Bump core version to 6.1.2 (#5317)

* WIP Fix compile errors

* Fix compile errors 2

* Fix test fails due to new Validation messages

* Ignore validation issues

Ignore two validation issues:

Two 'side is inherently a collection' warnings are now thrown for the following expressions:

NamingSystem nsd-1 uniqueId.type = 'uuid'
Observation obs-7 code != component.code

There is also a general error ignored because the StructureDefinition for StructureDefinition is actually for FHIR 3.0.1, and contains an invalid expression in constraint sdf-9. This is remedied in the expression used in 3.0.2, but a full update of all profile structure definitions is out of scope for this PR.

* Fix property name

* Add changelog

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/changes.yaml

@@ -9,4 +9,7 @@
         <li>Logback (All): 1.4.4 -&gt; 1.4.7</li>
         <li>H2 Database (JPA): 2.1.214 -&gt; 2.2.220</li>
         <li>Thymeleaf (Testpage Overlay): 3.0.14.RELEASE -&gt; 3.1.2.RELEASE</li>
+        <li>xpp3 (All): 1.1.4c.0 -&gt; 1.1.6</li>
+        <li>HtmlUnit (All): 2.67.0 -&gt; 2.70.0</li>
+        <li>org.hl7.fhir.core (All): 6.0.22.2 -&gt; 6.1.2</li>
    </ul>"

hapi-fhir-jpaserver-model/pom.xml

@@ -26,21 +26,13 @@
 					<groupId>junit</groupId>
 					<artifactId>junit</artifactId>
 				</exclusion>
-				<!-- remove xpp3 fat jar and replace it with non-bundled versions -->
+
-				<exclusion>
+
-					<groupId>xpp3</groupId>
-					<artifactId>xpp3</artifactId>
-				</exclusion>
 			</exclusions>
 		</dependency>
 
 
-		<!-- This dependency replaces the version of xpp3 that's bundled with Ucum with one that's Java 9+ compatible -->
+
-		<dependency>
-			<groupId>org.codelibs</groupId>
-			<artifactId>xpp3</artifactId>
-			<version>1.1.4c.0</version>
-		</dependency>
 
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4.java

@@ -39,6 +39,7 @@ import org.hl7.fhir.r4.model.ResourceType;
 import org.hl7.fhir.r4.model.TypeDetails;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.utils.FHIRPathEngine;
+import org.hl7.fhir.r4.utils.FHIRPathUtilityClasses.FunctionDetails;
 
 import java.util.Collections;
 import java.util.HashMap;

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR4B.java

@@ -39,6 +39,7 @@ import org.hl7.fhir.r4b.model.ResourceType;
 import org.hl7.fhir.r4b.model.TypeDetails;
 import org.hl7.fhir.r4b.model.ValueSet;
 import org.hl7.fhir.r4b.utils.FHIRPathEngine;
+import org.hl7.fhir.r4b.utils.FHIRPathUtilityClasses.FunctionDetails;
 
 import java.util.Collections;
 import java.util.HashMap;

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorR5.java

@@ -38,6 +38,7 @@ import org.hl7.fhir.r5.model.ResourceType;
 import org.hl7.fhir.r5.model.TypeDetails;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.utils.FHIRPathEngine;
+import org.hl7.fhir.r5.utils.FHIRPathUtilityClasses.FunctionDetails;
 
 import java.util.Collections;
 import java.util.HashMap;

hapi-fhir-server-mdm/pom.xml

@@ -60,20 +60,11 @@
 					<groupId>junit</groupId>
 					<artifactId>junit</artifactId>
 				</exclusion>
-				<!-- remove xpp3 fat jar and replace it with non-bundled versions -->
+
-				<exclusion>
-					<groupId>xpp3</groupId>
-					<artifactId>xpp3</artifactId>
-				</exclusion>
 			</exclusions>
 		</dependency>
 
-		<!-- These two dependencies replaces the version of xpp3 that's bundled with Ucum with one that's Java 9+ compatible -->
+
-		<dependency>
-			<groupId>org.codelibs</groupId>
-			<artifactId>xpp3</artifactId>
-			<version>1.1.4c.0</version>
-		</dependency>
 
