1108 lines
45 KiB
Java

package ca.uhn.fhir.parser;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2015 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.*;
import java.io.IOException;
import java.io.Reader;
import java.io.StringWriter;
import java.io.Writer;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import java.util.ListIterator;
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 ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.primitive.*;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.IBase;
import org.hl7.fhir.instance.model.IBaseResource;
import org.hl7.fhir.instance.model.IPrimitiveType;
import org.hl7.fhir.instance.model.api.IAnyResource;
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.IDomainResource;
import org.hl7.fhir.instance.model.api.INarrative;
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.RuntimeChildDeclaredExtensionDefinition;
import ca.uhn.fhir.context.RuntimeChildNarrativeDefinition;
import ca.uhn.fhir.context.RuntimeChildUndeclaredExtensionDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.BundleEntry;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IElement;
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.BaseContainedDt;
import ca.uhn.fhir.model.base.composite.BaseNarrativeDt;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
import ca.uhn.fhir.model.base.resource.BaseBinary;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.rest.method.BaseMethodBinding;
import ca.uhn.fhir.util.NonPrettyPrintWriterWrapper;
import ca.uhn.fhir.util.PrettyPrintWriterWrapper;
import ca.uhn.fhir.util.XmlUtil;
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()}.
*/
public XmlParser(FhirContext theContext) {
super(theContext);
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);
}
// XMLEventReader streamReader;
// try {
// streamReader = myXmlInputFactory.createXMLEventReader(theReader);
// } catch (XMLStreamException e) {
// throw new DataFormatException(e);
// } catch (FactoryConfigurationError e) {
// throw new ConfigurationException("Failed to initialize STaX event factory", e);
// }
// return streamReader;
}
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;
} else {
NonPrettyPrintWriterWrapper retVal = new NonPrettyPrintWriterWrapper(eventWriter);
return retVal;
}
}
private <T> T doXmlLoop(XMLEventReader streamReader, ParserState<T> parserState) {
ourLog.trace("Entering XML parsing loop with state: {}", parserState);
try {
while (streamReader.hasNext()) {
XMLEvent nextEvent = streamReader.nextEvent();
try {
if (nextEvent.isStartElement()) {
StartElement elem = nextEvent.asStartElement();
String namespaceURI = elem.getName().getNamespaceURI();
if ("extension".equals(elem.getName().getLocalPart())) {
Attribute urlAttr = elem.getAttributeByName(new QName("url"));
if (urlAttr == null || isBlank(urlAttr.getValue())) {
throw new DataFormatException("Extension element has no 'url' attribute");
}
parserState.enteringNewElementExtension(elem, urlAttr.getValue(), false);
} else if ("modifierExtension".equals(elem.getName().getLocalPart())) {
Attribute urlAttr = elem.getAttributeByName(new QName("url"));
if (urlAttr == null || isBlank(urlAttr.getValue())) {
throw new DataFormatException("Extension element has no 'url' attribute");
}
parserState.enteringNewElementExtension(elem, urlAttr.getValue(), true);
} else {
String elementName = elem.getName().getLocalPart();
parserState.enteringNewElement(namespaceURI, elementName);
}
for (@SuppressWarnings("unchecked")
Iterator<Attribute> iter = elem.getAttributes(); iter.hasNext();) {
Attribute next = iter.next();
// if
// (next.getName().getLocalPart().equals("value")) {
parserState.attributeValue(next.getName().getLocalPart(), next.getValue());
// }
}
} else if (nextEvent.isAttribute()) {
Attribute elem = (Attribute) nextEvent;
String name = (elem.getName().getLocalPart());
parserState.attributeValue(name, elem.getValue());
} else if (nextEvent.isEndElement()) {
parserState.endingElement();
