Java tutorial
package ca.uhn.fhir.parser; /* * #%L * HAPI FHIR - Core Library * %% * Copyright (C) 2014 - 2016 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 ca.uhn.fhir.model.api.BaseBundle; 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.IBaseElement; 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.IBaseReference; 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.BaseRuntimeElementCompositeDefinition; 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.RuntimeChildDeclaredExtensionDefinition; 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.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; } else { 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); } 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); } 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()) { 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()); 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"); 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 && nextEntry.getResource().getId().getBaseUrl() != null) { 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"); 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 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) theElement; String encodedValue = "id".equals(childName) ? value.getIdPart() : value.getValue(); if (value != null) { theEventWriter.writeStartElement(childName); theEventWriter.writeAttribute("value", encodedValue); encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource); theEventWriter.writeEndElement(); } break; } case PRIMITIVE_DATATYPE: { IPrimitiveType<?> pd = (IPrimitiveType<?>) 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) theElement; if (dt.hasContent()) { encodeXhtml(dt, theEventWriter); } break; } case PRIMITIVE_XHTML_HL7ORG: { IBaseXhtml dt = (IBaseXhtml) theElement; if (dt.isEmpty()) { break; } else { // 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; } 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 = nextChild.getExtensionUrl(); 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, 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, 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 = 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()); } else { 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(); } }