org.hl7.fhir.r5.elementmodel.XmlParser Maven / Gradle / Ivy
package org.hl7.fhir.r5.elementmodel;
import java.io.ByteArrayInputStream;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.SAXParserFactory;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMResult;
import javax.xml.transform.sax.SAXSource;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.PropertyRepresentation;
import org.hl7.fhir.r5.model.Enumeration;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.UserDataNames;
import org.hl7.fhir.r5.utils.formats.XmlLocationAnnotator;
import org.hl7.fhir.r5.utils.formats.XmlLocationData;
import org.hl7.fhir.utilities.ElementDecoration;
import org.hl7.fhir.utilities.StringPair;
import org.hl7.fhir.utilities.FileUtilities;
import org.hl7.fhir.utilities.MarkedToMoveToAdjunctPackage;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.xhtml.CDANarrativeFormat;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.utilities.xhtml.XhtmlParser;
import org.hl7.fhir.utilities.xml.IXMLWriter;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.hl7.fhir.utilities.xml.XMLWriter;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.xml.sax.ErrorHandler;
import org.xml.sax.InputSource;
import org.xml.sax.SAXParseException;
import org.xml.sax.XMLReader;
@MarkedToMoveToAdjunctPackage
public class XmlParser extends ParserBase {
private boolean allowXsiLocation;
private String version;
private boolean elideElements;
public XmlParser(IWorkerContext context) {
super(context);
}
private String schemaPath;
private boolean markedXhtml;
public String getSchemaPath() {
return schemaPath;
}
public void setSchemaPath(String schemaPath) {
this.schemaPath = schemaPath;
}
public boolean isAllowXsiLocation() {
return allowXsiLocation;
}
public void setAllowXsiLocation(boolean allowXsiLocation) {
this.allowXsiLocation = allowXsiLocation;
}
public List parse(InputStream inStream) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
byte[] content = FileUtilities.streamToBytes(inStream);
ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "xml", content, false);
ByteArrayInputStream stream = new ByteArrayInputStream(content);
Document doc = null;
try {
DocumentBuilderFactory factory = XMLUtil.newXXEProtectedDocumentBuilderFactory();
// xxe protection
factory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
factory.setFeature("http://xml.org/sax/features/external-general-entities", false);
factory.setFeature("http://xml.org/sax/features/external-parameter-entities", false);
factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
factory.setXIncludeAware(false);
factory.setExpandEntityReferences(false);
factory.setNamespaceAware(true);
if (policy == ValidationPolicy.EVERYTHING) {
// The SAX interface appears to not work when reporting the correct version/encoding.
// if we can, we'll inspect the header/encoding ourselves
stream.mark(1024);
version = checkHeader(focusFragment.getErrors(), stream);
stream.reset();
// use a slower parser that keeps location data
TransformerFactory transformerFactory = XMLUtil.newXXEProtectedTransformerFactory();
Transformer nullTransformer = transformerFactory.newTransformer();
DocumentBuilder docBuilder = factory.newDocumentBuilder();
doc = docBuilder.newDocument();
DOMResult domResult = new DOMResult(doc);
SAXParserFactory spf = XMLUtil.newXXEProtectedSaxParserFactory();
spf.setNamespaceAware(true);
spf.setValidating(false);
XMLReader xmlReader = XMLUtil.getXXEProtectedXMLReader(spf);
XmlLocationAnnotator locationAnnotator = new XmlLocationAnnotator(xmlReader, doc);
InputSource inputSource = new InputSource(stream);
