5771 patch operation failing for complex extension (#5776)
* initial failing test * tightening initial test. * fix with changelog * addressing comment from code review. * clean up from code analysis recommendations --------- Co-authored-by: peartree <etienne.poirier@smilecdr.com>
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Etienne Poirier
GitHub
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@ -0,0 +1,6 @@
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---
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type: fix
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issue: 5771
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jira: SMILE-7837
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title: "Previously, a Patch operation would fail when adding a complex extension, i.e. an extension
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comprised of another extension. This issue has been fixed."
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@ -12,6 +12,7 @@ import org.hl7.fhir.r4.model.BooleanType;
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import org.hl7.fhir.r4.model.CodeType;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.Coding;
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import org.hl7.fhir.r4.model.DateTimeType;
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import org.hl7.fhir.r4.model.Extension;
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import org.hl7.fhir.r4.model.HumanName;
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import org.hl7.fhir.r4.model.Identifier;
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@ -37,6 +38,7 @@ import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.equalTo;
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import static org.hamcrest.Matchers.hasSize;
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import static org.hamcrest.Matchers.is;
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import static org.hamcrest.Matchers.notNullValue;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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@ -531,6 +533,59 @@ public class FhirPatchApplyR4Test {
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assertThat(patient.getExtension().get(0).getValueAsPrimitive().getValueAsString(), is(equalTo("foo")));
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}
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@Test
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public void testAddExtensionWithExtension() {
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final String extensionUrl = "http://foo/fhir/extension/foo";
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final String innerExtensionUrl = "http://foo/fhir/extension/innerExtension";
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final String innerExtensionValue = "2021-07-24T13:23:30-04:00";
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FhirPatch svc = new FhirPatch(ourCtx);
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Patient patient = new Patient();
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Parameters patch = new Parameters();
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Parameters.ParametersParameterComponent addOperation = createPatchAddOperation("Patient", "extension", null);
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addOperation
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.addPart()
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.setName("value")
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.addPart(
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new Parameters.ParametersParameterComponent()
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.setName("url")
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.setValue(new UriType(extensionUrl))
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)
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.addPart(
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new Parameters.ParametersParameterComponent()
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.setName("extension")
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.addPart(
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new Parameters.ParametersParameterComponent()
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.setName("url")
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.setValue(new UriType(innerExtensionUrl))
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)
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.addPart(
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new Parameters.ParametersParameterComponent()
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.setName("value")
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.setValue(new DateTimeType(innerExtensionValue))
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)
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);
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patch.addParameter(addOperation);
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ourLog.info("Patch:\n{}", ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patch));
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svc.apply(patient, patch);
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ourLog.debug("Outcome:\n{}", ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
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//Then: it adds the new extension correctly.
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assertThat(patient.getExtension(), hasSize(1));
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Extension extension = patient.getExtension().get(0);
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assertThat(extension.getUrl(), is(equalTo(extensionUrl)));
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Extension innerExtension = extension.getExtensionFirstRep();
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assertThat(innerExtension, notNullValue());
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assertThat(innerExtension.getUrl(), is(equalTo(innerExtensionUrl)));
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assertThat(innerExtension.getValue().primitiveValue(), is(equalTo(innerExtensionValue)));
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}
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private Parameters.ParametersParameterComponent createPatchAddOperation(String thePath, String theName, Type theValue) {
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return createPatchOperation("add", thePath, theName, theValue, null);
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}
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@ -30,10 +30,10 @@ import ca.uhn.fhir.util.IModelVisitor2;
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import ca.uhn.fhir.util.ParametersUtil;
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import jakarta.annotation.Nonnull;
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import jakarta.annotation.Nullable;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.Validate;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseEnumeration;
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import org.hl7.fhir.instance.model.api.IBaseExtension;
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import org.hl7.fhir.instance.model.api.IBaseParameters;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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@ -49,7 +49,6 @@ import java.util.Optional;
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import java.util.Set;
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import static org.apache.commons.lang3.StringUtils.defaultString;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public class FhirPatch {
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@ -319,12 +318,9 @@ public class FhirPatch {
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if (valuePartValue.isPresent()) {
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newValue = valuePartValue.get();
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} else {
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newValue = theChildDefinition.getChildElement().newInstance();
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List<IBase> partParts = valuePart.map(this::extractPartsFromPart).orElse(Collections.emptyList());
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if (valuePart.isPresent()) {
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IBase theValueElement = valuePart.get();
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populateNewValue(theChildDefinition, newValue, theValueElement);
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}
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newValue = createAndPopulateNewElement(theChildDefinition, partParts);
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}
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if (IBaseEnumeration.class.isAssignableFrom(
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@ -350,31 +346,65 @@ public class FhirPatch {
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return newValue;
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}
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private void populateNewValue(ChildDefinition theChildDefinition, IBase theNewValue, IBase theValueElement) {
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List<IBase> valuePartParts = myContext.newTerser().getValues(theValueElement, "part");
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for (IBase nextValuePartPart : valuePartParts) {
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@Nonnull
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private List<IBase> extractPartsFromPart(IBase theParametersParameterComponent) {
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return myContext.newTerser().getValues(theParametersParameterComponent, "part");
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}
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/**
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* this method will instantiate an element according to the provided Definition and it according to
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* the properties found in thePartParts. a part usually represent a datatype as a name/value[X] pair.
