Merge remote-tracking branch 'origin/master' into do-20240916-core-bu…

…mp-6-3-25
hapifhir · Sep 30, 2024 · 2cca8bf · 2cca8bf
2 parents 6dad5f6 + 6bb72e4
commit 2cca8bf
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diff --git a/hapi-deployable-pom/pom.xml b/hapi-deployable-pom/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>7.5.0-SNAPSHOT</version>
+		 <version>7.5.1-SNAPSHOT</version>
 
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>

diff --git a/hapi-fhir-android/pom.xml b/hapi-fhir-android/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-base/pom.xml b/hapi-fhir-base/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-bom/pom.xml b/hapi-fhir-bom/pom.xml
@@ -4,15 +4,15 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>ca.uhn.hapi.fhir</groupId>
 	<artifactId>hapi-fhir-bom</artifactId>
-	<version>7.5.0-SNAPSHOT</version>
+	<version>7.5.1-SNAPSHOT</version>
 
 	<packaging>pom</packaging>
 	<name>HAPI FHIR BOM</name>
 
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-checkstyle/pom.xml b/hapi-fhir-checkstyle/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-cli/hapi-fhir-cli-app/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-cli/pom.xml b/hapi-fhir-cli/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-client-okhttp/pom.xml b/hapi-fhir-client-okhttp/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-client/pom.xml b/hapi-fhir-client/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-converter/pom.xml b/hapi-fhir-converter/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-dist/pom.xml b/hapi-fhir-dist/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-docs/pom.xml b/hapi-fhir-docs/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/...ocs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6261-upgrade-to-jakarta-mail.yaml b/...ocs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6261-upgrade-to-jakarta-mail.yaml
@@ -0,0 +1,5 @@
+---
+type: change
+issue: 6261
+title: "Upgrading to Jakarta had caused a problem with the version of java-simple-mail that was in use. This has been updated to be conformant
+with the Jakarta Mail APIs. Thanks to Thomas Papke(@thopap) for the contribution!"
diff --git a/.../fhir/changelog/7_6_0/6262-fix-cds-hooks-invocation-when-extension-passed-in-request.yaml b/.../fhir/changelog/7_6_0/6262-fix-cds-hooks-invocation-when-extension-passed-in-request.yaml
@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 6262
+title: "Previously, when a `extension` was passed in as a part of the CDS hooks request, it would result in a `400 service not found`. This behaviour has now been fixed."
diff --git a/...cs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6290-mssql-migration-trim-fix.yaml b/...cs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6290-mssql-migration-trim-fix.yaml
@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 6290
+title: "Previously, a specific migration task was using the `TRIM()` function, which does not exist in MSSQL 2012. This was causing migrations targeting MSSQL 2012 to fail. 
+This has been corrected and replaced with usage of a combination of LTRIM() and RTRIM(). Thanks to Primož Delopst at Better for the contribution!"
diff --git a/...hir/changelog/7_6_0/6305-search-missing-qualifier-does-not-work-reference-parameters.yaml b/...hir/changelog/7_6_0/6305-search-missing-qualifier-does-not-work-reference-parameters.yaml
@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 6305
+title: "Previously, when having StorageSettings#getIndexMissingFields() == IndexEnabledEnum.DISABLED (default value) 
+and attempting to search with the missing qualifier against a resource type with multiple search parameters of type reference, 
+the returned results would be incorrect. This has been fixed."
diff --git a/...7_6_0/6317-fix-resource-duplication-for-composite-unique-sp-with-date-time-component.yaml b/...7_6_0/6317-fix-resource-duplication-for-composite-unique-sp-with-date-time-component.yaml
@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 6317
+title: "Previously, defining a unique combo Search Parameter with the DateTime component and submitting multiple 
+resources with the same dateTime element (e.g. Observation.effectiveDateTime) resulted in duplicate resource creation. 
+This has been fixed."
+
diff --git a/hapi-fhir-jacoco/pom.xml b/hapi-fhir-jacoco/pom.xml
@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-jaxrsserver-base/pom.xml b/hapi-fhir-jaxrsserver-base/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-jpa/pom.xml b/hapi-fhir-jpa/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-jpaserver-base/pom.xml b/hapi-fhir-jpaserver-base/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
@@ -1972,7 +1972,7 @@ private void attemptComboUniqueSpProcessing(
 			 * The loop allows us to create multiple combo index joins if there
 			 * are multiple AND expressions for the related parameters.
 			 */
-			while (validateParamValuesAreValidForComboParam(theRequest, theParams, comboParamNames)) {
+			while (validateParamValuesAreValidForComboParam(theRequest, theParams, comboParamNames, comboParam)) {
 				applyComboSearchParam(theQueryStack, theParams, theRequest, comboParamNames, comboParam);
 			}
 		}
@@ -2068,7 +2068,10 @@ private void applyComboSearchParam(
 	 * (e.g. <code>?date=gt2024-02-01</code>), etc.
 	 */
 	private boolean validateParamValuesAreValidForComboParam(
-			RequestDetails theRequest, @Nonnull SearchParameterMap theParams, List<String> theComboParamNames) {
+			RequestDetails theRequest,
+			@Nonnull SearchParameterMap theParams,
+			List<String> theComboParamNames,
+			RuntimeSearchParam theComboParam) {
 		boolean paramValuesAreValidForCombo = true;
 		List<List<IQueryParameterType>> paramOrValues = new ArrayList<>(theComboParamNames.size());
 
