honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Fix broken test

This commit is contained in:
James Agnew 2018-11-01 10:25:13 -04:00
parent 4315900ac0
commit bb59e2d73a
1 changed files with 195 additions and 198 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

343
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
View File

@ -96,21 +96,23 @@ public class FhirTerser {
/**
* Clones all values from a source object into the equivalent fields in a target object
* @param theSource The source object (must not be null)
* @param theTarget The target object to copy values into (must not be null)
*
* @param theSource The source object (must not be null)
* @param theTarget The target object to copy values into (must not be null)
* @param theIgnoreMissingFields The ignore fields in the target which do not exist (if false, an exception will be thrown if the target is unable to accept a value from the source)
* @return Returns the target (which will be the same object that was passed into theTarget) for easy chaining
*/
public void cloneInto(IBase theSource, IBase theTarget, boolean theIgnoreMissingFields) {
public IBase cloneInto(IBase theSource, IBase theTarget, boolean theIgnoreMissingFields) {
Validate.notNull(theSource, "theSource must not be null");
Validate.notNull(theTarget, "theTarget must not be null");
if (theSource instanceof IPrimitiveType<?>) {
if (theTarget instanceof IPrimitiveType<?>) {
((IPrimitiveType<?>)theTarget).setValueAsString(((IPrimitiveType<?>)theSource).getValueAsString());
return;
((IPrimitiveType<?>) theTarget).setValueAsString(((IPrimitiveType<?>) theSource).getValueAsString());
return theSource;
}
if (theIgnoreMissingFields) {
return;
return theSource;
}
throw new DataFormatException("Can not copy value from primitive of type " + theSource.getClass().getName() + " into type " + theTarget.getClass().getName());
}
@ -120,10 +122,10 @@ public class FhirTerser {
List<BaseRuntimeChildDefinition> children = sourceDef.getChildren();
if (sourceDef instanceof RuntimeExtensionDtDefinition) {
children = ((RuntimeExtensionDtDefinition)sourceDef).getChildrenIncludingUrl();
children = ((RuntimeExtensionDtDefinition) sourceDef).getChildrenIncludingUrl();
}
for (BaseRuntimeChildDefinition nextChild : children) {
for (BaseRuntimeChildDefinition nextChild : children)
for (IBase nextValue : nextChild.getAccessor().getValues(theSource)) {
String elementName = nextChild.getChildNameByDatatype(nextValue.getClass());
BaseRuntimeChildDefinition targetChild = targetDef.getChildByName(elementName);
@ -134,13 +136,14 @@ public class FhirTerser {
throw new DataFormatException("Type " + theTarget.getClass().getName() + " does not have a child with name " + elementName);
}
BaseRuntimeElementDefinition<?> childDef = targetChild.getChildByName(elementName);
IBase target = childDef.newInstance();
BaseRuntimeElementDefinition<?> element = myContext.getElementDefinition(nextValue.getClass());
IBase target = element.newInstance();
targetChild.getMutator().addValue(theTarget, target);
cloneInto(nextValue, target, theIgnoreMissingFields);
}
}
return theTarget;
}
/**
@ -154,10 +157,8 @@ public class FhirTerser {
* {@link BaseResourceReferenceDt#getResource()}) or embedded resources (e.g. Bundle.entry.resource)
* </p>
*
* @param theResource
* The resource instance to search. Must not be null.
* @param theType
* The type to search for. Must not be null.
* @param theResource The resource instance to search. Must not be null.
* @param theType The type to search for. Must not be null.