if (parserState.isComplete()) {
return parserState.getObject();
}
} else if (nextEvent.isCharacters()) {
parserState.string(nextEvent.asCharacters().getData());
}
parserState.xmlEvent(nextEvent);
} catch (DataFormatException e) {
throw new DataFormatException("DataFormatException at [" + nextEvent.getLocation().toString() + "]: " + e.getMessage(), e);
}
}
return null;
} catch (XMLStreamException e) {
throw new DataFormatException(e);
}
}
@Override
public String encodeBundleToString(Bundle theBundle) throws DataFormatException {
StringWriter stringWriter = new StringWriter();
encodeBundleToWriter(theBundle, stringWriter);
return stringWriter.toString();
}
@Override
public void encodeBundleToWriter(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);
}
}
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, "self", theBundle.getLinkSelf());
writeAtomLink(eventWriter, "first", theBundle.getLinkFirst());
writeAtomLink(eventWriter, "previous", theBundle.getLinkPrevious());
writeAtomLink(eventWriter, "next", theBundle.getLinkNext());
writeAtomLink(eventWriter, "last", theBundle.getLinkLast());
writeAtomLink(eventWriter, "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());
writeOptionalTagWithTextNode(eventWriter, "published", theBundle.getPublished());
if (StringUtils.isNotBlank(theBundle.getAuthorName().getValue())) {
eventWriter.writeStartElement("author");
writeTagWithTextNode(eventWriter, "name", theBundle.getAuthorName());
writeOptionalTagWithTextNode(eventWriter, "uri", theBundle.getAuthorUri());
eventWriter.writeEndElement();
}
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()) {
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) {
if (nextEntry.getId().isEmpty() == false) {
writeTagWithTextNode(eventWriter, "id", nextEntry.getId());
} else {
writeTagWithTextNode(eventWriter, "id", nextEntry.getResource().getId());
}
}
writeOptionalTagWithTextNode(eventWriter, "updated", nextEntry.getUpdated());
writeOptionalTagWithTextNode(eventWriter, "published", nextEntry.getPublished());
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);
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");
writeOptionalTagWithValue(theEventWriter, "versionId", bundleId.getVersionIdPart());
if (updated != null) {
writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
}
theEventWriter.writeEndElement();
}
String bundleBaseUrl = theBundle.getLinkBase().getValue();
writeOptionalTagWithValue(theEventWriter, "type", theBundle.getType().getValue());
writeOptionalTagWithValue(theEventWriter, "base", bundleBaseUrl);
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;
}
writeOptionalTagWithValue(theEventWriter, "base", determineResourceBaseUrl(bundleBaseUrl, nextEntry));
IResource resource = nextEntry.getResource();
if (resource != null && !resource.isEmpty() && !deleted) {
theEventWriter.writeStartElement("resource");
encodeResourceToXmlStreamWriter(resource, theEventWriter, false);
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.getTransactionOperation().isEmpty() == false || nextEntry.getLinkSearch().isEmpty() == false) {
theEventWriter.writeStartElement("transaction");
writeOptionalTagWithValue(theEventWriter, "operation", nextEntry.getTransactionOperation().getValue());
writeOptionalTagWithValue(theEventWriter, "url", nextEntry.getLinkSearch().getValue());
theEventWriter.writeEndElement();
}
if (deleted) {
theEventWriter.writeStartElement("deleted");
writeOptionalTagWithValue(theEventWriter, "type", nextEntry.getId().getResourceType());
writeOptionalTagWithValue(theEventWriter, "id", nextEntry.getId().getIdPart());
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 nextValue, String childName, BaseRuntimeElementDefinition<?> childDef,
String theExtensionUrl, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
if (nextValue.isEmpty()) {
if (childDef.getChildType() == ChildTypeEnum.CONTAINED_RESOURCES && getContainedResources().isEmpty() == false && theIncludedResource == false) {
// We still want to go in..
