package ca.uhn.fhir.parser;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* 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%
*/
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.IOException;
import java.io.Reader;
import java.io.StringWriter;
import java.io.Writer;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import javax.xml.namespace.QName;
import javax.xml.stream.FactoryConfigurationError;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLStreamConstants;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamWriter;
import javax.xml.stream.events.Attribute;
import javax.xml.stream.events.Characters;
import javax.xml.stream.events.Comment;
import javax.xml.stream.events.EntityReference;
import javax.xml.stream.events.Namespace;
import javax.xml.stream.events.StartElement;
import javax.xml.stream.events.XMLEvent;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
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.IBaseResource;
import org.hl7.fhir.instance.model.api.IBaseXhtml;
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 ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
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.RuntimeChildExtension;
import ca.uhn.fhir.context.RuntimeChildNarrativeDefinition;
import ca.uhn.fhir.context.RuntimeChildUndeclaredExtensionDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.api.BaseBundle;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.BundleEntry;
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.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.XhtmlDt;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.ElementUtil;
import ca.uhn.fhir.util.NonPrettyPrintWriterWrapper;
import ca.uhn.fhir.util.PrettyPrintWriterWrapper;
import ca.uhn.fhir.util.XmlUtil;
/**
* This class is the FHIR XML parser/encoder. Users should not interact with this class directly, but should use
* {@link FhirContext#newXmlParser()} to get an instance.
*/
public class XmlParser extends BaseParser /*implements IParser */{
static final String ATOM_NS = "http://www.w3.org/2005/Atom";
static final String FHIR_NS = "http://hl7.org/fhir";
static final String OPENSEARCH_NS = "http://a9.com/-/spec/opensearch/1.1/";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParser.class);
static final String RESREF_DISPLAY = "display";
static final String RESREF_REFERENCE = "reference";
static final String TOMBSTONES_NS = "http://purl.org/atompub/tombstones/1.0";
static final String XHTML_NS = "http://www.w3.org/1999/xhtml";
// private static final Set<String> RESOURCE_NAMESPACES;
private FhirContext myContext;
private boolean myPrettyPrint;
/**
* Do not use this constructor, the recommended way to obtain a new instance of the XML parser is to invoke
* {@link FhirContext#newXmlParser()}.
*
* @param theParserErrorHandler
*/
public XmlParser(FhirContext theContext, IParserErrorHandler theParserErrorHandler) {
super(theContext, theParserErrorHandler);
myContext = theContext;
}
private XMLEventReader createStreamReader(Reader theReader) {
try {
return XmlUtil.createXmlReader(theReader);
} catch (FactoryConfigurationError e1) {
throw new ConfigurationException("Failed to initialize STaX event factory", e1);
} catch (XMLStreamException e1) {
throw new DataFormatException(e1);
}
}
private XMLStreamWriter createXmlWriter(Writer theWriter) throws XMLStreamException {
XMLStreamWriter eventWriter;
eventWriter = XmlUtil.createXmlStreamWriter(theWriter);
eventWriter = decorateStreamWriter(eventWriter);
return eventWriter;
}
private XMLStreamWriter decorateStreamWriter(XMLStreamWriter eventWriter) {
if (myPrettyPrint) {
PrettyPrintWriterWrapper retVal = new PrettyPrintWriterWrapper(eventWriter);
return retVal;
}
NonPrettyPrintWriterWrapper retVal = new NonPrettyPrintWriterWrapper(eventWriter);
return retVal;
}
@Override
public void doEncodeBundleToWriter(Bundle theBundle, Writer theWriter) throws DataFormatException {
try {
XMLStreamWriter eventWriter = createXmlWriter(theWriter);
if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
encodeBundleToWriterDstu2(theBundle, eventWriter);
} else {
encodeBundleToWriterDstu1(theBundle, eventWriter);
}
} catch (XMLStreamException e) {
throw new ConfigurationException("Failed to initialize STaX event factory", e);
}
}
@Override
public void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws DataFormatException {
XMLStreamWriter eventWriter;
try {
eventWriter = createXmlWriter(theWriter);
encodeResourceToXmlStreamWriter(theResource, eventWriter, false, false);
eventWriter.flush();
} catch (XMLStreamException e) {
throw new ConfigurationException("Failed to initialize STaX event factory", e);
}
}
@Override
public <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) {
XMLEventReader streamReader = createStreamReader(theReader);
return parseResource(theResourceType, streamReader);
}
private <T> T doXmlLoop(XMLEventReader streamReader, ParserState<T> parserState) {
ourLog.trace("Entering XML parsing loop with state: {}", parserState);
try {
List<String> heldComments = new ArrayList<String>(1);
while (streamReader.hasNext()) {
XMLEvent nextEvent = streamReader.nextEvent();
try {
switch (nextEvent.getEventType()) {
case XMLStreamConstants.START_ELEMENT: {
StartElement elem = nextEvent.asStartElement();
String namespaceURI = elem.getName().getNamespaceURI();
if ("extension".equals(elem.getName().getLocalPart())) {
