Merge branch 'master' into 3400-bulk-export-rules-incorrectly-applied…

…-to-group-and-patient-exports

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java

@@ -199,8 +199,6 @@ protected Iterable<CompositeChildElement> compositeChildIterator(IBase theCompos
 				} else if (myNext.getDef() instanceof RuntimeChildNarrativeDefinition) {
 					if (isSuppressNarratives() || isSummaryMode()) {
 						continue;
-					} else if (theContainedResource) {
-						continue;
 					}
 				} else if (myNext.getDef() instanceof RuntimeChildContainedResources) {
 					if (theContainedResource) {

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java

@@ -534,8 +534,6 @@ private void encodeCompositeElementChildrenToStreamWriter(RuntimeResourceDefinit
 						beginArray(theEventWriter, nextChildSpecificName);
 						inArray = true;
 						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, null, theContainedResource, nextChildElem, force, theEncodeContext);
-					} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theContainedResource) {
-						// suppress narratives from contained resources
 					} else {
 						encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, nextValue, childDef, nextChildSpecificName, theContainedResource, nextChildElem, false, theEncodeContext);
 					}

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java

@@ -446,8 +446,6 @@ private void encodeCompositeElementToStreamWriter(IBaseResource theResource, IBa
 							}
 						}
 						encodeChildElementToStreamWriter(theResource, theEventWriter, nextChild, nextValue, childName, childDef, getExtensionUrl(extension.getUrl()), theContainedResource, nextChildElem, theEncodeContext);
-					} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theContainedResource) {
-						// suppress narratives from contained resources
 					} else {
 						encodeChildElementToStreamWriter(theResource, theEventWriter, nextChild, nextValue, childName, childDef, extensionUrl, theContainedResource, nextChildElem, theEncodeContext);
 					}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/IResourceSupportedSvc.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.rest.api;
 
+/*-
+ * #%L
+ * HAPI FHIR - Core Library
+ * %%
+ * Copyright (C) 2014 - 2022 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://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%
+ */
+
 public interface IResourceSupportedSvc {
 	boolean isSupported(String theResourceName);
 }

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

@@ -242,27 +242,27 @@ public static <T> T notNull(final T argument, final String name) {
 	public static Pair<String, String> getCompletedDate(String theIncompleteDateStr) {
 
 		if (StringUtils.isBlank(theIncompleteDateStr)) 
-			return new ImmutablePair<String, String>(null, null);
+			return new ImmutablePair<>(null, null);
 
 		String lbStr, upStr;
 		// YYYY only, return the last day of the year
 		if (theIncompleteDateStr.length() == 4)  {
 			lbStr = theIncompleteDateStr + "-01-01"; // first day of the year
 			upStr = theIncompleteDateStr + "-12-31"; // last day of the year
-			return new ImmutablePair<String, String>(lbStr, upStr);
+			return new ImmutablePair<>(lbStr, upStr);
 		}
 
 		// Not YYYY-MM, no change
 		if (theIncompleteDateStr.length() != 7)
-			return new ImmutablePair<String, String>(theIncompleteDateStr, theIncompleteDateStr);
+			return new ImmutablePair<>(theIncompleteDateStr, theIncompleteDateStr);
 
 		// YYYY-MM Only
-		Date lb=null;
+		Date lb;
 		try {
 			// first day of the month
 			lb = new SimpleDateFormat("yyyy-MM-dd").parse(theIncompleteDateStr+"-01");   
 		} catch (ParseException e) {
-			return new ImmutablePair<String, String>(theIncompleteDateStr, theIncompleteDateStr);
+			return new ImmutablePair<>(theIncompleteDateStr, theIncompleteDateStr);
 		}
 
 		// last day of the month
@@ -278,7 +278,7 @@ public static Pair<String, String> getCompletedDate(String theIncompleteDateStr)
 	    lbStr = new SimpleDateFormat("yyyy-MM-dd").format(lb);  
 	    upStr = new SimpleDateFormat("yyyy-MM-dd").format(ub);  
 
