RDF Parser 0.1
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@ -627,6 +627,23 @@ public class FhirContext {
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return new JsonParser(this, myParserErrorHandler);
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return new JsonParser(this, myParserErrorHandler);
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}
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}
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/**
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* Create and return a new RDF parser.
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*
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* <p>
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* Thread safety: <b>Parsers are not guaranteed to be thread safe</b>. Create a new parser instance for every thread
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* or every message being parsed/encoded.
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* </p>
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* <p>
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* Performance Note: <b>This method is cheap</b> to call, and may be called once for every message being processed
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* without incurring any performance penalty
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* </p>
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*/
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public IParser newRDFParser() {
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return new RDFParser(this, myParserErrorHandler);
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}
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/**
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/**
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* Instantiates a new client instance. This method requires an interface which is defined specifically for your use
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* Instantiates a new client instance. This method requires an interface which is defined specifically for your use
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* cases to contain methods for each of the RESTful operations you wish to implement (e.g. "read ImagingStudy",
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* cases to contain methods for each of the RESTful operations you wish to implement (e.g. "read ImagingStudy",
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@ -0,0 +1,777 @@
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package ca.uhn.fhir.parser;
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/*-
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* #%L
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* HAPI FHIR - Core Library
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* %%
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* Copyright (C) 2014 - 2019 University Health Network
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import ca.uhn.fhir.context.*;
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import ca.uhn.fhir.model.api.*;
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import ca.uhn.fhir.model.base.composite.BaseCodingDt;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.model.primitive.InstantDt;
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import ca.uhn.fhir.model.primitive.XhtmlDt;
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import ca.uhn.fhir.narrative.INarrativeGenerator;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.util.ElementUtil;
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import ca.uhn.fhir.util.NonPrettyPrintWriterWrapper;
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import ca.uhn.fhir.util.PrettyPrintWriterWrapper;
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import ca.uhn.fhir.util.RDFUtil;
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import org.apache.commons.lang3.StringUtils;
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import org.hl7.fhir.instance.model.api.*;
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//import org.apache.jena.rdf.model.*;
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//import org.apache.jena.util.FileManager;
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import javax.xml.namespace.QName;
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import javax.xml.stream.*;
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import javax.xml.stream.events.*;
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import java.io.Reader;
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import java.io.Writer;
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import java.util.ArrayList;
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import java.util.Iterator;
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import java.util.List;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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/**
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* This class is the FHIR RDF parser/encoder. Users should not interact with this class directly, but should use
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* {@link FhirContext#newRDFParser()} to get an instance.
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*/
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public class RDFParser extends BaseParser /* implements IParser */ {
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private static final String FHIR_NS = "http://hl7.org/fhir";
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RDFParser.class);
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// private static final Set<String> RESOURCE_NAMESPACES;
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private FhirContext myContext;
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private boolean myPrettyPrint;
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/**
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* Do not use this constructor, the recommended way to obtain a new instance of the RDF parser is to invoke
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* {@link FhirContext#newRDFParser()}.
