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hapi-fhir
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Refactor to support all new tests

This commit is contained in:
Tadgh 2021-04-29 17:01:19 -04:00
parent 78271a2931
commit ac7c684437
4 changed files with 97 additions and 23 deletions
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109
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
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@ -33,17 +33,20 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
import ca.uhn.fhir.mdm.util.CanonicalIdentifier;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.TerserUtil;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
@ -122,11 +125,7 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
@SuppressWarnings("unchecked")
T newResource = (T) missingResourceDef.newInstance();
if (newResource instanceof IBaseHasExtensions) {
IBaseExtension<?, ?> extension = ((IBaseHasExtensions) newResource).addExtension();
extension.setUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
extension.setValue(myContext.getPrimitiveBoolean(true));
}
tryToAddPlaceholderExtensionToResource(newResource);
IFhirResourceDao<T> placeholderResourceDao = myDaoRegistry.getResourceDao(theType);
ourLog.debug("Automatically creating empty placeholder resource: {}", newResource.getIdElement().getValue());
@ -146,26 +145,98 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
return Optional.ofNullable(valueOf);
}
private <T extends IBaseResource> void tryToAddPlaceholderExtensionToResource(T newResource) {
if (newResource instanceof IBaseHasExtensions) {
IBaseExtension<?, ?> extension = ((IBaseHasExtensions) newResource).addExtension();
extension.setUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
extension.setValue(myContext.getPrimitiveBoolean(true));
}
}
private <T extends IBaseResource> void tryToCopyIdentifierFromReferenceToTargetResource(IBaseReference theSourceReference, RuntimeResourceDefinition theTargetResourceDef, T theTargetResource) {
boolean referenceHasIdentifier = theSourceReference.hasIdentifier();
if (referenceHasIdentifier) {
BaseRuntimeChildDefinition targetIdentifier = theTargetResourceDef.getChildByName("identifier");
if (targetIdentifier != null) {
BaseRuntimeElementDefinition<?> identifierElement = targetIdentifier.getChildByName("identifier");
String identifierElementName = identifierElement.getName();
boolean targetHasIdentifierElement = identifierElementName.equals("Identifier");
if (targetHasIdentifierElement) {
// boolean referenceHasIdentifier = theSourceReference.hasIdentifier();
CanonicalIdentifier referenceMatchUrlIdentifier = extractIdentifierFromUrl(theSourceReference.getReferenceElement().getValue());
CanonicalIdentifier referenceIdentifier = extractIdentifierReference(theSourceReference);
BaseRuntimeElementCompositeDefinition<?> referenceElement = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theSourceReference.getClass());
BaseRuntimeChildDefinition referenceIdentifierChild = referenceElement.getChildByName("identifier");
Optional<IBase> identifierOpt = referenceIdentifierChild.getAccessor().getFirstValueOrNull(theSourceReference);
identifierOpt.ifPresent(theIBase -> targetIdentifier.getMutator().addValue(theTargetResource, theIBase));
}
if (referenceIdentifier == null && referenceMatchUrlIdentifier != null) {
addMatchUrlIdentifierToTargetResource(theTargetResourceDef, theTargetResource, referenceMatchUrlIdentifier);
} else if (referenceIdentifier!= null && referenceMatchUrlIdentifier == null) {
addSubjectIdentifierToTargetResource(theSourceReference, theTargetResourceDef, theTargetResource);
} else if (referenceIdentifier != null && referenceMatchUrlIdentifier != null) {
if (referenceIdentifier.equals(referenceMatchUrlIdentifier)) {
addSubjectIdentifierToTargetResource(theSourceReference, theTargetResourceDef, theTargetResource);
} else {
addSubjectIdentifierToTargetResource(theSourceReference, theTargetResourceDef, theTargetResource);
addMatchUrlIdentifierToTargetResource(theTargetResourceDef, theTargetResource, referenceMatchUrlIdentifier);
}
}
}
private <T extends IBaseResource> void addSubjectIdentifierToTargetResource(IBaseReference theSourceReference, RuntimeResourceDefinition theTargetResourceDef, T theTargetResource) {
BaseRuntimeChildDefinition targetIdentifier = theTargetResourceDef.getChildByName("identifier");
if (targetIdentifier != null) {
BaseRuntimeElementDefinition<?> identifierElement = targetIdentifier.getChildByName("identifier");
String identifierElementName = identifierElement.getName();
boolean targetHasIdentifierElement = identifierElementName.equals("Identifier");
if (targetHasIdentifierElement) {
BaseRuntimeElementCompositeDefinition<?> referenceElement = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theSourceReference.getClass());
BaseRuntimeChildDefinition referenceIdentifierChild = referenceElement.getChildByName("identifier");
Optional<IBase> identifierOpt = referenceIdentifierChild.getAccessor().getFirstValueOrNull(theSourceReference);
identifierOpt.ifPresent(theIBase -> targetIdentifier.getMutator().addValue(theTargetResource, theIBase));
}
}
}
private <T extends IBaseResource> void addMatchUrlIdentifierToTargetResource(RuntimeResourceDefinition theTargetResourceDef, T theTargetResource, CanonicalIdentifier referenceMatchUrlIdentifier) {
BaseRuntimeChildDefinition identifierDefinition = theTargetResourceDef.getChildByName("identifier");
IBase identifierIBase = identifierDefinition.getChildByName("identifier").newInstance(identifierDefinition.getInstanceConstructorArguments());
IBase systemIBase = TerserUtil.newElement(myContext, "uri", referenceMatchUrlIdentifier.getSystemElement().getValueAsString());
IBase valueIBase = TerserUtil.newElement(myContext, "string", referenceMatchUrlIdentifier.getValueElement().getValueAsString());
//Set system in the IBase Identifier
BaseRuntimeElementDefinition<?> elementDefinition = myContext.getElementDefinition(identifierIBase.getClass());
BaseRuntimeChildDefinition systemDefinition = elementDefinition.getChildByName("system");
systemDefinition.getMutator().setValue(identifierIBase, systemIBase);
BaseRuntimeChildDefinition valueDefinition = elementDefinition.getChildByName("value");
valueDefinition.getMutator().setValue(identifierIBase, valueIBase);
//Set Value in the IBase identifier
identifierDefinition.getMutator().addValue(theTargetResource, identifierIBase);
}
private CanonicalIdentifier extractIdentifierReference(IBaseReference theSourceReference) {
Optional<IBase> identifier = myContext.newFhirPath().evaluateFirst(theSourceReference, "identifier", IBase.class);
if (!identifier.isPresent()) {
return null;
} else {
CanonicalIdentifier canonicalIdentifier = new CanonicalIdentifier();
Optional<IPrimitiveType> system = myContext.newFhirPath().evaluateFirst(identifier.get(), "system", IPrimitiveType.class);
Optional<IPrimitiveType> value = myContext.newFhirPath().evaluateFirst(identifier.get(), "value", IPrimitiveType.class);
system.ifPresent(theIPrimitiveType -> canonicalIdentifier.setSystem(theIPrimitiveType.getValueAsString()));
value.ifPresent(theIPrimitiveType -> canonicalIdentifier.setValue(theIPrimitiveType.getValueAsString()));
return canonicalIdentifier;
}
}
private CanonicalIdentifier extractIdentifierFromUrl(String theValue) {
if (!theValue.contains("identifier=")) {
return null;
}
CanonicalIdentifier identifier = new CanonicalIdentifier();
String identifierString = theValue.substring(theValue.indexOf("=") + 1);
String[] split = identifierString.split("\\|");
if (split.length != 2) {
throw new IllegalArgumentException("Can't create a placeholder reference with identifier " + theValue + ". It is not a valid identifier");
}
identifier.setSystem(split[0]);
identifier.setValue(split[1]);
return identifier;
}
@Override
public void validateTypeOrThrowException(Class<? extends IBaseResource> theType) {
myDaoRegistry.getDaoOrThrowException(theType);