* @return Returns a list of all matching elements
*/
public <T extends IBase> List<T> getAllPopulatedChildElementsOfType(IBaseResource theResource, final Class<T> theType) {
@ -274,7 +275,7 @@ public class FhirTerser {
.collect(Collectors.toList());
if (theAddExtension
&& (!(theCurrentObj instanceof IBaseExtension) || (extensionDts.isEmpty() && theSubList.size() == 1))) {
&& (!(theCurrentObj instanceof IBaseExtension) || (extensionDts.isEmpty() && theSubList.size() == 1))) {
extensionDts.add(createEmptyExtensionDt((ISupportsUndeclaredExtensions) theCurrentObj, extensionUrl));
}
@ -286,7 +287,7 @@ public class FhirTerser {
extensionDts = ((IBaseExtension) theCurrentObj).getExtension();
if (theAddExtension
&& (extensionDts.isEmpty() && theSubList.size() == 1)) {
&& (extensionDts.isEmpty() && theSubList.size() == 1)) {
extensionDts.add(createEmptyExtensionDt((IBaseExtension) theCurrentObj, extensionUrl));
}
@ -311,7 +312,7 @@ public class FhirTerser {
.collect(Collectors.toList());
if (theAddExtension
&& (!(theCurrentObj instanceof IBaseExtension) || (extensions.isEmpty() && theSubList.size() == 1))) {
&& (!(theCurrentObj instanceof IBaseExtension) || (extensions.isEmpty() && theSubList.size() == 1))) {
extensions.add(createEmptyExtension((IBaseHasExtensions) theCurrentObj, extensionUrl));
}
@ -396,7 +397,7 @@ public class FhirTerser {
.collect(Collectors.toList());
if (theAddExtension
&& (!(theCurrentObj instanceof IBaseExtension) || (extensions.isEmpty() && theSubList.size() == 1))) {
&& (!(theCurrentObj instanceof IBaseExtension) || (extensions.isEmpty() && theSubList.size() == 1))) {
extensions.add(createEmptyModifierExtension((IBaseHasModifierExtensions) theCurrentObj, extensionUrl));
}
@ -478,7 +479,7 @@ public class FhirTerser {
* type {@link Object}.
*
* @param theResource The resource instance to be accessed. Must not be null.
* @param thePath The path for the element to be accessed.
* @param thePath The path for the element to be accessed.
* @return A list of values of type {@link Object}.
*/
public List<Object> getValues(IBaseResource theResource, String thePath) {
@ -492,8 +493,8 @@ public class FhirTerser {
* type {@link Object}.
*
* @param theResource The resource instance to be accessed. Must not be null.
* @param thePath The path for the element to be accessed.
* @param theCreate When set to <code>true</code>, the terser will create a null-valued element where none exists.
* @param thePath The path for the element to be accessed.
* @param theCreate When set to <code>true</code>, the terser will create a null-valued element where none exists.
* @return A list of values of type {@link Object}.
*/
public List<Object> getValues(IBaseResource theResource, String thePath, boolean theCreate) {
@ -506,9 +507,9 @@ public class FhirTerser {
* Returns values stored in an element identified by its path. The list of values is of
* type {@link Object}.
*
* @param theResource The resource instance to be accessed. Must not be null.
* @param thePath The path for the element to be accessed.
* @param theCreate When set to <code>true</code>, the terser will create a null-valued element where none exists.
* @param theResource The resource instance to be accessed. Must not be null.
* @param thePath The path for the element to be accessed.
* @param theCreate When set to <code>true</code>, the terser will create a null-valued element where none exists.
* @param theAddExtension When set to <code>true</code>, the terser will add a null-valued extension where one or more such extensions already exist.
* @return A list of values of type {@link Object}.
*/
@ -522,10 +523,10 @@ public class FhirTerser {
* Returns values stored in an element identified by its path. The list of values is of
* type <code>theWantedClass</code>.
*
* @param theResource The resource instance to be accessed. Must not be null.
* @param thePath The path for the element to be accessed.
* @param theResource The resource instance to be accessed. Must not be null.
* @param thePath The path for the element to be accessed.
* @param theWantedClass The desired class to be returned in a list.
* @param <T> Type declared by <code>theWantedClass</code>
* @param <T> Type declared by <code>theWantedClass</code>
* @return A list of values of type <code>theWantedClass</code>.
*/
public <T> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass) {
@ -538,11 +539,11 @@ public class FhirTerser {
* Returns values stored in an element identified by its path. The list of values is of
* type <code>theWantedClass</code>.
