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Merge remote-tracking branch 'origin/master' into 5235-questions-on-fhir-resource-validation

This commit is contained in:
Martha Mitran 2024-01-11 15:00:38 -08:00
parent 3ccb548036 01c748163d
commit d3b1d75dce
11 changed files with 260 additions and 33 deletions
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38
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
View File

@ -49,6 +49,7 @@ import jakarta.annotation.Nullable;
import org.apache.commons.io.output.StringBuilderWriter;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseCoding;
@ -82,6 +83,7 @@ import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.startsWith;
@SuppressWarnings("WeakerAccess")
public abstract class BaseParser implements IParser {
@ -328,11 +330,7 @@ public abstract class BaseParser implements IParser {
Validate.notNull(theWriter, "theWriter can not be null");
Validate.notNull(theEncodeContext, "theEncodeContext can not be null");
if (myContext.getVersion().getVersion() == FhirVersionEnum.R4B
&& theResource.getStructureFhirVersionEnum() == FhirVersionEnum.R5) {
// TODO: remove once we've bumped the core lib version
} else if (theResource.getStructureFhirVersionEnum()
!= myContext.getVersion().getVersion()) {
if (theResource.getStructureFhirVersionEnum() != myContext.getVersion().getVersion()) {
throw new IllegalArgumentException(Msg.code(1829) + "This parser is for FHIR version "
+ myContext.getVersion().getVersion() + " - Can not encode a structure for version "
+ theResource.getStructureFhirVersionEnum());
@ -444,10 +442,6 @@ public abstract class BaseParser implements IParser {
return myContainedResources;
}
void setContainedResources(FhirTerser.ContainedResources theContainedResources) {
myContainedResources = theContainedResources;
}
@Override
public Set<String> getDontStripVersionsFromReferencesAtPaths() {
return myDontStripVersionsFromReferencesAtPaths;
@ -1010,6 +1004,32 @@ public abstract class BaseParser implements IParser {
return theFhirVersionEnum == apiFhirVersion || apiFhirVersion.isOlderThan(theFhirVersionEnum);
}
protected void containResourcesInReferences(IBaseResource theResource) {
/*
* If a UUID is present in Bundle.entry.fullUrl but no value is present
* in Bundle.entry.resource.id, the resource has a discrete identity which
* should be copied into the resource ID. It will not be serialized in
* Resource.id because it's a placeholder/UUID value, but its presence there
* informs the serializer that we don't need to contain this resource.
*/
if (theResource instanceof IBaseBundle) {
List<Pair<String, IBaseResource>> entries =
BundleUtil.getBundleEntryFullUrlsAndResources(getContext(), (IBaseBundle) theResource);
for (Pair<String, IBaseResource> nextEntry : entries) {
String fullUrl = nextEntry.getKey();
IBaseResource resource = nextEntry.getValue();
if (startsWith(fullUrl, "urn:")) {
if (resource != null && resource.getIdElement().getValue() == null) {
resource.getIdElement().setValue(fullUrl);
}
}
}
}
myContainedResources = getContext().newTerser().containResources(theResource);
}
class ChildNameAndDef {
private final BaseRuntimeElementDefinition<?> myChildDef;

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -892,7 +892,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
if (!theContainedResource) {
setContainedResources(getContext().newTerser().containResources(theResource));
containResourcesInReferences(theResource);
}
RuntimeResourceDefinition resDef = getContext().getResourceDefinition(theResource);

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/RDFParser.java
View File

@ -191,7 +191,7 @@ public class RDFParser extends BaseParser {
}
if (!containedResource) {
setContainedResources(getContext().newTerser().containResources(resource));
containResourcesInReferences(resource);
}
if (!(resource instanceof IAnyResource)) {
@ -238,7 +238,9 @@ public class RDFParser extends BaseParser {
rdfModel.createProperty(FHIR_NS + NODE_ROLE), rdfModel.createProperty(FHIR_NS + TREE_ROOT));
}
if (resourceId != null && resourceId.getIdPart() != null) {
if (resourceId != null
&& resourceId.getIdPart() != null
&& !resourceId.getValue().startsWith("urn:")) {
parentResource.addProperty(
rdfModel.createProperty(FHIR_NS + RESOURCE_ID),
createFhirValueBlankNode(rdfModel, resourceId.getIdPart()));