Attribute urlAttr = elem.getAttributeByName(new QName("url"));
String url;
if (urlAttr == null || isBlank(urlAttr.getValue())) {
getErrorHandler().missingRequiredElement(new ParseLocation("extension"), "url");
url = null;
} else {
url = urlAttr.getValue();
}
parserState.enteringNewElementExtension(elem, url, false, getServerBaseUrl());
} else if ("modifierExtension".equals(elem.getName().getLocalPart())) {
Attribute urlAttr = elem.getAttributeByName(new QName("url"));
String url;
if (urlAttr == null || isBlank(urlAttr.getValue())) {
getErrorHandler().missingRequiredElement(new ParseLocation("modifierExtension"), "url");
url = null;
} else {
url = urlAttr.getValue();
}
parserState.enteringNewElementExtension(elem, url, true, getServerBaseUrl());
} else {
String elementName = elem.getName().getLocalPart();
parserState.enteringNewElement(namespaceURI, elementName);
}
if (!heldComments.isEmpty()) {
for (String next : heldComments) {
parserState.commentPre(next);
}
heldComments.clear();
}
@SuppressWarnings("unchecked")
Iterator<Attribute> attributes = elem.getAttributes();
for (Iterator<Attribute> iter = attributes; iter.hasNext();) {
Attribute next = iter.next();
parserState.attributeValue(next.getName().getLocalPart(), next.getValue());
}
break;
}
case XMLStreamConstants.END_DOCUMENT:
case XMLStreamConstants.END_ELEMENT: {
if (!heldComments.isEmpty()) {
for (String next : heldComments) {
parserState.commentPost(next);
}
heldComments.clear();
}
parserState.endingElement();
// if (parserState.isComplete()) {
// return parserState.getObject();
// }
break;
}
case XMLStreamConstants.CHARACTERS: {
parserState.string(nextEvent.asCharacters().getData());
break;
}
case XMLStreamConstants.COMMENT: {
Comment comment = (Comment) nextEvent;
String commentText = comment.getText();
heldComments.add(commentText);
break;
}
}
parserState.xmlEvent(nextEvent);
} catch (DataFormatException e) {
throw new DataFormatException("DataFormatException at [" + nextEvent.getLocation().toString() + "]: " + e.getMessage(), e);
}
}
return parserState.getObject();
} catch (XMLStreamException e) {
throw new DataFormatException(e);
}
}
@Override
public String encodeBundleToString(Bundle theBundle) throws DataFormatException {
StringWriter stringWriter = new StringWriter();
try {
encodeBundleToWriter(theBundle, stringWriter);
} catch (IOException e) {
throw new InternalErrorException("IOException writing to StringWriter - Should not happen", e);
}
return stringWriter.toString();
}
private void encodeBundleToWriterDstu1(Bundle theBundle, XMLStreamWriter eventWriter) throws XMLStreamException {
eventWriter.writeStartElement("feed");
eventWriter.writeDefaultNamespace(ATOM_NS);
writeTagWithTextNode(eventWriter, "title", theBundle.getTitle());
writeTagWithTextNode(eventWriter, "id", theBundle.getBundleId());
writeAtomLink(eventWriter, Constants.LINK_SELF, theBundle.getLinkSelf());
writeAtomLink(eventWriter, Constants.LINK_FIRST, theBundle.getLinkFirst());
writeAtomLink(eventWriter, Constants.LINK_PREVIOUS, theBundle.getLinkPrevious());
writeAtomLink(eventWriter, Constants.LINK_NEXT, theBundle.getLinkNext());
writeAtomLink(eventWriter, Constants.LINK_LAST, theBundle.getLinkLast());
writeAtomLink(eventWriter, Constants.LINK_FHIR_BASE, theBundle.getLinkBase());
if (theBundle.getTotalResults().getValue() != null) {
eventWriter.writeStartElement("os", "totalResults", OPENSEARCH_NS);
eventWriter.writeNamespace("os", OPENSEARCH_NS);
eventWriter.writeCharacters(theBundle.getTotalResults().getValue().toString());
eventWriter.writeEndElement();
}
writeOptionalTagWithTextNode(eventWriter, "updated", theBundle.getUpdated());
writeAuthor(eventWriter, theBundle);
writeCategories(eventWriter, theBundle.getCategories());
for (BundleEntry nextEntry : theBundle.getEntries()) {
boolean deleted = false;
if (nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false) {
deleted = true;
eventWriter.writeStartElement("at", "deleted-entry", TOMBSTONES_NS);
eventWriter.writeNamespace("at", TOMBSTONES_NS);
if (nextEntry.getDeletedResourceId().isEmpty()) {
//TODO: Use of a deprecated method should be resolved.
writeOptionalAttribute(eventWriter, "ref", nextEntry.getId().getValueAsString());
} else {
writeOptionalAttribute(eventWriter, "ref", nextEntry.getDeletedResourceId().getValueAsString());
}
writeOptionalAttribute(eventWriter, "when", nextEntry.getDeletedAt().getValueAsString());
if (nextEntry.getDeletedByEmail().isEmpty() == false || nextEntry.getDeletedByName().isEmpty() == false) {
eventWriter.writeStartElement(TOMBSTONES_NS, "by");
if (nextEntry.getDeletedByName().isEmpty() == false) {
eventWriter.writeStartElement(TOMBSTONES_NS, "name");
eventWriter.writeCharacters(nextEntry.getDeletedByName().getValue());
eventWriter.writeEndElement();
}
if (nextEntry.getDeletedByEmail().isEmpty() == false) {
eventWriter.writeStartElement(TOMBSTONES_NS, "email");
eventWriter.writeCharacters(nextEntry.getDeletedByEmail().getValue());
eventWriter.writeEndElement();
}
eventWriter.writeEndElement();
}
if (nextEntry.getDeletedComment().isEmpty() == false) {
eventWriter.writeStartElement(TOMBSTONES_NS, "comment");
eventWriter.writeCharacters(nextEntry.getDeletedComment().getValue());
eventWriter.writeEndElement();
}
} else {
eventWriter.writeStartElement("entry");
}
writeOptionalTagWithTextNode(eventWriter, "title", nextEntry.getTitle());
if (!deleted) {
//TODO: Use of a deprecated method should be resolved.