*
* @param theResource The resource instance to be accessed. Must not be null.
* @param thePath The path for the element to be accessed.
* @param theResource The resource instance to be accessed. Must not be null.
* @param thePath The path for the element to be accessed.
* @param theWantedClass The desired class to be returned in a list.
* @param theCreate When set to <code>true</code>, the terser will create a null-valued element where none exists.
* @param <T> Type declared by <code>theWantedClass</code>
* @param theCreate When set to <code>true</code>, the terser will create a null-valued element where none exists.
* @param <T> Type declared by <code>theWantedClass</code>
* @return A list of values of type <code>theWantedClass</code>.
*/
public <T> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass, boolean theCreate) {
@ -555,12 +556,12 @@ public class FhirTerser {
* Returns values stored in an element identified by its path. The list of values is of
* type <code>theWantedClass</code>.
*
* @param theResource The resource instance to be accessed. Must not be null.
* @param thePath The path for the element to be accessed.
* @param theWantedClass The desired class to be returned in a list.
* @param theCreate When set to <code>true</code>, the terser will create a null-valued element where none exists.
* @param theResource The resource instance to be accessed. Must not be null.
* @param thePath The path for the element to be accessed.
* @param theWantedClass The desired class to be returned in a list.
* @param theCreate When set to <code>true</code>, the terser will create a null-valued element where none exists.
* @param theAddExtension When set to <code>true</code>, the terser will add a null-valued extension where one or more such extensions already exist.
* @param <T> Type declared by <code>theWantedClass</code>
* @param <T> Type declared by <code>theWantedClass</code>
* @return A list of values of type <code>theWantedClass</code>.
*/
public <T> List<T> getValues(IBaseResource theResource, String thePath, Class<T> theWantedClass, boolean theCreate, boolean theAddExtension) {
@ -607,8 +608,8 @@ public class FhirTerser {
* belonging to resource <code>theTarget</code>
*
* @param theCompartmentName The name of the compartment
* @param theSource The potential member of the compartment
* @param theTarget The owner of the compartment. Note that both the resource type and ID must be filled in on this IIdType or the method will throw an {@link IllegalArgumentException}
* @param theSource The potential member of the compartment
* @param theTarget The owner of the compartment. Note that both the resource type and ID must be filled in on this IIdType or the method will throw an {@link IllegalArgumentException}
* @return <code>true</code> if <code>theSource</code> is in the compartment
* @throws IllegalArgumentException If theTarget does not contain both a resource type and ID
*/
@ -684,7 +685,7 @@ public class FhirTerser {
}
private void visit(IBase theElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, IModelVisitor2 theCallback, List<IBase> theContainingElementPath,
List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
List<BaseRuntimeChildDefinition> theChildDefinitionPath, List<BaseRuntimeElementDefinition<?>> theElementDefinitionPath) {
if (theChildDefinition != null) {
theChildDefinitionPath.add(theChildDefinition);
}
@ -692,7 +693,7 @@ public class FhirTerser {
theElementDefinitionPath.add(theDefinition);
theCallback.acceptElement(theElement, Collections.unmodifiableList(theContainingElementPath), Collections.unmodifiableList(theChildDefinitionPath),
Collections.unmodifiableList(theElementDefinitionPath));
Collections.unmodifiableList(theElementDefinitionPath));
/*
* Visit undeclared extensions
@ -710,85 +711,85 @@ public class FhirTerser {
* Now visit the children of the given element
*/