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*
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* @param theParserErrorHandler the Parser Error Handler
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*/
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public RDFParser(FhirContext theContext, IParserErrorHandler theParserErrorHandler) {
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super(theContext, theParserErrorHandler);
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myContext = theContext;
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}
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private XMLEventReader createStreamReader(Reader theReader) {
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try {
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return RDFUtil.createXmlReader(theReader);
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} catch (FactoryConfigurationError e1) {
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throw new ConfigurationException("Failed to initialize STaX event factory", e1);
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} catch (XMLStreamException e1) {
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throw new DataFormatException(e1);
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}
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}
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private XMLStreamWriter createRDFWriter(Writer theWriter) throws XMLStreamException {
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XMLStreamWriter eventWriter;
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eventWriter = RDFUtil.createXmlStreamWriter(theWriter);
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eventWriter = decorateStreamWriter(eventWriter);
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return eventWriter;
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}
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private XMLStreamWriter decorateStreamWriter(XMLStreamWriter eventWriter) {
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if (myPrettyPrint) {
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return new PrettyPrintWriterWrapper(eventWriter);
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}
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return new NonPrettyPrintWriterWrapper(eventWriter);
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}
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@Override
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public void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter, EncodeContext theEncodeContext) throws DataFormatException {
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XMLStreamWriter eventWriter;
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try {
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eventWriter = createRDFWriter(theWriter);
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encodeResourceToRDFStreamWriter(theResource, eventWriter, false, theEncodeContext);
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eventWriter.flush();
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} catch (XMLStreamException e) {
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throw new ConfigurationException("Failed to initialize STaX event factory", e);
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}
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}
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@Override
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public <T extends IBaseResource> T doParseResource(Class<T> theResourceType, Reader theReader) {
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XMLEventReader streamReader = createStreamReader(theReader);
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return parseResource(theResourceType, streamReader);
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}
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private <T> T doRDFLoop(XMLEventReader streamReader, ParserState<T> parserState) {
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ourLog.trace("Entering RDF parsing loop with state: {}", parserState);
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try {
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List<String> heldComments = new ArrayList<>(1);
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while (streamReader.hasNext()) {
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XMLEvent nextEvent = streamReader.nextEvent();
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try {
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switch (nextEvent.getEventType()) {
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case XMLStreamConstants.START_ELEMENT: {
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StartElement elem = nextEvent.asStartElement();
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String namespaceURI = elem.getName().getNamespaceURI();
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if ("extension".equals(elem.getName().getLocalPart())) {
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Attribute urlAttr = elem.getAttributeByName(new QName("url"));
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String url;
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if (urlAttr == null || isBlank(urlAttr.getValue())) {
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getErrorHandler().missingRequiredElement(new ParseLocation().setParentElementName("extension"), "url");
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url = null;
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} else {
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url = urlAttr.getValue();
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}
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parserState.enteringNewElementExtension(elem, url, false, getServerBaseUrl());
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} else if ("modifierExtension".equals(elem.getName().getLocalPart())) {
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Attribute urlAttr = elem.getAttributeByName(new QName("url"));
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String url;
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if (urlAttr == null || isBlank(urlAttr.getValue())) {
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getErrorHandler().missingRequiredElement(new ParseLocation().setParentElementName("modifierExtension"), "url");
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url = null;
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} else {
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url = urlAttr.getValue();