if (nextEntry.getId().isEmpty() == false) {
//TODO: Use of a deprecated method should be resolved.
writeTagWithTextNode(eventWriter, "id", nextEntry.getId());
} else {
writeTagWithTextNode(eventWriter, "id", nextEntry.getResource().getId());
}
}
//TODO: Use of a deprecated method should be resolved.
writeOptionalTagWithTextNode(eventWriter, "updated", nextEntry.getUpdated());
writeOptionalTagWithTextNode(eventWriter, "published", nextEntry.getPublished());
writeAuthor(eventWriter, nextEntry);
writeCategories(eventWriter, nextEntry.getCategories());
if (!nextEntry.getLinkSelf().isEmpty()) {
writeAtomLink(eventWriter, "self", nextEntry.getLinkSelf());
}
if (!nextEntry.getLinkAlternate().isEmpty()) {
writeAtomLink(eventWriter, "alternate", nextEntry.getLinkAlternate());
}
if (!nextEntry.getLinkSearch().isEmpty()) {
writeAtomLink(eventWriter, "search", nextEntry.getLinkSearch());
}
IResource resource = nextEntry.getResource();
if (resource != null && !resource.isEmpty() && !deleted) {
eventWriter.writeStartElement("content");
eventWriter.writeAttribute("type", "text/xml");
encodeResourceToXmlStreamWriter(resource, eventWriter, false, true);
eventWriter.writeEndElement(); // content
} else {
ourLog.debug("Bundle entry contains null resource");
}
if (!nextEntry.getSummary().isEmpty()) {
eventWriter.writeStartElement("summary");
eventWriter.writeAttribute("type", "xhtml");
encodeXhtml(nextEntry.getSummary(), eventWriter);
eventWriter.writeEndElement();
}
eventWriter.writeEndElement(); // entry
}
eventWriter.writeEndElement();
eventWriter.close();
}
private void encodeBundleToWriterDstu2(Bundle theBundle, XMLStreamWriter theEventWriter) throws XMLStreamException {
theEventWriter.writeStartElement("Bundle");
theEventWriter.writeDefaultNamespace(FHIR_NS);
writeOptionalTagWithValue(theEventWriter, "id", theBundle.getId().getIdPart());
InstantDt updated = (InstantDt) theBundle.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
IdDt bundleId = theBundle.getId();
if (bundleId != null && isNotBlank(bundleId.getVersionIdPart()) || (updated != null && !updated.isEmpty())) {
theEventWriter.writeStartElement("meta");
//FIXME potential null acces bundleId may be null at this time due to the OR clause
writeOptionalTagWithValue(theEventWriter, "versionId", bundleId.getVersionIdPart());
if (updated != null) {
writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
}
theEventWriter.writeEndElement();
}
writeOptionalTagWithValue(theEventWriter, "type", theBundle.getType().getValue());
writeOptionalTagWithValue(theEventWriter, "total", theBundle.getTotalResults().getValueAsString());
writeBundleResourceLink(theEventWriter, "first", theBundle.getLinkFirst());
writeBundleResourceLink(theEventWriter, "previous", theBundle.getLinkPrevious());
writeBundleResourceLink(theEventWriter, "next", theBundle.getLinkNext());
writeBundleResourceLink(theEventWriter, "last", theBundle.getLinkLast());
writeBundleResourceLink(theEventWriter, "self", theBundle.getLinkSelf());
for (BundleEntry nextEntry : theBundle.getEntries()) {
theEventWriter.writeStartElement("entry");
boolean deleted = false;
if (nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false) {
deleted = true;
}
writeBundleResourceLink(theEventWriter, "alternate", nextEntry.getLinkAlternate());
if (nextEntry.getResource() != null && isNotBlank(nextEntry.getResource().getIdElement().getValue()) && (nextEntry.getResource().getId().getBaseUrl() != null || nextEntry.getResource().getId().getValueAsString().startsWith("urn:"))) {
writeOptionalTagWithValue(theEventWriter, "fullUrl", nextEntry.getResource().getId().getValue());
}
IResource resource = nextEntry.getResource();
if (resource != null && !resource.isEmpty() && !deleted) {
theEventWriter.writeStartElement("resource");
encodeResourceToXmlStreamWriter(resource, theEventWriter, false, true);
theEventWriter.writeEndElement(); // content
} else {
ourLog.debug("Bundle entry contains null resource");
}
if (nextEntry.getSearchMode().isEmpty() == false || nextEntry.getScore().isEmpty() == false) {
theEventWriter.writeStartElement("search");
writeOptionalTagWithValue(theEventWriter, "mode", nextEntry.getSearchMode().getValueAsString());
writeOptionalTagWithValue(theEventWriter, "score", nextEntry.getScore().getValueAsString());
theEventWriter.writeEndElement();
// IResource nextResource = nextEntry.getResource();
}
if (nextEntry.getTransactionMethod().isEmpty() == false || nextEntry.getLinkSearch().isEmpty() == false) {
theEventWriter.writeStartElement("request");
writeOptionalTagWithValue(theEventWriter, "method", nextEntry.getTransactionMethod().getValue());
writeOptionalTagWithValue(theEventWriter, "url", nextEntry.getLinkSearch().getValue());
theEventWriter.writeEndElement();
}
if (deleted) {
theEventWriter.writeStartElement("deleted");
//TODO: Use of a deprecated method should be resolved.