-		return new ImmutablePair<String, String>(lbStr, upStr);
+		return new ImmutablePair<>(lbStr, upStr);
 	}
 
 	public static Date getEndOfDay(Date theDate) {

hapi-fhir-bom/pom.xml

@@ -21,8 +21,13 @@
                 <artifactId>hapi-fhir-base</artifactId>
                 <version>${project.version}</version>
             </dependency>
-            <dependency>
-                <groupId>${project.groupId}</groupId>
+			  <dependency>
+				  <groupId>${project.groupId}</groupId>
+				  <artifactId>hapi-fhir-checkstyle</artifactId>
+				  <version>${project.version}</version>
+			  </dependency>
+			  <dependency>
+				  <groupId>${project.groupId}</groupId>
                 <artifactId>hapi-fhir-utilities</artifactId>
                 <version>${project.version}</version>
             </dependency>

hapi-fhir-checkstyle/pom.xml

@@ -42,7 +42,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-deploy-plugin</artifactId>
 				<configuration>
-					<skip>false</skip>
+					<skip>true</skip>
 				</configuration>
 			</plugin>
 		</plugins>

hapi-fhir-dist/pom.xml

@@ -92,8 +92,6 @@
 					<classifier>javadoc</classifier>
 					<scope>provided</scope>
 				</dependency>
-
-
 				<dependency>
 					<groupId>ca.uhn.hapi.fhir</groupId>
 					<artifactId>hapi-fhir-structures-dstu2</artifactId>

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/2791-partition-based-access-control-is-not-enforced-on-opaque-pagination-links.yml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 2791
+jira: 3710
+title: "Users were able to access data on partitions they did not have access to by using pagination links generated by users who did have access."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3374-chained-common-search-params.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 3374
+title: "Chained searches will handle common search parameters correctly when the `Index Contained Resources` configuration parameter is enabled."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3392-nullpointerexception-rest-hook-subscription-is-not-being-triggered-when-cross-partition-is.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 3392
+title: "When cross-partition reference Mode is used, the rest-hook subscriptions on a partition enabled server would
+   cause a NPE. Cause of this is from the reloading of the subscription when the server is restarted.
+   This issue has been fixed. Also fixed issue with revinclude for rest-hook subscription not working."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3394-bulk-export-permissions-are-over-permissive.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 3394
+title: "Bulk export permissions were over-permissive in RuleBulkExportImpl. This has been corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2022-02-17"
+codename: "Sojourner"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/1466-encode-narratives-of-encoded-resources.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 1466
+title: "The XML and JSON Parsers are now encoding narratives of contained resources. 
+  Narratives were skipped before for contained resources. This was a rule which was only valid in STU1 (https://www.hl7.org/fhir/DSTU1/narrative.html), and was removed in DSTU2+ "

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3346-always-use-integers-for-date-ordinals.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 3346
+title: "When searching for date search parameters on Postgres, ordinals could sometimes be
+  represented as strings, causing a search failure. This has been corrected."

hapi-fhir-jpa/pom.xml

@@ -41,16 +41,6 @@
 			<groupId>org.hibernate</groupId>
 			<artifactId>hibernate-java8</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.hibernate</groupId>
-			<artifactId>hibernate-ehcache</artifactId>
-			<exclusions>
-				<exclusion>
-					<groupId>net.sf.ehcache</groupId>
-					<artifactId>ehcache-core</artifactId>
-				</exclusion>
-			</exclusions>
-		</dependency>
 		<dependency>
 			<groupId>org.hibernate.validator</groupId>
 			<artifactId>hibernate-validator</artifactId>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BeanPostProcessorConfig.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.config;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 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://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%
+ */
+
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/FhirContextDstu2Config.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.config;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 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://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%
+ */
+
 import ca.uhn.fhir.context.FhirContext;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Primary;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HapiJpaConfig.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.config;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 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://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%
+ */
+
 import ca.uhn.fhir.jpa.api.IDaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.batch.config.NonPersistedBatchConfigurer;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/ValidationSupportConfig.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.config;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 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://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%
+ */
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/FhirContextDstu3Config.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.config.dstu3;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 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://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%
+ */
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.ParserOptions;
 import org.springframework.context.annotation.Bean;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/FhirContextR4Config.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.config.r4;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 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://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%
+ */
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.ParserOptions;
 import org.springframework.context.annotation.Bean;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/FhirContextR5Config.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.config.r5;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 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://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%
+ */
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.ParserOptions;
 import org.springframework.context.annotation.Bean;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/util/HapiEntityManagerFactoryUtil.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.config.util;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2022 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://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%
+ */
+
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect;
 import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;