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}
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parserState.enteringNewElementExtension(elem, url, true, getServerBaseUrl());
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} else {
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String elementName = elem.getName().getLocalPart();
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parserState.enteringNewElement(namespaceURI, elementName);
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}
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if (!heldComments.isEmpty()) {
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for (String next : heldComments) {
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parserState.commentPre(next);
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}
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heldComments.clear();
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}
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for (Iterator<Attribute> attributes = elem.getAttributes(); attributes.hasNext(); ) {
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Attribute next = attributes.next();
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parserState.attributeValue(next.getName().getLocalPart(), next.getValue());
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}
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break;
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}
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case XMLStreamConstants.END_DOCUMENT:
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case XMLStreamConstants.END_ELEMENT: {
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if (!heldComments.isEmpty()) {
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for (String next : heldComments) {
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parserState.commentPost(next);
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}
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heldComments.clear();
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}
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parserState.endingElement();
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// if (parserState.isComplete()) {
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// return parserState.getObject();
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// }
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break;
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}
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case XMLStreamConstants.CHARACTERS: {
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parserState.string(nextEvent.asCharacters().getData());
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break;
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}
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case XMLStreamConstants.COMMENT: {
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Comment comment = (Comment) nextEvent;
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String commentText = comment.getText();
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heldComments.add(commentText);
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break;
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}
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}
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parserState.xmlEvent(nextEvent);
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} catch (DataFormatException e) {
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throw new DataFormatException("DataFormatException at [" + nextEvent.getLocation().toString() + "]: " + e.getMessage(), e);
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}
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}
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return parserState.getObject();
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} catch (XMLStreamException e) {
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throw new DataFormatException(e);
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}
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}
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private void encodeChildElementToStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, BaseRuntimeChildDefinition theChildDefinition, IBase theElement, String theChildName, BaseRuntimeElementDefinition<?> childDef,
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String theExtensionUrl, boolean theIncludedResource, CompositeChildElement theParent, EncodeContext theEncodeContext) throws XMLStreamException, DataFormatException {
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/*
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* Often the two values below will be the same thing. There are cases though
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* where they will not be. An example would be Observation.value, which is
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* a choice type. If the value contains a Quantity, then:
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* childGenericName = "value"
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* theChildName = "valueQuantity"
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*/
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String childGenericName = theChildDefinition.getElementName();
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theEncodeContext.pushPath(childGenericName, false);
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try {
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if (theElement == null || theElement.isEmpty()) {
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if (!isChildContained(childDef, theIncludedResource)) {
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return;
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}
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}
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writeCommentsPre(theEventWriter, theElement);
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switch (childDef.getChildType()) {
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case ID_DATATYPE: {
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IIdType value = (IIdType) theElement;
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String encodedValue = "id".equals(theChildName) ? value.getIdPart() : value.getValue();
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if (StringUtils.isNotBlank(encodedValue) || !hasNoExtensions(value)) {
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theEventWriter.writeStartElement(theChildName);
