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Builds the hapi fhir base. Requires Common lang, commons-text, and guava be built first.
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package ca.uhn.fhir.parser;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeChildContainedResources;
import ca.uhn.fhir.context.RuntimeChildDeclaredExtensionDefinition;
import ca.uhn.fhir.context.RuntimeChildNarrativeDefinition;
import ca.uhn.fhir.context.RuntimeChildUndeclaredExtensionDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IPrimitiveDatatype;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.base.composite.BaseContainedDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.parser.json.BaseJsonLikeArray;
import ca.uhn.fhir.parser.json.BaseJsonLikeObject;
import ca.uhn.fhir.parser.json.BaseJsonLikeValue;
import ca.uhn.fhir.parser.json.BaseJsonLikeValue.ScalarType;
import ca.uhn.fhir.parser.json.BaseJsonLikeValue.ValueType;
import ca.uhn.fhir.parser.json.BaseJsonLikeWriter;
import ca.uhn.fhir.parser.json.JsonLikeStructure;
import ca.uhn.fhir.parser.json.jackson.JacksonStructure;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.util.ElementUtil;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.text.WordUtils;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBooleanDatatype;
import org.hl7.fhir.instance.model.api.IBaseDecimalDatatype;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions;
import org.hl7.fhir.instance.model.api.IBaseIntegerDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IDomainResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.INarrative;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.io.IOException;
import java.io.Reader;
import java.io.Writer;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.ID_DATATYPE;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.PRIMITIVE_DATATYPE;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
* This class is the FHIR JSON parser/encoder. Users should not interact with this class directly, but should use
* {@link FhirContext#newJsonParser()} to get an instance.
*/
public class JsonParser extends BaseParser implements IJsonLikeParser {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParser.HeldExtension.class);
private boolean myPrettyPrint;
private Boolean myIsSupportsFhirComment;
/**
* Do not use this constructor, the recommended way to obtain a new instance of the JSON parser is to invoke
* {@link FhirContext#newJsonParser()}.
*
* @param theParserErrorHandler
*/
public JsonParser(FhirContext theContext, IParserErrorHandler theParserErrorHandler) {
super(theContext, theParserErrorHandler);
}
private boolean addToHeldComments(
int valueIdx, List theCommentsToAdd, ArrayList> theListToAddTo) {
if (theCommentsToAdd.size() > 0) {
theListToAddTo.ensureCapacity(valueIdx);
while (theListToAddTo.size() <= valueIdx) {
theListToAddTo.add(null);
}
if (theListToAddTo.get(valueIdx) == null) {
theListToAddTo.set(valueIdx, new ArrayList<>());
}
theListToAddTo.get(valueIdx).addAll(theCommentsToAdd);
return true;
}
return false;
}
private boolean addToHeldExtensions(
int valueIdx,
List> ext,
ArrayList> list,
boolean theIsModifier,
CompositeChildElement theChildElem,
CompositeChildElement theParent,
EncodeContext theEncodeContext,
boolean theContainedResource,
IBase theContainingElement) {
boolean retVal = false;
if (ext.size() > 0) {
Boolean encodeExtension = null;
for (IBaseExtension next : ext) {
if (next.isEmpty()) {
continue;
}
// Make sure we respect _summary and _elements
if (encodeExtension == null) {
encodeExtension =
isEncodeExtension(theParent, theEncodeContext, theContainedResource, theContainingElement);
}
if (encodeExtension) {
HeldExtension extension = new HeldExtension(next, theIsModifier, theChildElem, theParent);
list.ensureCapacity(valueIdx);
while (list.size() <= valueIdx) {
list.add(null);
}
ArrayList extensionList = list.get(valueIdx);
if (extensionList == null) {
extensionList = new ArrayList<>();
list.set(valueIdx, extensionList);
}
extensionList.add(extension);
retVal = true;
}
}
}
return retVal;
}
private void addToHeldIds(int theValueIdx, ArrayList theListToAddTo, String theId) {
theListToAddTo.ensureCapacity(theValueIdx);
while (theListToAddTo.size() <= theValueIdx) {
theListToAddTo.add(null);
}
if (theListToAddTo.get(theValueIdx) == null) {
theListToAddTo.set(theValueIdx, theId);
}
}
// private void assertObjectOfType(JsonLikeValue theResourceTypeObj, Object theValueType, String thePosition) {
// if (theResourceTypeObj == null) {
// throw new DataFormatException(Msg.code(1836) + "Invalid JSON content detected, missing required element: '" +
// thePosition + "'");
// }
//
// if (theResourceTypeObj.getValueType() != theValueType) {
// throw new DataFormatException(Msg.code(1837) + "Invalid content of element " + thePosition + ", expected " +
// theValueType);
// }
// }
private void beginArray(BaseJsonLikeWriter theEventWriter, String arrayName) throws IOException {
theEventWriter.beginArray(arrayName);
}
private void beginObject(BaseJsonLikeWriter theEventWriter, String arrayName) throws IOException {
theEventWriter.beginObject(arrayName);
}
private BaseJsonLikeWriter createJsonWriter(Writer theWriter) throws IOException {
JsonLikeStructure jsonStructure = new JacksonStructure();
return jsonStructure.getJsonLikeWriter(theWriter);
}
public void doEncodeResourceToJsonLikeWriter(
IBaseResource theResource, BaseJsonLikeWriter theEventWriter, EncodeContext theEncodeContext)
throws IOException {
if (myPrettyPrint) {
theEventWriter.setPrettyPrint(myPrettyPrint);
}
theEventWriter.init();
RuntimeResourceDefinition resDef = getContext().getResourceDefinition(theResource);
encodeResourceToJsonStreamWriter(resDef, theResource, theEventWriter, null, false, theEncodeContext);
theEventWriter.flush();
}
@Override
protected void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter, EncodeContext theEncodeContext)
throws IOException {
BaseJsonLikeWriter eventWriter = createJsonWriter(theWriter);
doEncodeResourceToJsonLikeWriter(theResource, eventWriter, theEncodeContext);
eventWriter.close();
}
@Override
protected void doEncodeToWriter(IBase theElement, Writer theWriter, EncodeContext theEncodeContext)
throws IOException, DataFormatException {
BaseJsonLikeWriter eventWriter = createJsonWriter(theWriter);
eventWriter.beginObject();
encodeCompositeElementToStreamWriter(null, null, theElement, eventWriter, false, null, theEncodeContext);
eventWriter.endObject();
eventWriter.close();
}
@Override
public T doParseResource(Class theResourceType, Reader theReader) {
JsonLikeStructure jsonStructure = new JacksonStructure();
jsonStructure.load(theReader);
T retVal = doParseResource(theResourceType, jsonStructure);
return retVal;
}
public T doParseResource(Class theResourceType, JsonLikeStructure theJsonStructure) {
BaseJsonLikeObject object = theJsonStructure.getRootObject();
BaseJsonLikeValue resourceTypeObj = object.get("resourceType");
if (resourceTypeObj == null || !resourceTypeObj.isString() || isBlank(resourceTypeObj.getAsString())) {
throw new DataFormatException(
Msg.code(1838) + "Invalid JSON content detected, missing required element: 'resourceType'");
}
String resourceType = resourceTypeObj.getAsString();
ParserState state =
