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>
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@ -151,6 +151,10 @@
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<groupId>net.bytebuddy</groupId>
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<artifactId>byte-buddy</artifactId>
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</dependency>
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<dependency>
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<groupId>com.sun.xml.bind</groupId>
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<artifactId>jaxb-impl</artifactId>
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</dependency>
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</ignoredDependencies>
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<ignoredResourcePatterns>
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<ignoredResourcePattern>.*\.txt$</ignoredResourcePattern>
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@ -24,15 +24,21 @@ import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.util.BundleUtil;
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import ca.uhn.fhir.validation.*;
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import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.IValidationContext;
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import ca.uhn.fhir.validation.IValidatorModule;
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import ca.uhn.fhir.validation.ResultSeverityEnum;
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import ca.uhn.fhir.validation.SchemaBaseValidator;
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import ca.uhn.fhir.validation.SingleValidationMessage;
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import ca.uhn.fhir.validation.ValidationContext;
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import com.helger.commons.error.IError;
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import com.helger.commons.error.list.IErrorList;
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import com.helger.schematron.ISchematronResource;
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import com.helger.schematron.SchematronHelper;
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import com.helger.schematron.svrl.jaxb.SchematronOutputType;
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import com.helger.schematron.xslt.SchematronResourceSCH;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.oclc.purl.dsdl.svrl.SchematronOutputType;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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@ -2,6 +2,7 @@
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ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionRefersToUnknownCs=Unknown CodeSystem URI "{0}" referenced from ValueSet
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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}
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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.
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ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.valueSetExpandedUsingPreExpansion=ValueSet was expanded using a pre-calculated expansion
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@ -18,4 +18,6 @@
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* Lucene(HAPI FHIR JPA Server): 5.5.5 -> 8.7.0
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* Spring Boot (JPA Starter): 2.2.6.RELEASE -> 2.4.1
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* JANSI (CLI): 1.18 -> 2.1.1
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* PH-Schematron (SCH Validator): 5.2.0 -> 5.6.5
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* PH-Commons (SCH Validator): 5.3.8 -> 9.5.4
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"
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@ -521,6 +521,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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/*
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* ValueSet is pre-expanded in database so let's use that
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*/
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String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "valueSetExpandedUsingPreExpansion");
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theAccumulator.addMessage(msg);
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expandConcepts(theAccumulator, termValueSet, theFilter, theAdd);
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}
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@ -812,7 +812,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
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Optional<ValueSet.ValueSetExpansionContainsComponent> first = stream.findFirst();
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if (!first.isPresent()) {
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String failureMessage = String.format("Expanded ValueSet %s did not contain concept [%s|%s|%s] with [%d] designations", theValueSet.getId(), theSystem, theCode, theDisplay, theDesignationCount);
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String expandedValueSetString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(theValueSet);
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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);
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fail(failureMessage);
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return null;
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} else {
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@ -655,6 +655,11 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
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CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
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ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
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// If this ever fails, it just means that new codes have been added to the
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// code system used by this test, so the numbers below may also need to be
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// updated
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assertEquals(24, codeSystem.getConcept().size());
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ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
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ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
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@ -662,9 +667,11 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
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ValueSetExpansionOptions options = new ValueSetExpansionOptions()
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.setOffset(0)
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.setCount(23);
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.setCount(24);
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ValueSet expandedValueSet = myTermSvc.expandValueSet(options, valueSet);
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ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
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String expandedValueSetString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet);
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ourLog.info("Expanded ValueSet:\n" + expandedValueSetString);
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assertThat(expandedValueSetString, containsString("ValueSet was expanded using a pre-calculated expansion"));
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assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
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assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffset(), expandedValueSet.getExpansion().getOffset());
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@ -672,9 +679,9 @@ public class ValueSetExpansionR4Test extends BaseTermR4Test {
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assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
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assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
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assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
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assertEquals(23, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
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assertEquals(24, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
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assertEquals(23, expandedValueSet.getExpansion().getContains().size());
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assertEquals(24, expandedValueSet.getExpansion().getContains().size());
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ValueSet.ValueSetExpansionContainsComponent concept = assertExpandedValueSetContainsConcept(expandedValueSet, "http://acme.org", "8450-9", "Systolic blood pressure--expiration", 2);
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10
pom.xml
10
pom.xml
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@ -767,8 +767,8 @@
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<maven_assembly_plugin_version>3.1.0</maven_assembly_plugin_version>
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<maven_license_plugin_version>1.8</maven_license_plugin_version>
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<resteasy_version>4.0.0.Beta3</resteasy_version>
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<ph_schematron_version>5.2.0</ph_schematron_version>
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<ph_commons_version>9.3.8</ph_commons_version>
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<ph_schematron_version>5.6.5</ph_schematron_version>
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<ph_commons_version>9.5.4</ph_commons_version>
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<plexus_compiler_api_version>2.8.8</plexus_compiler_api_version>
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<servicemix_saxon_version>9.8.0-15</servicemix_saxon_version>
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<servicemix_xmlresolver_version>1.2_5</servicemix_xmlresolver_version>
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@ -892,6 +892,12 @@
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<groupId>com.helger</groupId>
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<artifactId>ph-schematron</artifactId>
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<version>${ph_schematron_version}</version>
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<exclusions>
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<exclusion>
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<groupId>jakarta.xml.bind</groupId>
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<artifactId>jakarta.xml.bind-api</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>com.helger</groupId>
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