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if (StringUtils.isNotBlank(encodedValue)) {
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theEventWriter.writeAttribute("value", encodedValue);
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}
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encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource, theEncodeContext);
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theEventWriter.writeEndElement();
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}
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break;
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}
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case PRIMITIVE_DATATYPE: {
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IPrimitiveType<?> pd = (IPrimitiveType) theElement;
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String value = pd.getValueAsString();
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if (value != null || !hasNoExtensions(pd)) {
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theEventWriter.writeStartElement(theChildName);
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String elementId = getCompositeElementId(theElement);
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if (isNotBlank(elementId)) {
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theEventWriter.writeAttribute("id", elementId);
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}
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if (value != null) {
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theEventWriter.writeAttribute("value", value);
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}
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encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource, theEncodeContext);
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theEventWriter.writeEndElement();
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}
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break;
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}
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case RESOURCE_BLOCK:
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case COMPOSITE_DATATYPE: {
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theEventWriter.writeStartElement(theChildName);
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String elementId = getCompositeElementId(theElement);
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if (isNotBlank(elementId)) {
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theEventWriter.writeAttribute("id", elementId);
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}
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if (isNotBlank(theExtensionUrl)) {
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theEventWriter.writeAttribute("url", theExtensionUrl);
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}
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encodeCompositeElementToStreamWriter(theResource, theElement, theEventWriter, theIncludedResource, theParent, theEncodeContext);
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theEventWriter.writeEndElement();
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break;
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}
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case CONTAINED_RESOURCE_LIST:
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case CONTAINED_RESOURCES: {
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/*
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* Disable per #103 for (IResource next : value.getContainedResources()) { if (getContainedResources().getResourceId(next) != null) { continue; }
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* theEventWriter.writeStartElement("contained"); encodeResourceToRDFStreamWriter(next, theEventWriter, true, fixContainedResourceId(next.getId().getValue()));
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* theEventWriter.writeEndElement(); }
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*/
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for (IBaseResource next : getContainedResources().getContainedResources()) {
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IIdType resourceId = getContainedResources().getResourceId(next);
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theEventWriter.writeStartElement("contained");
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encodeResourceToRDFStreamWriter(next, theEventWriter, true, fixContainedResourceId(resourceId.getValue()), theEncodeContext);
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theEventWriter.writeEndElement();
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}
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break;
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}
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case RESOURCE: {
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IBaseResource resource = (IBaseResource) theElement;
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String resourceName = myContext.getResourceDefinition(resource).getName();
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if (!super.shouldEncodeResource(resourceName)) {
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break;
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}
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theEventWriter.writeStartElement(theChildName);
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theEncodeContext.pushPath(resourceName, true);
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encodeResourceToRDFStreamWriter(resource, theEventWriter, false, theEncodeContext);
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theEncodeContext.popPath();
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theEventWriter.writeEndElement();
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break;
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}
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case PRIMITIVE_XHTML: {
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XhtmlDt dt = (XhtmlDt) theElement;
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if (dt.hasContent()) {
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encodeXhtml(dt, theEventWriter);
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}
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break;
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}
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case PRIMITIVE_XHTML_HL7ORG: {
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IBaseXhtml dt = (IBaseXhtml) theElement;