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>

hapi-fhir-storage-cr/pom.xml

@@ -19,7 +19,7 @@
 
 	<properties>
 		<org.antlr-version>4.10.1</org.antlr-version>
-		<org.codelibs.xpp3-version>1.1.4c.0</org.codelibs.xpp3-version>
+		<xpp3-version>1.1.6</xpp3-version>
 		<spring-security-core.version>5.7.8</spring-security-core.version>
 	</properties>
 
@@ -40,16 +40,6 @@
 				<groupId>ca.uhn.hapi.fhir</groupId>
 				<artifactId>hapi-fhir-validation</artifactId>
 				<version>${project.version}</version>
-				<exclusions>
-					<exclusion>
-						<groupId>xpp3</groupId>
-						<artifactId>xpp3_min</artifactId>
-					</exclusion>
-					<exclusion>
-						<groupId>xmlpull</groupId>
-						<artifactId>xmlpull</artifactId>
-					</exclusion>
-				</exclusions>
 			</dependency>
 			<dependency>
 				<groupId>ca.uhn.hapi.fhir</groupId>
@@ -169,9 +159,9 @@
 		</dependency>
 
 		<dependency>
-			<groupId>org.codelibs</groupId>
+			<groupId>org.ogce</groupId>
 			<artifactId>xpp3</artifactId>
-			<version>${org.codelibs.xpp3-version}</version>
+			<version>${xpp3-version}</version>
 		</dependency>
 
 		<dependency>

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java

@@ -86,7 +86,8 @@ public class ValidatorResourceFetcher implements IValidatorResourceFetcher {
 	}
 
 	@Override
-	public boolean resolveURL(IResourceValidator iResourceValidator, Object o, String s, String s1, String s2)
+	public boolean resolveURL(
+			IResourceValidator iResourceValidator, Object o, String s, String s1, String s2, boolean isCanonical)
 			throws IOException, FHIRException {
 		return true;
 	}

hapi-fhir-structures-dstu3/pom.xml

@@ -176,7 +176,7 @@
 			<optional>true</optional>
 		</dependency>
 		<dependency>
-			<groupId>xpp3</groupId>
+			<groupId>org.ogce</groupId>
 			<artifactId>xpp3</artifactId>
 			<optional>true</optional>
 		</dependency>

hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/fluentpath/FhirPathDstu3.java

@@ -12,6 +12,7 @@ import org.hl7.fhir.dstu3.model.ExpressionNode;
 import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.TypeDetails;
 import org.hl7.fhir.dstu3.utils.FHIRPathEngine;
+import org.hl7.fhir.dstu3.utils.FHIRPathUtilityClasses.FunctionDetails;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.PathEngineException;
 import org.hl7.fhir.instance.model.api.IBase;

hapi-fhir-structures-hl7org-dstu2/pom.xml

@@ -71,7 +71,7 @@
 		</dependency>
 
 		<dependency>
-			<groupId>xpp3</groupId>
+			<groupId>org.ogce</groupId>
 			<artifactId>xpp3</artifactId>
 			<optional>true</optional>
 		</dependency>

hapi-fhir-structures-r4/pom.xml

@@ -78,7 +78,7 @@
 			<optional>true</optional>
 		</dependency>
 		<dependency>
-			<groupId>xpp3</groupId>
+			<groupId>org.ogce</groupId>
 			<artifactId>xpp3</artifactId>
 			<optional>true</optional>
 		</dependency>

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/fluentpath/FhirPathR4.java

@@ -16,6 +16,7 @@ import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.TypeDetails;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.hl7.fhir.r4.utils.FHIRPathEngine;
+import org.hl7.fhir.r4.utils.FHIRPathUtilityClasses.FunctionDetails;
 
 import java.util.List;
 import java.util.Optional;

hapi-fhir-structures-r4b/pom.xml

@@ -70,7 +70,7 @@
 			<optional>true</optional>
 		</dependency>
 		<dependency>
-			<groupId>xpp3</groupId>
+			<groupId>org.ogce</groupId>
 			<artifactId>xpp3</artifactId>
 			<optional>true</optional>
 		</dependency>

hapi-fhir-structures-r4b/src/main/java/org/hl7/fhir/r4b/hapi/fhirpath/FhirPathR4B.java