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java
View File

@ -682,7 +682,7 @@ public class XmlParser extends BaseParser {
}
if (!theContainedResource) {
setContainedResources(getContext().newTerser().containResources(theResource));
containResourcesInReferences(theResource);
}
theEventWriter.writeStartElement(resDef.getName());

55
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BundleUtil.java
View File

@ -153,7 +153,42 @@ public class BundleUtil {
return getLinkUrlOfType(theContext, theBundle, theLinkRelation, false);
}
/**
* Returns a collection of Pairs, one for each entry in the bundle. Each pair will contain
* the values of Bundle.entry.fullUrl, and Bundle.entry.resource respectively. Nulls
* are possible in either or both values in the Pair.
*
* @since 7.0.0
*/
@SuppressWarnings("unchecked")
public static List<Pair<String, IBaseResource>> getBundleEntryFullUrlsAndResources(
FhirContext theContext, IBaseBundle theBundle) {
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
List<IBase> entries = entryChild.getAccessor().getValues(theBundle);
BaseRuntimeElementCompositeDefinition<?> entryChildElem =
(BaseRuntimeElementCompositeDefinition<?>) entryChild.getChildByName("entry");
BaseRuntimeChildDefinition resourceChild = entryChildElem.getChildByName("resource");
BaseRuntimeChildDefinition urlChild = entryChildElem.getChildByName("fullUrl");
List<Pair<String, IBaseResource>> retVal = new ArrayList<>(entries.size());
for (IBase nextEntry : entries) {
String fullUrl = urlChild.getAccessor()
.getFirstValueOrNull(nextEntry)
.map(t -> (((IPrimitiveType<?>) t).getValueAsString()))
.orElse(null);
IBaseResource resource = (IBaseResource)
resourceChild.getAccessor().getFirstValueOrNull(nextEntry).orElse(null);
retVal.add(Pair.of(fullUrl, resource));
}
return retVal;
}
public static List<Pair<String, IBaseResource>> getBundleEntryUrlsAndResources(
FhirContext theContext, IBaseBundle theBundle) {
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
@ -173,19 +208,15 @@ public class BundleUtil {
List<Pair<String, IBaseResource>> retVal = new ArrayList<>(entries.size());
for (IBase nextEntry : entries) {
String url = null;
IBaseResource resource = null;
String url = requestChild
.getAccessor()
.getFirstValueOrNull(nextEntry)
.flatMap(e -> urlChild.getAccessor().getFirstValueOrNull(e))
.map(t -> ((IPrimitiveType<?>) t).getValueAsString())
.orElse(null);
for (IBase nextEntryValue : requestChild.getAccessor().getValues(nextEntry)) {
for (IBase nextUrlValue : urlChild.getAccessor().getValues(nextEntryValue)) {
url = ((IPrimitiveType<String>) nextUrlValue).getValue();
}
}
// Should return 0..1 only
for (IBase nextValue : resourceChild.getAccessor().getValues(nextEntry)) {
resource = (IBaseResource) nextValue;
}
IBaseResource resource = (IBaseResource)
resourceChild.getAccessor().getFirstValueOrNull(nextEntry).orElse(null);
retVal.add(Pair.of(url, resource));
}

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5589-dont-contain-resources-with-fullurl.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: fix
issue: 5589
title: "When encoding a Bundle, if resources in bundle entries had a value in
`Bundle.entry.fullUrl` but no value in `Bundle.entry.resource.id`, the parser
sometimes incorrectly moved these resources to be contained within other
resources when serializing the bundle. This has been corrected."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5589-dont-encode-placeholder-ids-in-rdf.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 5589
title: "When encoding resources using the RDF parser, placeholder IDs (i.e. resource IDs
starting with `urn:`) were not omitted as they are in the XML and JSON parsers. This has
been corrected."