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* it may also represent a complex type like an Extension.
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*
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* @param theDefinition wrapper around the runtime definition of the element to be populated
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* @param thePartParts list of Part to populate the element that will be created from theDefinition
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* @return an element that was created from theDefinition and populated with the parts
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*/
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private IBase createAndPopulateNewElement(ChildDefinition theDefinition, List<IBase> thePartParts) {
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IBase newElement = theDefinition.getChildElement().newInstance();
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for (IBase nextValuePartPart : thePartParts) {
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String name = myContext
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.newTerser()
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.getSingleValue(nextValuePartPart, PARAMETER_NAME, IPrimitiveType.class)
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.map(IPrimitiveType::getValueAsString)
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.orElse(null);
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if (isNotBlank(name)) {
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Optional<IBase> value =
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myContext.newTerser().getSingleValue(nextValuePartPart, "value[x]", IBase.class);
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if (StringUtils.isBlank(name)) {
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continue;
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}
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Optional<IBase> value = myContext.newTerser().getSingleValue(nextValuePartPart, "value[x]", IBase.class);
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if (value.isPresent()) {
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// we have a dataType. let's extract its value and assign it.
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BaseRuntimeChildDefinition partChildDef =
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theChildDefinition.getChildElement().getChildByName(name);
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theDefinition.getChildElement().getChildByName(name);
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if (partChildDef == null) {
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name = name + "[x]";
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partChildDef = theChildDefinition.getChildElement().getChildByName(name);
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}
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partChildDef.getMutator().addValue(theNewValue, value.get());
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partChildDef = theDefinition.getChildElement().getChildByName(name);
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}
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partChildDef.getMutator().addValue(newElement, value.get());
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// a part represent a datatype or a complexType but not both at the same time.
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continue;
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}
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List<IBase> part = extractPartsFromPart(nextValuePartPart);
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if (!part.isEmpty()) {
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// we have a complexType. let's find its definition and recursively process
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// them till all complexTypes are processed.
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ChildDefinition childDefinition = findChildDefinition(newElement, name);
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IBase childNewValue = createAndPopulateNewElement(childDefinition, part);
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childDefinition.getChildDef().getMutator().setValue(newElement, childNewValue);
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}
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}
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return newElement;
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}
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private void deleteSingleElement(IBase theElementToDelete) {
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@ -390,17 +420,6 @@ public class FhirPatch {
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}
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return true;
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}
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@Override
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public boolean acceptUndeclaredExtension(
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IBaseExtension<?, ?> theNextExt,
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List<IBase> theContainingElementPath,
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List<BaseRuntimeChildDefinition> theChildDefinitionPath,
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List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
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theNextExt.setUrl(null);
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theNextExt.setValue(null);
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return true;
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}
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});
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}
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@ -565,7 +584,7 @@ public class FhirPatch {
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* If the value is a Resource or a datatype, we can put it into the part.value and that will cover
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* all of its children. If it's an infrastructure element though, such as Patient.contact we can't
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* just put it into part.value because it isn't an actual type. So we have to put all of its
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* childen in instead.
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* children in instead.
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*/
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if (valueDef.isStandardType()) {
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ParametersUtil.addPart(myContext, operation, PARAMETER_VALUE, value);
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