SAXSource saxSource = new SAXSource(locationAnnotator, inputSource);
nullTransformer.transform(saxSource, domResult);
} else {
DocumentBuilder builder = factory.newDocumentBuilder();
builder.setErrorHandler(new NullErrorHandler());
doc = builder.parse(stream);
}
} catch (Exception e) {
if (e.getMessage().contains("lineNumber:") && e.getMessage().contains("columnNumber:")) {
int line = Utilities.parseInt(extractVal(e.getMessage(), "lineNumber"), 0);
int col = Utilities.parseInt(extractVal(e.getMessage(), "columnNumber"), 0);
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, line, col, "(xml)", IssueType.INVALID, e.getMessage().substring(e.getMessage().lastIndexOf(";")+1).trim(), IssueSeverity.FATAL);
} else {
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, 0, 0, "(xml)", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
}
doc = null;
}
if (doc != null) {
focusFragment.setElement(parse(focusFragment.getErrors(), doc));
}
List res = new ArrayList<>();
res.add(focusFragment);
return res;
}
private String extractVal(String src, String name) {
src = src.substring(src.indexOf(name)+name.length()+1);
src = src.substring(0, src.indexOf(";")).trim();
return src;
}
private void checkForProcessingInstruction(List errors, Document document) throws FHIRFormatError {
if (policy == ValidationPolicy.EVERYTHING && FormatUtilities.FHIR_NS.equals(document.getDocumentElement().getNamespaceURI())) {
Node node = document.getFirstChild();
while (node != null) {
if (node.getNodeType() == Node.PROCESSING_INSTRUCTION_NODE)
logError(errors, ValidationMessage.NO_RULE_DATE, line(document, false), col(document, false), "(document)", IssueType.INVALID, context.formatMessage(
I18nConstants.NO_PROCESSING_INSTRUCTIONS_ALLOWED_IN_RESOURCES), IssueSeverity.ERROR);
node = node.getNextSibling();
}
}
}
private int line(Node node, boolean end) {
XmlLocationData loc = node == null ? null : (XmlLocationData) node.getUserData(XmlLocationData.LOCATION_DATA_KEY);
return loc == null ? 0 : end ? loc.getEndLine() : loc.getStartLine();
}
private int col(Node node, boolean end) {
XmlLocationData loc = node == null ? null : (XmlLocationData) node.getUserData(XmlLocationData.LOCATION_DATA_KEY);
return loc == null ? 0 : end ? loc.getEndColumn() : loc.getStartColumn();
}
public Element parse(List errors, Document doc) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
checkForProcessingInstruction(errors, doc);
org.w3c.dom.Element element = doc.getDocumentElement();
return parse(errors, element);
}
public Element parse(List errors, org.w3c.dom.Element element) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
String ns = element.getNamespaceURI();
String name = element.getLocalName();
String path = "/"+pathPrefix(ns)+name;
StructureDefinition sd = getDefinition(errors, line(element, false), col(element, false), (ns == null ? "noNamespace" : ns), name);
if (sd == null)
return null;
Element result = new Element(element.getLocalName(), new Property(context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities())).setFormat(FhirFormat.XML);
result.setPath(element.getLocalName());
checkElement(errors, element, result, path, result.getProperty(), false);
result.markLocation(line(element, false), col(element, false));
result.setType(element.getLocalName());
parseChildren(errors, path, element, result);
result.numberChildren();
return result;
}
private String pathPrefix(String ns) {
if (Utilities.noString(ns))
return "";
if (ns.equals(FormatUtilities.FHIR_NS))
return "f:";
if (ns.equals(FormatUtilities.XHTML_NS))
return "h:";
if (ns.equals("urn:hl7-org:v3"))
