hapifhir · madduci · Nov 6, 2024 · Nov 7, 2024 · Nov 7, 2024 · Nov 7, 2024
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml
@@ -5,4 +5,40 @@
       (dependent HAPI modules listed in brackets):
       <ul>
       <li>org.hl7.fhir.core (Base): 6.3.25 -&gt; 6.4.0</li>
+      <li>spring-boot-bom (Base): 3.2.6 -&gt; 3.3.5</li>
+      <li>spring-retry (Base): 2.0.6 -&gt; 2.0.10</li>
+      <li>spring-data-bom (Base): 2023.1.6 -&gt; 2024.0.5</li>
+      <li>spring (Base): 6.1.8 -&gt; 6.1.14</li>
+      <li>slf4j-api (Base): 2.0.13 -&gt; 2.0.16</li>
+      <li>log4j-to-slf4j (Base): 2.19.0 -&gt; 2.24.1</li>
+      <li>jackson (Base): 2.17.1 -&gt; 2.18.1</li>
+      <li>jackson-databind (Base): 2.17.1 -&gt; 2.18.1</li>
+      <li>opentelemetry-instrumentation-bom (Base): 2.8.0 -&gt; 2.9.0</li>
+      <li>resteasy (Base): 6.2.9.Final -&gt; 6.2.10.Final</li>
+      <li>logback-classic (Base): 1.4.14 -&gt; 1.5.12</li>
+      <li>owasp-java-html-sanitizer (Base): 20211018.2 -&gt; 20240325.1</li>
+      <li>graphql-java (Base): 21.5 -&gt; 22.3</li>
+      <li>simple-java-mail (Base): 8.11.2 -&gt; 8.12.2</li>
+      <li>okio-jvm (Base): 3.4.0 -&gt; 3.9.1</li>
+      <li>commons-cli (Base): 1.5.0 -&gt; 1.9.0</li>
+      <li>org.jetbrains.annotations (Base): 23.0.0 -&gt; 26.0.1</li>
+      <li>xmlunit-core (Base): 2.4.0 -&gt; 2.10.0</li>
+      <li>jboss-logging (Tinder): 3.4.2.Final -&gt; 3.6.1.Final</li>
+      <li>springdoc-openapi-starter-webmvc-ui (Server): 2.2.0 -&gt; 2.6.0</li>
+      <li>ace-builds (Server): 1.22.0 -&gt; 1.36.3</li>
+      <li>bootstrap (Server): 4.5.2 -&gt; 4.6.2</li>
+      <li>Eonasdan-bootstrap-datetimepicker (Server): 4.17.47 -&gt; 4.17.49</li>
+      <li>font-awesome (Server): 5.8.2 -&gt; 5.15.4</li>
+      <li>swagger-ui (Server): 4.1.3 -&gt; 4.19.1</li>
+      <li>httpcore (Client): 4.4.13 -&gt; 4.4.16</li>
+      <li>httpclient (Client): 4.5.13 -&gt; 4.5.14</li>
+      <li>flyway (JPA): 9.4.0 -&gt; 10.20.1</li>
+      <li>hibernate (JPA): 6.4.1.Final -&gt; 6.6.2.Final</li>
+      <li>hibernate-search (JPA): 7.0.0.Final -&gt; 7.2.1.Final</li>
+      <li>elastic-apm (JPA): 1.44.0 -&gt; 1.52.0</li>
+      <li>elastic-search (JPA): 8.14.3 -&gt; 8.15.3</li>
+      <li>lucene (JPA): 9.8.0 -&gt; 9.12.0</li>
+      <li>postgresql (JPA): 42.7.3 -&gt; 42.7.4</li>
+      <li>mysql-connector-j (JPA): 8.2.0 -&gt; 9.1.0</li>
+      <li>ojdbc11 (JPA): 23.3.0.23.09 -&gt; 23.6.0.24.10</li>
       </ul>"
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/upgrade.md b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/upgrade.md
@@ -0,0 +1,3 @@
+## Entities annotations
+
+The `@Embedded` Annotation is no longer allowed, in presences of the `@Entity` one.
diff --git a/...hir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java b/...hir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IBatch2WorkChunkRepository.java
@@ -150,6 +150,6 @@ List<String> fetchAllChunkIdsForStepWithStatus(
 			@Param("status") WorkChunkStatusEnum theStatus);
 