writeOptionalTagWithValue(theEventWriter, "type", nextEntry.getId().getResourceType());
//TODO: Use of a deprecated method should be resolved.
writeOptionalTagWithValue(theEventWriter, "id", nextEntry.getId().getIdPart());
//TODO: Use of a deprecated method should be resolved.
writeOptionalTagWithValue(theEventWriter, "versionId", nextEntry.getId().getVersionIdPart());
writeOptionalTagWithValue(theEventWriter, "instant", nextEntry.getDeletedAt().getValueAsString());
theEventWriter.writeEndElement();
}
theEventWriter.writeEndElement(); // entry
}
theEventWriter.writeEndElement();
theEventWriter.close();
}
private void encodeChildElementToStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, IBase theElement, String childName, BaseRuntimeElementDefinition<?> childDef,
String theExtensionUrl, boolean theIncludedResource, CompositeChildElement theParent) throws XMLStreamException, DataFormatException {
if (theElement == null || theElement.isEmpty()) {
if (isChildContained(childDef, theIncludedResource)) {
// We still want to go in..
} else {
return;
}
}
writeCommentsPre(theEventWriter, theElement);
switch (childDef.getChildType()) {
case ID_DATATYPE: {
IIdType value = IIdType.class.cast(theElement);
String encodedValue = "id".equals(childName) ? value.getIdPart() : value.getValue();
theEventWriter.writeStartElement(childName);
theEventWriter.writeAttribute("value", encodedValue);
encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource);
theEventWriter.writeEndElement();
break;
}
case PRIMITIVE_DATATYPE: {
IPrimitiveType<?> pd = IPrimitiveType.class.cast(theElement);
String value = pd.getValueAsString();
if (value != null || super.hasExtensions(pd)) {
theEventWriter.writeStartElement(childName);
String elementId = getCompositeElementId(theElement);
if (isNotBlank(elementId)) {
theEventWriter.writeAttribute("id", elementId);
}
if (value != null) {
theEventWriter.writeAttribute("value", value);
}
encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource);
theEventWriter.writeEndElement();
}
break;
}
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
theEventWriter.writeStartElement(childName);
String elementId = getCompositeElementId(theElement);
if (isNotBlank(elementId)) {
theEventWriter.writeAttribute("id", elementId);
}
if (isNotBlank(theExtensionUrl)) {
theEventWriter.writeAttribute("url", theExtensionUrl);
}
encodeCompositeElementToStreamWriter(theResource, theElement, theEventWriter, theIncludedResource, theParent);
theEventWriter.writeEndElement();
break;
}
case CONTAINED_RESOURCE_LIST:
case CONTAINED_RESOURCES: {
/*
* Disable per #103 for (IResource next : value.getContainedResources()) { if (getContainedResources().getResourceId(next) != null) { continue; }
* theEventWriter.writeStartElement("contained"); encodeResourceToXmlStreamWriter(next, theEventWriter, true, fixContainedResourceId(next.getId().getValue()));
* theEventWriter.writeEndElement(); }
*/
for (IBaseResource next : getContainedResources().getContainedResources()) {
IIdType resourceId = getContainedResources().getResourceId(next);
theEventWriter.writeStartElement("contained");
encodeResourceToXmlStreamWriter(next, theEventWriter, true, fixContainedResourceId(resourceId.getValue()));
theEventWriter.writeEndElement();
}
break;
}
case RESOURCE: {
theEventWriter.writeStartElement(childName);
IBaseResource resource = (IBaseResource) theElement;
encodeResourceToXmlStreamWriter(resource, theEventWriter, false, true);
theEventWriter.writeEndElement();
break;
}
case PRIMITIVE_XHTML: {
XhtmlDt dt = XhtmlDt.class.cast(theElement);
if (dt.hasContent()) {
encodeXhtml(dt, theEventWriter);
}
break;
}
case PRIMITIVE_XHTML_HL7ORG: {
IBaseXhtml dt = IBaseXhtml.class.cast(theElement);
if (!dt.isEmpty()) {
// TODO: this is probably not as efficient as it could be
XhtmlDt hdt = new XhtmlDt();
hdt.setValueAsString(dt.getValueAsString());
encodeXhtml(hdt, theEventWriter);
}
break;
}
case EXTENSION_DECLARED:
case UNDECL_EXT: {
throw new IllegalStateException("state should not happen: " + childDef.getName());
}
}
writeCommentsPost(theEventWriter, theElement);
}
private void encodeCompositeElementToStreamWriter(IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter, boolean theContainedResource, CompositeChildElement theParent)
throws XMLStreamException, DataFormatException {
for (CompositeChildElement nextChildElem : super.compositeChildIterator(theElement, theContainedResource, theParent)) {
BaseRuntimeChildDefinition nextChild = nextChildElem.getDef();
if (nextChild.getElementName().equals("url") && theElement instanceof IBaseExtension) {
/*
* XML encoding is a one-off for extensions. The URL element goes in an attribute
* instead of being encoded as a normal element, only for XML encoding
*/
continue;
}
if (nextChild instanceof RuntimeChildNarrativeDefinition) {
INarrativeGenerator gen = myContext.getNarrativeGenerator();
INarrative narr;
if (theResource instanceof IResource) {
narr = ((IResource) theResource).getText();
} else if (theResource instanceof IDomainResource) {
narr = ((IDomainResource) theResource).getText();
} else {
narr = null;
}
//FIXME potential null access on narr see line 623
if (gen != null && narr.isEmpty()) {
gen.generateNarrative(myContext, theResource, narr);
}
if (narr != null && narr.isEmpty() == false) {
RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