} else {
return;
}
}
switch (childDef.getChildType()) {
case PRIMITIVE_DATATYPE: {
IPrimitiveType<?> pd = (IPrimitiveType<?>) nextValue;
String value = pd.getValueAsString();
if (value != null) {
theEventWriter.writeStartElement(childName);
theEventWriter.writeAttribute("value", value);
encodeExtensionsIfPresent(theResource, theEventWriter, nextValue, theIncludedResource);
theEventWriter.writeEndElement();
}
break;
}
case RESOURCE_BLOCK:
case COMPOSITE_DATATYPE: {
theEventWriter.writeStartElement(childName);
if (isNotBlank(theExtensionUrl)) {
theEventWriter.writeAttribute("url", theExtensionUrl);
}
BaseRuntimeElementCompositeDefinition<?> childCompositeDef = (BaseRuntimeElementCompositeDefinition<?>) childDef;
encodeCompositeElementToStreamWriter(theResource, nextValue, theEventWriter, childCompositeDef, theIncludedResource);
theEventWriter.writeEndElement();
break;
}
case RESOURCE_REF: {
BaseResourceReferenceDt ref = (BaseResourceReferenceDt) nextValue;
if (!ref.isEmpty()) {
theEventWriter.writeStartElement(childName);
encodeResourceReferenceToStreamWriter(theEventWriter, ref);
theEventWriter.writeEndElement();
}
break;
}
case CONTAINED_RESOURCES: {
BaseContainedDt value = (BaseContainedDt) nextValue;
/*
* 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()) {
IdDt 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) nextValue;
encodeResourceToXmlStreamWriter(resource, theEventWriter, false);
theEventWriter.writeEndElement();
break;
}
case PRIMITIVE_XHTML: {
XhtmlDt dt = (XhtmlDt) nextValue;
if (dt.hasContent()) {
encodeXhtml(dt, theEventWriter);
}
break;
}
case EXTENSION_DECLARED:
case UNDECL_EXT: {
throw new IllegalStateException("state should not happen: " + childDef.getName());
}
}
}
private void encodeCompositeElementChildrenToStreamWriter(IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter, List<? extends BaseRuntimeChildDefinition> children,
boolean theIncludedResource) throws XMLStreamException, DataFormatException {
for (BaseRuntimeChildDefinition nextChild : children) {
if (nextChild.getElementName().equals("extension") || nextChild.getElementName().equals("modifierExtension")) {
continue;
}
if (nextChild instanceof RuntimeChildNarrativeDefinition && !theIncludedResource) {
INarrativeGenerator gen = myContext.getNarrativeGenerator();
if (theResource instanceof IResource) {
BaseNarrativeDt<?> narr = ((IResource) theResource).getText();
if (gen != null && narr.isEmpty()) {
String resourceProfile = myContext.getResourceDefinition(theResource).getResourceProfile();
gen.generateNarrative(resourceProfile, theResource, narr);
}
if (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, theIncludedResource);
continue;
}
} else {
INarrative narr1 = ((IDomainResource) theResource).getText();
BaseNarrativeDt<?> narr2 = null;
if (gen != null && narr1.isEmpty()) {
// TODO: need to implement this
String resourceProfile = myContext.getResourceDefinition(theResource).getResourceProfile();
gen.generateNarrative(resourceProfile, theResource, null);
}
if (narr2 != null) {
RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
String childName = nextChild.getChildNameByDatatype(child.getDatatype());
BaseRuntimeElementDefinition<?> type = child.getChildByName(childName);
encodeChildElementToStreamWriter(theResource, theEventWriter, narr2, childName, type, null, theIncludedResource);
continue;
}
}
}
List<? extends IBase> values = nextChild.getAccessor().getValues(theElement);
if (values == null || values.isEmpty()) {
continue;
}
for (IBase nextValue : values) {
if ((nextValue == null || nextValue.isEmpty()) && !(nextValue instanceof BaseContainedDt)) {
continue;
}
Class<? extends IBase> type = nextValue.getClass();
String childName = nextChild.getChildNameByDatatype(type);
String extensionUrl = nextChild.getExtensionUrl();
BaseRuntimeElementDefinition<?> childDef = nextChild.getChildElementDefinitionByDatatype(type);
if (childDef == null) {
super.throwExceptionForUnknownChildType(nextChild, type);
}
if (nextValue instanceof IBaseExtension && myContext.getVersion().getVersion() == FhirVersionEnum.DSTU1) {
// This is called for the Query resource in DSTU1 only
extensionUrl = ((IBaseExtension<?>) nextValue).getUrl();
encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, extensionUrl, theIncludedResource);
} else if (extensionUrl != null && childName.equals("extension") == false) {
RuntimeChildDeclaredExtensionDefinition extDef = (RuntimeChildDeclaredExtensionDefinition) nextChild;
if (extDef.isModifier()) {
theEventWriter.writeStartElement("modifierExtension");
} else {
theEventWriter.writeStartElement("extension");
}
theEventWriter.writeAttribute("url", extensionUrl);
encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, null, theIncludedResource);
theEventWriter.writeEndElement();