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if (!dt.isEmpty()) {
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// TODO: this is probably not as efficient as it could be
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XhtmlDt hdt = new XhtmlDt();
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hdt.setValueAsString(dt.getValueAsString());
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encodeXhtml(hdt, theEventWriter);
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}
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break;
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}
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case EXTENSION_DECLARED:
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case UNDECL_EXT: {
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throw new IllegalStateException("state should not happen: " + childDef.getName());
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}
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}
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writeCommentsPost(theEventWriter, theElement);
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} finally {
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theEncodeContext.popPath();
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}
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}
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private void encodeCompositeElementToStreamWriter(IBaseResource theResource, IBase theElement, XMLStreamWriter theEventWriter, boolean theContainedResource, CompositeChildElement theParent, EncodeContext theEncodeContext)
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throws XMLStreamException, DataFormatException {
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for (CompositeChildElement nextChildElem : super.compositeChildIterator(theElement, theContainedResource, theParent, theEncodeContext)) {
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BaseRuntimeChildDefinition nextChild = nextChildElem.getDef();
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if (nextChild.getElementName().equals("url") && theElement instanceof IBaseExtension) {
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/*
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* RDF encoding is a one-off for extensions. The URL element goes in an attribute
|
||||||
|
* instead of being encoded as a normal element, only for RDF 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.populateResourceNarrative(myContext, theResource);
|
||||||
|
}
|
||||||
|
if (narr != null && !narr.isEmpty()) {
|
||||||
|
RuntimeChildNarrativeDefinition child = (RuntimeChildNarrativeDefinition) nextChild;
|
||||||
|
String childName = nextChild.getChildNameByDatatype(child.getDatatype());
|
||||||
|
BaseRuntimeElementDefinition<?> type = child.getChildByName(childName);
|
||||||
|
encodeChildElementToStreamWriter(theResource, theEventWriter, nextChild, narr, childName, type, null, theContainedResource, nextChildElem, theEncodeContext);
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (nextChild instanceof RuntimeChildContainedResources) {
|
||||||
|
encodeChildElementToStreamWriter(theResource, theEventWriter, nextChild, null, nextChild.getChildNameByDatatype(null), nextChild.getChildElementDefinitionByDatatype(null), null, theContainedResource, nextChildElem, theEncodeContext);
|
||||||
|
} else {
|
||||||
|
|
||||||
|
List<? extends IBase> values = nextChild.getAccessor().getValues(theElement);
|
||||||
|
values = super.preProcessValues(nextChild, theResource, values, nextChildElem, theEncodeContext);
|
||||||
|
|
||||||
|
if (values == null || values.isEmpty()) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
for (IBase nextValue : values) {
|
||||||
|
if ((nextValue == null || nextValue.isEmpty())) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
|
||||||
|
ChildNameAndDef childNameAndDef = super.getChildNameAndDef(nextChild, nextValue);
|
||||||
|
if (childNameAndDef == null) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
|
||||||
|
String childName = childNameAndDef.getChildName();
|
||||||
|
BaseRuntimeElementDefinition<?> childDef = childNameAndDef.getChildDef();
|
||||||
|
String extensionUrl = getExtensionUrl(nextChild.getExtensionUrl());
|
||||||
|
|
||||||
|
if (extensionUrl != null && !childName.equals("extension")) {
|
||||||
|
encodeExtension(theResource, theEventWriter, theContainedResource, nextChildElem, nextChild, nextValue, childName, extensionUrl, childDef, theEncodeContext);
|
||||||
|
} else if (nextChild instanceof RuntimeChildExtension) {
|
||||||
|
IBaseExtension<?, ?> extension = (IBaseExtension<?, ?>) nextValue;
|
||||||
|
if ((extension.getValue() == null || extension.getValue().isEmpty())) {
|
||||||
|
if (extension.getExtension().isEmpty()) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
encodeChildElementToStreamWriter(theResource, theEventWriter, nextChild, nextValue, childName, childDef, getExtensionUrl(extension.getUrl()), theContainedResource, nextChildElem, theEncodeContext);
|
||||||
|
} else if (!(nextChild instanceof RuntimeChildNarrativeDefinition) || !theContainedResource) {
|
||||||
|
encodeChildElementToStreamWriter(theResource, theEventWriter, nextChild, nextValue, childName, childDef, extensionUrl, theContainedResource, nextChildElem, theEncodeContext);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private void encodeExtension(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, CompositeChildElement nextChildElem, BaseRuntimeChildDefinition nextChild, IBase nextValue, String childName, String extensionUrl, BaseRuntimeElementDefinition<?> childDef, EncodeContext theEncodeContext)
|
||||||
|
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, nextChild, nextValue, childName, childDef, null, theContainedResource, nextChildElem, theEncodeContext);
|
||||||
|
theEventWriter.writeEndElement();
|
||||||
|
}
|
||||||
|
|
||||||
|
private void encodeExtensionsIfPresent(IBaseResource theResource, XMLStreamWriter theWriter, IBase theElement, boolean theIncludedResource, EncodeContext theEncodeContext) throws XMLStreamException, DataFormatException {
|
||||||
|
if (theElement instanceof ISupportsUndeclaredExtensions) {
|
||||||
|
ISupportsUndeclaredExtensions res = (ISupportsUndeclaredExtensions) theElement;
|
||||||
|
encodeUndeclaredExtensions(theResource, theWriter, toBaseExtensionList(res.getUndeclaredExtensions()), "extension", theIncludedResource, theEncodeContext);
|
||||||
|
encodeUndeclaredExtensions(theResource, theWriter, toBaseExtensionList(res.getUndeclaredModifierExtensions()), "modifierExtension", theIncludedResource, theEncodeContext);
|
||||||
|
}
|
||||||
|