@@ -16,6 +16,7 @@ import org.hl7.fhir.r4b.model.IdType;
 import org.hl7.fhir.r4b.model.TypeDetails;
 import org.hl7.fhir.r4b.model.ValueSet;
 import org.hl7.fhir.r4b.utils.FHIRPathEngine;
+import org.hl7.fhir.r4b.utils.FHIRPathUtilityClasses.FunctionDetails;
 
 import java.util.List;
 import java.util.Optional;

hapi-fhir-structures-r5/pom.xml

@@ -67,7 +67,7 @@
 			<optional>true</optional>
 		</dependency>
 		<dependency>
-			<groupId>xpp3</groupId>
+			<groupId>org.ogce</groupId>
 			<artifactId>xpp3</artifactId>
 			<optional>true</optional>
 		</dependency>

hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/ctx/HapiWorkerContext.java

@@ -162,6 +162,12 @@ public final class HapiWorkerContext extends I18nBase implements IWorkerContext
 		throw new UnsupportedOperationException(Msg.code(209));
 	}
 
+	@Override
+	public void validateCodeBatchByRef(
+			ValidationOptions validationOptions, List<? extends CodingValidationRequest> list, String s) {
+		throw new UnsupportedOperationException(Msg.code(2430));
+	}
+
 	@Override
 	public ValueSetExpansionOutcome expandVS(
 			ValueSet theValueSet, boolean cacheOk, boolean heiarchical, boolean incompleteOk) {

hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/fhirpath/FhirPathR5.java

@@ -16,6 +16,7 @@ import org.hl7.fhir.r5.model.IdType;
 import org.hl7.fhir.r5.model.TypeDetails;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.utils.FHIRPathEngine;
+import org.hl7.fhir.r5.utils.FHIRPathUtilityClasses.FunctionDetails;
 
 import java.util.List;
 import java.util.Optional;

hapi-fhir-validation/pom.xml

@@ -79,19 +79,11 @@
 					<groupId>org.apache.commons</groupId>
 					<artifactId>commons-collections4</artifactId>
 				</exclusion>
-				<exclusion>
+
-					<groupId>xpp3</groupId>
-					<artifactId>xpp3</artifactId>
-				</exclusion>
 			</exclusions>
 		</dependency>
 
-		<!-- These two dependencies replaces the version of xpp3 that's bundled with Ucum with one that's Java 9+ compatible -->
+
-		<dependency>
-			<groupId>org.codelibs</groupId>
-			<artifactId>xpp3</artifactId>
-			<version>1.1.4c.0</version>
-		</dependency>
 
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
@@ -103,10 +95,6 @@
             <groupId>org.fhir</groupId>
             <artifactId>ucum</artifactId>
 			  <exclusions>
-				  <exclusion>
-					  <groupId>xpp3</groupId>
-					  <artifactId>xpp3</artifactId>
-				  </exclusion>
 				  <exclusion>
 					  <groupId>junit</groupId>
 					  <artifactId>junit</artifactId>

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/FhirInstanceValidator.java

@@ -13,6 +13,7 @@ import org.hl7.fhir.r5.model.Base;
 import org.hl7.fhir.r5.model.TypeDetails;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.utils.FHIRPathEngine;
+import org.hl7.fhir.r5.utils.FHIRPathUtilityClasses.FunctionDetails;
 import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor;
 import org.hl7.fhir.r5.utils.validation.IValidatorResourceFetcher;
 import org.hl7.fhir.r5.utils.validation.constants.BestPracticeWarningLevel;

hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/VersionSpecificWorkerContextWrapper.java

@@ -613,6 +613,13 @@ public class VersionSpecificWorkerContextWrapper extends I18nBase implements IWo
 		}
 	}
 
+	@Override
+	public void validateCodeBatchByRef(
+			ValidationOptions validationOptions, List<? extends CodingValidationRequest> list, String s) {
+		ValueSet valueSet = fetchResource(ValueSet.class, s);
+		validateCodeBatch(validationOptions, list, valueSet);
+	}
+
 	@Nonnull
 	private ValidationResult doValidation(
 			IBaseResource theValueSet,

hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidatorDstu3Test.java

@@ -91,6 +91,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyBoolean;
 import static org.mockito.ArgumentMatchers.nullable;
 import static org.mockito.Mockito.anyString;
 import static org.mockito.Mockito.mock;
@@ -682,8 +683,10 @@ public class FhirInstanceValidatorDstu3Test {
 					} else if (t.getMessage().contains("sdf-15") && t.getMessage().contains("The name 'kind' is not valid for any of the possible types")) {
 						// Find constraint sdf-15 fails with stricter core validation.
 						return false;
-					}
+					} else if (t.getMessage().contains("side is inherently a collection") && t.getMessage().endsWith("may fail or return false if there is more than one item in the content being evaluated")) {
-					else {
+						// Some DSTU3 FHIRPath expressions now produce warnings if a singleton is compared to a collection that potentially has > 1 elements
+						return false;
+					} else {
 						return true;
 					}
 				})
@@ -1338,7 +1341,7 @@ public class FhirInstanceValidatorDstu3Test {
 		myInstanceVal.setValidatorPolicyAdvisor(policyAdvisor);
 		myVal.validateWithResult(input);
 