return "v3:";
if (ns.equals("urn:hl7-org:sdtc"))
return "sdtc:";
if (ns.equals("urn:ihe:pharm"))
return "pharm:";
if (ns.equals("http://ns.electronichealth.net.au/Ci/Cda/Extensions/3.0"))
return "ext:";
return "?:";
}
private boolean empty(org.w3c.dom.Element element) {
for (int i = 0; i < element.getAttributes().getLength(); i++) {
String n = element.getAttributes().item(i).getNodeName();
if (!n.equals("xmlns") && !n.startsWith("xmlns:"))
return false;
}
if (!Utilities.noString(element.getTextContent().trim()))
return false;
Node n = element.getFirstChild();
while (n != null) {
if (n.getNodeType() == Node.ELEMENT_NODE)
return false;
n = n.getNextSibling();
}
return true;
}
private void checkElement(List errors, org.w3c.dom.Element element, Element e, String path, Property prop, boolean xsiTypeChecked) throws FHIRFormatError {
if (policy == ValidationPolicy.EVERYTHING) {
if (empty(element) && FormatUtilities.FHIR_NS.equals(element.getNamespaceURI())) // this rule only applies to FHIR Content
logError(errors, ValidationMessage.NO_RULE_DATE, line(element, false), col(element, false), path, IssueType.INVALID, context.formatMessage(I18nConstants.ELEMENT_MUST_HAVE_SOME_CONTENT), IssueSeverity.ERROR);
String ns = prop.getXmlNamespace();
String elementNs = element.getNamespaceURI();
if (elementNs == null) {
elementNs = "noNamespace";
}
if (!elementNs.equals(ns)) {
logError(errors, ValidationMessage.NO_RULE_DATE, line(element, false), col(element, false), path, IssueType.INVALID, context.formatMessage(I18nConstants.WRONG_NAMESPACE__EXPECTED_, ns), IssueSeverity.ERROR);
}
if (!xsiTypeChecked) {
String xsiType = element.getAttributeNS(FormatUtilities.NS_XSI, "type");
if (!Utilities.noString(xsiType)) {
String actualType = prop.getXmlTypeName();
if (xsiType.equals(actualType)) {
logError(errors, "2023-10-12", line(element, false), col(element, false), path, IssueType.INVALID, context.formatMessage(I18nConstants.XSI_TYPE_UNNECESSARY), IssueSeverity.INFORMATION);
} else {
StructureDefinition sd = findLegalConstraint(xsiType, actualType);
if (sd != null) {
e.setType(sd.getType());
e.setExplicitType(xsiType);
} else {
logError(errors, "2023-10-12", line(element, false), col(element, false), path, IssueType.INVALID, context.formatMessage(I18nConstants.XSI_TYPE_WRONG, xsiType, actualType), IssueSeverity.ERROR);
}
}
}
}
}
}
private StructureDefinition findLegalConstraint(String xsiType, String actualType) {
StructureDefinition sdA = context.fetchTypeDefinition(actualType);
StructureDefinition sd = context.fetchTypeDefinition(xsiType);
while (sd != null) {
if (sd == sdA) {
return sd;
}
sd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
}
return null;
}
public Element parse(List errors, org.w3c.dom.Element base, String type) throws Exception {
StructureDefinition sd = getDefinition(errors, 0, 0, FormatUtilities.FHIR_NS, type);
Element result = new Element(base.getLocalName(), new Property(context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities())).setFormat(FhirFormat.XML).setNativeObject(base);
result.setPath(base.getLocalName());
String path = "/"+pathPrefix(base.getNamespaceURI())+base.getLocalName();
checkElement(errors, base, result, path, result.getProperty(), false);
result.setType(base.getLocalName());
parseChildren(errors, path, base, result);
result.numberChildren();
return result;
}
private void parseChildren(List errors, String path, org.w3c.dom.Element node, Element element) throws FHIRFormatError, FHIRException, IOException, DefinitionException {
// this parsing routine retains the original order in a the XML file, to support validation