ParserState.getPreResourceInstance(this, theResourceType, getContext(), true, getErrorHandler());
state.enteringNewElement(null, resourceType);
parseChildren(object, state);
state.endingElement();
state.endingElement();
@SuppressWarnings("unchecked")
T retVal = (T) state.getObject();
return retVal;
}
private void encodeChildElementToStreamWriter(
RuntimeResourceDefinition theResDef,
IBaseResource theResource,
BaseJsonLikeWriter theEventWriter,
IBase theNextValue,
BaseRuntimeElementDefinition theChildDef,
String theChildName,
boolean theContainedResource,
CompositeChildElement theChildElem,
boolean theForceEmpty,
EncodeContext theEncodeContext)
throws IOException {
switch (theChildDef.getChildType()) {
case ID_DATATYPE: {
IIdType value = (IIdType) theNextValue;
String encodedValue = "id".equals(theChildName) ? value.getIdPart() : value.getValue();
if (isBlank(encodedValue)) {
break;
}
if (theChildName != null) {
write(theEventWriter, theChildName, encodedValue);
} else {
theEventWriter.write(encodedValue);
}
break;
}
case PRIMITIVE_DATATYPE: {
final IPrimitiveType value = (IPrimitiveType) theNextValue;
final String valueStr = value.getValueAsString();
if (isBlank(valueStr)) {
if (theForceEmpty) {
theEventWriter.writeNull();
}
break;
}
// check for the common case first - String value types
Object valueObj = value.getValue();
if (valueObj instanceof String) {
if (theChildName != null) {
theEventWriter.write(theChildName, valueStr);
} else {
theEventWriter.write(valueStr);
}
break;
} else if (valueObj instanceof Long) {
if (theChildName != null) {
theEventWriter.write(theChildName, (long) valueObj);
} else {
theEventWriter.write((long) valueObj);
}
break;
}
if (value instanceof IBaseIntegerDatatype) {
if (theChildName != null) {
write(theEventWriter, theChildName, ((IBaseIntegerDatatype) value).getValue());
} else {
theEventWriter.write(((IBaseIntegerDatatype) value).getValue());
}
} else if (value instanceof IBaseDecimalDatatype) {
BigDecimal decimalValue = ((IBaseDecimalDatatype) value).getValue();
decimalValue = new BigDecimal(decimalValue.toString()) {
private static final long serialVersionUID = 1L;
@Override
public String toString() {
return value.getValueAsString();
}
};
if (theChildName != null) {
write(theEventWriter, theChildName, decimalValue);
} else {
theEventWriter.write(decimalValue);
}
} else if (value instanceof IBaseBooleanDatatype) {
if (theChildName != null) {
write(theEventWriter, theChildName, ((IBaseBooleanDatatype) value).getValue());
} else {
Boolean booleanValue = ((IBaseBooleanDatatype) value).getValue();
if (booleanValue != null) {
theEventWriter.write(booleanValue.booleanValue());
}
}
} else {
if (theChildName != null) {
write(theEventWriter, theChildName, valueStr);
} else {
theEventWriter.write(valueStr);
}
}
break;
}
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
if (theChildName != null) {
theEventWriter.beginObject(theChildName);
} else {
theEventWriter.beginObject();
}
encodeCompositeElementToStreamWriter(
theResDef,
theResource,
theNextValue,
theEventWriter,
theContainedResource,
theChildElem,
theEncodeContext);
theEventWriter.endObject();
break;
}
case CONTAINED_RESOURCE_LIST:
case CONTAINED_RESOURCES: {
List containedResources = getContainedResources().getContainedResources();
if (containedResources.size() > 0) {
beginArray(theEventWriter, theChildName);
for (IBaseResource next : containedResources) {
IIdType resourceId = getContainedResources().getResourceId(next);
String value = resourceId.getValue();
encodeResourceToJsonStreamWriter(
theResDef,
next,
theEventWriter,
null,
true,
fixContainedResourceId(value),
theEncodeContext);
}
theEventWriter.endArray();
}
break;
}
case PRIMITIVE_XHTML_HL7ORG:
case PRIMITIVE_XHTML: {
if (!isSuppressNarratives()) {
IPrimitiveType dt = (IPrimitiveType) theNextValue;
if (theChildName != null) {
write(theEventWriter, theChildName, dt.getValueAsString());
} else {
theEventWriter.write(dt.getValueAsString());
}
} else {
if (theChildName != null) {
// do nothing
} else {
theEventWriter.writeNull();
}
}
break;
}
case RESOURCE:
IBaseResource resource = (IBaseResource) theNextValue;
RuntimeResourceDefinition def = getContext().getResourceDefinition(resource);
theEncodeContext.pushPath(def.getName(), true);
encodeResourceToJsonStreamWriter(
def, resource, theEventWriter, theChildName, theContainedResource, theEncodeContext);
theEncodeContext.popPath();
break;
case UNDECL_EXT:
default:
throw new IllegalStateException(Msg.code(1839) + "Should not have this state here: "
+ theChildDef.getChildType().name());
}
}
private void encodeCompositeElementChildrenToStreamWriter(
RuntimeResourceDefinition theResDef,
IBaseResource theResource,
IBase theElement,
BaseJsonLikeWriter theEventWriter,
boolean theContainedResource,
CompositeChildElement theParent,
EncodeContext theEncodeContext)
throws IOException {
{
String elementId = getCompositeElementId(theElement);
if (isNotBlank(elementId)) {
write(theEventWriter, "id", elementId);
}
}
boolean haveWrittenExtensions = false;
Iterable compositeChildElements =
super.compositeChildIterator(theElement, theContainedResource, theParent, theEncodeContext);
for (CompositeChildElement nextChildElem : compositeChildElements) {
BaseRuntimeChildDefinition nextChild = nextChildElem.getDef();
if (nextChildElem.getDef().getElementName().equals("extension")
|| nextChildElem.getDef().getElementName().equals("modifierExtension")
|| nextChild instanceof RuntimeChildDeclaredExtensionDefinition) {
if (!haveWrittenExtensions) {
extractAndWriteExtensionsAsDirectChild(
theElement,
theEventWriter,
getContext().getElementDefinition(theElement.getClass()),
theResDef,
theResource,
nextChildElem,
theParent,
theEncodeContext,
theContainedResource);
haveWrittenExtensions = true;
}
continue;
}
if (nextChild instanceof RuntimeChildNarrativeDefinition) {
INarrativeGenerator gen = getContext().getNarrativeGenerator();
if (gen != null) {
INarrative narr;
if (theResource instanceof IResource) {
narr = ((IResource) theResource).getText();
} else if (theResource instanceof IDomainResource) {
narr = ((IDomainResource) theResource).getText();
} else {
narr = null;
}
if (narr != null && narr.isEmpty()) {
gen.populateResourceNarrative(getContext(), theResource);
if (!narr.isEmpty()) {
RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
String childName = nextChild.getChildNameByDatatype(child.getDatatype());
BaseRuntimeElementDefinition type = child.getChildByName(childName);
encodeChildElementToStreamWriter(
theResDef,
theResource,
theEventWriter,
narr,
type,
childName,
theContainedResource,
nextChildElem,
false,
theEncodeContext);
continue;
}
}
}
} else if (nextChild instanceof RuntimeChildContainedResources) {
String childName = nextChild.getValidChildNames().iterator().next();
BaseRuntimeElementDefinition child = nextChild.getChildByName(childName);
encodeChildElementToStreamWriter(
theResDef,
theResource,
theEventWriter,
null,
child,
childName,
theContainedResource,
nextChildElem,
false,
theEncodeContext);
continue;
}
List values = nextChild.getAccessor().getValues(theElement);
values = preProcessValues(nextChild, theResource, values, nextChildElem, theEncodeContext);
if (values == null || values.isEmpty()) {
continue;
}
String currentChildName = null;
boolean inArray = false;