-		verify(fetcher, times(3)).resolveURL(any(), any(), anyString(), anyString(), anyString());
+		verify(fetcher, times(3)).resolveURL(any(), any(), anyString(), anyString(), anyString(), anyBoolean());
 		verify(policyAdvisor, times(4)).policyForReference(any(), any(), anyString(), anyString());
 		verify(fetcher, times(4)).fetch(any(), any(), anyString());
 	}

hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java

@@ -110,6 +110,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyBoolean;
 import static org.mockito.ArgumentMatchers.anyString;
 import static org.mockito.ArgumentMatchers.nullable;
 import static org.mockito.Mockito.mock;
@@ -1273,7 +1274,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
 		ValidationResult output = myFhirValidator.validateWithResult(input);
 		logResultsAndReturnAll(output);
 		assertEquals(
-			"The value provided ('notvalidcode') is not in the value set 'ObservationStatus' (http://hl7.org/fhir/ValueSet/observation-status|4.0.1), and a code is required from this value set) (error message = Unknown code 'notvalidcode' for in-memory expansion of ValueSet 'http://hl7.org/fhir/ValueSet/observation-status')",
+			"The value provided ('notvalidcode') is not in the value set 'ObservationStatus' (http://hl7.org/fhir/ValueSet/observation-status|4.0.1), and a code is required from this value set  (error message = Unknown code 'notvalidcode' for in-memory expansion of ValueSet 'http://hl7.org/fhir/ValueSet/observation-status')",
 			output.getMessages().get(0).getMessage());
 	}
 
@@ -1516,7 +1517,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
 		myInstanceVal.setValidatorPolicyAdvisor(policyAdvisor);
 		myFhirValidator.validateWithResult(encoded);
 
-		verify(resourceFetcher, times(12)).resolveURL(any(), any(), anyString(), anyString(), anyString());
+		verify(resourceFetcher, times(12)).resolveURL(any(), any(), anyString(), anyString(), anyString(), anyBoolean());
 		verify(policyAdvisor, times(12)).policyForContained(any(), any(), any(), any(), any(), any(), any());
 	}
 

hapi-fhir-validation/src/test/java/org/hl7/fhir/r4b/validation/FhirInstanceValidatorR4BTest.java

@@ -77,6 +77,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyBoolean;
 import static org.mockito.ArgumentMatchers.anyString;
 import static org.mockito.ArgumentMatchers.nullable;
 import static org.mockito.Mockito.mock;
@@ -1177,7 +1178,7 @@ public class FhirInstanceValidatorR4BTest extends BaseTest {
 		ValidationResult output = myFhirValidator.validateWithResult(input);
 		logResultsAndReturnAll(output);
 		assertEquals(
-			"The value provided ('notvalidcode') is not in the value set 'ObservationStatus' (http://hl7.org/fhir/ValueSet/observation-status|4.3.0), and a code is required from this value set) (error message = Unknown code 'notvalidcode' for in-memory expansion of ValueSet 'http://hl7.org/fhir/ValueSet/observation-status')",
+			"The value provided ('notvalidcode') is not in the value set 'ObservationStatus' (http://hl7.org/fhir/ValueSet/observation-status|4.3.0), and a code is required from this value set  (error message = Unknown code 'notvalidcode' for in-memory expansion of ValueSet 'http://hl7.org/fhir/ValueSet/observation-status')",
 			output.getMessages().get(0).getMessage());
 	}
 
@@ -1382,7 +1383,7 @@ public class FhirInstanceValidatorR4BTest extends BaseTest {
 		myInstanceVal.setValidatorPolicyAdvisor(policyAdvisor);
 		myFhirValidator.validateWithResult(encoded);
 
