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>
This commit is contained in:
Etienne Poirier 2024-03-12 13:59:36 -04:00 committed by GitHub
parent 2f53a32f9d
commit fc4c31a779
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3 changed files with 113 additions and 33 deletions

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@ -0,0 +1,6 @@
---
type: fix
issue: 5771
jira: SMILE-7837
title: "Previously, a Patch operation would fail when adding a complex extension, i.e. an extension
comprised of another extension. This issue has been fixed."

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@ -12,6 +12,7 @@ import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeType; import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept; import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding; import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Extension; import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.HumanName; import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.Identifier; import org.hl7.fhir.r4.model.Identifier;
@ -37,6 +38,7 @@ import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.equalTo; import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.hasSize; import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.is; import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.notNullValue;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue; import static org.junit.jupiter.api.Assertions.assertTrue;
@ -531,6 +533,59 @@ public class FhirPatchApplyR4Test {
assertThat(patient.getExtension().get(0).getValueAsPrimitive().getValueAsString(), is(equalTo("foo"))); assertThat(patient.getExtension().get(0).getValueAsPrimitive().getValueAsString(), is(equalTo("foo")));
} }
@Test
public void testAddExtensionWithExtension() {
final String extensionUrl = "http://foo/fhir/extension/foo";
final String innerExtensionUrl = "http://foo/fhir/extension/innerExtension";
final String innerExtensionValue = "2021-07-24T13:23:30-04:00";
FhirPatch svc = new FhirPatch(ourCtx);
Patient patient = new Patient();
Parameters patch = new Parameters();
Parameters.ParametersParameterComponent addOperation = createPatchAddOperation("Patient", "extension", null);
addOperation
.addPart()
.setName("value")
.addPart(
new Parameters.ParametersParameterComponent()
.setName("url")
.setValue(new UriType(extensionUrl))
)
.addPart(
new Parameters.ParametersParameterComponent()
.setName("extension")
.addPart(
new Parameters.ParametersParameterComponent()
.setName("url")
.setValue(new UriType(innerExtensionUrl))
)
.addPart(
new Parameters.ParametersParameterComponent()
.setName("value")
.setValue(new DateTimeType(innerExtensionValue))
)
);
patch.addParameter(addOperation);
ourLog.info("Patch:\n{}", ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patch));
svc.apply(patient, patch);
ourLog.debug("Outcome:\n{}", ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
//Then: it adds the new extension correctly.
assertThat(patient.getExtension(), hasSize(1));
Extension extension = patient.getExtension().get(0);
assertThat(extension.getUrl(), is(equalTo(extensionUrl)));
Extension innerExtension = extension.getExtensionFirstRep();
assertThat(innerExtension, notNullValue());
assertThat(innerExtension.getUrl(), is(equalTo(innerExtensionUrl)));
assertThat(innerExtension.getValue().primitiveValue(), is(equalTo(innerExtensionValue)));
}
private Parameters.ParametersParameterComponent createPatchAddOperation(String thePath, String theName, Type theValue) { private Parameters.ParametersParameterComponent createPatchAddOperation(String thePath, String theName, Type theValue) {
return createPatchOperation("add", thePath, theName, theValue, null); return createPatchOperation("add", thePath, theName, theValue, null);
} }