 	@Query(
-			"SELECT new ca.uhn.fhir.batch2.model.BatchWorkChunkStatusDTO(e.myTargetStepId, e.myStatus, min(e.myStartTime), max(e.myEndTime), avg(e.myEndTime - e.myStartTime), count(*)) FROM Batch2WorkChunkEntity e WHERE e.myInstanceId=:instanceId GROUP BY e.myTargetStepId, e.myStatus")
+			"SELECT new ca.uhn.fhir.batch2.model.BatchWorkChunkStatusDTO(e.myTargetStepId, e.myStatus, min(e.myStartTime), max(e.myEndTime), avg(cast((e.myEndTime - e.myStartTime) as long)), count(*)) FROM Batch2WorkChunkEntity e WHERE e.myInstanceId=:instanceId GROUP BY e.myTargetStepId, e.myStatus")
 	List<BatchWorkChunkStatusDTO> fetchWorkChunkStatusForInstance(@Param("instanceId") String theInstanceId);
 }
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/PathContext.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/PathContext.java
@@ -20,9 +20,11 @@
 package ca.uhn.fhir.jpa.dao.search;
 
 import jakarta.annotation.Nonnull;
+import org.hibernate.search.engine.search.common.NamedValues;
 import org.hibernate.search.engine.search.predicate.SearchPredicate;
 import org.hibernate.search.engine.search.predicate.dsl.BooleanPredicateClausesStep;
 import org.hibernate.search.engine.search.predicate.dsl.ExistsPredicateFieldStep;
+import org.hibernate.search.engine.search.predicate.dsl.KnnPredicateFieldStep;
 import org.hibernate.search.engine.search.predicate.dsl.MatchAllPredicateOptionsStep;
 import org.hibernate.search.engine.search.predicate.dsl.MatchIdPredicateMatchingStep;
 import org.hibernate.search.engine.search.predicate.dsl.MatchNonePredicateFinalStep;
@@ -34,6 +36,8 @@
 import org.hibernate.search.engine.search.predicate.dsl.NotPredicateFinalStep;
 import org.hibernate.search.engine.search.predicate.dsl.PhrasePredicateFieldStep;
 import org.hibernate.search.engine.search.predicate.dsl.PredicateFinalStep;
+import org.hibernate.search.engine.search.predicate.dsl.PrefixPredicateFieldStep;
+import org.hibernate.search.engine.search.predicate.dsl.QueryStringPredicateFieldStep;
 import org.hibernate.search.engine.search.predicate.dsl.RangePredicateFieldStep;
 import org.hibernate.search.engine.search.predicate.dsl.RegexpPredicateFieldStep;
 import org.hibernate.search.engine.search.predicate.dsl.SearchPredicateFactory;
@@ -221,6 +225,11 @@ public WildcardPredicateFieldStep<?> wildcard() {
 		return myPredicateFactory.wildcard();
 	}
 
+	@Override
+	public PrefixPredicateFieldStep<?> prefix() {
+		return myPredicateFactory.prefix();
+	}
+
 	@Override
 	public RegexpPredicateFieldStep<?> regexp() {
 		return myPredicateFactory.regexp();
@@ -246,6 +255,11 @@ public SimpleQueryStringPredicateFieldStep<?> simpleQueryString() {
 		return myPredicateFactory.simpleQueryString();
 	}
 
+	@Override
+	public QueryStringPredicateFieldStep<?> queryString() {
+		return myPredicateFactory.queryString();
+	}
+
 	@Override
 	public ExistsPredicateFieldStep<?> exists() {
 		return myPredicateFactory.exists();
@@ -262,6 +276,16 @@ public NamedPredicateOptionsStep named(String path) {
 		return myPredicateFactory.named(path);
 	}
 
