HAPI FHIR Dependency Bumps (#5576)

* HAPI FHIR Dependency Bumps * Hibernate search 6 * Dep bumps * Bump mockito * Fix memory leak * Test cleanup * Test fix * Test fixes * Test fix * Test fix * Test fix * Test fix * Prepare to try and rework max clauses * Refactor large VS expansion * Spotless * Test fix * Version bump * Test fixes * Bump maven container * Build fix * Add license headers * Version bump * License headers
hapifhir · Jan 14, 2024 · 878e27b · 878e27b
1 parent 5286829
commit 878e27b
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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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-android/src/test/java/ca/uhn/fhir/android/client/GenericClientDstu3IT.java b/hapi-fhir-android/src/test/java/ca/uhn/fhir/android/client/GenericClientDstu3IT.java
@@ -209,7 +209,7 @@ public void testBinaryCreateWithNoContentType() throws Exception {
  @Test
  public void testClientFailures() {
  ResponseBody body = mock(ResponseBody.class);
- when(body.source()).thenThrow(IllegalStateException.class, RuntimeException.class);
+ when(body.byteStream()).thenThrow(IllegalStateException.class, RuntimeException.class);
 
  myHttpResponse = new Response.Builder()
  .request(myRequest)

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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BaseBatchJobParameters.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BaseBatchJobParameters.java
@@ -1,3 +1,22 @@
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2024 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http:https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
 package ca.uhn.fhir.model.api;
 
 import com.fasterxml.jackson.annotation.JsonProperty;

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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-SNAPSHOT</version>
 
  <packaging>pom</packaging>
  <name>HAPI FHIR BOM</name>
 
  <parent>
  <groupId>ca.uhn.hapi.fhir</groupId>
  <artifactId>hapi-deployable-pom</artifactId>
- <version>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>

diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/changes.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/changes.yaml
@@ -4,20 +4,24 @@
  title: "The version of a few dependencies have been bumped to the latest versions
  (dependent HAPI modules listed in brackets):
  <ul>
- <li>Jackson (Base): 2.15.3 -&gt; 2.16.0</li>
+ <li>Jackson (Base): 2.15.3 -&gt; 2.16.1</li>
  <li>SLF4j (Base): 2.0.3 -&gt; 2.0.9</li>
  <li>Logback (Base): 1.4.7 -&gt; 1.4.14</li>
  <li>Caffeine (Base): 3.1.1 -&gt; 3.1.8</li>
  <li>Spring Framework (JPA): 5.3.27 -&gt; 6.1.1</li>
  <li>Spring Boot (JPA-Starter): 5.3.27 -&gt; 6.2.0</li>
  <li>Spring Data BOM (JPA): 2021.2.2 -&gt; 2023.1.0</li>
- <li>Hibernate (JPA): 5.6.15.Final -&gt; 6.4.0.Final</li>
+ <li>Hibernate (JPA): 5.6.15.Final -&gt; 6.4.1.Final</li>
  <li>Hibernate Validator (JPA): 6.1.5.Final -&gt; 8.0.0.Final</li>
- <li>Hibernate Search (JPA): 6.1.6.Final -&gt; 6.2.2.Final</li>
+ <li>Hibernate Search (JPA): 6.1.6.Final -&gt; 7.0.0.Final</li>
  <li>Commons-DBCP2 (JPA): 2.9.0 -&gt; 2.11.0</li>
+ <li>DataSource-Proxy (JPA): 1.9 -&gt; 1.10</li>
  <li>Spring Boot (Boot+Starter): 2.7.12 -&gt; 3.1.4</li>
  <li>Jetty (CLI): 10.0.14 -&gt; 12.0.3</li>
  <li>Jansi (CLI): 2.4.0 -&gt; 2.4.1</li>
+ <li>Derby (CLI): 10.14.2.0 -&gt; 10.17.1.0</li>
+ <li>Commons-Lang3 (CLI): 3.12.0 -&gt; 3.14.0</li>
+ <li>Commons-CSV (CLI): 1.8 -&gt; 1.10.0</li>
  <li>Phloc Schematron (Schematron Validator): 5.6.5 -&gt; 7.1.2</li>
  <li>RestEasy (JAX-RS Server): 5.0.2.Final -&gt; 6.2.5.Final</li>
  </ul>"

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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
@@ -53,7 +53,7 @@
  </dependency>
  <dependency>
  <groupId>org.hibernate.search</groupId>
- <artifactId>hibernate-search-mapper-orm-orm6</artifactId>
+ <artifactId>hibernate-search-mapper-orm</artifactId>
  <exclusions>
  <exclusion>
  <groupId>org.apache.logging.log4j</groupId>

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>6.11.9-SNAPSHOT</version>
+ <version>6.11.10-SNAPSHOT</version>
 
  <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
  </parent>
@@ -340,11 +340,7 @@
  </dependency>
  <dependency>
  <groupId>org.apache.lucene</groupId>
- <artifactId>lucene-analyzers-phonetic</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.lucene</groupId>
- <artifactId>lucene-backward-codecs</artifactId>
+ <artifactId>lucene-analysis-phonetic</artifactId>
  </dependency>
  <!-- Misc -->
  <dependency>

diff --git a/...-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessor.java b/...-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessor.java
@@ -111,7 +111,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
 
  @SuppressWarnings("rawtypes")
  @Autowired
- private IMdmLinkDao myMdmLinkDao;
+ protected IMdmLinkDao myMdmLinkDao;
 
  @Autowired
  private MdmExpansionCacheSvc myMdmExpansionCacheSvc;

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
@@ -582,7 +582,7 @@ private Map<String, List<IResourceLookup<JpaPid>>> translateForcedIdToPids(
  return retVal;
  }
 
- RequestPartitionId replaceDefault(RequestPartitionId theRequestPartitionId) {
+ public RequestPartitionId replaceDefault(RequestPartitionId theRequestPartitionId) {
  if (myPartitionSettings.getDefaultPartitionId() != null) {
  if (!theRequestPartitionId.isAllPartitions() && theRequestPartitionId.hasDefaultPartitionId()) {
  List<Integer> partitionIds = theRequestPartitionId.getPartitionIds().stream()
@@ -712,7 +712,7 @@ public void addResolvedPidToForcedId(
  }
 
  @VisibleForTesting
- void setPartitionSettingsForUnitTest(PartitionSettings thePartitionSettings) {
+ public void setPartitionSettingsForUnitTest(PartitionSettings thePartitionSettings) {
  myPartitionSettings = thePartitionSettings;
  }
 

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SynchronousSearchSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SynchronousSearchSvcImpl.java
@@ -71,7 +71,7 @@ public class SynchronousSearchSvcImpl implements ISynchronousSearchSvc {
  private JpaStorageSettings myStorageSettings;
 
  @Autowired
- private SearchBuilderFactory mySearchBuilderFactory;
+ protected SearchBuilderFactory mySearchBuilderFactory;
 
  @Autowired
  private DaoRegistry myDaoRegistry;