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@ -30,10 +30,10 @@ import ca.uhn.fhir.util.IModelVisitor2;
import ca.uhn.fhir.util.ParametersUtil; import ca.uhn.fhir.util.ParametersUtil;
import jakarta.annotation.Nonnull; import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable; import jakarta.annotation.Nullable;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate; import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase; import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseEnumeration; import org.hl7.fhir.instance.model.api.IBaseEnumeration;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseParameters; import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType; import org.hl7.fhir.instance.model.api.IIdType;
@ -49,7 +49,6 @@ import java.util.Optional;
import java.util.Set; import java.util.Set;
import static org.apache.commons.lang3.StringUtils.defaultString; import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirPatch { public class FhirPatch {
@ -319,12 +318,9 @@ public class FhirPatch {
if (valuePartValue.isPresent()) { if (valuePartValue.isPresent()) {
newValue = valuePartValue.get(); newValue = valuePartValue.get();
} else { } else {
newValue = theChildDefinition.getChildElement().newInstance(); List<IBase> partParts = valuePart.map(this::extractPartsFromPart).orElse(Collections.emptyList());
if (valuePart.isPresent()) { newValue = createAndPopulateNewElement(theChildDefinition, partParts);
IBase theValueElement = valuePart.get();
populateNewValue(theChildDefinition, newValue, theValueElement);
}
} }
if (IBaseEnumeration.class.isAssignableFrom( if (IBaseEnumeration.class.isAssignableFrom(
@ -350,31 +346,65 @@ public class FhirPatch {
return newValue; return newValue;
} }
private void populateNewValue(ChildDefinition theChildDefinition, IBase theNewValue, IBase theValueElement) { @Nonnull
List<IBase> valuePartParts = myContext.newTerser().getValues(theValueElement, "part"); private List<IBase> extractPartsFromPart(IBase theParametersParameterComponent) {
for (IBase nextValuePartPart : valuePartParts) { return myContext.newTerser().getValues(theParametersParameterComponent, "part");
}
/**
* this method will instantiate an element according to the provided Definition and it according to
* the properties found in thePartParts. a part usually represent a datatype as a name/value[X] pair.
* it may also represent a complex type like an Extension.
*
* @param theDefinition wrapper around the runtime definition of the element to be populated
* @param thePartParts list of Part to populate the element that will be created from theDefinition
* @return an element that was created from theDefinition and populated with the parts
*/
private IBase createAndPopulateNewElement(ChildDefinition theDefinition, List<IBase> thePartParts) {
IBase newElement = theDefinition.getChildElement().newInstance();
for (IBase nextValuePartPart : thePartParts) {
String name = myContext String name = myContext
.newTerser() .newTerser()
.getSingleValue(nextValuePartPart, PARAMETER_NAME, IPrimitiveType.class) .getSingleValue(nextValuePartPart, PARAMETER_NAME, IPrimitiveType.class)
.map(IPrimitiveType::getValueAsString) .map(IPrimitiveType::getValueAsString)
.orElse(null); .orElse(null);
if (isNotBlank(name)) {
Optional<IBase> value = if (StringUtils.isBlank(name)) {
myContext.newTerser().getSingleValue(nextValuePartPart, "value[x]", IBase.class); continue;
if (value.isPresent()) { }
BaseRuntimeChildDefinition partChildDef = Optional<IBase> value = myContext.newTerser().getSingleValue(nextValuePartPart, "value[x]", IBase.class);
theChildDefinition.getChildElement().getChildByName(name);
if (partChildDef == null) { if (value.isPresent()) {
name = name + "[x]"; // we have a dataType. let's extract its value and assign it.
partChildDef = theChildDefinition.getChildElement().getChildByName(name); BaseRuntimeChildDefinition partChildDef =
} theDefinition.getChildElement().getChildByName(name);
partChildDef.getMutator().addValue(theNewValue, value.get()); if (partChildDef == null) {
name = name + "[x]";
partChildDef = theDefinition.getChildElement().getChildByName(name);
} }
partChildDef.getMutator().addValue(newElement, value.get());
// a part represent a datatype or a complexType but not both at the same time.
continue;
}
List<IBase> part = extractPartsFromPart(nextValuePartPart);
if (!part.isEmpty()) {
// we have a complexType. let's find its definition and recursively process
// them till all complexTypes are processed.
ChildDefinition childDefinition = findChildDefinition(newElement, name);
IBase childNewValue = createAndPopulateNewElement(childDefinition, part);
childDefinition.getChildDef().getMutator().setValue(newElement, childNewValue);
} }
} }
return newElement;
} }
private void deleteSingleElement(IBase theElementToDelete) { private void deleteSingleElement(IBase theElementToDelete) {
@ -390,17 +420,6 @@ public class FhirPatch {
} }
return true; return true;
} }
@Override
public boolean acceptUndeclaredExtension(
IBaseExtension<?, ?> theNextExt,
List<IBase> theContainingElementPath,
List<BaseRuntimeChildDefinition> theChildDefinitionPath,
List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
theNextExt.setUrl(null);
theNextExt.setValue(null);
return true;
}
}); });
} }
@ -565,7 +584,7 @@ public class FhirPatch {
* If the value is a Resource or a datatype, we can put it into the part.value and that will cover * If the value is a Resource or a datatype, we can put it into the part.value and that will cover
* all of its children. If it's an infrastructure element though, such as Patient.contact we can't * all of its children. If it's an infrastructure element though, such as Patient.contact we can't
* just put it into part.value because it isn't an actual type. So we have to put all of its * just put it into part.value because it isn't an actual type. So we have to put all of its
* childen in instead. * children in instead.
*/ */
if (valueDef.isStandardType()) { if (valueDef.isStandardType()) {
ParametersUtil.addPart(myContext, operation, PARAMETER_VALUE, value); ParametersUtil.addPart(myContext, operation, PARAMETER_VALUE, value);