ArrayList> extensions = new ArrayList<>(0);
ArrayList> modifierExtensions = new ArrayList<>(0);
ArrayList> comments = new ArrayList<>(0);
ArrayList ids = new ArrayList<>(0);
int valueIdx = 0;
for (IBase nextValue : values) {
if (nextValue == null || nextValue.isEmpty()) {
if (nextValue instanceof BaseContainedDt) {
if (theContainedResource || getContainedResources().isEmpty()) {
continue;
}
} else {
continue;
}
}
BaseParser.ChildNameAndDef childNameAndDef = super.getChildNameAndDef(nextChild, nextValue);
if (childNameAndDef == null) {
continue;
}
/*
* Often the two values below will be the same thing. There are cases though
* where they will not be. An example would be Observation.value, which is
* a choice type. If the value contains a Quantity, then:
* nextChildGenericName = "value"
* nextChildSpecificName = "valueQuantity"
*/
String nextChildSpecificName = childNameAndDef.getChildName();
String nextChildGenericName = nextChild.getElementName();
theEncodeContext.pushPath(nextChildGenericName, false);
BaseRuntimeElementDefinition childDef = childNameAndDef.getChildDef();
boolean primitive = childDef.getChildType() == ChildTypeEnum.PRIMITIVE_DATATYPE;
if ((childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES
|| childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCE_LIST)
&& theContainedResource) {
continue;
}
boolean force = false;
if (primitive) {
if (nextValue instanceof ISupportsUndeclaredExtensions) {
List ext = ((ISupportsUndeclaredExtensions) nextValue).getUndeclaredExtensions();
force |= addToHeldExtensions(
valueIdx,
ext,
extensions,
false,
nextChildElem,
theParent,
theEncodeContext,
theContainedResource,
theElement);
ext = ((ISupportsUndeclaredExtensions) nextValue).getUndeclaredModifierExtensions();
force |= addToHeldExtensions(
valueIdx,
ext,
modifierExtensions,
true,
nextChildElem,
theParent,
theEncodeContext,
theContainedResource,
theElement);
} else {
if (nextValue instanceof IBaseHasExtensions) {
IBaseHasExtensions element = (IBaseHasExtensions) nextValue;
List> ext = element.getExtension();
force |= addToHeldExtensions(
valueIdx,
ext,
extensions,
false,
nextChildElem,
theParent,
theEncodeContext,
theContainedResource,
theElement);
}
if (nextValue instanceof IBaseHasModifierExtensions) {
IBaseHasModifierExtensions element = (IBaseHasModifierExtensions) nextValue;
List> ext = element.getModifierExtension();
force |= addToHeldExtensions(
valueIdx,
ext,
modifierExtensions,
true,
nextChildElem,
theParent,
theEncodeContext,
theContainedResource,
theElement);
}
}
if (nextValue.hasFormatComment()) {
force |= addToHeldComments(valueIdx, nextValue.getFormatCommentsPre(), comments);
force |= addToHeldComments(valueIdx, nextValue.getFormatCommentsPost(), comments);
}
String elementId = getCompositeElementId(nextValue);
if (isNotBlank(elementId)) {
force = true;
addToHeldIds(valueIdx, ids, elementId);
}
}
if (currentChildName == null || !currentChildName.equals(nextChildSpecificName)) {
if (inArray) {
theEventWriter.endArray();
}
BaseRuntimeChildDefinition replacedParentDefinition = nextChild.getReplacedParentDefinition();
if (nextChild.isMultipleCardinality()
|| (replacedParentDefinition != null && replacedParentDefinition.isMultipleCardinality())) {
beginArray(theEventWriter, nextChildSpecificName);
inArray = true;
encodeChildElementToStreamWriter(
theResDef,
theResource,
theEventWriter,
nextValue,
childDef,
null,
theContainedResource,
nextChildElem,
force,
theEncodeContext);
} else {
encodeChildElementToStreamWriter(
theResDef,
theResource,
theEventWriter,
nextValue,
childDef,
nextChildSpecificName,
theContainedResource,
nextChildElem,
false,
theEncodeContext);
}
currentChildName = nextChildSpecificName;
} else {
encodeChildElementToStreamWriter(
theResDef,
theResource,
theEventWriter,
nextValue,
childDef,
null,
theContainedResource,
nextChildElem,
force,
theEncodeContext);
}
valueIdx++;
theEncodeContext.popPath();
}
if (inArray) {
theEventWriter.endArray();
}
if (!extensions.isEmpty()
|| !modifierExtensions.isEmpty()
|| (!comments.isEmpty() && isSupportsFhirComment())) {
if (inArray) {
// If this is a repeatable field, the extensions go in an array too
beginArray(theEventWriter, '_' + currentChildName);
} else {
beginObject(theEventWriter, '_' + currentChildName);
}
for (int i = 0; i < valueIdx; i++) {
boolean haveContent = false;
List heldExts = Collections.emptyList();
List heldModExts = Collections.emptyList();
if (extensions.size() > i
&& extensions.get(i) != null
&& !extensions.get(i).isEmpty()) {
haveContent = true;
heldExts = extensions.get(i);
}
if (modifierExtensions.size() > i
&& modifierExtensions.get(i) != null
&& !modifierExtensions.get(i).isEmpty()) {
haveContent = true;
heldModExts = modifierExtensions.get(i);
}
ArrayList nextComments;
if (comments.size() > i) {
nextComments = comments.get(i);
} else {
nextComments = null;
}
if (nextComments != null && !nextComments.isEmpty()) {
haveContent = true;
}
String elementId = null;
if (ids.size() > i) {
elementId = ids.get(i);
haveContent |= isNotBlank(elementId);
}
if (!haveContent) {
theEventWriter.writeNull();
} else {
if (inArray) {
theEventWriter.beginObject();
}
if (isNotBlank(elementId)) {
write(theEventWriter, "id", elementId);
}
if (nextComments != null && !nextComments.isEmpty()) {
if (isSupportsFhirComment()) {
beginArray(theEventWriter, "fhir_comments");
for (String next : nextComments) {
theEventWriter.write(next);
}
theEventWriter.endArray();
}
}
writeExtensionsAsDirectChild(
theResource,
theEventWriter,
theResDef,
heldExts,
heldModExts,
theEncodeContext,
theContainedResource);
if (inArray) {
theEventWriter.endObject();
}
}
}
if (inArray) {
theEventWriter.endArray();
} else {
theEventWriter.endObject();
}
}
}
}
private boolean isSupportsFhirComment() {
if (myIsSupportsFhirComment == null) {
myIsSupportsFhirComment = isFhirVersionLessThanOrEqualTo(FhirVersionEnum.DSTU2_1);
}
return myIsSupportsFhirComment;
}
private void encodeCompositeElementToStreamWriter(
RuntimeResourceDefinition theResDef,
IBaseResource theResource,
IBase theNextValue,
BaseJsonLikeWriter theEventWriter,
boolean theContainedResource,
CompositeChildElement theParent,
EncodeContext theEncodeContext)
throws IOException, DataFormatException {
writeCommentsPreAndPost(theNextValue, theEventWriter);
encodeCompositeElementChildrenToStreamWriter(
theResDef,
theResource,
theNextValue,
theEventWriter,
theContainedResource,
theParent,
theEncodeContext);
}
@Override
public void encodeResourceToJsonLikeWriter(IBaseResource theResource, BaseJsonLikeWriter theJsonLikeWriter)
throws IOException, DataFormatException {
Validate.notNull(theResource, "theResource can not be null");
Validate.notNull(theJsonLikeWriter, "theJsonLikeWriter can not be null");
if (theResource.getStructureFhirVersionEnum()
!= getContext().getVersion().getVersion()) {
throw new IllegalArgumentException(Msg.code(1840) + "This parser is for FHIR version "
+ getContext().getVersion().getVersion() + " - Can not encode a structure for version "
+ theResource.getStructureFhirVersionEnum());
}
EncodeContext encodeContext = new EncodeContext();
String resourceName = getContext().getResourceType(theResource);
encodeContext.pushPath(resourceName, true);
doEncodeResourceToJsonLikeWriter(theResource, theJsonLikeWriter, encodeContext);