} else if (nextChild instanceof RuntimeChildNarrativeDefinition && theIncludedResource) {
// suppress narratives from contained resources
} else {
encodeChildElementToStreamWriter(theResource, theEventWriter, nextValue, childName, childDef, extensionUrl, theIncludedResource);
}
}
}
}
private void encodeCompositeElementToStreamWriter(IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter, BaseRuntimeElementCompositeDefinition<?> theElementDefinition,
boolean theIncludedResource) throws XMLStreamException, DataFormatException {
encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource);
encodeCompositeElementChildrenToStreamWriter(theResource, theElement, theEventWriter, theElementDefinition.getExtensions(), theIncludedResource);
encodeCompositeElementChildrenToStreamWriter(theResource, theElement, theEventWriter, theElementDefinition.getChildren(), theIncludedResource);
}
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);
}
}
/**
* 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 encodeResourceReferenceToStreamWriter(XMLStreamWriter theEventWriter, BaseResourceReferenceDt theRef) throws XMLStreamException {
String reference = determineReferenceText(theRef);
if (StringUtils.isNotBlank(reference)) {
theEventWriter.writeStartElement(RESREF_REFERENCE);
theEventWriter.writeAttribute("value", reference);
theEventWriter.writeEndElement();
}
if (!(theRef.getDisplayElement().isEmpty())) {
theEventWriter.writeStartElement(RESREF_DISPLAY);
theEventWriter.writeAttribute("value", theRef.getDisplayElement().getValue());
theEventWriter.writeEndElement();
}
}
private void encodeResourceToStreamWriterInDstu2Format(RuntimeResourceDefinition theResDef, IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter,
BaseRuntimeElementCompositeDefinition<?> resDef, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
/*
* DSTU2 requires extensions to come in a specific spot within the encoded content - This is a bit of a messy way to make that happen, but hopefully this won't matter as much once we use the
* HL7 structures
*/
List<BaseRuntimeChildDefinition> preExtensionChildren = new ArrayList<BaseRuntimeChildDefinition>();
List<BaseRuntimeChildDefinition> postExtensionChildren = new ArrayList<BaseRuntimeChildDefinition>();
List<BaseRuntimeChildDefinition> children = resDef.getChildren();
for (BaseRuntimeChildDefinition next : children) {
if (next.getElementName().equals("text")) {
preExtensionChildren.add(next);
} else if (next.getElementName().equals("contained")) {
preExtensionChildren.add(next);
} else {
postExtensionChildren.add(next);
}
}
encodeCompositeElementChildrenToStreamWriter(theResource, theElement, theEventWriter, preExtensionChildren, theIncludedResource);
encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource);
encodeCompositeElementChildrenToStreamWriter(theResource, theElement, theEventWriter, resDef.getExtensions(), theIncludedResource);
encodeCompositeElementChildrenToStreamWriter(theResource, theElement, theEventWriter, postExtensionChildren, theIncludedResource);
}
@Override
public String encodeResourceToString(IBaseResource theResource) throws DataFormatException {
if (theResource == null) {
throw new NullPointerException("Resource can not be null");
}
Writer stringWriter = new StringWriter();
encodeResourceToWriter(theResource, stringWriter);
return stringWriter.toString();
}
@Override
public void encodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws DataFormatException {
XMLStreamWriter eventWriter;
try {
eventWriter = createXmlWriter(theWriter);
encodeResourceToXmlStreamWriter(theResource, eventWriter, false);
eventWriter.flush();
} catch (XMLStreamException e) {
throw new ConfigurationException("Failed to initialize STaX event factory", e);
}
}
private void encodeResourceToXmlStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theIncludedResource) throws XMLStreamException, DataFormatException {
String resourceId = null;
if (theResource instanceof IResource) {
// HAPI structs
IResource iResource = (IResource) theResource;
if (StringUtils.isNotBlank(iResource.getId().getValue())) {
resourceId = iResource.getId().getIdPart();
}
} else {
// HL7 structs
IAnyResource resource = (IAnyResource) theResource;
if (StringUtils.isNotBlank(resource.getId())) {
resourceId = resource.getId();
}
}
encodeResourceToXmlStreamWriter(theResource, theEventWriter, theIncludedResource, resourceId);
}
private void encodeResourceToXmlStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, String 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
encodeCompositeElementToStreamWriter(theResource, theResource, theEventWriter, resDef, theContainedResource);
} else {
if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
// DSTU2+
IResource resource = (IResource) theResource;
writeOptionalTagWithValue(theEventWriter, "id", theResourceId);
