Bump ph-schematron from 5.2.0 to 5.6.5 (#2184)

* Bump ph-schematron from 5.2.0 to 5.6.5

Bumps [ph-schematron](https://github.com/phax/ph-schematron) from 5.2.0 to 5.6.5.
- [Release notes](https://github.com/phax/ph-schematron/releases)
- [Commits](https://github.com/phax/ph-schematron/compare/ph-schematron-parent-pom-5.2.0...ph-schematron-parent-pom-5.6.5)

Signed-off-by: dependabot[bot] <support@github.com>

* Fix compile error

* Build fix

* Add test logging

* Test fix

* Resolve classpath duplicates

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>

hapi-deployable-pom/pom.xml

@@ -151,6 +151,10 @@
 							<groupId>net.bytebuddy</groupId>
 							<artifactId>byte-buddy</artifactId>
 						</dependency>
+						<dependency>
+							<groupId>com.sun.xml.bind</groupId>
+							<artifactId>jaxb-impl</artifactId>
+						</dependency>
 					</ignoredDependencies>
 					<ignoredResourcePatterns>
 						<ignoredResourcePattern>.*\.txt$</ignoredResourcePattern>

hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/schematron/SchematronBaseValidator.java

@@ -24,15 +24,21 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.util.BundleUtil;
-import ca.uhn.fhir.validation.*;
+import ca.uhn.fhir.validation.FhirValidator;
+import ca.uhn.fhir.validation.IValidationContext;
+import ca.uhn.fhir.validation.IValidatorModule;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+import ca.uhn.fhir.validation.SchemaBaseValidator;
+import ca.uhn.fhir.validation.SingleValidationMessage;
+import ca.uhn.fhir.validation.ValidationContext;
 import com.helger.commons.error.IError;
 import com.helger.commons.error.list.IErrorList;
 import com.helger.schematron.ISchematronResource;
 import com.helger.schematron.SchematronHelper;
+import com.helger.schematron.svrl.jaxb.SchematronOutputType;
 import com.helger.schematron.xslt.SchematronResourceSCH;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.oclc.purl.dsdl.svrl.SchematronOutputType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -2,6 +2,7 @@
 ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionRefersToUnknownCs=Unknown CodeSystem URI "{0}" referenced from ValueSet
 ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.valueSetNotYetExpanded=ValueSet "{0}" has not yet been pre-expanded. Performing in-memory expansion without parameters. Current status: {1} | {2}
 ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.valueSetNotYetExpanded_OffsetNotAllowed=ValueSet expansion can not combine "offset" with "ValueSet.compose.exclude" unless the ValueSet has been pre-expanded. ValueSet "{0}" must be pre-expanded for this operation to work.
+ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.valueSetExpandedUsingPreExpansion=ValueSet was expanded using a pre-calculated expansion
 
 
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_0/changes.yaml

@@ -18,4 +18,6 @@
 * Lucene(HAPI FHIR JPA Server): 5.5.5 -> 8.7.0
 * Spring Boot (JPA Starter): 2.2.6.RELEASE -> 2.4.1
 * JANSI (CLI):  1.18 -> 2.1.1
+* PH-Schematron (SCH Validator): 5.2.0 -> 5.6.5
+* PH-Commons (SCH Validator): 5.3.8 -> 9.5.4
 "

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java

@@ -521,6 +521,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
 		/*
 		 * ValueSet is pre-expanded in database so let's use that
 		 */
+		String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "valueSetExpandedUsingPreExpansion");
+		theAccumulator.addMessage(msg);
 		expandConcepts(theAccumulator, termValueSet, theFilter, theAdd);
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -812,7 +812,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
 
 		Optional<ValueSet.ValueSetExpansionContainsComponent> first = stream.findFirst();
 		if (!first.isPresent()) {
-			String failureMessage = String.format("Expanded ValueSet %s did not contain concept [%s|%s|%s] with [%d] designations", theValueSet.getId(), theSystem, theCode, theDisplay, theDesignationCount);
+			String expandedValueSetString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(theValueSet);
+			String failureMessage = String.format("Expanded ValueSet %s did not contain concept [%s|%s|%s] with [%d] designations. Outcome:\n%s", theValueSet.getId(), theSystem, theCode, theDisplay, theDesignationCount, expandedValueSetString);
 			fail(failureMessage);
 			return null;
 		} else {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4Test.java

@@ -655,6 +655,11 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
 		CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
 		ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
 
+		// If this ever fails, it just means that new codes have been added to the
+		// code system used by this test, so the numbers below may also need to be
+		// updated
+		assertEquals(24, codeSystem.getConcept().size());
+
 		ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
 		ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
 
@@ -662,9 +667,11 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
 
 		ValueSetExpansionOptions options = new ValueSetExpansionOptions()
 			.setOffset(0)
-			.setCount(23);
+			.setCount(24);
 		ValueSet expandedValueSet = myTermSvc.expandValueSet(options, valueSet);
-		ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
+		String expandedValueSetString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet);
+		ourLog.info("Expanded ValueSet:\n" + expandedValueSetString);
+		assertThat(expandedValueSetString, containsString("ValueSet was expanded using a pre-calculated expansion"));
 
 		assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
 		assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffset(), expandedValueSet.getExpansion().getOffset());
@@ -672,9 +679,9 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
 		assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
 		assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
 		assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
-		assertEquals(23, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
+		assertEquals(24, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
 
-		assertEquals(23, expandedValueSet.getExpansion().getContains().size());
+		assertEquals(24, expandedValueSet.getExpansion().getContains().size());
 
 		ValueSet.ValueSetExpansionContainsComponent concept = assertExpandedValueSetContainsConcept(expandedValueSet, "http://acme.org", "8450-9", "Systolic blood pressure--expiration", 2);
 

pom.xml

@@ -767,8 +767,8 @@
 		<maven_assembly_plugin_version>3.1.0</maven_assembly_plugin_version>
 		<maven_license_plugin_version>1.8</maven_license_plugin_version>
 		<resteasy_version>4.0.0.Beta3</resteasy_version>
-		<ph_schematron_version>5.2.0</ph_schematron_version>
+		<ph_schematron_version>5.6.5</ph_schematron_version>
-		<ph_commons_version>9.3.8</ph_commons_version>
+		<ph_commons_version>9.5.4</ph_commons_version>
 		<plexus_compiler_api_version>2.8.8</plexus_compiler_api_version>
 		<servicemix_saxon_version>9.8.0-15</servicemix_saxon_version>
 		<servicemix_xmlresolver_version>1.2_5</servicemix_xmlresolver_version>
@@ -892,6 +892,12 @@
 				<groupId>com.helger</groupId>
 				<artifactId>ph-schematron</artifactId>
 				<version>${ph_schematron_version}</version>
+				<exclusions>
+					<exclusion>
+						<groupId>jakarta.xml.bind</groupId>
+						<artifactId>jakarta.xml.bind-api</artifactId>
+               </exclusion>
+				</exclusions>
 			</dependency>
 			<dependency>
 				<groupId>com.helger</groupId>