6
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServerUtils.java
View File

@ -682,12 +682,6 @@ public class RestfulServerUtils {
}
private static FhirContext getContextForVersion(FhirContext theContext, FhirVersionEnum theForVersion) {
// TODO: remove once we've bumped the core lib version
if (theContext.getVersion().getVersion() == FhirVersionEnum.R4B && theForVersion == FhirVersionEnum.R5) {
return theContext;
}
FhirContext context = theContext;
if (context.getVersion().getVersion() != theForVersion) {
context = myFhirContextMap.get(theForVersion);

85
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
View File

@ -27,7 +27,6 @@ import org.hl7.fhir.r4.model.DocumentReference;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Medication;
import org.hl7.fhir.r4.model.MedicationDispense;
@ -37,13 +36,13 @@ import org.hl7.fhir.r4.model.Meta;
import org.hl7.fhir.r4.model.Narrative;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.PrimitiveType;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.QuestionnaireResponse;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.Type;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
@ -54,6 +53,7 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Date;
@ -1200,6 +1200,87 @@ public class JsonParserR4Test extends BaseTest {
assertEquals(expected, actual);
}
@Test
public void testEncodeBundleWithCrossReferenceFullUrlsAndNoIds() {
Bundle bundle = createBundleWithCrossReferenceFullUrlsAndNoIds();
String output = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
ourLog.info(output);
assertThat(output, not(containsString("\"contained\"")));
assertThat(output, not(containsString("\"id\"")));
assertThat(output, stringContainsInOrder(
"\"fullUrl\": \"urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7\",",
"\"resourceType\": \"Patient\"",
"\"fullUrl\": \"urn:uuid:71d7ab79-a001-41dc-9a8e-b3e478ce1cbb\"",
"\"resourceType\": \"Observation\"",
"\"reference\": \"urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7\""
));
}
@Test
public void testEncodeBundleWithCrossReferenceFullUrlsAndNoIds_NestedInParameters() {
Parameters parameters = createBundleWithCrossReferenceFullUrlsAndNoIds_NestedInParameters();
String output = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(parameters);
ourLog.info(output);
assertThat(output, not(containsString("\"contained\"")));
assertThat(output, not(containsString("\"id\"")));
assertThat(output, stringContainsInOrder(
"\"resourceType\": \"Parameters\"",
"\"name\": \"resource\"",
"\"fullUrl\": \"urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7\",",
"\"resourceType\": \"Patient\"",
"\"fullUrl\": \"urn:uuid:71d7ab79-a001-41dc-9a8e-b3e478ce1cbb\"",
"\"resourceType\": \"Observation\"",
"\"reference\": \"urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7\""
));
}
@Test
public void testParseBundleWithCrossReferenceFullUrlsAndNoIds() {
Bundle bundle = createBundleWithCrossReferenceFullUrlsAndNoIds();
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
Bundle parsedBundle = ourCtx.newJsonParser().parseResource(Bundle.class, encoded);
assertEquals("urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7", parsedBundle.getEntry().get(0).getFullUrl());
assertEquals("urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7", parsedBundle.getEntry().get(0).getResource().getId());
assertEquals("urn:uuid:71d7ab79-a001-41dc-9a8e-b3e478ce1cbb", parsedBundle.getEntry().get(1).getFullUrl());
assertEquals("urn:uuid:71d7ab79-a001-41dc-9a8e-b3e478ce1cbb", parsedBundle.getEntry().get(1).getResource().getId());
}
@Nonnull
public static Bundle createBundleWithCrossReferenceFullUrlsAndNoIds() {
Bundle bundle = new Bundle();
Patient patient = new Patient();
patient.setActive(true);
bundle
.addEntry()
.setResource(patient)
.setFullUrl("urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7");
Observation observation = new Observation();
observation.getSubject().setReference("urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7").setResource(patient);
bundle
.addEntry()
.setResource(observation)
.setFullUrl("urn:uuid:71d7ab79-a001-41dc-9a8e-b3e478ce1cbb");
return bundle;
}
@Nonnull
public static Parameters createBundleWithCrossReferenceFullUrlsAndNoIds_NestedInParameters() {
Parameters retVal = new Parameters();
retVal
.addParameter()
.setName("resource")
.setResource(createBundleWithCrossReferenceFullUrlsAndNoIds());
return retVal;
}
@Test
public void testPreCommentsToFhirComments() {