if (theElement instanceof IBaseHasExtensions) {
|
||||||
|
IBaseHasExtensions res = (IBaseHasExtensions) theElement;
|
||||||
|
encodeUndeclaredExtensions(theResource, theWriter, res.getExtension(), "extension", theIncludedResource, theEncodeContext);
|
||||||
|
}
|
||||||
|
if (theElement instanceof IBaseHasModifierExtensions) {
|
||||||
|
IBaseHasModifierExtensions res = (IBaseHasModifierExtensions) theElement;
|
||||||
|
encodeUndeclaredExtensions(theResource, theWriter, res.getModifierExtension(), "modifierExtension", theIncludedResource, theEncodeContext);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private void encodeResourceToRDFStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theIncludedResource, EncodeContext theEncodeContext) throws XMLStreamException, DataFormatException {
|
||||||
|
IIdType resourceId = null;
|
||||||
|
|
||||||
|
if (StringUtils.isNotBlank(theResource.getIdElement().getIdPart())) {
|
||||||
|
resourceId = theResource.getIdElement();
|
||||||
|
if (theResource.getIdElement().getValue().startsWith("urn:")) {
|
||||||
|
resourceId = null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (!theIncludedResource) {
|
||||||
|
if (!super.shouldEncodeResourceId(theResource, theEncodeContext)) {
|
||||||
|
resourceId = null;
|
||||||
|
} else if (theEncodeContext.getResourcePath().size() == 1 && getEncodeForceResourceId() != null) {
|
||||||
|
resourceId = getEncodeForceResourceId();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
encodeResourceToRDFStreamWriter(theResource, theEventWriter, theIncludedResource, resourceId, theEncodeContext);
|
||||||
|
}
|
||||||
|
|
||||||
|
private void encodeResourceToRDFStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, IIdType theResourceId, EncodeContext theEncodeContext) throws XMLStreamException {
|
||||||
|
RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
|
||||||
|
if (resDef == null) {
|
||||||
|
throw new ConfigurationException("Unknown resource type: " + theResource.getClass());
|
||||||
|
}
|
||||||
|
|
||||||
|
if (!theContainedResource) {
|
||||||
|
super.containResourcesForEncoding(theResource);
|
||||||
|
}
|
||||||
|
|
||||||
|
theEventWriter.writeStartElement(resDef.getName());
|
||||||
|
theEventWriter.writeDefaultNamespace(FHIR_NS);
|
||||||
|
|
||||||
|
if (theResource instanceof IAnyResource) {
|
||||||
|
// HL7.org Structures
|
||||||
|
if (theResourceId != null) {
|
||||||
|
writeCommentsPre(theEventWriter, theResourceId);
|
||||||
|
theEventWriter.writeStartElement("id");
|
||||||
|
theEventWriter.writeAttribute("value", theResourceId.getIdPart());
|
||||||
|
encodeExtensionsIfPresent(theResource, theEventWriter, theResourceId, false, theEncodeContext);
|
||||||
|
theEventWriter.writeEndElement();
|
||||||
|
writeCommentsPost(theEventWriter, theResourceId);
|
||||||
|
}
|
||||||
|
|
||||||
|
encodeCompositeElementToStreamWriter(theResource, theResource, theEventWriter, theContainedResource, new CompositeChildElement(resDef, theEncodeContext), theEncodeContext);
|
||||||
|
|
||||||
|
} else {
|
||||||
|
|
||||||
|
// DSTU2+
|
||||||
|
|
||||||
|
IResource resource = (IResource) theResource;
|
||||||
|
if (theResourceId != null) {
|
||||||
|
/* writeCommentsPre(theEventWriter, theResourceId);
|
||||||
|
writeOptionalTagWithValue(theEventWriter, "id", theResourceId.getIdPart());
|
||||||
|
writeCommentsPost(theEventWriter, theResourceId);*/
|
||||||
|
theEventWriter.writeStartElement("id");
|
||||||
|
theEventWriter.writeAttribute("value", theResourceId.getIdPart());
|
||||||
|
encodeExtensionsIfPresent(theResource, theEventWriter, theResourceId, false, theEncodeContext);
|
||||||
|
theEventWriter.writeEndElement();
|
||||||
|
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), theEncodeContext);
|
||||||
|
|
||||||
|
if (super.shouldEncodeResourceMeta(resource) && !ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles)) {
|
||||||
|
theEventWriter.writeStartElement("meta");
|
||||||
|
if (shouldEncodePath(resource, "meta.versionId")) {
|
||||||
|
writeOptionalTagWithValue(theEventWriter, "versionId", versionIdPart);
|
||||||
|
}
|
||||||
|
if (updated != null) {
|
||||||
|
if (shouldEncodePath(resource, "meta.lastUpdated")) {
|
||||||
|
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, theEncodeContext);
|
||||||
|
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, theEncodeContext), theEncodeContext);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
theEventWriter.writeEndElement();
|
||||||
|
}
|
||||||
|
|
||||||
|
private void encodeUndeclaredExtensions(IBaseResource theResource, XMLStreamWriter theEventWriter, List<? extends IBaseExtension<?, ?>> theExtensions, String tagName, boolean theIncludedResource, EncodeContext theEncodeContext)
|
||||||
|
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, extDef, value, childName, childDef, null, theIncludedResource, null, theEncodeContext);
|
||||||
|
}
|
||||||
|
|
||||||
|
// child extensions
|
||||||
|
encodeExtensionsIfPresent(theResource, theEventWriter, next, theIncludedResource, theEncodeContext);
|
||||||
|
|
||||||
|
theEventWriter.writeEndElement();
|
||||||
|
|
||||||
|
writeCommentsPost(theEventWriter, next);
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private void encodeXhtml(XhtmlDt theDt, XMLStreamWriter theEventWriter) throws XMLStreamException {
|
||||||
|
if (theDt == null || theDt.getValue() == null) {
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
List<XMLEvent> events = RDFUtil.parse(theDt.getValue());
|
||||||
|
boolean firstElement = true;
|
||||||
|
|
||||||
|
for (XMLEvent event : events) {
|
||||||
|
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;
|
||||||
|
}
|
||||||
|
|
||||||
|
private <T extends IBaseResource> T parseResource(Class<T> theResourceType, XMLEventReader theStreamReader) {
|
||||||
|
ParserState<T> parserState = ParserState.getPreResourceInstance(this, theResourceType, myContext, false, getErrorHandler());
|
||||||
|
return doRDFLoop(theStreamReader, 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<>(theList.size());
|
||||||
|
retVal.addAll(theList);
|
||||||
|
return retVal;
|
||||||
|
}
|
||||||
|
|
||||||
|
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 writeOptionalTagWithValue(XMLStreamWriter theEventWriter, String theName, String theValue) throws XMLStreamException {
|
||||||
|
if (StringUtils.isNotBlank(theValue)) {
|
||||||
|
theEventWriter.writeStartElement(theName);
|
||||||
|
theEventWriter.writeAttribute("value", theValue);
|
||||||
|
theEventWriter.writeEndElement();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
File diff suppressed because it is too large
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Reference in New Issue