reapComments(node, element);
List properties = element.getProperty().getChildProperties(element.getName(), XMLUtil.getXsiType(node));
Property cgProp = getChoiceGroupProp(properties);
Property mtProp = cgProp == null ? null : getTextProp(cgProp.getChildProperties(null, null));
String text = mtProp == null ? XMLUtil.getDirectText(node).trim() : null;
int line = line(node, false);
int col = col(node, false);
if (!Utilities.noString(text)) {
Property property = getTextProp(properties);
if (property != null) {
if ("ED.data[x]".equals(property.getDefinition().getId()) || (property.getDefinition()!=null && property.getDefinition().getBase()!=null && "ED.data[x]".equals(property.getDefinition().getBase().getPath()))) {
if ("B64".equals(node.getAttribute("representation"))) {
Element n = new Element("dataBase64Binary", property, "base64Binary", text).markLocation(line, col).setFormat(FhirFormat.XML);
n.setPath(element.getPath()+"."+property.getName());
element.getChildren().add(n);
} else {
Element n = new Element("dataString", property, "string", text).markLocation(line, col).setFormat(FhirFormat.XML);
n.setPath(element.getPath()+"."+property.getName());
element.getChildren().add(n);
}
} else {
Element n = new Element(property.getName(), property, property.getType(), text).markLocation(line, col).setFormat(FhirFormat.XML);
n.setPath(element.getPath()+"."+property.getName());
element.getChildren().add(n);
}
} else {
Node n = node.getFirstChild();
while (n != null) {
if (n.getNodeType() == Node.TEXT_NODE && !Utilities.noString(n.getTextContent().trim())) {
Node nt = n; // try to find the nearest element for a line/col location
boolean end = false;
while (nt.getPreviousSibling() != null && nt.getNodeType() != Node.ELEMENT_NODE) {
nt = nt.getPreviousSibling();
end = true;
}
while (nt.getNextSibling() != null && nt.getNodeType() != Node.ELEMENT_NODE) {
nt = nt.getNextSibling();
end = false;
}
line = line(nt, end);
col = col(nt, end);
logError(errors, ValidationMessage.NO_RULE_DATE, line, col, path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.TEXT_SHOULD_NOT_BE_PRESENT, Utilities.makeSingleLine(n.getTextContent().trim())), IssueSeverity.ERROR);
}
n = n.getNextSibling();
}
}
}
for (int i = 0; i < node.getAttributes().getLength(); i++) {
Node attr = node.getAttributes().item(i);
String value = attr.getNodeValue();
if (!validAttrValue(value)) {
logError(errors, ValidationMessage.NO_RULE_DATE, line, col, path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.XML_ATTR_VALUE_INVALID, attr.getNodeName()), IssueSeverity.ERROR);
}
if (!(attr.getNodeName().equals("xmlns") || attr.getNodeName().startsWith("xmlns:"))) {
Property property = getAttrProp(properties, attr.getLocalName(), attr.getNamespaceURI());
if (property != null) {
String av = attr.getNodeValue();
if (ToolingExtensions.hasExtension(property.getDefinition(), ToolingExtensions.EXT_DATE_FORMAT))
av = convertForDateFormatFromExternal(ToolingExtensions.readStringExtension(property.getDefinition(), ToolingExtensions.EXT_DATE_FORMAT), av);
if (property.getName().equals("value") && element.isPrimitive())
element.setValue(av);
else {
String[] vl = {av};
if (property.isList() && av.contains(" ")) {
vl = av.split(" ");
}
for (String v : vl) {
Element n = new Element(property.getName(), property, property.getType(), v).markLocation(line, col).setFormat(FhirFormat.XML);
n.setPath(element.getPath()+"."+property.getName());
element.getChildren().add(n);
}
}
} else {
boolean ok = false;
if (FormatUtilities.FHIR_NS.equals(node.getNamespaceURI())) {
