Backport for 7.4.2 (#6303)

* version bumps and change log

* cherry pick 6420

* various updates to changelogs

* build formatting changes

---------

Co-authored-by: jdar <[email protected]>
Co-authored-by: Etienne Poirier <[email protected]>

hapi-deployable-pom/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>7.4.1-SNAPSHOT</version>
+		 <version>7.4.2</version>
 
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TaskChunker.java

@@ -20,10 +20,12 @@
  * #L%
  */
 
+import com.google.common.collect.Streams;
 import jakarta.annotation.Nonnull;
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Iterator;
 import java.util.List;
 import java.util.function.Consumer;
 import java.util.stream.Stream;
@@ -57,4 +59,9 @@ public void chunk(Collection<T> theInput, int theChunkSize, Consumer<List<T>> th
 	public <T> Stream<List<T>> chunk(Stream<T> theStream, int theChunkSize) {
 		return StreamUtil.partition(theStream, theChunkSize);
 	}
+
+	@Nonnull
+	public void chunk(Iterator<T> theIterator, int theChunkSize, Consumer<List<T>> theListConsumer) {
+		chunk(Streams.stream(theIterator), theChunkSize).forEach(theListConsumer);
+	}
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java

@@ -159,7 +159,8 @@ public enum VersionEnum {
 
 	V7_3_0,
 	V7_4_0,
-	V7_4_1;
+	V7_4_1,
+	V7_4_2;
 
 	public static VersionEnum latestVersion() {
 		VersionEnum[] values = VersionEnum.values();

hapi-fhir-base/src/test/java/ca/uhn/fhir/util/TaskChunkerTest.java

@@ -3,14 +3,21 @@
 import jakarta.annotation.Nonnull;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
 import org.mockito.ArgumentCaptor;
 import org.mockito.Captor;
 import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
 
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
 import java.util.List;
 import java.util.function.Consumer;
 import java.util.stream.IntStream;
+import java.util.stream.Stream;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.times;
@@ -43,8 +50,32 @@ public void testChunk() {
 
 	@Nonnull
 	private static List<Integer> newIntRangeList(int startInclusive, int endExclusive) {
-		List<Integer> input = IntStream.range(startInclusive, endExclusive).boxed().toList();
-		return input;
+		return IntStream.range(startInclusive, endExclusive).boxed().toList();
+	}
+
+	@ParameterizedTest
+	@MethodSource("testIteratorChunkArguments")
+	void testIteratorChunk(List<Integer> theListToChunk, List<List<Integer>> theExpectedChunks) {
+	    // given
+		Iterator<Integer> iter = theListToChunk.iterator();
+		ArrayList<List<Integer>> result = new ArrayList<>();
+
+	    // when
+		new TaskChunker<Integer>().chunk(iter, 3, result::add);
+
+	    // then
+	    assertEquals(theExpectedChunks, result);
+	}
+
+	public static Stream<Arguments> testIteratorChunkArguments() {
+		return Stream.of(
+			Arguments.of(Collections.emptyList(), Collections.emptyList()),
+			Arguments.of(List.of(1), List.of(List.of(1))),
+			Arguments.of(List.of(1,2), List.of(List.of(1,2))),
+			Arguments.of(List.of(1,2,3), List.of(List.of(1,2,3))),
+			Arguments.of(List.of(1,2,3,4), List.of(List.of(1,2,3), List.of(4))),
+			Arguments.of(List.of(1,2,3,4,5,6,7,8,9), List.of(List.of(1,2,3), List.of(4,5,6), List.of(7,8,9)))
+		);
 	}
 
 }

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>7.4.1-SNAPSHOT</version>
+	<version>7.4.2</version>
 
 	<packaging>pom</packaging>
 	<name>HAPI FHIR BOM</name>
 
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-checkstyle/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

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>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

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>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../pom.xml</relativePath>
 	</parent>

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_2/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2024-09-20"
+codename: "Copernicus"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6216-fulltext-searching-not-returning-expected-results.yml

@@ -0,0 +1,8 @@
+---
+type: fix
+issue: 6216
+jira: SMILE-8806
+title: "Previously, searches combining the `_text` query parameter (using Lucene/Elasticsearch) with query parameters 
+using the database (e.g. `identifier` or `date`) could miss matches when more than 500 results match the `_text` query 
+parameter.  This has been fixed, but may be slow if many results match the `_text` query and must be checked against the 
+database parameters."

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpa/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>7.4.1-SNAPSHOT</version>
+		<version>7.4.2</version>
 
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java

@@ -32,6 +32,7 @@
 import ca.uhn.fhir.jpa.dao.search.ExtendedHSearchSearchBuilder;
 import ca.uhn.fhir.jpa.dao.search.IHSearchSortHelper;
 import ca.uhn.fhir.jpa.dao.search.LastNOperation;
+import ca.uhn.fhir.jpa.dao.search.SearchScrollQueryExecutorAdaptor;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.search.ExtendedHSearchBuilderConsumeAdvancedQueryClausesParams;
@@ -40,6 +41,7 @@
 import ca.uhn.fhir.jpa.search.autocomplete.ValueSetAutocompleteOptions;
 import ca.uhn.fhir.jpa.search.autocomplete.ValueSetAutocompleteSearch;
 import ca.uhn.fhir.jpa.search.builder.ISearchQueryExecutor;
+import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
 import ca.uhn.fhir.jpa.search.builder.SearchQueryExecutors;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
@@ -183,6 +185,19 @@ public ISearchQueryExecutor searchNotScrolled(
 		return doSearch(theResourceName, theParams, null, theMaxResultsToFetch, theRequestDetails);
 	}
 
+	@Transactional
+	@Override
+	public ISearchQueryExecutor searchScrolled(
+			String theResourceType, SearchParameterMap theParams, RequestDetails theRequestDetails) {
+		validateHibernateSearchIsEnabled();
+
+		SearchQueryOptionsStep<?, Long, SearchLoadingOptionsStep, ?, ?> searchQueryOptionsStep =
+				getSearchQueryOptionsStep(theResourceType, theParams, null);
+		logQuery(searchQueryOptionsStep, theRequestDetails);
+
+		return new SearchScrollQueryExecutorAdaptor(searchQueryOptionsStep.scroll(SearchBuilder.getMaximumPageSize()));
+	}
+
 	// keep this in sync with supportsSomeOf();
 	@SuppressWarnings("rawtypes")
 	private ISearchQueryExecutor doSearch(

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFulltextSearchSvc.java

@@ -62,6 +62,17 @@ ISearchQueryExecutor searchNotScrolled(
 			Integer theMaxResultsToFetch,
 			RequestDetails theRequestDetails);
 
+	/**
+	 * Query the index for a complete iterator of ALL results. (scrollable search result).
+	 *
+	 * @param theResourceName      e.g. Patient
+	 * @param theParams            The search query
+	 * @param theRequestDetails The request details
+	 * @return Iterator of result PIDs
+	 */
+	ISearchQueryExecutor searchScrolled(
+			String theResourceName, SearchParameterMap theParams, RequestDetails theRequestDetails);
+
 	/**
 	 * Autocomplete search for NIH $expand contextDirection=existing
 	 * @param theOptions operation options