}
private void encodeResourceToJsonStreamWriter(
RuntimeResourceDefinition theResDef,
IBaseResource theResource,
BaseJsonLikeWriter theEventWriter,
String theObjectNameOrNull,
boolean theContainedResource,
EncodeContext theEncodeContext)
throws IOException {
IIdType resourceId = null;
if (StringUtils.isNotBlank(theResource.getIdElement().getIdPart())) {
resourceId = theResource.getIdElement();
if (theResource.getIdElement().getValue().startsWith("urn:")) {
resourceId = null;
}
}
if (!theContainedResource) {
if (!super.shouldEncodeResourceId(theResource, theEncodeContext)) {
resourceId = null;
} else if (theEncodeContext.getResourcePath().size() == 1 && getEncodeForceResourceId() != null) {
resourceId = getEncodeForceResourceId();
}
}
encodeResourceToJsonStreamWriter(
theResDef,
theResource,
theEventWriter,
theObjectNameOrNull,
theContainedResource,
resourceId,
theEncodeContext);
}
private void encodeResourceToJsonStreamWriter(
RuntimeResourceDefinition theResDef,
IBaseResource theResource,
BaseJsonLikeWriter theEventWriter,
String theObjectNameOrNull,
boolean theContainedResource,
IIdType theResourceId,
EncodeContext theEncodeContext)
throws IOException {
if (!super.shouldEncodeResource(theResDef.getName())) {
return;
}
if (!theContainedResource) {
containResourcesInReferences(theResource);
}
RuntimeResourceDefinition resDef = getContext().getResourceDefinition(theResource);
if (theObjectNameOrNull == null) {
theEventWriter.beginObject();
} else {
beginObject(theEventWriter, theObjectNameOrNull);
}
write(theEventWriter, "resourceType", resDef.getName());
if (theResourceId != null && theResourceId.hasIdPart()) {
write(theEventWriter, "id", theResourceId.getIdPart());
final List extensions = new ArrayList<>(0);
final List modifierExtensions = new ArrayList<>(0);
// Undeclared extensions
extractUndeclaredExtensions(
theResourceId, extensions, modifierExtensions, null, null, theEncodeContext, theContainedResource);
boolean haveExtension = !extensions.isEmpty();
if (theResourceId.hasFormatComment() || haveExtension) {
beginObject(theEventWriter, "_id");
if (theResourceId.hasFormatComment()) {
writeCommentsPreAndPost(theResourceId, theEventWriter);
}
if (haveExtension) {
writeExtensionsAsDirectChild(
theResource,
theEventWriter,
theResDef,
extensions,
modifierExtensions,
theEncodeContext,
theContainedResource);
}
theEventWriter.endObject();
}
}
if (theResource instanceof IResource) {
parseMetaForDSTU2(theResDef, theResource, theEventWriter, theContainedResource, theEncodeContext, resDef);
}
encodeCompositeElementToStreamWriter(
theResDef,
theResource,
theResource,
theEventWriter,
theContainedResource,
new CompositeChildElement(resDef, theEncodeContext),
theEncodeContext);
theEventWriter.endObject();
}
private void parseMetaForDSTU2(
RuntimeResourceDefinition theResDef,
IBaseResource theResource,
BaseJsonLikeWriter theEventWriter,
boolean theContainedResource,
EncodeContext theEncodeContext,
RuntimeResourceDefinition resDef)
throws IOException {
IResource resource = (IResource) theResource;
// Object securityLabelRawObj =
List securityLabels =
extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
List profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
profiles = super.getProfileTagsForEncoding(resource, profiles);
TagList tags = getMetaTagsForEncoding(resource, theEncodeContext);
InstantDt updated = (InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
IdDt resourceId = resource.getId();
String versionIdPart = resourceId.getVersionIdPart();
if (isBlank(versionIdPart)) {
versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
}
List, Object>> extensionMetadataKeys = getExtensionMetadataKeys(resource);
if (super.shouldEncodeResourceMeta(resource)
&& (ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false)
|| !extensionMetadataKeys.isEmpty()) {
beginObject(theEventWriter, "meta");
if (shouldEncodePath(resource, "meta.versionId")) {
writeOptionalTagWithTextNode(theEventWriter, "versionId", versionIdPart);
}
if (shouldEncodePath(resource, "meta.lastUpdated")) {
writeOptionalTagWithTextNode(theEventWriter, "lastUpdated", updated);
}
if (profiles != null && profiles.isEmpty() == false) {
beginArray(theEventWriter, "profile");
for (IIdType profile : profiles) {
if (profile != null && isNotBlank(profile.getValue())) {
theEventWriter.write(profile.getValue());
}
}
theEventWriter.endArray();
}
if (securityLabels.isEmpty() == false) {
beginArray(theEventWriter, "security");
for (BaseCodingDt securityLabel : securityLabels) {
theEventWriter.beginObject();
theEncodeContext.pushPath("security", false);
encodeCompositeElementChildrenToStreamWriter(
resDef,
resource,
securityLabel,
theEventWriter,
theContainedResource,
null,
theEncodeContext);
theEncodeContext.popPath();
theEventWriter.endObject();
}
theEventWriter.endArray();
}
if (tags != null && tags.isEmpty() == false) {
beginArray(theEventWriter, "tag");
for (Tag tag : tags) {
if (tag.isEmpty()) {
continue;
}
theEventWriter.beginObject();
writeOptionalTagWithTextNode(theEventWriter, "system", tag.getScheme());
writeOptionalTagWithTextNode(theEventWriter, "code", tag.getTerm());
writeOptionalTagWithTextNode(theEventWriter, "display", tag.getLabel());
writeOptionalTagWithTextNode(theEventWriter, "version", tag.getVersion());
write(theEventWriter, "userSelected", tag.getUserSelectedBoolean());
theEventWriter.endObject();
}
theEventWriter.endArray();
}
addExtensionMetadata(
theResDef,
theResource,
theContainedResource,
extensionMetadataKeys,
resDef,
theEventWriter,
theEncodeContext);
theEventWriter.endObject(); // end meta
}
}
private void addExtensionMetadata(
RuntimeResourceDefinition theResDef,
IBaseResource theResource,
boolean theContainedResource,
List, Object>> extensionMetadataKeys,
RuntimeResourceDefinition resDef,
BaseJsonLikeWriter theEventWriter,
EncodeContext theEncodeContext)
throws IOException {
if (extensionMetadataKeys.isEmpty()) {
return;
}
ExtensionDt metaResource = new ExtensionDt();
for (Map.Entry, Object> entry : extensionMetadataKeys) {
metaResource.addUndeclaredExtension((ExtensionDt) entry.getValue());
}
encodeCompositeElementToStreamWriter(
theResDef,
theResource,
metaResource,
theEventWriter,
theContainedResource,
new CompositeChildElement(resDef, theEncodeContext),
theEncodeContext);
}
/**
* This is useful only for the two cases where extensions are encoded as direct children (e.g. not in some object
* called _name): resource extensions, and extension extensions
*/
private void extractAndWriteExtensionsAsDirectChild(
IBase theElement,
BaseJsonLikeWriter theEventWriter,
BaseRuntimeElementDefinition theElementDef,
RuntimeResourceDefinition theResDef,
IBaseResource theResource,
CompositeChildElement theChildElem,
CompositeChildElement theParent,
EncodeContext theEncodeContext,
boolean theContainedResource)
throws IOException {
List extensions = new ArrayList<>(0);
List modifierExtensions = new ArrayList<>(0);
// Undeclared extensions
extractUndeclaredExtensions(
theElement,
extensions,
modifierExtensions,
theChildElem,
theParent,
theEncodeContext,
theContainedResource);
// Declared extensions
if (theElementDef != null) {
extractDeclaredExtensions(theElement, theElementDef, extensions, modifierExtensions, theChildElem);
}
// Write the extensions