if (attr.getLocalName().equals("schemaLocation") && FormatUtilities.NS_XSI.equals(attr.getNamespaceURI())) {
ok = ok || allowXsiLocation;
}
} else
ok = ok || (attr.getLocalName().equals("schemaLocation")); // xsi:schemalocation allowed for non FHIR content
ok = ok || (hasTypeAttr(element) && attr.getLocalName().equals("type") && FormatUtilities.NS_XSI.equals(attr.getNamespaceURI())); // xsi:type allowed if element says so
if (!ok) {
logError(errors, ValidationMessage.NO_RULE_DATE, line(node, false), col(node, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.UNDEFINED_ATTRIBUTE__ON__FOR_TYPE__PROPERTIES__, attr.getNodeName(), node.getNodeName(), element.fhirType(), properties), IssueSeverity.ERROR);
}
}
}
}
String lastName = null;
int repeatCount = 0;
Node child = node.getFirstChild();
while (child != null) {
if (child.getNodeType() == Node.ELEMENT_NODE) {
Property property = getElementProp(properties, child.getLocalName(), child.getNamespaceURI());
if (property != null) {
if (property.getName().equals(lastName)) {
repeatCount++;
} else {
lastName = property.getName();
repeatCount = 0;
}
if (!property.isChoice() && "xhtml".equals(property.getType())) {
XhtmlNode xhtml;
if (property.getDefinition().hasRepresentation(PropertyRepresentation.CDATEXT))
xhtml = new CDANarrativeFormat().convert((org.w3c.dom.Element) child);
else {
XhtmlParser xp = new XhtmlParser();
xhtml = xp.parseHtmlNode((org.w3c.dom.Element) child);
if (policy == ValidationPolicy.EVERYTHING) {
for (StringPair s : xp.getValidationIssues()) {
logError(errors, "2022-11-17", line(child, false), col(child, false), path, IssueType.INVALID, context.formatMessage(s.getName(), s.getValue()), IssueSeverity.ERROR);
}
}
}
Element n = new Element(property.getName(), property, "xhtml", new XhtmlComposer(XhtmlComposer.XML, false).compose(xhtml)).setXhtml(xhtml).markLocation(line(child, false), col(child, false)).setFormat(FhirFormat.XML).setNativeObject(child);
n.setPath(element.getPath()+"."+property.getName());
element.getChildren().add(n);
} else {
String npath = path+"/"+pathPrefix(child.getNamespaceURI())+child.getLocalName();
String name = child.getLocalName();
if (!property.isChoice() && !name.equals(property.getName())) {
name = property.getName();
}
Element n = new Element(name, property).markLocation(line(child, false), col(child, false)).setFormat(FhirFormat.XML).setNativeObject(child);
if (property.isList()) {
n.setPath(element.getPath()+"."+property.getName()+"["+repeatCount+"]");
} else {
n.setPath(element.getPath()+"."+property.getName());
}
boolean xsiTypeChecked = false;
boolean ok = true;
if (property.isChoice()) {
if (property.getDefinition().hasRepresentation(PropertyRepresentation.TYPEATTR)) {
String xsiType = ((org.w3c.dom.Element) child).getAttributeNS(FormatUtilities.NS_XSI, "type");
if (Utilities.noString(xsiType)) {
if (ToolingExtensions.hasExtension(property.getDefinition(), "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaulttype")) {
xsiType = ToolingExtensions.readStringExtension(property.getDefinition(), "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaulttype");
n.setType(xsiType);
} else {
logError(errors, ValidationMessage.NO_RULE_DATE, line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.NO_TYPE_FOUND_ON_, child.getLocalName()), IssueSeverity.ERROR);
ok = false;
}
} else {
if (xsiType.contains(":"))
xsiType = xsiType.substring(xsiType.indexOf(":")+1);
n.setType(xsiType);
n.setExplicitType(xsiType);
}
xsiTypeChecked = true;
} else
n.setType(n.getType());
}
checkElement(errors, (org.w3c.dom.Element) child, n, npath, n.getProperty(), xsiTypeChecked);
