf-fhir-auth/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-fhir/dsf-fhir-rest-adapter/pom.xml b/dsf-fhir/dsf-fhir-rest-adapter/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-fhir/dsf-fhir-server-jetty/pom.xml b/dsf-fhir/dsf-fhir-server-jetty/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-fhir/dsf-fhir-server/pom.xml b/dsf-fhir/dsf-fhir-server/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/...ir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/OrganizationAffiliationDaoJdbc.java b/...ir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/OrganizationAffiliationDaoJdbc.java
@@ -72,7 +72,7 @@ public List<OrganizationAffiliation> readActiveNotDeletedByMemberOrganizationIde
 			{
 				List<OrganizationAffiliation> affiliations = new ArrayList<>();
 
-				if (result.next())
+				while (result.next())
 				{
 					OrganizationAffiliation oA = getResource(result, 1);
 					String organizationIdentifier = result.getString(2);

diff --git a/...sf-fhir-server/src/test/java/org/highmed/dsf/fhir/dao/OrganizationAffiliationDaoTest.java b/...sf-fhir-server/src/test/java/org/highmed/dsf/fhir/dao/OrganizationAffiliationDaoTest.java
@@ -1,10 +1,12 @@
 package org.highmed.dsf.fhir.dao;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 
 import java.sql.Connection;
+import java.sql.SQLException;
 import java.util.List;
 import java.util.UUID;
 
@@ -70,38 +72,21 @@ public void testReadActiveNotDeletedByMemberOrganizationIdentifier() throws Exce
 
 		try (Connection connection = getDao().newReadWriteTransaction())
 		{
-			Organization memberOrg = new Organization();
-			memberOrg.setActive(true);
-			memberOrg.addIdentifier().setSystem(identifierSystem).setValue(identifierValue);
+			Organization memberOrg = createAndStoreOrganizationInDb(identifierValue, connection);
+			Organization parentOrg = createAndStoreOrganizationInDb(parentIdentifier, connection);
 
-			Organization parentOrg = new Organization();
-			parentOrg.setActive(true);
-			parentOrg.addIdentifier().setSystem(identifierSystem).setValue(parentIdentifier);
-
-			Organization createdMemberOrg = organizationDao.createWithTransactionAndId(connection, memberOrg,
-					UUID.randomUUID());
-
-			Organization createdParentOrg = organizationDao.createWithTransactionAndId(connection, parentOrg,
-					UUID.randomUUID());
-
-			OrganizationAffiliation affiliation = new OrganizationAffiliation();
-			affiliation.setActive(true);
-			affiliation.getParticipatingOrganization()
-					.setReference("Organization/" + createdMemberOrg.getIdElement().getIdPart());
-			affiliation.getOrganization().setReference("Organization/" + createdParentOrg.getIdElement().getIdPart());
-
-			OrganizationAffiliation createdAffiliation = getDao().createWithTransactionAndId(connection, affiliation,
-					UUID.randomUUID());
+			OrganizationAffiliation affiliation = createAndStoreOrganizationAffiliationInDb(parentOrg, memberOrg,
+					connection);
 
 			List<OrganizationAffiliation> affiliations = getDao()
 					.readActiveNotDeletedByMemberOrganizationIdentifierIncludingOrganizationIdentifiersWithTransaction(
 							connection, identifierValue);
 			assertNotNull(affiliations);
 			assertEquals(1, affiliations.size());
-			assertEquals(createdAffiliation.getIdElement().getIdPart(), affiliations.get(0).getIdElement().getIdPart());
+			assertEquals(affiliation.getIdElement().getIdPart(), affiliations.get(0).getIdElement().getIdPart());
 			assertTrue(affiliations.get(0).hasParticipatingOrganization());
 			assertTrue(affiliations.get(0).getParticipatingOrganization().hasReference());
-			assertEquals("Organization/" + createdMemberOrg.getIdElement().getIdPart(),
+			assertEquals("Organization/" + memberOrg.getIdElement().getIdPart(),
 					affiliations.get(0).getParticipatingOrganization().getReference());
 			assertTrue(affiliations.get(0).getParticipatingOrganization().hasIdentifier());
 			assertTrue(affiliations.get(0).getParticipatingOrganization().getIdentifier().hasSystem());
@@ -112,7 +97,7 @@ public void testReadActiveNotDeletedByMemberOrganizationIdentifier() throws Exce
 					affiliations.get(0).getParticipatingOrganization().getIdentifier().getValue());
 			assertTrue(affiliations.get(0).hasOrganization());
 			assertTrue(affiliations.get(0).getOrganization().hasReference());
-			assertEquals("Organization/" + createdParentOrg.getIdElement().getIdPart(),
+			assertEquals("Organization/" + parentOrg.getIdElement().getIdPart(),
 					affiliations.get(0).getOrganization().getReference());
 			assertTrue(affiliations.get(0).getOrganization().hasIdentifier());
 			assertTrue(affiliations.get(0).getOrganization().getIdentifier().hasSystem());
@@ -122,6 +107,62 @@ public void testReadActiveNotDeletedByMemberOrganizationIdentifier() throws Exce
 		}
 	}
 