writeExtensionsAsDirectChild(
theResource,
theEventWriter,
theResDef,
extensions,
modifierExtensions,
theEncodeContext,
theContainedResource);
}
private void extractDeclaredExtensions(
IBase theResource,
BaseRuntimeElementDefinition resDef,
List extensions,
List modifierExtensions,
CompositeChildElement theChildElem) {
for (RuntimeChildDeclaredExtensionDefinition nextDef : resDef.getExtensionsNonModifier()) {
for (IBase nextValue : nextDef.getAccessor().getValues(theResource)) {
if (nextValue != null) {
if (nextValue.isEmpty()) {
continue;
}
extensions.add(new HeldExtension(nextDef, nextValue, theChildElem));
}
}
}
for (RuntimeChildDeclaredExtensionDefinition nextDef : resDef.getExtensionsModifier()) {
for (IBase nextValue : nextDef.getAccessor().getValues(theResource)) {
if (nextValue != null) {
if (nextValue.isEmpty()) {
continue;
}
modifierExtensions.add(new HeldExtension(nextDef, nextValue, theChildElem));
}
}
}
}
private void extractUndeclaredExtensions(
IBase theElement,
List extensions,
List modifierExtensions,
CompositeChildElement theChildElem,
CompositeChildElement theParent,
EncodeContext theEncodeContext,
boolean theContainedResource) {
if (theElement instanceof ISupportsUndeclaredExtensions) {
ISupportsUndeclaredExtensions element = (ISupportsUndeclaredExtensions) theElement;
List ext = element.getUndeclaredExtensions();
for (ExtensionDt next : ext) {
if (next == null || next.isEmpty()) {
continue;
}
extensions.add(new HeldExtension(next, false, theChildElem, theParent));
}
ext = element.getUndeclaredModifierExtensions();
for (ExtensionDt next : ext) {
if (next == null || next.isEmpty()) {
continue;
}
modifierExtensions.add(new HeldExtension(next, true, theChildElem, theParent));
}
} else {
if (theElement instanceof IBaseHasExtensions) {
IBaseHasExtensions element = (IBaseHasExtensions) theElement;
List> ext = element.getExtension();
Boolean encodeExtension = null;
for (IBaseExtension next : ext) {
if (next == null
|| (ElementUtil.isEmpty(next.getValue())
&& next.getExtension().isEmpty())) {
continue;
}
// Make sure we respect _elements and _summary
if (encodeExtension == null) {
encodeExtension = isEncodeExtension(theParent, theEncodeContext, theContainedResource, element);
}
if (encodeExtension) {
HeldExtension extension = new HeldExtension(next, false, theChildElem, theParent);
extensions.add(extension);
}
}
}
if (theElement instanceof IBaseHasModifierExtensions) {
IBaseHasModifierExtensions element = (IBaseHasModifierExtensions) theElement;
List> ext = element.getModifierExtension();
for (IBaseExtension next : ext) {
if (next == null || next.isEmpty()) {
continue;
}
HeldExtension extension = new HeldExtension(next, true, theChildElem, theParent);
modifierExtensions.add(extension);
}
}
}
}
private boolean isEncodeExtension(
CompositeChildElement theParent,
EncodeContext theEncodeContext,
boolean theContainedResource,
IBase theElement) {
BaseRuntimeElementDefinition runtimeElementDefinition =
getContext().getElementDefinition(theElement.getClass());
boolean retVal = true;
if (runtimeElementDefinition instanceof BaseRuntimeElementCompositeDefinition) {
BaseRuntimeElementCompositeDefinition definition =
(BaseRuntimeElementCompositeDefinition) runtimeElementDefinition;
BaseRuntimeChildDefinition childDef = definition.getChildByName("extension");
CompositeChildElement c = new CompositeChildElement(theParent, childDef, theEncodeContext);
retVal = c.shouldBeEncoded(theContainedResource);
}
return retVal;
}
@Override
public EncodingEnum getEncoding() {
return EncodingEnum.JSON;
}
private BaseJsonLikeArray grabJsonArray(BaseJsonLikeObject theObject, String nextName, String thePosition) {
BaseJsonLikeValue object = theObject.get(nextName);
if (object == null || object.isNull()) {
return null;
}
if (!object.isArray()) {
throw new DataFormatException(
Msg.code(1841) + "Syntax error parsing JSON FHIR structure: Expected ARRAY at element '"
+ thePosition + "', found '" + object.getJsonType() + "'");
}
return object.getAsArray();
}
private void parseAlternates(
BaseJsonLikeValue theAlternateVal,
ParserState theState,
String theElementName,
String theAlternateName) {
if (theAlternateVal == null || theAlternateVal.isNull()) {
return;
}
if (theAlternateVal.isArray()) {
BaseJsonLikeArray array = theAlternateVal.getAsArray();
if (array.size() > 1) {
throw new DataFormatException(Msg.code(1842) + "Unexpected array of length " + array.size()
+ " (expected 0 or 1) for element: " + theElementName);
}
if (array.size() == 0) {
return;
}
parseAlternates(array.get(0), theState, theElementName, theAlternateName);
return;
}
BaseJsonLikeValue alternateVal = theAlternateVal;
if (alternateVal.isObject() == false) {
getErrorHandler()
.incorrectJsonType(
null, theAlternateName, ValueType.OBJECT, null, alternateVal.getJsonType(), null);
return;
}
BaseJsonLikeObject alternate = alternateVal.getAsObject();
for (Iterator keyIter = alternate.keyIterator(); keyIter.hasNext(); ) {
String nextKey = keyIter.next();
BaseJsonLikeValue nextVal = alternate.get(nextKey);
if ("extension".equals(nextKey)) {
boolean isModifier = false;
BaseJsonLikeArray array = nextVal.getAsArray();
parseExtension(theState, array, isModifier);
} else if ("modifierExtension".equals(nextKey)) {
boolean isModifier = true;
BaseJsonLikeArray array = nextVal.getAsArray();
parseExtension(theState, array, isModifier);
} else if ("id".equals(nextKey)) {
if (nextVal.isString()) {
theState.attributeValue("id", nextVal.getAsString());
} else {
getErrorHandler()
.incorrectJsonType(
null,
"id",
ValueType.SCALAR,
ScalarType.STRING,
nextVal.getJsonType(),
nextVal.getDataType());
}
} else if ("fhir_comments".equals(nextKey)) {
parseFhirComments(nextVal, theState);
}
}
}
private void parseChildren(BaseJsonLikeObject theObject, ParserState theState) {
int allUnderscoreNames = 0;
int handledUnderscoreNames = 0;
for (Iterator keyIter = theObject.keyIterator(); keyIter.hasNext(); ) {
String nextName = keyIter.next();
if ("resourceType".equals(nextName)) {
if (theState.isToplevelResourceElement()) {
continue;
}
} else if ("extension".equals(nextName)) {
BaseJsonLikeArray array = grabJsonArray(theObject, nextName, "extension");
parseExtension(theState, array, false);
continue;
} else if ("modifierExtension".equals(nextName)) {
BaseJsonLikeArray array = grabJsonArray(theObject, nextName, "modifierExtension");
parseExtension(theState, array, true);
continue;
} else if (nextName.equals("fhir_comments")) {
parseFhirComments(theObject.get(nextName), theState);
continue;
} else if (nextName.charAt(0) == '_') {
allUnderscoreNames++;
continue;
}
BaseJsonLikeValue nextVal = theObject.get(nextName);
String alternateName = '_' + nextName;
BaseJsonLikeValue alternateVal = theObject.get(alternateName);
if (alternateVal != null) {
handledUnderscoreNames++;
}
parseChildren(theState, nextName, nextVal, alternateVal, alternateName, false);
}
// if (elementId != null) {
// IBase object = (IBase) theState.getObject();
// if (object instanceof IIdentifiableElement) {
// ((IIdentifiableElement) object).setElementSpecificId(elementId);
// } else if (object instanceof IBaseResource) {
// ((IBaseResource) object).getIdElement().setValue(elementId);
// }
// }
/*
* This happens if an element has an extension but no actual value. I.e.