element.getChildren().add(n);
if (ok) {
if (property.isResource())
parseResource(errors, npath, (org.w3c.dom.Element) child, n, property);
else
parseChildren(errors, npath, (org.w3c.dom.Element) child, n);
}
}
} else {
if (cgProp != null) {
property = getElementProp(cgProp.getChildProperties(null, null), child.getLocalName(), child.getNamespaceURI());
if (property != null) {
if (cgProp.getName().equals(lastName)) {
repeatCount++;
} else {
lastName = cgProp.getName();
repeatCount = 0;
}
String npath = path+"/"+pathPrefix(cgProp.getXmlNamespace())+cgProp.getName();
String name = cgProp.getName();
Element cgn = new Element(cgProp.getName(), cgProp).setFormat(FhirFormat.XML);
cgn.setPath(element.getPath()+"."+cgProp.getName()+"["+repeatCount+"]");
element.getChildren().add(cgn);
npath = npath+"/"+pathPrefix(child.getNamespaceURI())+child.getLocalName();
name = child.getLocalName();
Element n = new Element(name, property).markLocation(line(child, false), col(child, false)).setFormat(FhirFormat.XML).setNativeObject(child);
cgn.getChildren().add(n);
n.setPath(element.getPath()+"."+property.getName());
checkElement(errors, (org.w3c.dom.Element) child, n, npath, n.getProperty(), false);
parseChildren(errors, npath, (org.w3c.dom.Element) child, n);
}
}
if (property == null) {
logError(errors, ValidationMessage.NO_RULE_DATE, line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.UNDEFINED_ELEMENT_, child.getLocalName(), path), IssueSeverity.ERROR);
}
}
} else if (child.getNodeType() == Node.TEXT_NODE && !Utilities.noString(child.getTextContent().trim()) && mtProp != null) {
if (cgProp.getName().equals(lastName)) {
repeatCount++;
} else {
lastName = cgProp.getName();
repeatCount = 0;
}
String npath = path+"/"+pathPrefix(cgProp.getXmlNamespace())+cgProp.getName();
String name = cgProp.getName();
Element cgn = new Element(cgProp.getName(), cgProp).setFormat(FhirFormat.XML);
cgn.setPath(element.getPath()+"."+cgProp.getName()+"["+repeatCount+"]");
element.getChildren().add(cgn);
npath = npath+"/text()";
name = mtProp.getName();
Element n = new Element(name, mtProp, mtProp.getType(), child.getTextContent().trim()).markLocation(line(child, false), col(child, false)).setFormat(FhirFormat.XML).setNativeObject(child);
cgn.getChildren().add(n);
n.setPath(element.getPath()+"."+mtProp.getName());
} else if (child.getNodeType() == Node.CDATA_SECTION_NODE) {
logError(errors, ValidationMessage.NO_RULE_DATE, line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.CDATA_IS_NOT_ALLOWED), IssueSeverity.ERROR);
} else if (!Utilities.existsInList(child.getNodeType(), 3, 8)) {
logError(errors, ValidationMessage.NO_RULE_DATE, line(child, false), col(child, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.NODE_TYPE__IS_NOT_ALLOWED, Integer.toString(child.getNodeType())), IssueSeverity.ERROR);
}
child = child.getNextSibling();
}
}
private Property getChoiceGroupProp(List properties) {
for (Property p : properties) {
if (p.getDefinition().hasExtension(ToolingExtensions.EXT_ID_CHOICE_GROUP)) {
return p;
}
}
return null;
}
private boolean validAttrValue(String value) {
if (version == null) {
return true;
}
if (version.equals("1.0")) {
boolean ok = true;
for (char ch : value.toCharArray()) {
if (ch <= 0x1F && !Utilities.existsInList(ch, '\r', '\n', '\t')) {
ok = false;
}
}
return ok;
} else
return true;
}
private Property getElementProp(List properties, String nodeName, String namespace) {
List propsSortedByLongestFirst = new ArrayList(properties);
// sort properties according to their name longest first, so .requestOrganizationReference comes first before .request[x]