switch (theDefinition.getChildType()) {
case ID_DATATYPE:
case PRIMITIVE_XHTML_HL7ORG:
case PRIMITIVE_XHTML:
case PRIMITIVE_DATATYPE:
// These are primitive types, so we don't need to visit their children
break;
case RESOURCE:
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
BaseRuntimeElementCompositeDefinition<?> childDef = (BaseRuntimeElementCompositeDefinition<?>) theDefinition;
for (BaseRuntimeChildDefinition nextChild : childDef.getChildrenAndExtension()) {
List<? extends IBase> values = nextChild.getAccessor().getValues(theElement);
if (values != null) {
for (IBase nextValue : values) {
if (nextValue == null) {
continue;
}
if (nextValue.isEmpty()) {
continue;
}
BaseRuntimeElementDefinition<?> childElementDef;
childElementDef = nextChild.getChildElementDefinitionByDatatype(nextValue.getClass());
if (childElementDef == null) {
StringBuilder b = new StringBuilder();
b.append("Found value of type[");
b.append(nextValue.getClass().getSimpleName());
b.append("] which is not valid for field[");
b.append(nextChild.getElementName());
b.append("] in ");
b.append(childDef.getName());
b.append(" - Valid types: ");
for (Iterator<String> iter = new TreeSet<String>(nextChild.getValidChildNames()).iterator(); iter.hasNext();) {
BaseRuntimeElementDefinition<?> childByName = nextChild.getChildByName(iter.next());
b.append(childByName.getImplementingClass().getSimpleName());
if (iter.hasNext()) {
b.append(", ");
}
case ID_DATATYPE:
case PRIMITIVE_XHTML_HL7ORG:
case PRIMITIVE_XHTML:
case PRIMITIVE_DATATYPE:
// These are primitive types, so we don't need to visit their children
break;
case RESOURCE:
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
BaseRuntimeElementCompositeDefinition<?> childDef = (BaseRuntimeElementCompositeDefinition<?>) theDefinition;
for (BaseRuntimeChildDefinition nextChild : childDef.getChildrenAndExtension()) {
List<? extends IBase> values = nextChild.getAccessor().getValues(theElement);
if (values != null) {
for (IBase nextValue : values) {
if (nextValue == null) {
continue;
}
throw new DataFormatException(b.toString());
}
if (nextValue.isEmpty()) {
continue;
}
BaseRuntimeElementDefinition<?> childElementDef;
childElementDef = nextChild.getChildElementDefinitionByDatatype(nextValue.getClass());
if (nextChild instanceof RuntimeChildDirectResource) {
// Don't descend into embedded resources
theContainingElementPath.add(nextValue);
theChildDefinitionPath.add(nextChild);
theElementDefinitionPath.add(myContext.getElementDefinition(nextValue.getClass()));
theCallback.acceptElement(nextValue, Collections.unmodifiableList(theContainingElementPath), Collections.unmodifiableList(theChildDefinitionPath),
if (childElementDef == null) {
StringBuilder b = new StringBuilder();
b.append("Found value of type[");
b.append(nextValue.getClass().getSimpleName());
b.append("] which is not valid for field[");
b.append(nextChild.getElementName());
b.append("] in ");
b.append(childDef.getName());
b.append(" - Valid types: ");
for (Iterator<String> iter = new TreeSet<String>(nextChild.getValidChildNames()).iterator(); iter.hasNext(); ) {
BaseRuntimeElementDefinition<?> childByName = nextChild.getChildByName(iter.next());
b.append(childByName.getImplementingClass().getSimpleName());
if (iter.hasNext()) {
b.append(", ");
}
}
throw new DataFormatException(b.toString());
}
if (nextChild instanceof RuntimeChildDirectResource) {
// Don't descend into embedded resources
theContainingElementPath.add(nextValue);
theChildDefinitionPath.add(nextChild);
theElementDefinitionPath.add(myContext.getElementDefinition(nextValue.getClass()));
theCallback.acceptElement(nextValue, Collections.unmodifiableList(theContainingElementPath), Collections.unmodifiableList(theChildDefinitionPath),
Collections.unmodifiableList(theElementDefinitionPath));
theChildDefinitionPath.remove(theChildDefinitionPath.size() - 1);
