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Jr 20241008 merge data absent reason (#6370) 

* handle single cardinality case

* multiple cardinality case

* change log
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JasonRoberts-smile 2024-10-15 11:47:32 -04:00 committed by GitHub
parent 239bf8d441
commit b08c59528d
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3 changed files with 160 additions and 9 deletions
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58
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TerserUtil.java
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@ -26,10 +26,12 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.tuple.Triple;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
@ -93,6 +95,8 @@ public final class TerserUtil {
private static final Logger ourLog = getLogger(TerserUtil.class);
private static final String EQUALS_DEEP = "equalsDeep";
public static final String DATA_ABSENT_REASON_EXTENSION_URI =
"http://hl7.org/fhir/StructureDefinition/data-absent-reason";
private TerserUtil() {}
@ -266,6 +270,15 @@ public final class TerserUtil {
return theItems.stream().anyMatch(i -> equals(i, theItem, method));
}
private static boolean hasDataAbsentReason(IBase theItem) {
if (theItem instanceof IBaseHasExtensions) {
IBaseHasExtensions hasExtensions = (IBaseHasExtensions) theItem;
return hasExtensions.getExtension().stream()
.anyMatch(t -> StringUtils.equals(t.getUrl(), DATA_ABSENT_REASON_EXTENSION_URI));
}
return false;
}
/**
* Merges all fields on the provided instance. <code>theTo</code> will contain a union of all values from <code>theFrom</code>
* instance and <code>theTo</code> instance.
@ -695,24 +708,36 @@ public final class TerserUtil {
BaseRuntimeChildDefinition childDefinition,
List<IBase> theFromFieldValues,
List<IBase> theToFieldValues) {
for (IBase theFromFieldValue : theFromFieldValues) {
if (contains(theFromFieldValue, theToFieldValues)) {
if (!theFromFieldValues.isEmpty() && theToFieldValues.stream().anyMatch(TerserUtil::hasDataAbsentReason)) {
// If the to resource has a data absent reason, and there is potentially real data incoming
// in the from resource, we should clear the data absent reason because it won't be absent anymore.
theToFieldValues = removeDataAbsentReason(theTo, childDefinition, theToFieldValues);
}
for (IBase fromFieldValue : theFromFieldValues) {
if (contains(fromFieldValue, theToFieldValues)) {
continue;
}
IBase newFieldValue = newElement(theTerser, childDefinition, theFromFieldValue, null);
if (theFromFieldValue instanceof IPrimitiveType) {
if (hasDataAbsentReason(fromFieldValue) && !theToFieldValues.isEmpty()) {
// if the from field value asserts a reason the field isn't populated, but the to field is populated,
// we don't want to overwrite real data with the extension
continue;
}
IBase newFieldValue = newElement(theTerser, childDefinition, fromFieldValue, null);
if (fromFieldValue instanceof IPrimitiveType) {
try {
Method copyMethod = getMethod(theFromFieldValue, "copy");
Method copyMethod = getMethod(fromFieldValue, "copy");
if (copyMethod != null) {
newFieldValue = (IBase) copyMethod.invoke(theFromFieldValue, new Object[] {});
newFieldValue = (IBase) copyMethod.invoke(fromFieldValue, new Object[] {});
}
} catch (Throwable t) {
((IPrimitiveType) newFieldValue)
.setValueAsString(((IPrimitiveType) theFromFieldValue).getValueAsString());
((IPrimitiveType<?>) newFieldValue)
.setValueAsString(((IPrimitiveType<?>) fromFieldValue).getValueAsString());
}
} else {
theTerser.cloneInto(theFromFieldValue, newFieldValue, true);
theTerser.cloneInto(fromFieldValue, newFieldValue, true);
}
try {
@ -724,6 +749,21 @@ public final class TerserUtil {
}
}
private static List<IBase> removeDataAbsentReason(
IBaseResource theResource, BaseRuntimeChildDefinition theFieldDefinition, List<IBase> theFieldValues) {
for (int i = 0; i < theFieldValues.size(); i++) {
if (hasDataAbsentReason(theFieldValues.get(i))) {
try {
theFieldDefinition.getMutator().remove(theResource, i);
} catch (UnsupportedOperationException e) {
// the field must be single-valued, just clear it
theFieldDefinition.getMutator().setValue(theResource, null);
}
}
}
return theFieldDefinition.getAccessor().getValues(theResource);
}
/**
* Clones the specified resource.
*

