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Fix #369 - FhirTerser cloneInto method fails if target contains extension

This commit is contained in:
jamesagnew 2016-05-23 09:20:40 -04:00
parent 635398a754
commit ee031667c5
6 changed files with 412 additions and 96 deletions
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8
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeChildExtension.java
View File

@ -46,6 +46,14 @@ public class RuntimeChildExtension extends RuntimeChildAny {
public Set<String> getValidChildNames() {
return Collections.singleton(getElementName());
}
@Override
public BaseRuntimeElementDefinition<?> getChildByName(String theName) {
if ("extension".equals(theName) || "modifierExtension".equals(theName)) {
return super.getChildByName("extensionExtension");
}
return super.getChildByName(theName);
}
// @Override
// public BaseRuntimeElementDefinition<?> getChildElementDefinitionByDatatype(Class<? extends IBase> theDatatype) {

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeExtensionDtDefinition.java
View File

@ -43,6 +43,10 @@ public class RuntimeExtensionDtDefinition extends RuntimeCompositeDatatypeDefini
return myChildren;
}
public List<BaseRuntimeChildDefinition> getChildrenIncludingUrl() {
return super.getChildren();
}
@Override
public void sealAndInitialize(FhirContext theContext, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
super.sealAndInitialize(theContext, theClassToElementDefinitions);

37
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
View File

@ -48,6 +48,7 @@ import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeChildChoiceDefinition;
import ca.uhn.fhir.context.RuntimeChildDirectResource;
import ca.uhn.fhir.context.RuntimeExtensionDtDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.model.api.ExtensionDt;
@ -88,16 +89,17 @@ public class FhirTerser {
addUndeclaredExtensions(nextExt, theDefinition, theChildDefinition, theCallback);
}
}
if (theElement instanceof IBaseHasExtensions) {
for (IBaseExtension<?, ?> nextExt : ((IBaseHasExtensions)theElement).getExtension()) {
if (nextExt == null) {
continue;
}
theCallback.acceptElement(nextExt.getValue(), null, theChildDefinition, theDefinition);
addUndeclaredExtensions(nextExt, theDefinition, theChildDefinition, theCallback);
}
}
// Commented out because FhirTerserDstu3Test#testGetResourceReferenceInExtension
// if (theElement instanceof IBaseHasExtensions) {
// for (IBaseExtension<?, ?> nextExt : ((IBaseHasExtensions)theElement).getExtension()) {
// if (nextExt == null) {
// continue;
// }
// theCallback.acceptElement(nextExt.getValue(), null, theChildDefinition, theDefinition);
// addUndeclaredExtensions(nextExt, theDefinition, theChildDefinition, theCallback);
// }
// }
if (theElement instanceof IBaseHasModifierExtensions) {
for (IBaseExtension<?, ?> nextExt : ((IBaseHasModifierExtensions)theElement).getModifierExtension()) {
@ -137,18 +139,25 @@ public class FhirTerser {
BaseRuntimeElementCompositeDefinition<?> sourceDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theSource.getClass());
BaseRuntimeElementCompositeDefinition<?> targetDef = (BaseRuntimeElementCompositeDefinition<?>) myContext.getElementDefinition(theTarget.getClass());
for (BaseRuntimeChildDefinition nextChild : sourceDef.getChildren()) {
List<BaseRuntimeChildDefinition> children = sourceDef.getChildren();
if (sourceDef instanceof RuntimeExtensionDtDefinition) {
children = ((RuntimeExtensionDtDefinition)sourceDef).getChildrenIncludingUrl();
}
for (BaseRuntimeChildDefinition nextChild : children) {
for (IBase nextValue : nextChild.getAccessor().getValues(theSource)) {
BaseRuntimeChildDefinition targetChild = targetDef.getChildByName(nextChild.getElementName());
String elementName = nextChild.getChildNameByDatatype(nextValue.getClass());
BaseRuntimeChildDefinition targetChild = targetDef.getChildByName(elementName);
if (targetChild == null) {
if (theIgnoreMissingFields) {
continue;
} else {
throw new DataFormatException("Type " + theTarget.getClass().getName() + " does not have a child with name " + nextChild.getElementName());
throw new DataFormatException("Type " + theTarget.getClass().getName() + " does not have a child with name " + elementName);
}
}
IBase target = targetChild.getChildByName(nextChild.getElementName()).newInstance();
BaseRuntimeElementDefinition<?> childDef = targetChild.getChildByName(elementName);
IBase target = childDef.newInstance();
targetChild.getMutator().addValue(theTarget, target);
cloneInto(nextValue, target, theIgnoreMissingFields);
}