String childName = nextChild.getChildNameByDatatype(child.getDatatype());
BaseRuntimeElementDefinition<?> type = child.getChildByName(childName);
encodeChildElementToStreamWriter(theResource, theEventWriter, narr, childName, type, null, theContainedResource, nextChildElem);
continue;
}
}
if (nextChild instanceof RuntimeChildContainedResources) {
encodeChildElementToStreamWriter(theResource, theEventWriter, null, nextChild.getChildNameByDatatype(null), nextChild.getChildElementDefinitionByDatatype(null), null, theContainedResource, nextChildElem);
} else {
List<? extends IBase> values = nextChild.getAccessor().getValues(theElement);
values = super.preProcessValues(nextChild, theResource, values, nextChildElem);
if (values == null || values.isEmpty()) {
continue;
}
for (IBase nextValue : values) {
if ((nextValue == null || nextValue.isEmpty())) {
continue;
}
BaseParser.ChildNameAndDef childNameAndDef = super.getChildNameAndDef(nextChild, nextValue);
if (childNameAndDef == null) {
continue;
}
String childName = childNameAndDef.getChildName();
BaseRuntimeElementDefinition<?> childDef = childNameAndDef.getChildDef();
String extensionUrl = getExtensionUrl(nextChild.getExtensionUrl());
if (nextValue instanceof IBaseExtension && myContext.getVersion().getVersion() == FhirVersionEnum.DSTU1) {
// This is called for the Query resource in DSTU1 only
extensionUrl = getExtensionUrl(((IBaseExtension<?, ?>) nextValue).getUrl());
encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, extensionUrl, theContainedResource, nextChildElem);
} else if (extensionUrl != null && childName.equals("extension") == false) {
encodeExtension(theResource, theEventWriter, theContainedResource, nextChildElem, nextChild, nextValue, childName, extensionUrl, childDef);
} else if (nextChild instanceof RuntimeChildExtension) {
IBaseExtension<?, ?> extension = (IBaseExtension<?, ?>) nextValue;
if ((extension.getValue() == null || extension.getValue().isEmpty())) {
if (extension.getExtension().isEmpty()) {
continue;
}
}
encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, getExtensionUrl(extension.getUrl()), theContainedResource, nextChildElem);
} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theContainedResource) {
// suppress narratives from contained resources
} else {
encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, extensionUrl, theContainedResource, nextChildElem);
}
}
}
}
}
private void encodeExtension(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, CompositeChildElement nextChildElem, BaseRuntimeChildDefinition nextChild, IBase nextValue, String childName, String extensionUrl, BaseRuntimeElementDefinition<?> childDef)
throws XMLStreamException {
BaseRuntimeDeclaredChildDefinition extDef = (BaseRuntimeDeclaredChildDefinition) nextChild;
if (extDef.isModifier()) {
theEventWriter.writeStartElement("modifierExtension");
} else {
theEventWriter.writeStartElement("extension");
}
String elementId = getCompositeElementId(nextValue);
if (isNotBlank(elementId)) {
theEventWriter.writeAttribute("id", elementId);
}
theEventWriter.writeAttribute("url", extensionUrl);
encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, null, theContainedResource, nextChildElem);
theEventWriter.writeEndElement();
}
private void encodeExtensionsIfPresent(IBaseResource theResource, XMLStreamWriter theWriter, IBase theElement, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
if (theElement instanceof ISupportsUndeclaredExtensions) {
ISupportsUndeclaredExtensions res = (ISupportsUndeclaredExtensions) theElement;
encodeUndeclaredExtensions(theResource, theWriter, toBaseExtensionList(res.getUndeclaredExtensions()), "extension", theIncludedResource);
encodeUndeclaredExtensions(theResource, theWriter, toBaseExtensionList(res.getUndeclaredModifierExtensions()), "modifierExtension", theIncludedResource);
}
if (theElement instanceof IBaseHasExtensions) {
IBaseHasExtensions res = (IBaseHasExtensions) theElement;
encodeUndeclaredExtensions(theResource, theWriter, res.getExtension(), "extension", theIncludedResource);
}
if (theElement instanceof IBaseHasModifierExtensions) {
IBaseHasModifierExtensions res = (IBaseHasModifierExtensions) theElement;
encodeUndeclaredExtensions(theResource, theWriter, res.getModifierExtension(), "modifierExtension", theIncludedResource);
}
}
private void encodeResourceToXmlStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theIncludedResource, boolean theSubResource) throws XMLStreamException, DataFormatException {
IIdType resourceId = null;
if (StringUtils.isNotBlank(theResource.getIdElement().getIdPart())) {
resourceId = theResource.getIdElement();
if (theResource.getIdElement().getValue().startsWith("urn:")) {
resourceId = null;
}
if (myContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU1)) {
resourceId = null;
}
}
if (!theIncludedResource) {
if (super.shouldEncodeResourceId(theResource) == false) {
resourceId = null;
} else if (theSubResource == false && getEncodeForceResourceId() != null) {
resourceId = getEncodeForceResourceId();
}
}
encodeResourceToXmlStreamWriter(theResource, theEventWriter, theIncludedResource, resourceId);
}
private void encodeResourceToXmlStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, IIdType theResourceId) throws XMLStreamException {
if (!theContainedResource) {
super.containResourcesForEncoding(theResource);
}
RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
if (resDef == null) {