theContainingElementPath.remove(theContainingElementPath.size() - 1);
theElementDefinitionPath.remove(theElementDefinitionPath.size() - 1);
} else {
visit(nextValue, nextChild, childElementDef, theCallback, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
theChildDefinitionPath.remove(theChildDefinitionPath.size() - 1);
theContainingElementPath.remove(theContainingElementPath.size() - 1);
theElementDefinitionPath.remove(theElementDefinitionPath.size() - 1);
} else {
visit(nextValue, nextChild, childElementDef, theCallback, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
}
}
}
}
break;
}
break;
}
case CONTAINED_RESOURCES: {
BaseContainedDt value = (BaseContainedDt) theElement;
for (IResource next : value.getContainedResources()) {
BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(next);
visit(next, null, def, theCallback, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
case CONTAINED_RESOURCES: {
BaseContainedDt value = (BaseContainedDt) theElement;
for (IResource next : value.getContainedResources()) {
BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(next);
visit(next, null, def, theCallback, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
}
break;
}
break;
}
case EXTENSION_DECLARED:
case UNDECL_EXT: {
throw new IllegalStateException("state should not happen: " + theDefinition.getChildType());
}
case CONTAINED_RESOURCE_LIST: {
if (theElement != null) {
BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition(theElement.getClass());
visit(theElement, null, def, theCallback, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
case EXTENSION_DECLARED:
case UNDECL_EXT: {
throw new IllegalStateException("state should not happen: " + theDefinition.getChildType());
}
case CONTAINED_RESOURCE_LIST: {
if (theElement != null) {
BaseRuntimeElementDefinition<?> def = myContext.getElementDefinition(theElement.getClass());
visit(theElement, null, def, theCallback, theContainingElementPath, theChildDefinitionPath, theElementDefinitionPath);
}
break;
}
break;
}
}
if (theChildDefinition != null) {
@ -806,10 +807,8 @@ public class FhirTerser {
* {@link BaseResourceReferenceDt#getResource()}) or embedded resources (e.g. Bundle.entry.resource)
* </p>
*
* @param theResource
* The resource to visit
* @param theVisitor
* The visitor
* @param theResource The resource to visit
* @param theVisitor The visitor
*/
public void visit(IBaseResource theResource, IModelVisitor theVisitor) {
BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
@ -818,7 +817,7 @@ public class FhirTerser {
/**
* Visit all elements in a given resource
*
* <p>
* THIS ALTERNATE METHOD IS STILL EXPERIMENTAL
*
* <p>
@ -826,10 +825,8 @@ public class FhirTerser {
* {@link BaseResourceReferenceDt#getResource()}) or embedded resources (e.g. Bundle.entry.resource)
* </p>
*
* @param theResource
* The resource to visit
* @param theVisitor
* The visitor
* @param theResource The resource to visit
* @param theVisitor The visitor
*/
void visit(IBaseResource theResource, IModelVisitor2 theVisitor) {
BaseRuntimeElementCompositeDefinition<?> def = myContext.getResourceDefinition(theResource);
@ -837,7 +834,7 @@ public class FhirTerser {
}
private void visit(IdentityHashMap<Object, Object> theStack, IBaseResource theResource, IBase theElement, List<String> thePathToElement, BaseRuntimeChildDefinition theChildDefinition,
BaseRuntimeElementDefinition<?> theDefinition, IModelVisitor theCallback) {
BaseRuntimeElementDefinition<?> theDefinition, IModelVisitor theCallback) {
List<String> pathToElement = addNameToList(thePathToElement, theChildDefinition);
if (theStack.put(theElement, theElement) != null) {
@ -852,7 +849,7 @@ public class FhirTerser {
}
if (theElement instanceof IBaseReference) {
IBaseResource target = ((IBaseReference)theElement).getResource();
IBaseResource target = ((IBaseReference) theElement).getResource();
if (target != null) {