198
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/util/FhirTerserDstu2Test.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.model.dstu2.composite.MoneyDt;
import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.model.dstu2.resource.Organization;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.MarkdownDt;
@ -39,28 +40,114 @@ public class FhirTerserDstu2Test {
private static FhirContext ourCtx = FhirContext.forDstu2();
@Test
public void testGetResourceReferenceInExtension() {
public void testCloneIntoComposite() {
QuantityDt source = new QuantityDt();
source.setCode("CODE");
MoneyDt target = new MoneyDt();
ourCtx.newTerser().cloneInto(source, target, true);
assertEquals("CODE", target.getCode());
}
@Test
public void testCloneIntoCompositeMismatchedFields() {
QuantityDt source = new QuantityDt();
source.setSystem("SYSTEM");
source.setUnit("UNIT");
IdentifierDt target = new IdentifierDt();
ourCtx.newTerser().cloneInto(source, target, true);
assertEquals("SYSTEM", target.getSystem());
try {
ourCtx.newTerser().cloneInto(source, target, false);
fail();
} catch (DataFormatException e) {
// good
}
}
/**
* See #369
*/
@Test
public void testCloneIntoExtension() {
Patient patient = new Patient();
patient.addUndeclaredExtension(new ExtensionDt(false, "http://example.com", new StringDt("FOO")));
Patient target = new Patient();
ourCtx.newTerser().cloneInto(patient, target, false);
List<ExtensionDt> exts = target.getUndeclaredExtensionsByUrl("http://example.com");
assertEquals(1, exts.size());
assertEquals("FOO", ((StringDt)exts.get(0).getValue()).getValue());
}
@Test
public void testCloneIntoPrimitive() {
StringDt source = new StringDt("STR");
MarkdownDt target = new MarkdownDt();
ourCtx.newTerser().cloneInto(source, target, true);
assertEquals("STR", target.getValueAsString());
}
@Test
public void testCloneIntoPrimitiveFails() {
StringDt source = new StringDt("STR");
MoneyDt target = new MoneyDt();
ourCtx.newTerser().cloneInto(source, target, true);
assertTrue(target.isEmpty());
try {
ourCtx.newTerser().cloneInto(source, target, false);
fail();
} catch (DataFormatException e) {
// good
}
}
/**
* See #369
*/
@Test
public void testCloneIntoValues() {
Observation obs = new Observation();
obs.setValue(new StringDt("AAA"));
obs.setComments("COMMENTS");
Observation target = new Observation();
ourCtx.newTerser().cloneInto(obs, target, false);
assertEquals("AAA", ((StringDt)obs.getValue()).getValue());
assertEquals("COMMENTS", obs.getComments());
}
@Test
public void testGetAllPopulatedChildElementsOfTypeDescendsIntoContained() {
Patient p = new Patient();
p.addName().addFamily("PATIENT");
Organization o = new Organization();
o.setName("ORG");
ResourceReferenceDt ref = new ResourceReferenceDt(o);
ExtensionDt ext = new ExtensionDt(false, "urn:foo", ref);
p.addUndeclaredExtension(ext);
o.getNameElement().setValue("ORGANIZATION");
p.getContained().getContainedResources().add(o);
FhirTerser t = ourCtx.newTerser();
List<StringDt> strings = t.getAllPopulatedChildElementsOfType(p, StringDt.class);
assertEquals(2, strings.size());
assertThat(strings, containsInAnyOrder(new StringDt("PATIENT"), new StringDt("ORGANIZATION")));
List<IBaseReference> refs = ourCtx.newTerser().getAllPopulatedChildElementsOfType(p, IBaseReference.class);
assertEquals(1, refs.size());
assertSame(ref, refs.get(0));
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Test
public void testGetAllPopulatedChildElementsOfTypeDoesntDescendIntoEmbedded() {
Patient p = new Patient();
@ -79,79 +166,21 @@ public class FhirTerserDstu2Test {
}
@Test
public void testCloneIntoPrimitive() {
StringDt source = new StringDt("STR");
MarkdownDt target = new MarkdownDt();
ourCtx.newTerser().cloneInto(source, target, true);
assertEquals("STR", target.getValueAsString());
}
@Test
public void testCloneIntoPrimitiveFails() {
StringDt source = new StringDt("STR");
MoneyDt target = new MoneyDt();
ourCtx.newTerser().cloneInto(source, target, true);
assertTrue(target.isEmpty());
try {
ourCtx.newTerser().cloneInto(source, target, false);
fail();
} catch (DataFormatException e) {
// good
}
}
@Test
public void testCloneIntoComposite() {
QuantityDt source = new QuantityDt();
source.setCode("CODE");
MoneyDt target = new MoneyDt();
ourCtx.newTerser().cloneInto(source, target, true);
assertEquals("CODE", target.getCode());
}
@Test
public void testCloneIntoCompositeMismatchedFields() {
QuantityDt source = new QuantityDt();
source.setSystem("SYSTEM");
source.setUnit("UNIT");
IdentifierDt target = new IdentifierDt();
ourCtx.newTerser().cloneInto(source, target, true);
assertEquals("SYSTEM", target.getSystem());
try {
ourCtx.newTerser().cloneInto(source, target, false);
fail();
} catch (DataFormatException e) {
// good
}
}
@Test
public void testGetAllPopulatedChildElementsOfTypeDescendsIntoContained() {
public void testGetResourceReferenceInExtension() {
Patient p = new Patient();
p.addName().addFamily("PATIENT");
Organization o = new Organization();
o.getNameElement().setValue("ORGANIZATION");
p.getContained().getContainedResources().add(o);
FhirTerser t = ourCtx.newTerser();
List<StringDt> strings = t.getAllPopulatedChildElementsOfType(p, StringDt.class);
assertEquals(2, strings.size());
assertThat(strings, containsInAnyOrder(new StringDt("PATIENT"), new StringDt("ORGANIZATION")));
o.setName("ORG");
ResourceReferenceDt ref = new ResourceReferenceDt(o);
ExtensionDt ext = new ExtensionDt(false, "urn:foo", ref);
p.addUndeclaredExtension(ext);
List<IBaseReference> refs = ourCtx.newTerser().getAllPopulatedChildElementsOfType(p, IBaseReference.class);
assertEquals(1, refs.size());
assertSame(ref, refs.get(0));
}
@Test
public void testVisitWithModelVisitor2() {
IModelVisitor2 visitor = mock(IModelVisitor2.class);
@ -178,6 +207,11 @@ public class FhirTerserDstu2Test {
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
/**
* See http://stackoverflow.com/questions/182636/how-to-determine-the-class-of-a-generic-type
*/