throw new ConfigurationException("Unknown resource type: " + theResource.getClass());
}
theEventWriter.writeStartElement(resDef.getName());
theEventWriter.writeDefaultNamespace(FHIR_NS);
if (theResource instanceof IAnyResource) {
// HL7.org Structures
if (theResourceId != null) {
writeCommentsPre(theEventWriter, theResourceId);
writeOptionalTagWithValue(theEventWriter, "id", theResourceId.getIdPart());
writeCommentsPost(theEventWriter, theResourceId);
}
encodeCompositeElementToStreamWriter(theResource, theResource, theEventWriter, theContainedResource, new CompositeChildElement(resDef));
} else {
if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
// DSTU2+
IResource resource = (IResource) theResource;
if (theResourceId != null) {
writeCommentsPre(theEventWriter, theResourceId);
writeOptionalTagWithValue(theEventWriter, "id", theResourceId.getIdPart());
writeCommentsPost(theEventWriter, theResourceId);
}
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<BaseCodingDt> securityLabels = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
List<? extends IIdType> profiles = extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
profiles = super.getProfileTagsForEncoding(resource, profiles);
TagList tags = getMetaTagsForEncoding((resource));
if (super.shouldEncodeResourceMeta(resource) && ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false) {
theEventWriter.writeStartElement("meta");
writeOptionalTagWithValue(theEventWriter, "versionId", versionIdPart);
if (updated != null) {
writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
}
for (IIdType profile : profiles) {
theEventWriter.writeStartElement("profile");
theEventWriter.writeAttribute("value", profile.getValue());
theEventWriter.writeEndElement();
}
for (BaseCodingDt securityLabel : securityLabels) {
theEventWriter.writeStartElement("security");
encodeCompositeElementToStreamWriter(resource, securityLabel, theEventWriter, theContainedResource, null);
theEventWriter.writeEndElement();
}
if (tags != null) {
for (Tag tag : tags) {
if (tag.isEmpty()) {
continue;
}
theEventWriter.writeStartElement("tag");
writeOptionalTagWithValue(theEventWriter, "system", tag.getScheme());
writeOptionalTagWithValue(theEventWriter, "code", tag.getTerm());
writeOptionalTagWithValue(theEventWriter, "display", tag.getLabel());
theEventWriter.writeEndElement();
}
}
theEventWriter.writeEndElement();
}
if (theResource instanceof IBaseBinary) {
IBaseBinary bin = (IBaseBinary) theResource;
writeOptionalTagWithValue(theEventWriter, "contentType", bin.getContentType());
writeOptionalTagWithValue(theEventWriter, "content", bin.getContentAsBase64());
} else {
encodeCompositeElementToStreamWriter(theResource, theResource, theEventWriter, theContainedResource, new CompositeChildElement(resDef));
}
} else {
// DSTU1
if (theResourceId != null && theContainedResource && theResourceId.hasIdPart()) {
theEventWriter.writeAttribute("id", theResourceId.getIdPart());
}
if (theResource instanceof IBaseBinary) {
IBaseBinary bin = (IBaseBinary) theResource;
if (bin.getContentType() != null) {
theEventWriter.writeAttribute("contentType", bin.getContentType());
}
theEventWriter.writeCharacters(bin.getContentAsBase64());
} else {
encodeCompositeElementToStreamWriter(theResource, theResource, theEventWriter, theContainedResource, new CompositeChildElement(resDef));
}
}
}
theEventWriter.writeEndElement();
}
@Override
public void encodeTagListToWriter(TagList theTagList, Writer theWriter) throws IOException {
try {
XMLStreamWriter eventWriter = createXmlWriter(theWriter);
eventWriter.writeStartElement(TagList.ELEMENT_NAME_LC);
eventWriter.writeDefaultNamespace(FHIR_NS);
for (Tag next : theTagList) {
eventWriter.writeStartElement(TagList.ATTR_CATEGORY);
if (isNotBlank(next.getTerm())) {
eventWriter.writeAttribute(Tag.ATTR_TERM, next.getTerm());
}
if (isNotBlank(next.getLabel())) {
eventWriter.writeAttribute(Tag.ATTR_LABEL, next.getLabel());
}
if (isNotBlank(next.getScheme())) {
eventWriter.writeAttribute(Tag.ATTR_SCHEME, next.getScheme());
}
eventWriter.writeEndElement();
}
eventWriter.writeEndElement();
eventWriter.close();
} catch (XMLStreamException e) {
throw new ConfigurationException("Failed to initialize STaX event factory", e);
}
}
private void encodeUndeclaredExtensions(IBaseResource theResource, XMLStreamWriter theEventWriter, List<? extends IBaseExtension<?, ?>> theExtensions, String tagName, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
for (IBaseExtension<?, ?> next : theExtensions) {
if (next == null || (ElementUtil.isEmpty(next.getValue()) && next.getExtension().isEmpty())) {
continue;
}
writeCommentsPre(theEventWriter, next);
theEventWriter.writeStartElement(tagName);
String elementId = getCompositeElementId(next);
if (isNotBlank(elementId)) {
theEventWriter.writeAttribute("id", elementId);
}
String url = getExtensionUrl(next.getUrl());
theEventWriter.writeAttribute("url", url);
if (next.getValue() != null) {
IBaseDatatype value = next.getValue();
RuntimeChildUndeclaredExtensionDefinition extDef = myContext.getRuntimeChildUndeclaredExtensionDefinition();
String childName = extDef.getChildNameByDatatype(value.getClass());
BaseRuntimeElementDefinition<?> childDef;
if (childName == null) {
childDef = myContext.getElementDefinition(value.getClass());
if (childDef == null) {
throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
}