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6370-data-absent-merge.yaml Normal file
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@ -0,0 +1,6 @@
---
type: add
issue: 6370
title: "When using the FHIR `TerserUtil` to merge two resource, if one resource has real data in a particular field,
and the other resource has a `data-absent-reason` extension in the same field, the real data will be given
precedence in the merged resource, and the extension will be ignored."

105
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/TerserUtilTest.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.util;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.r4.model.Address;
@ -10,10 +11,12 @@ import org.hl7.fhir.r4.model.Claim;
import org.hl7.fhir.r4.model.Condition;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.Enumeration;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
@ -21,9 +24,14 @@ import org.hl7.fhir.r4.model.PrimitiveType;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.StringType;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import java.util.Date;
import java.util.List;
import java.util.UUID;
import java.util.stream.Stream;
import static org.assertj.core.api.Assertions.assertThat;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ -118,6 +126,7 @@ class TerserUtilTest {
]
}
""";
public static final String DATA_ABSENT_REASON_EXTENSION_URI = "http://hl7.org/fhir/StructureDefinition/data-absent-reason";
@Test
void cloneIdentifierIntoResource() {
@ -417,6 +426,102 @@ class TerserUtilTest {
assertThat(c2.getRecorder().getResource()).isSameAs(practitioner);
}
@ParameterizedTest
@MethodSource("singleCardinalityArguments")
public void testMergeWithDataAbsentReason_singleCardinality(
Enumeration<Observation.ObservationStatus> theFromStatus,
Enumeration<Observation.ObservationStatus> theToStatus,
Enumeration<Observation.ObservationStatus> theExpectedStatus) {
Observation fromObservation = new Observation();
fromObservation.setStatusElement(theFromStatus);
Observation toObservation = new Observation();
toObservation.setStatusElement(theToStatus);
TerserUtil.mergeField(ourFhirContext, "status", fromObservation, toObservation);
if (theExpectedStatus == null) {
assertThat(toObservation.hasStatus()).isFalse();
} else {
assertThat(toObservation.getStatusElement().getCode()).isEqualTo(theExpectedStatus.getCode());
}
}
private static Stream<Arguments> singleCardinalityArguments() {
return Stream.of(
Arguments.of(null, null, null),
Arguments.of(statusFromEnum(Observation.ObservationStatus.FINAL), null, statusFromEnum(Observation.ObservationStatus.FINAL)),
Arguments.of(null, statusFromEnum(Observation.ObservationStatus.FINAL), statusFromEnum(Observation.ObservationStatus.FINAL)),
Arguments.of(statusFromEnum(Observation.ObservationStatus.FINAL), statusFromEnum(Observation.ObservationStatus.PRELIMINARY), statusFromEnum(Observation.ObservationStatus.FINAL)),
Arguments.of(statusWithDataAbsentReason(), null, statusWithDataAbsentReason()),
Arguments.of(null, statusWithDataAbsentReason(), statusWithDataAbsentReason()),
Arguments.of(statusWithDataAbsentReason(), statusWithDataAbsentReason(), statusWithDataAbsentReason()),
Arguments.of(statusFromEnum(Observation.ObservationStatus.FINAL), statusWithDataAbsentReason(), statusFromEnum(Observation.ObservationStatus.FINAL)),
Arguments.of(statusWithDataAbsentReason(), statusFromEnum(Observation.ObservationStatus.FINAL), statusFromEnum(Observation.ObservationStatus.FINAL))
);
}
private static Enumeration<Observation.ObservationStatus> statusFromEnum(Observation.ObservationStatus theStatus) {
return new Enumeration<>(new Observation.ObservationStatusEnumFactory(), theStatus);