256
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/util/FhirTerserDstu3Test.java Normal file
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@ -0,0 +1,256 @@
package ca.uhn.fhir.util;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import java.lang.reflect.ParameterizedType;
import java.lang.reflect.Type;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.Identifier;
import org.hl7.fhir.dstu3.model.MarkdownType;
import org.hl7.fhir.dstu3.model.Money;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Organization;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Patient.LinkType;
import org.hl7.fhir.dstu3.model.Quantity;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.junit.AfterClass;
import org.junit.Test;
import org.mockito.ArgumentCaptor;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.DataFormatException;
public class FhirTerserDstu3Test {
private static FhirContext ourCtx = FhirContext.forDstu3();
@Test
public void testCloneIntoComposite() {
Quantity source = new Quantity();
source.setCode("CODE");
Money target = new Money();
ourCtx.newTerser().cloneInto(source, target, true);
assertEquals("CODE", target.getCode());
}
@Test
public void testCloneIntoCompositeMismatchedFields() {
Quantity source = new Quantity();
source.setSystem("SYSTEM");
source.setUnit("UNIT");
Identifier target = new Identifier();
ourCtx.newTerser().cloneInto(source, target, true);
assertEquals("SYSTEM", target.getSystem());
try {
ourCtx.newTerser().cloneInto(source, target, false);
fail();
} catch (DataFormatException e) {
// good
}
}
/**
* See #369
*/
@Test
public void testCloneIntoExtension() {
Patient patient = new Patient();
patient.addExtension(new Extension("http://example.com", new StringType("FOO")));
Patient target = new Patient();
ourCtx.newTerser().cloneInto(patient, target, false);
List<Extension> exts = target.getExtensionsByUrl("http://example.com");
assertEquals(1, exts.size());
assertEquals("FOO", ((StringType)exts.get(0).getValue()).getValue());
}
@Test
public void testCloneIntoPrimitive() {
StringType source = new StringType("STR");
MarkdownType target = new MarkdownType();
ourCtx.newTerser().cloneInto(source, target, true);
assertEquals("STR", target.getValueAsString());
}
@Test
public void testCloneIntoPrimitiveFails() {
StringType source = new StringType("STR");
Money target = new Money();
ourCtx.newTerser().cloneInto(source, target, true);
assertTrue(target.isEmpty());
try {
ourCtx.newTerser().cloneInto(source, target, false);
fail();
} catch (DataFormatException e) {
// good
}
}
/**
* See #369
*/
@Test
public void testCloneIntoValues() {
Observation obs = new Observation();
obs.setValue(new StringType("AAA"));
obs.setComment("COMMENTS");
Observation target = new Observation();
ourCtx.newTerser().cloneInto(obs, target, false);
assertEquals("AAA", ((StringType)obs.getValue()).getValue());
assertEquals("COMMENTS", obs.getComment());
}
@Test
public void testGetAllPopulatedChildElementsOfTypeDescendsIntoContained() {
Patient p = new Patient();
p.addName().addFamily("PATIENT");
Organization o = new Organization();
o.getNameElement().setValue("ORGANIZATION");
p.getContained().add(o);
FhirTerser t = ourCtx.newTerser();
List<StringType> strings = t.getAllPopulatedChildElementsOfType(p, StringType.class);
assertThat(toStrings(strings), containsInAnyOrder("PATIENT","ORGANIZATION"));
}
@Test
public void testGetAllPopulatedChildElementsOfTypeDoesntDescendIntoEmbedded() {
Patient p = new Patient();
p.addName().addFamily("PATIENT");
Bundle b = new Bundle();
b.addEntry().setResource(p);
b.addLink().setRelation("BUNDLE");