* if a resource has a "_status" element but no corresponding "status"
* element. This could be used to handle a null value with an extension
* for example.
*/
if (allUnderscoreNames > handledUnderscoreNames) {
for (Iterator keyIter = theObject.keyIterator(); keyIter.hasNext(); ) {
String alternateName = keyIter.next();
if (alternateName.startsWith("_") && alternateName.length() > 1) {
BaseJsonLikeValue nextValue = theObject.get(alternateName);
if (nextValue != null) {
if (nextValue.isObject()) {
String nextName = alternateName.substring(1);
if (theObject.get(nextName) == null) {
theState.enteringNewElement(null, nextName);
parseAlternates(nextValue, theState, alternateName, alternateName);
theState.endingElement();
}
} else {
getErrorHandler()
.incorrectJsonType(
null, alternateName, ValueType.OBJECT, null, nextValue.getJsonType(), null);
}
}
}
}
}
}
private void parseChildren(
ParserState theState,
String theName,
BaseJsonLikeValue theJsonVal,
BaseJsonLikeValue theAlternateVal,
String theAlternateName,
boolean theInArray) {
if (theName.equals("id")) {
if (!theJsonVal.isString()) {
getErrorHandler()
.incorrectJsonType(
null,
"id",
ValueType.SCALAR,
ScalarType.STRING,
theJsonVal.getJsonType(),
theJsonVal.getDataType());
}
}
if (theJsonVal.isArray()) {
BaseJsonLikeArray nextArray = theJsonVal.getAsArray();
BaseJsonLikeValue alternateVal = theAlternateVal;
if (alternateVal != null && alternateVal.isArray() == false) {
getErrorHandler()
.incorrectJsonType(
null, theAlternateName, ValueType.ARRAY, null, alternateVal.getJsonType(), null);
alternateVal = null;
}
BaseJsonLikeArray nextAlternateArray = BaseJsonLikeValue.asArray(alternateVal); // could be null
for (int i = 0; i < nextArray.size(); i++) {
BaseJsonLikeValue nextObject = nextArray.get(i);
BaseJsonLikeValue nextAlternate = null;
if (nextAlternateArray != null && nextAlternateArray.size() >= (i + 1)) {
nextAlternate = nextAlternateArray.get(i);
}
parseChildren(theState, theName, nextObject, nextAlternate, theAlternateName, true);
}
} else if (theJsonVal.isObject()) {
if (!theInArray && theState.elementIsRepeating(theName)) {
getErrorHandler().incorrectJsonType(null, theName, ValueType.ARRAY, null, ValueType.OBJECT, null);
}
theState.enteringNewElement(null, theName);
parseAlternates(theAlternateVal, theState, theAlternateName, theAlternateName);
BaseJsonLikeObject nextObject = theJsonVal.getAsObject();
boolean preResource = false;
if (theState.isPreResource()) {
BaseJsonLikeValue resType = nextObject.get("resourceType");
if (resType == null || !resType.isString()) {
throw new DataFormatException(Msg.code(1843)
+ "Missing required element 'resourceType' from JSON resource object, unable to parse");
}
theState.enteringNewElement(null, resType.getAsString());
preResource = true;
}
parseChildren(nextObject, theState);
if (preResource) {
theState.endingElement();
}
theState.endingElement();
} else if (theJsonVal.isNull()) {
theState.enteringNewElement(null, theName);
parseAlternates(theAlternateVal, theState, theAlternateName, theAlternateName);
theState.endingElement();
} else {
// must be a SCALAR
theState.enteringNewElement(null, theName);
String asString = theJsonVal.getAsString();
theState.attributeValue("value", asString);
parseAlternates(theAlternateVal, theState, theAlternateName, theAlternateName);
theState.endingElement();
}
}
private void parseExtension(ParserState theState, BaseJsonLikeArray theValues, boolean theIsModifier) {
int allUnderscoreNames = 0;
int handledUnderscoreNames = 0;
for (int i = 0; i < theValues.size(); i++) {
BaseJsonLikeObject nextExtObj = BaseJsonLikeValue.asObject(theValues.get(i));
BaseJsonLikeValue jsonElement = nextExtObj.get("url");
String url;
if (null == jsonElement || !(jsonElement.isScalar())) {
String parentElementName;
if (theIsModifier) {
parentElementName = "modifierExtension";
} else {
parentElementName = "extension";
}
getErrorHandler()
.missingRequiredElement(new ParseLocation().setParentElementName(parentElementName), "url");
url = null;
} else {
url = getExtensionUrl(jsonElement.getAsString());
}
theState.enteringNewElementExtension(null, url, theIsModifier, getServerBaseUrl());
for (Iterator keyIter = nextExtObj.keyIterator(); keyIter.hasNext(); ) {
String next = keyIter.next();
if ("url".equals(next)) {
continue;
} else if ("extension".equals(next)) {
BaseJsonLikeArray jsonVal = BaseJsonLikeValue.asArray(nextExtObj.get(next));
parseExtension(theState, jsonVal, false);
} else if ("modifierExtension".equals(next)) {
BaseJsonLikeArray jsonVal = BaseJsonLikeValue.asArray(nextExtObj.get(next));
parseExtension(theState, jsonVal, true);
} else if (next.charAt(0) == '_') {
allUnderscoreNames++;
continue;
} else {
BaseJsonLikeValue jsonVal = nextExtObj.get(next);
String alternateName = '_' + next;
BaseJsonLikeValue alternateVal = nextExtObj.get(alternateName);
if (alternateVal != null) {
handledUnderscoreNames++;
}
parseChildren(theState, next, jsonVal, alternateVal, alternateName, false);
}
}
/*
* This happens if an element has an extension but no actual value. I.e.
* if a resource has a "_status" element but no corresponding "status"
* element. This could be used to handle a null value with an extension
* for example.