}
private static Enumeration<Observation.ObservationStatus> statusWithDataAbsentReason() {
Enumeration<Observation.ObservationStatus> enumeration = new Enumeration<>(new Observation.ObservationStatusEnumFactory());
Enumeration<Enumerations.DataAbsentReason> extension = new Enumeration<>(new Enumerations.DataAbsentReasonEnumFactory(), Enumerations.DataAbsentReason.UNKNOWN);
enumeration.addExtension(DATA_ABSENT_REASON_EXTENSION_URI, extension);
return enumeration;
}
@ParameterizedTest
@MethodSource("multipleCardinalityArguments")
public void testMergeWithDataAbsentReason_multipleCardinality(
List<Identifier> theFromIdentifiers, List<Identifier> theToIdentifiers, List<Identifier> theExpectedIdentifiers) {
Observation fromObservation = new Observation();
theFromIdentifiers.forEach(fromObservation::addIdentifier);
Observation toObservation = new Observation();
theToIdentifiers.forEach(toObservation::addIdentifier);
TerserUtil.mergeField(ourFhirContext, "identifier", fromObservation, toObservation);
assertThat(toObservation.getIdentifier()).hasSize(theExpectedIdentifiers.size());
assertThat(toObservation.getIdentifier()).allMatch(t -> {
if (t.hasValue()) {
return theExpectedIdentifiers.stream().anyMatch(s -> StringUtils.equals(t.getValue(), s.getValue()));
} else if (t.hasExtension(DATA_ABSENT_REASON_EXTENSION_URI)) {
return theExpectedIdentifiers.stream().anyMatch(s -> s.hasExtension(DATA_ABSENT_REASON_EXTENSION_URI));
}
return false;
});
}
private static Stream<Arguments> multipleCardinalityArguments() {
return Stream.of(
Arguments.of(List.of(), List.of(), List.of()),
Arguments.of(List.of(identifierFromValue("identifier1")), List.of(), List.of(identifierFromValue("identifier1"))),
Arguments.of(List.of(), List.of(identifierFromValue("identifier1")), List.of(identifierFromValue("identifier1"))),
Arguments.of(List.of(identifierFromValue("identifier1")), List.of(identifierFromValue("identifier2")), List.of(identifierFromValue("identifier1"), identifierFromValue("identifier2"))),
Arguments.of(List.of(identifierWithDataAbsentReason()), List.of(), List.of(identifierWithDataAbsentReason())),
Arguments.of(List.of(), List.of(identifierWithDataAbsentReason()), List.of(identifierWithDataAbsentReason())),
Arguments.of(List.of(identifierWithDataAbsentReason()), List.of(identifierWithDataAbsentReason()), List.of(identifierWithDataAbsentReason())),
Arguments.of(List.of(identifierFromValue("identifier1")), List.of(identifierWithDataAbsentReason()), List.of(identifierFromValue("identifier1"))),
Arguments.of(List.of(identifierWithDataAbsentReason()), List.of(identifierFromValue("identifier1")), List.of(identifierFromValue("identifier1"))),
Arguments.of(List.of(identifierFromValue("identifier1"), identifierFromValue("identifier2")), List.of(identifierWithDataAbsentReason()), List.of(identifierFromValue("identifier1"), identifierFromValue("identifier2"))),
Arguments.of(List.of(identifierWithDataAbsentReason()), List.of(identifierFromValue("identifier1"), identifierFromValue("identifier2")), List.of(identifierFromValue("identifier1"), identifierFromValue("identifier2")))
);
}
private static Identifier identifierFromValue(String theValue) {
return new Identifier().setValue(theValue);
}
private static Identifier identifierWithDataAbsentReason() {
Identifier identifier = new Identifier();
Enumeration<Enumerations.DataAbsentReason> extension = new Enumeration<>(new Enumerations.DataAbsentReasonEnumFactory(), Enumerations.DataAbsentReason.UNKNOWN);
identifier.addExtension(DATA_ABSENT_REASON_EXTENSION_URI, extension);
return identifier;
}
@Test
void testCloneWithDuplicateNonPrimitives() {
Patient p1 = new Patient();