FhirTerser t = ourCtx.newTerser();
List<StringType> strings = t.getAllPopulatedChildElementsOfType(b, StringType.class);
assertEquals(1, strings.size());
assertThat(toStrings(strings), containsInAnyOrder("BUNDLE"));
}
@Test
public void testGetResourceReferenceInExtension() {
Patient p = new Patient();
p.addName().addFamily("PATIENT");
Organization o = new Organization();
o.setName("ORG");
Reference ref = new Reference(o);
Extension ext = new Extension("urn:foo", ref);
p.addExtension(ext);
FhirTerser t = ourCtx.newTerser();
List<IBaseReference> refs = t.getAllPopulatedChildElementsOfType(p, IBaseReference.class);
assertEquals(1, refs.size());
assertSame(ref, refs.get(0));
}
@Test
public void testVisitWithModelVisitor2() {
IModelVisitor2 visitor = mock(IModelVisitor2.class);
ArgumentCaptor<IBase> element = ArgumentCaptor.forClass(IBase.class);
ArgumentCaptor<List<IBase>> containingElementPath = ArgumentCaptor.forClass(getListClass(IBase.class));
ArgumentCaptor<List<BaseRuntimeChildDefinition>> childDefinitionPath = ArgumentCaptor.forClass(getListClass(BaseRuntimeChildDefinition.class));
ArgumentCaptor<List<BaseRuntimeElementDefinition<?>>> elementDefinitionPath = ArgumentCaptor.forClass(getListClass2());
when(visitor.acceptElement(element.capture(), containingElementPath.capture(), childDefinitionPath.capture(), elementDefinitionPath.capture())).thenReturn(true);
Patient p = new Patient();
p.addLink().getTypeElement().setValue(LinkType.REFER);
ourCtx.newTerser().visit(p, visitor);
assertEquals(3, element.getAllValues().size());
assertSame(p, element.getAllValues().get(0));
assertSame(p.getLinkFirstRep(), element.getAllValues().get(1));
assertSame(p.getLinkFirstRep().getTypeElement(), element.getAllValues().get(2));
assertEquals(3, containingElementPath.getAllValues().size());
// assertEquals(0, containingElementPath.getAllValues().get(0).size());
// assertEquals(1, containingElementPath.getAllValues().get(1).size());
// assertEquals(2, containingElementPath.getAllValues().get(2).size());
}
private List<String> toStrings(List<StringType> theStrings) {
ArrayList<String> retVal = new ArrayList<String>();
for (StringType next : theStrings) {
retVal.add(next.getValue());
}
return retVal;
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
/**
* See http://stackoverflow.com/questions/182636/how-to-determine-the-class-of-a-generic-type
*/
private static <T> Class<List<T>> getListClass(Class<T> theClass) {
return new ClassGetter<List<T>>() {
}.get();
}
/**
* See http://stackoverflow.com/questions/182636/how-to-determine-the-class-of-a-generic-type
*/
private static Class<List<BaseRuntimeElementDefinition<?>>> getListClass2() {
return new ClassGetter<List<BaseRuntimeElementDefinition<?>>>() {
}.get();
}
/**
* See http://stackoverflow.com/questions/182636/how-to-determine-the-class-of-a-generic-type
*/
private static abstract class ClassGetter<T> {
@SuppressWarnings("unchecked")
public final Class<T> get() {
final ParameterizedType superclass = (ParameterizedType) getClass().getGenericSuperclass();
Type type = superclass.getActualTypeArguments()[0];
if (type instanceof ParameterizedType) {
return (Class<T>) ((ParameterizedType) type).getOwnerType();
}
return (Class<T>) type;
}
}
}

5
src/changes/changes.xml
View File

@ -229,6 +229,11 @@
</ul>
]]>
</action>
<action type="fix" issue="369">
FhirTerser.cloneInto method failed to clone correctly if the source
had any extensions. Thanks to GitHub user @Virdulys for submitting and
providing a test case!
</action>
</release>
<release version="1.5" date="2016-04-20">
<action type="fix" issue="339">