childName = RuntimeChildUndeclaredExtensionDefinition.createExtensionChildName(childDef);
} else {
childDef = extDef.getChildElementDefinitionByDatatype(value.getClass());
if (childDef == null) {
throw new ConfigurationException("Unable to encode extension, unrecognized child element type: " + value.getClass().getCanonicalName());
}
}
encodeChildElementToStreamWriter(theResource, theEventWriter, value, childName, childDef, null, theIncludedResource, null);
}
// child extensions
encodeExtensionsIfPresent(theResource, theEventWriter, next, theIncludedResource);
theEventWriter.writeEndElement();
writeCommentsPost(theEventWriter, next);
}
}
private void encodeXhtml(XhtmlDt theDt, XMLStreamWriter theEventWriter) throws XMLStreamException {
if (theDt == null || theDt.getValue() == null) {
return;
}
boolean firstElement = true;
for (XMLEvent event : theDt.getValue()) {
switch (event.getEventType()) {
case XMLStreamConstants.ATTRIBUTE:
Attribute attr = (Attribute) event;
if (isBlank(attr.getName().getPrefix())) {
if (isBlank(attr.getName().getNamespaceURI())) {
theEventWriter.writeAttribute(attr.getName().getLocalPart(), attr.getValue());
} else {
theEventWriter.writeAttribute(attr.getName().getNamespaceURI(), attr.getName().getLocalPart(), attr.getValue());
}
} else {
theEventWriter.writeAttribute(attr.getName().getPrefix(), attr.getName().getNamespaceURI(), attr.getName().getLocalPart(), attr.getValue());
}
break;
case XMLStreamConstants.CDATA:
theEventWriter.writeCData(((Characters) event).getData());
break;
case XMLStreamConstants.CHARACTERS:
case XMLStreamConstants.SPACE:
String data = ((Characters) event).getData();
theEventWriter.writeCharacters(data);
break;
case XMLStreamConstants.COMMENT:
theEventWriter.writeComment(((Comment) event).getText());
break;
case XMLStreamConstants.END_ELEMENT:
theEventWriter.writeEndElement();
break;
case XMLStreamConstants.ENTITY_REFERENCE:
EntityReference er = (EntityReference) event;
theEventWriter.writeEntityRef(er.getName());
break;
case XMLStreamConstants.NAMESPACE:
Namespace ns = (Namespace) event;
theEventWriter.writeNamespace(ns.getPrefix(), ns.getNamespaceURI());
break;
case XMLStreamConstants.START_ELEMENT:
StartElement se = event.asStartElement();
if (firstElement) {
if (StringUtils.isBlank(se.getName().getPrefix())) {
String namespaceURI = se.getName().getNamespaceURI();
if (StringUtils.isBlank(namespaceURI)) {
namespaceURI = "http://www.w3.org/1999/xhtml";
}
theEventWriter.writeStartElement(se.getName().getLocalPart());
theEventWriter.writeDefaultNamespace(namespaceURI);
} else {
String prefix = se.getName().getPrefix();
String namespaceURI = se.getName().getNamespaceURI();
theEventWriter.writeStartElement(prefix, se.getName().getLocalPart(), namespaceURI);
theEventWriter.writeNamespace(prefix, namespaceURI);
}
firstElement = false;
} else {
if (isBlank(se.getName().getPrefix())) {
if (isBlank(se.getName().getNamespaceURI())) {
theEventWriter.writeStartElement(se.getName().getLocalPart());
} else {
if (StringUtils.isBlank(se.getName().getPrefix())) {
theEventWriter.writeStartElement(se.getName().getLocalPart());
// theEventWriter.writeDefaultNamespace(se.getName().getNamespaceURI());
} else {
theEventWriter.writeStartElement(se.getName().getNamespaceURI(), se.getName().getLocalPart());
}
}
} else {
theEventWriter.writeStartElement(se.getName().getPrefix(), se.getName().getLocalPart(), se.getName().getNamespaceURI());
}
for (Iterator<?> attrIter = se.getAttributes(); attrIter.hasNext();) {
Attribute next = (Attribute) attrIter.next();
theEventWriter.writeAttribute(next.getName().getLocalPart(), next.getValue());
}
}
break;
case XMLStreamConstants.DTD:
case XMLStreamConstants.END_DOCUMENT:
case XMLStreamConstants.ENTITY_DECLARATION:
case XMLStreamConstants.NOTATION_DECLARATION:
case XMLStreamConstants.PROCESSING_INSTRUCTION:
case XMLStreamConstants.START_DOCUMENT:
break;
}
}
}
@Override
public EncodingEnum getEncoding() {
return EncodingEnum.XML;
}
@Override
public <T extends IBaseResource> Bundle parseBundle(Class<T> theResourceType, Reader theReader) {
XMLEventReader streamReader = createStreamReader(theReader);
return parseBundle(streamReader, theResourceType);
}
private Bundle parseBundle(XMLEventReader theStreamReader, Class<? extends IBaseResource> theResourceType) {
ParserState<Bundle> parserState = ParserState.getPreAtomInstance(this, myContext, theResourceType, false, getErrorHandler());
return doXmlLoop(theStreamReader, parserState);
}
private <T extends IBaseResource> T parseResource(Class<T> theResourceType, XMLEventReader theStreamReader) {
ParserState<T> parserState = ParserState.getPreResourceInstance(this, theResourceType, myContext, false, getErrorHandler());
return doXmlLoop(theStreamReader, parserState);
}
@Override
public TagList parseTagList(Reader theReader) {
XMLEventReader streamReader = createStreamReader(theReader);
ParserState<TagList> parserState = ParserState.getPreTagListInstance(this, myContext, false, getErrorHandler());
return doXmlLoop(streamReader, parserState);
}
@Override
public IParser setPrettyPrint(boolean thePrettyPrint) {
myPrettyPrint = thePrettyPrint;
return this;
}
/**
* This is just to work around the fact that casting java.util.List<ca.uhn.fhir.model.api.ExtensionDt> to
* java.util.List<? extends org.hl7.fhir.instance.model.api.IBaseExtension<?, ?>> seems to be
* rejected by the compiler some of the time.