*/
if (allUnderscoreNames > handledUnderscoreNames) {
for (Iterator keyIter = nextExtObj.keyIterator(); keyIter.hasNext(); ) {
String alternateName = keyIter.next();
if (alternateName.startsWith("_") && alternateName.length() > 1) {
BaseJsonLikeValue nextValue = nextExtObj.get(alternateName);
if (nextValue != null) {
if (nextValue.isObject()) {
String nextName = alternateName.substring(1);
if (nextExtObj.get(nextName) == null) {
theState.enteringNewElement(null, nextName);
parseAlternates(nextValue, theState, alternateName, alternateName);
theState.endingElement();
}
} else {
getErrorHandler()
.incorrectJsonType(
null,
alternateName,
ValueType.OBJECT,
null,
nextValue.getJsonType(),
null);
}
}
}
}
}
theState.endingElement();
}
}
private void parseFhirComments(BaseJsonLikeValue theObject, ParserState theState) {
if (isSupportsFhirComment()) {
if (theObject.isArray()) {
BaseJsonLikeArray comments = theObject.getAsArray();
for (int i = 0; i < comments.size(); i++) {
BaseJsonLikeValue nextComment = comments.get(i);
if (nextComment.isString()) {
String commentText = nextComment.getAsString();
if (commentText != null) {
theState.commentPre(commentText);
}
}
}
}
}
}
@Override
public T parseResource(Class theResourceType, JsonLikeStructure theJsonLikeStructure)
throws DataFormatException {
/*****************************************************
* ************************************************* *
* ** NOTE: this duplicates most of the code in ** *
* ** BaseParser.parseResource(Class, Reader). ** *
* ** Unfortunately, there is no way to avoid ** *
* ** this without doing some refactoring of the ** *
* ** BaseParser class. ** *
* ************************************************* *
*****************************************************/
/*
* We do this so that the context can verify that the structure is for
* the correct FHIR version
*/
if (theResourceType != null) {
getContext().getResourceDefinition(theResourceType);
}
// Actually do the parse
T retVal = doParseResource(theResourceType, theJsonLikeStructure);
RuntimeResourceDefinition def = getContext().getResourceDefinition(retVal);
if ("Bundle".equals(def.getName())) {
BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
BaseRuntimeElementCompositeDefinition entryDef =
(BaseRuntimeElementCompositeDefinition) entryChild.getChildByName("entry");
List entries = entryChild.getAccessor().getValues(retVal);
if (entries != null) {
for (IBase nextEntry : entries) {
/**
* If Bundle.entry.fullUrl is populated, set the resource ID to that
*/
// TODO: should emit a warning and maybe notify the error handler if the resource ID doesn't match
// the
// fullUrl idPart
BaseRuntimeChildDefinition fullUrlChild = entryDef.getChildByName("fullUrl");
if (fullUrlChild == null) {
continue; // TODO: remove this once the data model in tinder plugin catches up to 1.2
}
List fullUrl = fullUrlChild.getAccessor().getValues(nextEntry);
if (fullUrl != null && !fullUrl.isEmpty()) {
IPrimitiveType value = (IPrimitiveType) fullUrl.get(0);
if (value.isEmpty() == false) {
List entryResources = entryDef.getChildByName("resource")
.getAccessor()
.getValues(nextEntry);
if (entryResources != null && entryResources.size() > 0) {
IBaseResource res = (IBaseResource) entryResources.get(0);
String versionId = res.getIdElement().getVersionIdPart();
res.setId(value.getValueAsString());
if (isNotBlank(versionId) && res.getIdElement().hasVersionIdPart() == false) {
res.setId(res.getIdElement().withVersion(versionId));
}
}
}
}
}
}
}
return retVal;
}
@Override
public IBaseResource parseResource(JsonLikeStructure theJsonLikeStructure) throws DataFormatException {
return parseResource(null, theJsonLikeStructure);
}
@Override
public IParser setPrettyPrint(boolean thePrettyPrint) {
myPrettyPrint = thePrettyPrint;
return this;
}
private void write(BaseJsonLikeWriter theEventWriter, String theChildName, Boolean theValue) throws IOException {
if (theValue != null) {
theEventWriter.write(theChildName, theValue.booleanValue());
}
}
// private void parseExtensionInDstu2Style(boolean theModifier, ParserState theState, String
// theParentExtensionUrl, String theExtensionUrl, JsonArray theValues) {
// String extUrl = UrlUtil.constructAbsoluteUrl(theParentExtensionUrl, theExtensionUrl);
// theState.enteringNewElementExtension(null, extUrl, theModifier);
//
// for (int extIdx = 0; extIdx < theValues.size(); extIdx++) {
// JsonObject nextExt = theValues.getJsonObject(extIdx);
// for (String nextKey : nextExt.keySet()) {
// // if (nextKey.startsWith("value") && nextKey.length() > 5 &&
// // myContext.getRuntimeChildUndeclaredExtensionDefinition().getChildByName(nextKey) != null) {
// JsonElement jsonVal = nextExt.get(nextKey);
// if (jsonVal.getValueType() == ValueType.ARRAY) {
// /*
// * Extension children which are arrays are sub-extensions. Any other value type should be treated as a value.
// */
// JsonArray arrayValue = (JsonArray) jsonVal;
// parseExtensionInDstu2Style(theModifier, theState, extUrl, nextKey, arrayValue);
// } else {
// parseChildren(theState, nextKey, jsonVal, null, null);
// }
// }
// }
//
// theState.endingElement();
// }
private void write(BaseJsonLikeWriter theEventWriter, String theChildName, BigDecimal theDecimalValue)
throws IOException {
theEventWriter.write(theChildName, theDecimalValue);
}
private void write(BaseJsonLikeWriter theEventWriter, String theChildName, Integer theValue) throws IOException {
theEventWriter.write(theChildName, theValue);
}
private void writeCommentsPreAndPost(IBase theNextValue, BaseJsonLikeWriter theEventWriter) throws IOException {
if (theNextValue.hasFormatComment()) {
if (isSupportsFhirComment()) {
beginArray(theEventWriter, "fhir_comments");
List pre = theNextValue.getFormatCommentsPre();
if (pre.isEmpty() == false) {
for (String next : pre) {
theEventWriter.write(next);
}
}
List post = theNextValue.getFormatCommentsPost();
if (post.isEmpty() == false) {
for (String next : post) {
theEventWriter.write(next);
}
}
theEventWriter.endArray();
}
}
}
private void writeExtensionsAsDirectChild(
IBaseResource theResource,
BaseJsonLikeWriter theEventWriter,
RuntimeResourceDefinition resDef,
List extensions,
List modifierExtensions,
EncodeContext theEncodeContext,
boolean theContainedResource)
throws IOException {
// Write Extensions
if (extensions.isEmpty() == false) {
theEncodeContext.pushPath("extension", false);
beginArray(theEventWriter, "extension");
for (HeldExtension next : extensions) {
next.write(resDef, theResource, theEventWriter, theEncodeContext, theContainedResource);
}
theEventWriter.endArray();
theEncodeContext.popPath();
}
// Write ModifierExtensions
if (modifierExtensions.isEmpty() == false) {
theEncodeContext.pushPath("modifierExtension", false);
beginArray(theEventWriter, "modifierExtension");
for (HeldExtension next : modifierExtensions) {
next.write(resDef, theResource, theEventWriter, theEncodeContext, theContainedResource);
}
theEventWriter.endArray();
theEncodeContext.popPath();
}
}
private void writeOptionalTagWithTextNode(
BaseJsonLikeWriter theEventWriter, String theElementName, IPrimitiveDatatype thePrimitive)
throws IOException {
if (thePrimitive == null) {
return;
}
String str = thePrimitive.getValueAsString();
writeOptionalTagWithTextNode(theEventWriter, theElementName, str);
}
private void writeOptionalTagWithTextNode(BaseJsonLikeWriter theEventWriter, String theElementName, String theValue)
throws IOException {
if (StringUtils.isNotBlank(theValue)) {
write(theEventWriter, theElementName, theValue);
}
}