+	@Override
+	public KnnPredicateFieldStep knn(int i) {
+		return myPredicateFactory.knn(i);
+	}
+
+	@Override
+	public PredicateFinalStep withParameters(Function<? super NamedValues, ? extends PredicateFinalStep> function) {
+		return myPredicateFactory.withParameters(function);
+	}
+
 	@Override
 	public <T> T extension(SearchPredicateFactoryExtension<T> extension) {
 		return myPredicateFactory.extension(extension);

diff --git a/...paserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java b/...paserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java
@@ -33,6 +33,8 @@
 import ca.uhn.fhir.util.VersionUtil;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
+import com.google.gson.JsonArray;
+import com.google.gson.JsonSerializer;
 import graphql.ExecutionResult;
 import graphql.GraphQL;
 import graphql.language.InterfaceTypeDefinition;
@@ -80,6 +82,7 @@ public class GraphQLProviderWithIntrospection extends GraphQLProvider {
 	private final ISearchParamRegistry mySearchParamRegistry;
 	private final VersionSpecificWorkerContextWrapper myContext;
 	private final IDaoRegistry myDaoRegistry;
+	private final Gson myGson;
 
 	/**
 	 * Constructor
@@ -97,6 +100,11 @@ public GraphQLProviderWithIntrospection(
 
 		myContext = VersionSpecificWorkerContextWrapper.newVersionSpecificWorkerContextWrapper(theValidationSupport);
 		myGenerator = new GraphQLSchemaGenerator(myContext, VersionUtil.getVersion());
+
+		GsonBuilder gsonBuilder = new GsonBuilder();
+		gsonBuilder.registerTypeAdapter(Collections.emptyList().getClass(), (JsonSerializer<Object>)
+				(src, typeOfSrc, context) -> new JsonArray());
+		myGson = gsonBuilder.create();
 	}
 
 	@Override
@@ -250,8 +258,7 @@ private String generateSchema(
 		ExecutionResult executionResult = build.execute(theQueryBody);
 
 		Map<String, Object> data = executionResult.toSpecification();
-		Gson gson = new GsonBuilder().create();
-		return gson.toJson(data);
+		return myGson.toJson(data);
 	}
 
 	@Nonnull

diff --git a/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTag.java b/hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceHistoryTag.java
@@ -20,7 +20,6 @@
 package ca.uhn.fhir.jpa.model.entity;
 
 import jakarta.persistence.Column;
-import jakarta.persistence.Embeddable;
 import jakarta.persistence.Entity;
 import jakarta.persistence.ForeignKey;
 import jakarta.persistence.GeneratedValue;
@@ -35,7 +34,6 @@
 
 import java.io.Serializable;
 
-@Embeddable
 @Entity
 @Table(
 		name = "HFJ_HISTORY_TAG",

diff --git a/...er-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamCoords.java b/...er-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamCoords.java
@@ -24,7 +24,6 @@
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import jakarta.annotation.Nullable;
 import jakarta.persistence.Column;
-import jakarta.persistence.Embeddable;
 import jakarta.persistence.Entity;
 import jakarta.persistence.EntityListeners;
 import jakarta.persistence.FetchType;
@@ -42,7 +41,6 @@
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hibernate.annotations.GenericGenerator;
 
-@Embeddable
 @EntityListeners(IndexStorageOptimizationListener.class)
 @Entity
 @Table(

diff --git a/...rver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamDate.java b/...rver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamDate.java
@@ -28,7 +28,6 @@
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.util.DateUtils;
 import jakarta.persistence.Column;
-import jakarta.persistence.Embeddable;
 import jakarta.persistence.Entity;
 import jakarta.persistence.EntityListeners;
 import jakarta.persistence.FetchType;
@@ -56,7 +55,6 @@
 import java.text.SimpleDateFormat;
 import java.util.Date;
 
-@Embeddable
 @EntityListeners(IndexStorageOptimizationListener.class)
 @Entity
 @Table(

diff --git a/...er-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamNumber.java b/...er-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamNumber.java
@@ -24,7 +24,6 @@
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.param.NumberParam;
 import jakarta.persistence.Column;
-import jakarta.persistence.Embeddable;
 import jakarta.persistence.Entity;
 import jakarta.persistence.EntityListeners;
 import jakarta.persistence.FetchType;
@@ -48,7 +47,6 @@
 import java.math.BigDecimal;
 import java.util.Objects;
 