-		verify(resourceFetcher, times(12)).resolveURL(any(), any(), anyString(), anyString(), anyString());
+		verify(resourceFetcher, times(12)).resolveURL(any(), any(), anyString(), anyString(), anyString(), anyBoolean());
 		verify(policyAdvisor, times(12)).policyForContained(any(), any(), any(), any(), any(), any(), any());
 	}
 
@@ -1433,7 +1434,7 @@ public class FhirInstanceValidatorR4BTest extends BaseTest {
 		ValidationResult output = myFhirValidator.validateWithResult(input);
 		List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
 		assertEquals(1, errors.size(), errors.toString());
-		assertThat(errors.get(0).getMessage(), containsString("The value provided ('BLAH') is not in the value set 'CurrencyCode' (http://hl7.org/fhir/ValueSet/currencies|4.3.0), and a code is required from this value set) (error message = Unknown code 'BLAH' for in-memory expansion of ValueSet 'http://hl7.org/fhir/ValueSet/currencies')"));
+		assertThat(errors.get(0).getMessage(), containsString("The value provided ('BLAH') is not in the value set 'CurrencyCode' (http://hl7.org/fhir/ValueSet/currencies|4.3.0), and a code is required from this value set  (error message = Unknown code 'BLAH' for in-memory expansion of ValueSet 'http://hl7.org/fhir/ValueSet/currencies')"));
 
 
 	}

hapi-fhir-validation/src/test/java/org/hl7/fhir/r5/validation/FhirInstanceValidatorR5Test.java

@@ -874,7 +874,7 @@ public class FhirInstanceValidatorR5Test {
 		logResultsAndReturnAll(output);
 		assertThat(
 			output.getMessages().get(0).getMessage(),
-			containsString("The value provided ('notvalidcode') is not in the value set 'Observation Status' (http://hl7.org/fhir/ValueSet/observation-status|5.0.0), and a code is required from this value set) (error message = Unknown code 'notvalidcode' for in-memory expansion of ValueSet 'http://hl7.org/fhir/ValueSet/observation-status')")
+			containsString("The value provided ('notvalidcode') is not in the value set 'Observation Status' (http://hl7.org/fhir/ValueSet/observation-status|5.0.0), and a code is required from this value set  (error message = Unknown code 'notvalidcode' for in-memory expansion of ValueSet 'http://hl7.org/fhir/ValueSet/observation-status')")
 			);
 	}
 

pom.xml

@@ -897,12 +897,10 @@
 	</licenses>
 
 	<properties>
-		<fhir_core_version>6.0.22.2</fhir_core_version>
+		<fhir_core_version>6.1.2</fhir_core_version>
 		<spotless_version>2.37.0</spotless_version>
-		<ucum_version>1.0.3</ucum_version>
 		<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>
 
-		<ucum_version>1.0.3</ucum_version>
 
 		<!-- configure timestamp in MANIFEST.MF for maven-war-provider -->
 		<maven.build.timestamp.format>yyyy-MM-dd'T'HH:mm:ss'Z'</maven.build.timestamp.format>
@@ -982,6 +980,7 @@
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 		<ebay_cors_filter_version>1.0.1</ebay_cors_filter_version>
 		<elastic_apm_version>1.28.4</elastic_apm_version>
+		<ucum_version>1.0.8</ucum_version>
 
 		<!-- CQL Support -->
 		<clinical-reasoning.version>3.0.0-PRE5</clinical-reasoning.version>
@@ -1396,7 +1395,7 @@
 			<dependency>
 				<groupId>net.sourceforge.htmlunit</groupId>
 				<artifactId>htmlunit</artifactId>
-				<version>2.67.0</version>
+				<version>2.70.0</version>
 				<exclusions>
 					<exclusion>
 						<!-- Don't let HTMLUnit bring in Jetty 9 -->
@@ -2190,14 +2189,9 @@
 				<scope>test</scope>
 			</dependency>
 			<dependency>
-				<groupId>xpp3</groupId>
+				<groupId>org.ogce</groupId>
 				<artifactId>xpp3</artifactId>
-				<version>1.1.4c</version>
+				<version>1.1.6</version>
-			</dependency>
-			<dependency>
-				<groupId>xpp3</groupId>
-				<artifactId>xpp3_xpath</artifactId>
-				<version>1.1.4c</version>
 			</dependency>
 			<dependency>
 				<groupId>org.flywaydb</groupId>