+	@Test
+	public void testSizeOfReadActiveNotDeletedByMemberOrganizationIdentifier() throws Exception
+	{
+		final String parentFooIdentifier = "parentFoo.org";
+		final String parentBarIdentifier = "parentBar.org";
+
+		try (Connection connection = getDao().newReadWriteTransaction())
+		{
+			Organization memberOrg = createAndStoreOrganizationInDb(identifierValue, connection);
+			Organization parentFooOrg = createAndStoreOrganizationInDb(parentFooIdentifier, connection);
+			Organization parentBarOrg = createAndStoreOrganizationInDb(parentBarIdentifier, connection);
+
+			createAndStoreOrganizationAffiliationInDb(parentFooOrg, memberOrg, connection);
+			createAndStoreOrganizationAffiliationInDb(parentBarOrg, memberOrg, connection);
+
+			List<OrganizationAffiliation> affiliations = getDao()
+					.readActiveNotDeletedByMemberOrganizationIdentifierIncludingOrganizationIdentifiersWithTransaction(
+							connection, identifierValue);
+			assertNotNull(affiliations);
+
+			assertEquals(2, affiliations.size());
+			assertEquals(identifierValue,
+					affiliations.get(0).getParticipatingOrganization().getIdentifier().getValue());
+			assertEquals(identifierValue,
+					affiliations.get(1).getParticipatingOrganization().getIdentifier().getValue());
+			assertNotEquals(affiliations.get(0).getOrganization().getIdentifier().getValue(),
+					affiliations.get(1).getOrganization().getIdentifier().getValue());
+			assertTrue(List.of(parentFooIdentifier, parentBarIdentifier)
+					.contains(affiliations.get(0).getOrganization().getIdentifier().getValue()));
+			assertTrue(List.of(parentFooIdentifier, parentBarIdentifier)
+					.contains(affiliations.get(1).getOrganization().getIdentifier().getValue()));
+		}
+	}
+
+	private Organization createAndStoreOrganizationInDb(String identifierValue, Connection connection)
+			throws SQLException
+	{
+		Organization memberOrg = new Organization();
+		memberOrg.setActive(true);
+		memberOrg.addIdentifier().setSystem(identifierSystem).setValue(identifierValue);
+
+		return organizationDao.createWithTransactionAndId(connection, memberOrg, UUID.randomUUID());
+	}
+
+	private OrganizationAffiliation createAndStoreOrganizationAffiliationInDb(Organization parent, Organization member,
+			Connection connection) throws SQLException
+	{
+		OrganizationAffiliation organizationAffiliation = new OrganizationAffiliation();
+		organizationAffiliation.setActive(true);
+		organizationAffiliation.getParticipatingOrganization()
+				.setReference("Organization/" + member.getIdElement().getIdPart());
+		organizationAffiliation.getOrganization().setReference("Organization/" + parent.getIdElement().getIdPart());
+
+		return getDao().createWithTransactionAndId(connection, organizationAffiliation, UUID.randomUUID());
+	}
+
 	@Override
 	@Test
 	public void testReadAccessTriggerAll() throws Exception

diff --git a/dsf-fhir/dsf-fhir-validation/pom.xml b/dsf-fhir/dsf-fhir-validation/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>
@@ -93,7 +93,7 @@
 				</configuration>
 				<!-- Workaround for exec maven plugin issue -->
 				<!-- https://github.com/mojohaus/exec-maven-plugin/issues/76 -->
-				<!-- <dependencies> <dependency> <groupId>org.highmed.dsf</groupId> <artifactId>dsf-tools-bundle-generator</artifactId> <version>0.5.0</version> </dependency> 
+				<!-- <dependencies> <dependency> <groupId>org.highmed.dsf</groupId> <artifactId>dsf-tools-bundle-generator</artifactId> <version>0.5.1</version> </dependency> 
 					</dependencies> -->
 			</plugin>
 		</plugins>

diff --git a/dsf-fhir/dsf-fhir-webservice-client/pom.xml b/dsf-fhir/dsf-fhir-webservice-client/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-fhir/dsf-fhir-websocket-client/pom.xml b/dsf-fhir/dsf-fhir-websocket-client/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-fhir-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-fhir/pom.xml b/dsf-fhir/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<modules>

diff --git a/dsf-mpi/dsf-mpi-client-pdq/pom.xml b/dsf-mpi/dsf-mpi-client-pdq/pom.xml
@@ -9,7 +9,7 @@
 	<parent>
 		<artifactId>dsf-mpi-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-mpi/dsf-mpi-client-stub/pom.xml b/dsf-mpi/dsf-mpi-client-stub/pom.xml
@@ -9,7 +9,7 @@
 	<parent>
 		<artifactId>dsf-mpi-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-mpi/dsf-mpi-client/pom.xml b/dsf-mpi/dsf-mpi-client/pom.xml
@@ -9,7 +9,7 @@
 	<parent>
 		<artifactId>dsf-mpi-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-mpi/pom.xml b/dsf-mpi/pom.xml
@@ -10,7 +10,7 @@
 	<parent>
 		<artifactId>dsf-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<modules>

diff --git a/dsf-openehr/dsf-openehr-client-impl/pom.xml b/dsf-openehr/dsf-openehr-client-impl/pom.xml
@@ -9,7 +9,7 @@
 	<parent>
 		<artifactId>dsf-openehr-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-openehr/dsf-openehr-client-stub/pom.xml b/dsf-openehr/dsf-openehr-client-stub/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<artifactId>dsf-openehr-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-openehr/dsf-openehr-client/pom.xml b/dsf-openehr/dsf-openehr-client/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<artifactId>dsf-openehr-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-openehr/dsf-openehr-model/pom.xml b/dsf-openehr/dsf-openehr-model/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<artifactId>dsf-openehr-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-openehr/pom.xml b/dsf-openehr/pom.xml
@@ -10,7 +10,7 @@
 	<parent>
 		<artifactId>dsf-pom</artifactId>
 		<groupId>org.highmed.dsf</groupId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<modules>

diff --git a/dsf-pseudonymization/dsf-pseudonymization-base/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-base/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-pseudonymization-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>

diff --git a/dsf-pseudonymization/dsf-pseudonymization-medic/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-medic/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-pseudonymization-pom</artifactId>
-		<version>0.5.0</version>
+		<version>0.5.1</version>
 	</parent>
 
 	<properties>