private static void write(BaseJsonLikeWriter theWriter, String theName, String theValue) throws IOException {
theWriter.write(theName, theValue);
}
private class HeldExtension implements Comparable {
private CompositeChildElement myChildElem;
private RuntimeChildDeclaredExtensionDefinition myDef;
private boolean myModifier;
private IBaseExtension myUndeclaredExtension;
private IBase myValue;
private CompositeChildElement myParent;
public HeldExtension(
IBaseExtension theUndeclaredExtension,
boolean theModifier,
CompositeChildElement theChildElem,
CompositeChildElement theParent) {
assert theUndeclaredExtension != null;
myUndeclaredExtension = theUndeclaredExtension;
myModifier = theModifier;
myChildElem = theChildElem;
myParent = theParent;
}
public HeldExtension(
RuntimeChildDeclaredExtensionDefinition theDef, IBase theValue, CompositeChildElement theChildElem) {
assert theDef != null;
assert theValue != null;
myDef = theDef;
myValue = theValue;
myChildElem = theChildElem;
}
@Override
public int compareTo(HeldExtension theArg0) {
String url1 = myDef != null ? myDef.getExtensionUrl() : myUndeclaredExtension.getUrl();
String url2 =
theArg0.myDef != null ? theArg0.myDef.getExtensionUrl() : theArg0.myUndeclaredExtension.getUrl();
url1 = defaultString(getExtensionUrl(url1));
url2 = defaultString(getExtensionUrl(url2));
return url1.compareTo(url2);
}
private void managePrimitiveExtension(
final IBase theValue,
final RuntimeResourceDefinition theResDef,
final IBaseResource theResource,
final BaseJsonLikeWriter theEventWriter,
final BaseRuntimeElementDefinition def,
final String childName,
EncodeContext theEncodeContext,
boolean theContainedResource)
throws IOException {
if (def.getChildType().equals(ID_DATATYPE) || def.getChildType().equals(PRIMITIVE_DATATYPE)) {
final List extensions = new ArrayList(0);
final List modifierExtensions = new ArrayList(0);
// Undeclared extensions
extractUndeclaredExtensions(
theValue,
extensions,
modifierExtensions,
myParent,
null,
theEncodeContext,
theContainedResource);
// Declared extensions
extractDeclaredExtensions(theValue, def, extensions, modifierExtensions, myParent);
boolean haveContent = false;
if (!extensions.isEmpty() || !modifierExtensions.isEmpty()) {
haveContent = true;
}
if (haveContent) {
beginObject(theEventWriter, '_' + childName);
writeExtensionsAsDirectChild(
theResource,
theEventWriter,
theResDef,
extensions,
modifierExtensions,
theEncodeContext,
theContainedResource);
theEventWriter.endObject();
}
}
}
public void write(
RuntimeResourceDefinition theResDef,
IBaseResource theResource,
BaseJsonLikeWriter theEventWriter,
EncodeContext theEncodeContext,
boolean theContainedResource)
throws IOException {
if (myUndeclaredExtension != null) {
writeUndeclaredExtension(
theResDef,
theResource,
theEventWriter,
myUndeclaredExtension,
theEncodeContext,
theContainedResource);
} else {
theEventWriter.beginObject();
writeCommentsPreAndPost(myValue, theEventWriter);
JsonParser.write(theEventWriter, "url", getExtensionUrl(myDef.getExtensionUrl()));
/*
* This makes sure that even if the extension contains a reference to a contained
* resource which has a HAPI-assigned ID we'll still encode that ID.
*
* See #327
*/
List preProcessedValue = preProcessValues(
myDef, theResource, Collections.singletonList(myValue), myChildElem, theEncodeContext);
// // Check for undeclared extensions on the declared extension
// // (grrrrrr....)
// if (myValue instanceof ISupportsUndeclaredExtensions) {
// ISupportsUndeclaredExtensions value = (ISupportsUndeclaredExtensions)myValue;
// List exts = value.getUndeclaredExtensions();
// if (exts.size() > 0) {
// ArrayList newValueList = new ArrayList();
// newValueList.addAll(preProcessedValue);
// newValueList.addAll(exts);
// preProcessedValue = newValueList;
// }
// }
myValue = preProcessedValue.get(0);
BaseRuntimeElementDefinition def = myDef.getChildElementDefinitionByDatatype(myValue.getClass());
if (def.getChildType() == ChildTypeEnum.RESOURCE_BLOCK) {
extractAndWriteExtensionsAsDirectChild(
myValue,
theEventWriter,
def,
theResDef,
theResource,
myChildElem,
null,
theEncodeContext,
theContainedResource);
} else {
String childName = myDef.getChildNameByDatatype(myValue.getClass());
encodeChildElementToStreamWriter(
theResDef,
theResource,
theEventWriter,
myValue,
def,
childName,
false,
myParent,
false,
theEncodeContext);
managePrimitiveExtension(
myValue,
theResDef,
theResource,
theEventWriter,
def,
childName,
theEncodeContext,
theContainedResource);
}
theEventWriter.endObject();
}
}
private void writeUndeclaredExtension(
RuntimeResourceDefinition theResDef,
IBaseResource theResource,
BaseJsonLikeWriter theEventWriter,
IBaseExtension ext,
EncodeContext theEncodeContext,
boolean theContainedResource)
throws IOException {
IBase value = ext.getValue();
final String extensionUrl = getExtensionUrl(ext.getUrl());
theEventWriter.beginObject();
writeCommentsPreAndPost(myUndeclaredExtension, theEventWriter);
String elementId = getCompositeElementId(ext);
if (isNotBlank(elementId)) {
JsonParser.write(theEventWriter, "id", getCompositeElementId(ext));
}
if (isBlank(extensionUrl)) {
ParseLocation loc = new ParseLocation(theEncodeContext.toString());
getErrorHandler().missingRequiredElement(loc, "url");
}
JsonParser.write(theEventWriter, "url", extensionUrl);
boolean noValue = value == null || value.isEmpty();
if (noValue && ext.getExtension().isEmpty()) {
ParseLocation loc = new ParseLocation(theEncodeContext.toString());
getErrorHandler().missingRequiredElement(loc, "value");
ourLog.debug("Extension with URL[{}] has no value", extensionUrl);
} else {
if (!noValue && !ext.getExtension().isEmpty()) {
ParseLocation loc = new ParseLocation(theEncodeContext.toString());
getErrorHandler().extensionContainsValueAndNestedExtensions(loc);
}
// Write child extensions
if (!ext.getExtension().isEmpty()) {
if (myModifier) {
beginArray(theEventWriter, "modifierExtension");
} else {
beginArray(theEventWriter, "extension");
}
for (Object next : ext.getExtension()) {
writeUndeclaredExtension(
theResDef,
theResource,
theEventWriter,
(IBaseExtension) next,
theEncodeContext,
theContainedResource);
}
theEventWriter.endArray();
}
// Write value
if (!noValue) {
theEncodeContext.pushPath("value", false);
/*
* Pre-process value - This is called in case the value is a reference
* since we might modify the text
*/
value = preProcessValues(
myDef, theResource, Collections.singletonList(value), myChildElem, theEncodeContext)
.get(0);
RuntimeChildUndeclaredExtensionDefinition extDef =
getContext().getRuntimeChildUndeclaredExtensionDefinition();
String childName = extDef.getChildNameByDatatype(value.getClass());
if (childName == null) {
childName = "value"
+ WordUtils.capitalize(getContext()
.getElementDefinition(value.getClass())
.getName());
}
BaseRuntimeElementDefinition childDef =
extDef.getChildElementDefinitionByDatatype(value.getClass());
if (childDef == null) {
throw new ConfigurationException(
Msg.code(1844) + "Unable to encode extension, unrecognized child element type: "
+ value.getClass().getCanonicalName());
}
encodeChildElementToStreamWriter(
theResDef,
theResource,
theEventWriter,
value,
childDef,
childName,
false,
myParent,
false,
theEncodeContext);
managePrimitiveExtension(
value,
theResDef,
theResource,
theEventWriter,
childDef,
childName,
theEncodeContext,
theContainedResource);
theEncodeContext.popPath();
}
}
// theEventWriter.name(myUndeclaredExtension.get);
theEventWriter.endObject();
}
}
}
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