*/
private <Q extends IBaseExtension<?, ?>> List<IBaseExtension<?, ?>> toBaseExtensionList(final List<Q> theList) {
List<IBaseExtension<?, ?>> retVal = new ArrayList<IBaseExtension<?, ?>>(theList.size());
retVal.addAll(theList);
return retVal;
}
private void writeAuthor(XMLStreamWriter theEventWriter, BaseBundle theBundle) throws XMLStreamException {
if (StringUtils.isNotBlank(theBundle.getAuthorName().getValue())) {
theEventWriter.writeStartElement("author");
writeTagWithTextNode(theEventWriter, "name", theBundle.getAuthorName());
writeOptionalTagWithTextNode(theEventWriter, "uri", theBundle.getAuthorUri());
theEventWriter.writeEndElement();
}
}
private void writeAtomLink(XMLStreamWriter theEventWriter, String theRel, StringDt theStringDt) throws XMLStreamException {
if (StringUtils.isNotBlank(theStringDt.getValue())) {
theEventWriter.writeStartElement("link");
theEventWriter.writeAttribute("rel", theRel);
theEventWriter.writeAttribute("href", theStringDt.getValue());
theEventWriter.writeEndElement();
}
}
private void writeBundleResourceLink(XMLStreamWriter theEventWriter, String theRel, StringDt theUrl) throws XMLStreamException {
if (theUrl.isEmpty() == false) {
theEventWriter.writeStartElement("link");
theEventWriter.writeStartElement("relation");
theEventWriter.writeAttribute("value", theRel);
theEventWriter.writeEndElement();
theEventWriter.writeStartElement("url");
theEventWriter.writeAttribute("value", theUrl.getValue());
theEventWriter.writeEndElement();
theEventWriter.writeEndElement();
}
}
private void writeCategories(XMLStreamWriter eventWriter, TagList categories) throws XMLStreamException {
if (categories != null) {
for (Tag next : categories) {
eventWriter.writeStartElement("category");
eventWriter.writeAttribute("term", defaultString(next.getTerm()));
eventWriter.writeAttribute("label", defaultString(next.getLabel()));
eventWriter.writeAttribute("scheme", defaultString(next.getScheme()));
eventWriter.writeEndElement();
}
}
}
private void writeCommentsPost(XMLStreamWriter theEventWriter, IBase theElement) throws XMLStreamException {
if (theElement != null && theElement.hasFormatComment()) {
for (String next : theElement.getFormatCommentsPost()) {
if (isNotBlank(next)) {
theEventWriter.writeComment(next);
}
}
}
}
private void writeCommentsPre(XMLStreamWriter theEventWriter, IBase theElement) throws XMLStreamException {
if (theElement != null && theElement.hasFormatComment()) {
for (String next : theElement.getFormatCommentsPre()) {
if (isNotBlank(next)) {
theEventWriter.writeComment(next);
}
}
}
}
private void writeOptionalAttribute(XMLStreamWriter theEventWriter, String theName, String theValue) throws XMLStreamException {
if (StringUtils.isNotBlank(theValue)) {
theEventWriter.writeAttribute(theName, theValue);
}
}
private void writeOptionalTagWithTextNode(XMLStreamWriter theEventWriter, String theTagName, InstantDt theInstantDt) throws XMLStreamException {
if (theInstantDt.getValue() != null) {
theEventWriter.writeStartElement(theTagName);
theEventWriter.writeCharacters(theInstantDt.getValueAsString());
theEventWriter.writeEndElement();
}
}
private void writeOptionalTagWithTextNode(XMLStreamWriter theEventWriter, String theElementName, StringDt theTextValue) throws XMLStreamException {
if (StringUtils.isNotBlank(theTextValue.getValue())) {
theEventWriter.writeStartElement(theElementName);
theEventWriter.writeCharacters(theTextValue.getValue());
theEventWriter.writeEndElement();
}
}
private void writeOptionalTagWithValue(XMLStreamWriter theEventWriter, String theName, String theValue) throws XMLStreamException {
if (StringUtils.isNotBlank(theValue)) {
theEventWriter.writeStartElement(theName);
theEventWriter.writeAttribute("value", theValue);
theEventWriter.writeEndElement();
}
}
private void writeTagWithTextNode(XMLStreamWriter theEventWriter, String theElementName, IdDt theIdDt) throws XMLStreamException {
theEventWriter.writeStartElement(theElementName);
if (StringUtils.isNotBlank(theIdDt.getValue())) {
theEventWriter.writeCharacters(theIdDt.getValue());
}
theEventWriter.writeEndElement();
}
private void writeTagWithTextNode(XMLStreamWriter theEventWriter, String theElementName, StringDt theStringDt) throws XMLStreamException {
theEventWriter.writeStartElement(theElementName);
if (StringUtils.isNotBlank(theStringDt.getValue())) {
theEventWriter.writeCharacters(theStringDt.getValue());
}
theEventWriter.writeEndElement();
}
}