@@ -2129,6 +2132,19 @@ private boolean validateParamValuesAreValidForComboParam(
 					break;
 				}
 			}
+
+			// Date params are not eligible for using composite unique index
+			// as index could contain date with different precision (e.g. DAY, SECOND)
+			if (nextParamDef.getParamType() == RestSearchParameterTypeEnum.DATE
+					&& theComboParam.getComboSearchParamType() == ComboSearchParamType.UNIQUE) {
+				ourLog.debug(
+						"Search with params {} is not a candidate for combo searching - "
+								+ "Unique combo search parameter '{}' has DATE type",
+						theComboParamNames,
+						nextParamName);
+				paramValuesAreValidForCombo = false;
+				break;
+			}
 		}
 
 		if (CartesianProductUtil.calculateCartesianProductSize(paramOrValues) > 500) {

diff --git a/.../src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java b/.../src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java
@@ -800,14 +800,19 @@ public Condition createPredicateParamMissingValue(MissingQueryParameterPredicate
 		subquery.addCustomColumns(1);
 		subquery.addFromTable(getTable());
 
+		String resourceType = theParams.getResourceTablePredicateBuilder().getResourceType();
+		RuntimeSearchParam paramDefinition =
+				mySearchParamRegistry.getRuntimeSearchParam(resourceType, theParams.getParamName());
+		List<String> pathList = paramDefinition.getPathsSplitForResourceType(resourceType);
+
 		Condition subQueryCondition = ComboCondition.and(
 				BinaryCondition.equalTo(
 						getResourceIdColumn(),
 						theParams.getResourceTablePredicateBuilder().getResourceIdColumn()),
-				BinaryCondition.equalTo(
-						getResourceTypeColumn(),
-						generatePlaceholder(
-								theParams.getResourceTablePredicateBuilder().getResourceType())));
+				BinaryCondition.equalTo(getResourceTypeColumn(), generatePlaceholder(resourceType)),
+				ComboCondition.or(pathList.stream()
+						.map(path -> BinaryCondition.equalTo(getColumnSourcePath(), generatePlaceholder(path)))
+						.toArray(BinaryCondition[]::new)));
 
 		subquery.addCondition(subQueryCondition);
 

diff --git a/hapi-fhir-jpaserver-elastic-test-utilities/pom.xml b/hapi-fhir-jpaserver-elastic-test-utilities/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

diff --git a/hapi-fhir-jpaserver-hfql/pom.xml b/hapi-fhir-jpaserver-hfql/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

diff --git a/hapi-fhir-jpaserver-ips/pom.xml b/hapi-fhir-jpaserver-ips/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-jpaserver-mdm/pom.xml b/hapi-fhir-jpaserver-mdm/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

diff --git a/hapi-fhir-jpaserver-model/pom.xml b/hapi-fhir-jpaserver-model/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/hapi-fhir-jpaserver-searchparam/pom.xml b/hapi-fhir-jpaserver-searchparam/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/...chparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java b/...chparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
@@ -566,7 +566,8 @@ private Set<String> extractParameterCombinationsForComboParam(
 				for (BaseResourceIndexedSearchParam nextParam : paramsListForCompositePart) {
 					IQueryParameterType nextParamAsClientParam = nextParam.toQueryParameterType();
 
-					if (nextParamAsClientParam instanceof DateParam) {
+					if (theParam.getComboSearchParamType() == ComboSearchParamType.NON_UNIQUE
+							&& nextParamAsClientParam instanceof DateParam) {
 						DateParam date = (DateParam) nextParamAsClientParam;
 						if (date.getPrecision() != TemporalPrecisionEnum.DAY) {
 							continue;

diff --git a/hapi-fhir-jpaserver-subscription/pom.xml b/hapi-fhir-jpaserver-subscription/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 
@@ -70,6 +70,11 @@
 			<artifactId>jakarta.servlet-api</artifactId>
 			<scope>provided</scope>
 		</dependency>
+		<dependency>
+			<groupId>jakarta.mail</groupId>
+			<artifactId>jakarta.mail-api</artifactId>
+			<optional>true</optional>
+		</dependency>
 
 		<!-- test dependencies -->
 		<dependency>

diff --git a/hapi-fhir-jpaserver-test-dstu2/pom.xml b/hapi-fhir-jpaserver-test-dstu2/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/...st-dstu2/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu2Test.java b/...st-dstu2/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu2Test.java
@@ -28,8 +28,8 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeMessage;
+import jakarta.mail.internet.InternetAddress;
+import jakarta.mail.internet.MimeMessage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;

diff --git a/hapi-fhir-jpaserver-test-dstu3/pom.xml b/hapi-fhir-jpaserver-test-dstu3/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.5.0-SNAPSHOT</version>
+		<version>7.5.1-SNAPSHOT</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

diff --git a/...rver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSenderImplTest.java b/...rver-test-dstu3/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSenderImplTest.java
@@ -17,8 +17,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeMessage;
+import jakarta.mail.internet.InternetAddress;
+import jakarta.mail.internet.MimeMessage;
 import java.util.Arrays;
 
 import static org.assertj.core.api.Assertions.assertThat;

diff --git a/...st-dstu3/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu3Test.java b/...st-dstu3/src/test/java/ca/uhn/fhir/jpa/subscription/email/EmailSubscriptionDstu3Test.java
@@ -26,8 +26,8 @@
 import org.junit.jupiter.api.extension.RegisterExtension;
 import org.springframework.beans.factory.annotation.Autowired;
 
-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeMessage;
+import jakarta.mail.internet.InternetAddress;
+import jakarta.mail.internet.MimeMessage;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;