if (target.getIdElement().hasIdPart() == false || target.getIdElement().isLocal()) {
RuntimeResourceDefinition targetDef = myContext.getResourceDefinition(target);
@ -862,65 +859,65 @@ public class FhirTerser {
}
switch (def.getChildType()) {
case ID_DATATYPE:
case PRIMITIVE_XHTML_HL7ORG:
case PRIMITIVE_XHTML:
case PRIMITIVE_DATATYPE:
// These are primitive types
break;
case RESOURCE:
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
BaseRuntimeElementCompositeDefinition<?> childDef = (BaseRuntimeElementCompositeDefinition<?>) def;
for (BaseRuntimeChildDefinition nextChild : childDef.getChildrenAndExtension()) {
case ID_DATATYPE:
case PRIMITIVE_XHTML_HL7ORG:
case PRIMITIVE_XHTML:
case PRIMITIVE_DATATYPE:
// These are primitive types
break;
case RESOURCE:
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
BaseRuntimeElementCompositeDefinition<?> childDef = (BaseRuntimeElementCompositeDefinition<?>) def;
for (BaseRuntimeChildDefinition nextChild : childDef.getChildrenAndExtension()) {
List<?> values = nextChild.getAccessor().getValues(theElement);
if (values != null) {
for (Object nextValueObject : values) {
IBase nextValue;
try {
nextValue = (IBase) nextValueObject;
} catch (ClassCastException e) {
String s = "Found instance of " + nextValueObject.getClass() + " - Did you set a field value to the incorrect type? Expected " + IBase.class.getName();
throw new ClassCastException(s);
}
if (nextValue == null) {
continue;
}
if (nextValue.isEmpty()) {
continue;
}
BaseRuntimeElementDefinition<?> childElementDef;
childElementDef = nextChild.getChildElementDefinitionByDatatype(nextValue.getClass());
List<?> values = nextChild.getAccessor().getValues(theElement);
if (values != null) {
for (Object nextValueObject : values) {
IBase nextValue;
try {
nextValue = (IBase) nextValueObject;
} catch (ClassCastException e) {
String s = "Found instance of " + nextValueObject.getClass() + " - Did you set a field value to the incorrect type? Expected " + IBase.class.getName();
throw new ClassCastException(s);
}
if (nextValue == null) {
continue;
}
if (nextValue.isEmpty()) {
continue;
}
BaseRuntimeElementDefinition<?> childElementDef;
childElementDef = nextChild.getChildElementDefinitionByDatatype(nextValue.getClass());
if (childElementDef == null) {
childElementDef = myContext.getElementDefinition(nextValue.getClass());
}
if (childElementDef == null) {
childElementDef = myContext.getElementDefinition(nextValue.getClass());
}
if (nextChild instanceof RuntimeChildDirectResource) {
// Don't descend into embedded resources
theCallback.acceptElement(theResource, nextValue, null, nextChild, childElementDef);
} else {
visit(theStack, theResource, nextValue, pathToElement, nextChild, childElementDef, theCallback);
if (nextChild instanceof RuntimeChildDirectResource) {
// Don't descend into embedded resources
theCallback.acceptElement(theResource, nextValue, null, nextChild, childElementDef);
} else {
visit(theStack, theResource, nextValue, pathToElement, nextChild, childElementDef, theCallback);
}
}
}
}
break;
}
break;
}
case CONTAINED_RESOURCES: {
BaseContainedDt value = (BaseContainedDt) theElement;
for (IResource next : value.getContainedResources()) {
def = myContext.getResourceDefinition(next);
visit(theStack, next, next, pathToElement, null, def, theCallback);
case CONTAINED_RESOURCES: {
BaseContainedDt value = (BaseContainedDt) theElement;
for (IResource next : value.getContainedResources()) {
def = myContext.getResourceDefinition(next);
visit(theStack, next, next, pathToElement, null, def, theCallback);
}
break;
}
case CONTAINED_RESOURCE_LIST:
case EXTENSION_DECLARED:
case UNDECL_EXT: {
throw new IllegalStateException("state should not happen: " + def.getChildType());
}
break;
}
case CONTAINED_RESOURCE_LIST:
case EXTENSION_DECLARED:
case UNDECL_EXT: {
throw new IllegalStateException("state should not happen: " + def.getChildType());
}
}
theStack.remove(theElement);