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
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@ -276,6 +276,7 @@ public class SearchParamWithInlineReferencesExtractor {
throw new InvalidRequestException(msg);
}
Class<? extends IBaseResource> matchResourceType = matchResourceDef.getImplementingClass();
//Attempt to find the target reference before creating a placeholder
Set<ResourcePersistentId> matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theRequest);
ResourcePersistentId match;

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
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@ -423,13 +423,13 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
List<Identifier> identifiers = placeholderPat.getIdentifier();
//inline match-url identifier
assertThat(identifiers.get(0).getSystem(), is(equalTo("http://foo")));
assertThat(identifiers.get(0).getValue(), is(equalTo("123")));
//subject identifier
assertThat(identifiers.get(1).getSystem(), is(equalTo("http://foo")));
assertThat(identifiers.get(1).getValue(), is(equalTo("123")));
//subject identifier
assertThat(identifiers.get(0).getSystem(), is(equalTo("http://bar")));
assertThat(identifiers.get(0).getValue(), is(equalTo("321")));
// Conditionally update a Patient with the same identifier
Patient patToConditionalUpdate = new Patient();

2
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/IdentifierUtil.java
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@ -49,6 +49,8 @@ public final class IdentifierUtil {
return retval;
}
/**
* Retrieves appropriate FHIR Identifier model instance based on the context version
*