InstantDt updated = (InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
//Object securityLabelRawObj = resource.getResourceMetadata().get(ResourceMetadataKeyEnum.SECURITY_LABELS);
List<BaseCodingDt> securityLabels = (List<BaseCodingDt>) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.SECURITY_LABELS);
IdDt resourceId = resource.getId();
if (resourceId != null && isNotBlank(resourceId.getVersionIdPart())
|| (updated != null && !updated.isEmpty())
|| (securityLabels != null && !securityLabels.isEmpty())) {
theEventWriter.writeStartElement("meta");
String versionIdPart = resourceId.getVersionIdPart();
if (isBlank(versionIdPart)) {
versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
}
writeOptionalTagWithValue(theEventWriter, "versionId", versionIdPart);
if (updated != null) {
writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
}
if (securityLabels != null) {
if (!securityLabels.isEmpty()) {
for (BaseCodingDt securityLabel : securityLabels) {
theEventWriter.writeStartElement("security");
UriDt system = securityLabel.getSystemElement();
if (system != null && !system.isEmpty())
writeOptionalTagWithValue(theEventWriter, "system", system.getValueAsString());
CodeDt code = securityLabel.getCodeElement();
if (code != null && !code.isEmpty())
writeOptionalTagWithValue(theEventWriter, "code", code.getValueAsString());
StringDt display = securityLabel.getDisplayElement();
if (display != null && !display.isEmpty())
writeOptionalTagWithValue(theEventWriter, "display", display.getValueAsString());
/*todo: handle version
StringDt version = securityLabel.getVersion();
if (version != null && ! version.isEmpty())
writeOptionalTagWithValue(theEventWriter, "version", version.getValueAsString());
*/
theEventWriter.writeEndElement();
}
}
}
theEventWriter.writeEndElement();
}
if (theResource instanceof BaseBinary) {
BaseBinary bin = (BaseBinary) theResource;
writeOptionalTagWithValue(theEventWriter, "contentType", bin.getContentType());
writeOptionalTagWithValue(theEventWriter, "content", bin.getContentAsBase64());
} else {
encodeResourceToStreamWriterInDstu2Format(resDef, theResource, theResource, theEventWriter, resDef, theContainedResource);
}
} else {
// DSTU1
if (theResourceId != null && theContainedResource) {
theEventWriter.writeAttribute("id", theResourceId);
}
if (theResource instanceof BaseBinary) {
BaseBinary bin = (BaseBinary) theResource;
if (bin.getContentType() != null) {
theEventWriter.writeAttribute("contentType", bin.getContentType());
}
theEventWriter.writeCharacters(bin.getContentAsBase64());
} else {
encodeCompositeElementToStreamWriter(theResource, theResource, theEventWriter, resDef, theContainedResource);
}
}
}
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 theWriter, List<? extends IBaseExtension<?>> theExtensions, String tagName, boolean theIncludedResource)
throws XMLStreamException, DataFormatException {
for (IBaseExtension<?> next : theExtensions) {
if (next == null) {
continue;
}
theWriter.writeStartElement(tagName);
String url = next.getUrl();
theWriter.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());
} else {
childName = RuntimeChildUndeclaredExtensionDefinition.createExtensionChildName(childDef);
}
} else {
childDef = extDef.getChildElementDefinitionByDatatype(value.getClass());
}
encodeChildElementToStreamWriter(theResource, theWriter, value, childName, childDef, null, theIncludedResource);
}
// child extensions
encodeExtensionsIfPresent(theResource, theWriter, next, theIncludedResource);
theWriter.writeEndElement();
}
}
private void encodeXhtml(XhtmlDt theDt, XMLStreamWriter theEventWriter) throws XMLStreamException {
if (theDt == null || theDt.getValue() == null || getSuppressNarratives()) {
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 <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(myContext, theResourceType, false);
return doXmlLoop(theStreamReader, parserState);
}
@Override
public <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) {
XMLEventReader streamReader = createStreamReader(theReader);
return parseResource(theResourceType, streamReader);
}
private <T extends IBaseResource> T parseResource(Class<T> theResourceType, XMLEventReader theStreamReader) {
ParserState<T> parserState = ParserState.getPreResourceInstance(theResourceType, myContext, false);
return doXmlLoop(theStreamReader, parserState);
}
@Override
public TagList parseTagList(Reader theReader) {
XMLEventReader streamReader = createStreamReader(theReader);
ParserState<TagList> parserState = ParserState.getPreTagListInstance(myContext, false);
return doXmlLoop(streamReader, parserState);
}
@Override
public IParser setPrettyPrint(boolean thePrettyPrint) {
myPrettyPrint = thePrettyPrint;
return this;
}
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 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();
}
}