32
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserTest.java
View File

@ -36,8 +36,11 @@ import org.eclipse.rdf4j.rio.RDFFormat;
import org.eclipse.rdf4j.rio.Rio;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Parameters;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.parallel.Execution;
import org.junit.jupiter.api.parallel.ExecutionMode;
import org.junit.jupiter.params.ParameterizedTest;
@ -59,6 +62,12 @@ import java.util.List;
import java.util.Optional;
import java.util.stream.Stream;
import static ca.uhn.fhir.parser.JsonParserR4Test.createBundleWithCrossReferenceFullUrlsAndNoIds;
import static ca.uhn.fhir.parser.JsonParserR4Test.createBundleWithCrossReferenceFullUrlsAndNoIds_NestedInParameters;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.hamcrest.core.IsNot.not;
import static org.junit.jupiter.api.Assertions.*;
public class RDFParserTest extends BaseTest {
@ -216,4 +225,27 @@ public class RDFParserTest extends BaseTest {
}
}
@Test
public void testEncodeBundleWithCrossReferenceFullUrlsAndNoIds() {
Bundle bundle = createBundleWithCrossReferenceFullUrlsAndNoIds();
String output = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(bundle);
ourLog.info(output);
assertThat(output, not(containsString("contained ")));
assertThat(output, not(containsString("id ")));
}
@Test
public void testEncodeBundleWithCrossReferenceFullUrlsAndNoIds_NestedInParameters() {
Parameters parameters = createBundleWithCrossReferenceFullUrlsAndNoIds_NestedInParameters();
String output = ourCtx.newRDFParser().setPrettyPrint(true).encodeResourceToString(parameters);
ourLog.info(output);
assertThat(output, not(containsString("contained ")));
assertThat(output, not(containsString("id ")));
}
}

54
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/XmlParserR4Test.java
View File

@ -1,8 +1,11 @@
package ca.uhn.fhir.parser;
import static ca.uhn.fhir.parser.JsonParserR4Test.createBundleWithCrossReferenceFullUrlsAndNoIds;
import static ca.uhn.fhir.parser.JsonParserR4Test.createBundleWithCrossReferenceFullUrlsAndNoIds_NestedInParameters;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.hamcrest.core.IsNot.not;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@ -304,5 +307,56 @@ public class XmlParserR4Test extends BaseTest {
}
@Test
public void testEncodeBundleWithCrossReferenceFullUrlsAndNoIds() {
Bundle bundle = createBundleWithCrossReferenceFullUrlsAndNoIds();
String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
ourLog.info(output);
assertThat(output, not(containsString("<contained")));
assertThat(output, not(containsString("<id")));
assertThat(output, stringContainsInOrder(
"<fullUrl value=\"urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7\"/>",
"<Patient xmlns=\"http://hl7.org/fhir\">",
"<fullUrl value=\"urn:uuid:71d7ab79-a001-41dc-9a8e-b3e478ce1cbb\"/>",
"<Observation xmlns=\"http://hl7.org/fhir\">",
"<reference value=\"urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7\"/>"
));
}
@Test
public void testEncodeBundleWithCrossReferenceFullUrlsAndNoIds_NestedInParameters() {
Parameters parameters = createBundleWithCrossReferenceFullUrlsAndNoIds_NestedInParameters();
String output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(parameters);
ourLog.info(output);
assertThat(output, not(containsString("\"contained\"")));
assertThat(output, not(containsString("\"id\"")));
assertThat(output, stringContainsInOrder(
"<Parameters xmlns=\"http://hl7.org/fhir\">",
"<fullUrl value=\"urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7\"/>",
"<Patient xmlns=\"http://hl7.org/fhir\">",
"<fullUrl value=\"urn:uuid:71d7ab79-a001-41dc-9a8e-b3e478ce1cbb\"/>",
"<Observation xmlns=\"http://hl7.org/fhir\">",
"<reference value=\"urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7\"/>"
));
}
@Test
public void testParseBundleWithCrossReferenceFullUrlsAndNoIds() {
Bundle bundle = createBundleWithCrossReferenceFullUrlsAndNoIds();
String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
Bundle parsedBundle = ourCtx.newXmlParser().parseResource(Bundle.class, encoded);
assertEquals("urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7", parsedBundle.getEntry().get(0).getFullUrl());
assertEquals("urn:uuid:9e9187c1-db6d-4b6f-adc6-976153c65ed7", parsedBundle.getEntry().get(0).getResource().getId());
assertEquals("urn:uuid:71d7ab79-a001-41dc-9a8e-b3e478ce1cbb", parsedBundle.getEntry().get(1).getFullUrl());
assertEquals("urn:uuid:71d7ab79-a001-41dc-9a8e-b3e478ce1cbb", parsedBundle.getEntry().get(1).getResource().getId());
}
}