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Make patch `add` actually add instead of replace. (#3800) 

* Fix some patch problems

* Changelog
This commit is contained in:
Tadgh 2022-07-15 12:29:16 -04:00 committed by GitHub
parent e0169fa6c7
commit ab4d9578e7
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4 changed files with 143 additions and 3 deletions
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1
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/model/RequestPartitionId.java
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@ -49,7 +49,6 @@ import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
public class RequestPartitionId implements IModelJson {
private static final RequestPartitionId ALL_PARTITIONS = new RequestPartitionId();
private static final ObjectMapper ourObjectMapper = new ObjectMapper().registerModule(new com.fasterxml.jackson.datatype.jsr310.JavaTimeModule());
@JsonProperty("partitionDate")
private final LocalDate myPartitionDate;
@JsonProperty("allPartitions")

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3796-fhirpath-patch-add.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 3796
jira: SMILE-4328
title: "Previously, the FHIRPath PATCH operation type `add` was replacing the entire element as opposed to adding the new element to the existing element. This has been corrected."

135
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/patch/FhirPatchApplyR4Test.java
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@ -6,20 +6,26 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Questionnaire;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.Type;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class FhirPatchApplyR4Test {
@ -218,6 +224,7 @@ public class FhirPatchApplyR4Test {
.addPart()
.setName("value")
.setValue(new StringType("2"));
operation = patch.addParameter();
operation.setName("operation");
operation
@ -236,6 +243,7 @@ public class FhirPatchApplyR4Test {
.addPart()
.setName("value")
.setValue(new Coding("http://smilecdr.com/fhir/document-type", "ADMIN", null));
operation = patch.addParameter();
operation.setName("operation");
operation
@ -259,8 +267,135 @@ public class FhirPatchApplyR4Test {
ourLog.info("Outcome:\n{}", ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals("{\"resourceType\":\"Questionnaire\",\"item\":[{\"linkId\":\"1\",\"code\":[{\"system\":\"https://smilecdr.com/fhir/document-type\",\"code\":\"CLINICAL\"}],\"text\":\"Test item\"},{\"linkId\":\"2\",\"code\":[{\"system\":\"http://smilecdr.com/fhir/document-type\",\"code\":\"ADMIN\"}],\"text\":\"Test Item 2\"}]}", ourCtx.newJsonParser().encodeResourceToString(patient));
}
@Test
public void testAddDoesNotReplaceHighCardinalityItems() {
FhirPatch svc = new FhirPatch(ourCtx);
//Given: We create a patient with an identifier
Patient patient = new Patient();
patient.addIdentifier().setSystem("first-system").setValue("first-value");
//Given: We create a patch request to add a second identifier.
Identifier theValue = new Identifier().setSystem("second-system").setValue("second-value");
Parameters patch = new Parameters();
patch.addParameter(createPatchAddOperation( "Patient", "identifier", theValue));
//When: We apply the patch
svc.apply(patient, patch);
ourLog.info("Outcome:\n{}", ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
//Then: New identifier is added, and does not overwrite.
assertThat(patient.getIdentifier(), hasSize(2));
assertThat(patient.getIdentifier().get(0).getSystem(), is(equalTo("first-system")));
assertThat(patient.getIdentifier().get(0).getValue(), is(equalTo("first-value")));
assertThat(patient.getIdentifier().get(1).getSystem(), is(equalTo("second-system")));
assertThat(patient.getIdentifier().get(1).getValue(), is(equalTo("second-value")));
}
@Test
public void testAddToHighCardinalityFieldSetsValueIfEmpty() {
FhirPatch svc = new FhirPatch(ourCtx);
Patient patient = new Patient();
//Given: We create a patch request to add an identifier.
Parameters patch = new Parameters();
Identifier theValue = new Identifier().setSystem("third-system").setValue("third-value");
patch.addParameter(createPatchAddOperation("Patient", "identifier", theValue));
//When: We apply the patch
svc.apply(patient, patch);
ourLog.info("Outcome:\n{}", ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
//Then: it applies the new identifier correctly.
assertThat(patient.getIdentifier(), hasSize(1));
assertThat(patient.getIdentifier().get(0).getSystem(), is(equalTo("third-system")));
assertThat(patient.getIdentifier().get(0).getValue(), is(equalTo("third-value")));
}
@Test
public void testReplaceToHighCardinalityFieldRemovesAllAndSetsValue() {
FhirPatch svc = new FhirPatch(ourCtx);
Patient patient = new Patient();
patient.addIdentifier().setSystem("first-system").setValue("first-value");
patient.addIdentifier().setSystem("second-system").setValue("second-value");
//Given: We create a patch request to add an identifier.
Identifier theValue = new Identifier().setSystem("third-system").setValue("third-value");
Parameters patch = new Parameters();
patch.addParameter(createPatchReplaceOperation("Patient.identifier", theValue));
//When: We apply the patch
svc.apply(patient, patch);
ourLog.info("Outcome:\n{}", ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
//Then: it applies the new identifier correctly.
assertThat(patient.getIdentifier(), hasSize(1));
assertThat(patient.getIdentifier().get(0).getSystem(), is(equalTo("third-system")));
assertThat(patient.getIdentifier().get(0).getValue(), is(equalTo("third-value")));
}
//TODO: https://github.com/hapifhir/hapi-fhir/issues/3796
@Test
public void testAddToSingleCardinalityFieldFailsWhenExists() {
FhirPatch svc = new FhirPatch(ourCtx);
Patient patient = new Patient();
patient.setActive(true);
//Given: We create a patch request to add a new active statuts
BooleanType theValue = new BooleanType(false);
Parameters patch = new Parameters();
patch.addParameter(createPatchAddOperation("Patient", "active", theValue));
//When: We apply the patch
svc.apply(patient, patch);
ourLog.info("Outcome:\n{}", ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
//TODO THIS SHOULD THROW AN EXCEPTION. you cannot `add` to a field that is already set.
}
private Parameters.ParametersParameterComponent createPatchAddOperation(String thePath, String theName, Type theValue) {
return createPatchOperation("add", thePath, theName, theValue, null);
}
private Parameters.ParametersParameterComponent createPatchReplaceOperation(String thePath, Type theValue) {
return createPatchOperation("replace", thePath, null , theValue, null);
}
private Parameters.ParametersParameterComponent createPatchInsertOperation(String thePath, Type theValue) {
return createPatchOperation("replace", thePath, null , theValue, null);
}
@Nonnull
private Parameters.ParametersParameterComponent createPatchOperation(String theType, String thePath, String theName, Type theValue, Integer theIndex) {
Parameters.ParametersParameterComponent operation = new Parameters.ParametersParameterComponent();
operation.setName("operation");
operation
.addPart()
.setName("type")
.setValue(new CodeType(theType));
operation
.addPart()
.setName("path")
.setValue(new StringType(thePath));
if (theName != null) {
operation
.addPart()
.setName("name")
.setValue(new StringType(theName));
}
if (theValue != null) {
operation.addPart()
.setName("value")
.setValue(theValue);
}
if (theIndex != null) {
operation.addPart()
.setName("index")
.setValue(new IntegerType(theIndex));
}
return operation;
}
public static String extractPartValuePrimitive(Parameters theDiff, int theIndex, String theParameterName, String thePartName) {

5
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/patch/FhirPatch.java
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@ -235,10 +235,11 @@ public class FhirPatch {
childDef.getMutator().addValue(next, nextNewValue);
}
} else {
} else if ("add".equals(type)) {
childDef.getMutator().addValue(next, newValue);
} else if ("replace".equals(type)) {
childDef.getMutator().setValue(next, newValue);
}
}