-@Embeddable
 @EntityListeners(IndexStorageOptimizationListener.class)
 @Entity
 @Table(

diff --git a/...-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java b/...-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantity.java
@@ -24,7 +24,6 @@
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.param.QuantityParam;
 import jakarta.persistence.Column;
-import jakarta.persistence.Embeddable;
 import jakarta.persistence.Entity;
 import jakarta.persistence.EntityListeners;
 import jakarta.persistence.FetchType;
@@ -50,7 +49,6 @@
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
 // @formatter:off
-@Embeddable
 @EntityListeners(IndexStorageOptimizationListener.class)
 @Entity
 @Table(

diff --git a/.../main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalized.java b/.../main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamQuantityNormalized.java
@@ -25,7 +25,6 @@
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.param.QuantityParam;
 import jakarta.persistence.Column;
-import jakarta.persistence.Embeddable;
 import jakarta.persistence.Entity;
 import jakarta.persistence.EntityListeners;
 import jakarta.persistence.FetchType;
@@ -52,7 +51,6 @@
 import static org.apache.commons.lang3.StringUtils.isBlank;
 
 // @formatter:off
-@Embeddable
 @EntityListeners(IndexStorageOptimizationListener.class)
 @Entity
 @Table(

diff --git a/...er-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamString.java b/...er-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamString.java
@@ -27,7 +27,6 @@
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.util.StringUtil;
 import jakarta.persistence.Column;
-import jakarta.persistence.Embeddable;
 import jakarta.persistence.Entity;
 import jakarta.persistence.EntityListeners;
 import jakarta.persistence.ForeignKey;
@@ -48,7 +47,6 @@
 import static org.apache.commons.lang3.StringUtils.defaultString;
 
 // @formatter:off
-@Embeddable
 @EntityListeners(IndexStorageOptimizationListener.class)
 @Entity
 @Table(

diff --git a/...ver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamToken.java b/...ver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamToken.java
@@ -26,7 +26,6 @@
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.param.TokenParam;
 import jakarta.persistence.Column;
-import jakarta.persistence.Embeddable;
 import jakarta.persistence.Entity;
 import jakarta.persistence.EntityListeners;
 import jakarta.persistence.FetchType;
@@ -52,7 +51,6 @@
 import static org.apache.commons.lang3.StringUtils.defaultString;
 import static org.apache.commons.lang3.StringUtils.trim;
 
-@Embeddable
 @EntityListeners(IndexStorageOptimizationListener.class)
 @Entity
 @Table(

diff --git a/...erver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamUri.java b/...erver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceIndexedSearchParamUri.java
@@ -25,7 +25,6 @@
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.param.UriParam;
 import jakarta.persistence.Column;
-import jakarta.persistence.Embeddable;
 import jakarta.persistence.Entity;
 import jakarta.persistence.EntityListeners;
 import jakarta.persistence.FetchType;
@@ -47,7 +46,6 @@
 import static ca.uhn.fhir.jpa.model.util.SearchParamHash.hashSearchParam;
 import static org.apache.commons.lang3.StringUtils.defaultString;
 
-@Embeddable
 @EntityListeners(IndexStorageOptimizationListener.class)
 @Entity
 @Table(

diff --git a/hapi-fhir-sql-migrate/pom.xml b/hapi-fhir-sql-migrate/pom.xml
@@ -54,13 +54,13 @@
 			<groupId>org.apache.derby</groupId>
 			<artifactId>derby</artifactId>
 			<scope>test</scope>
-			<version>10.16.1.1</version>
+			<version>10.17.1.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.derby</groupId>
 			<artifactId>derbytools</artifactId>
 			<scope>test</scope>
-			<version>10.16.1.1</version>
+			<version>10.17.1.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.postgresql</groupId>
@@ -80,13 +80,6 @@
 			<artifactId>logback-classic</artifactId>
 			<scope>test</scope>
 		</dependency>
-
-		<dependency>
-			<groupId>ca.uhn.hapi.fhir</groupId>
-			<artifactId>hapi-fhir-test-utilities</artifactId>
-			<version>${project.version}</version>
-			<scope>test</scope>
-		</dependency>
 		<dependency>
 			<groupId>org.testcontainers</groupId>
 			<artifactId>junit-jupiter</artifactId>
@@ -131,7 +124,6 @@
 		</dependency>
 
 		<!-- test -->
-
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-test-utilities</artifactId>