// and therefore the longer property names get evaluated first
Collections.sort(propsSortedByLongestFirst, new Comparator() {
@Override
public int compare(Property o1, Property o2) {
return o2.getName().length() - o1.getName().length();
}
});
// first scan, by namespace
for (Property p : propsSortedByLongestFirst) {
if (!p.getDefinition().hasRepresentation(PropertyRepresentation.XMLATTR) && !p.getDefinition().hasRepresentation(PropertyRepresentation.XMLTEXT)) {
if (p.getXmlName().equals(nodeName) && p.getXmlNamespace().equals(namespace))
return p;
}
}
for (Property p : propsSortedByLongestFirst) {
if (!p.getDefinition().hasRepresentation(PropertyRepresentation.XMLATTR) && !p.getDefinition().hasRepresentation(PropertyRepresentation.XMLTEXT)) {
if (p.getXmlName().equals(nodeName))
return p;
if (p.getName().endsWith("[x]") && nodeName.length() > p.getName().length()-3 && p.getName().substring(0, p.getName().length()-3).equals(nodeName.substring(0, p.getName().length()-3)))
return p;
}
}
return null;
}
private Property getAttrProp(List properties, String nodeName, String namespace) {
for (Property p : properties) {
if (p.getXmlName().equals(nodeName) && p.getDefinition().hasRepresentation(PropertyRepresentation.XMLATTR) && p.getXmlNamespace().equals(namespace)) {
return p;
}
}
if (namespace == null) {
for (Property p : properties) {
if (p.getXmlName().equals(nodeName) && p.getDefinition().hasRepresentation(PropertyRepresentation.XMLATTR)) {
return p;
}
}
}
return null;
}
private Property getTextProp(List properties) {
for (Property p : properties)
if (p.getDefinition().hasRepresentation(PropertyRepresentation.XMLTEXT))
return p;
return null;
}
private String convertForDateFormatFromExternal(String fmt, String av) throws FHIRException {
if ("v3".equals(fmt) || "YYYYMMDDHHMMSS.UUUU[+|-ZZzz]".equals(fmt)) {
try {
DateTimeType d = DateTimeType.parseV3(av);
return d.asStringValue();
} catch (Exception e) {
return av; // not at all clear what to do in this case.
}
}
throw new FHIRException(context.formatMessage(I18nConstants.UNKNOWN_DATA_FORMAT_, fmt));
}
private String convertForDateFormatToExternal(String fmt, String av) throws FHIRException {
if ("v3".equals(fmt) || "YYYYMMDDHHMMSS.UUUU[+|-ZZzz]".equals(fmt)) {
DateTimeType d = new DateTimeType(av);
return d.getAsV3();
} else
throw new FHIRException(context.formatMessage(I18nConstants.UNKNOWN_DATE_FORMAT_, fmt));
}
private void parseResource(List errors, String string, org.w3c.dom.Element container, Element parent, Property elementProperty) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
org.w3c.dom.Element res = XMLUtil.getFirstChild(container);
String name = res.getLocalName();
StructureDefinition sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
if (sd == null)
throw new FHIRFormatError(context.formatMessage(I18nConstants.CONTAINED_RESOURCE_DOES_NOT_APPEAR_TO_BE_A_FHIR_RESOURCE_UNKNOWN_NAME_, res.getLocalName()));
parent.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities()), SpecialElement.fromProperty(parent.getProperty()), elementProperty);
parent.setType(name);
parseChildren(errors, res.getLocalName(), res, parent);
}
private void reapComments(org.w3c.dom.Element element, Element context) {
Node node = element.getPreviousSibling();
while (node != null && node.getNodeType() != Node.ELEMENT_NODE) {
if (node.getNodeType() == Node.COMMENT_NODE)
context.getComments().add(0, node.getTextContent());
node = node.getPreviousSibling();
}
node = element.getLastChild();
while (node != null && node.getNodeType() != Node.ELEMENT_NODE) {
node = node.getPreviousSibling();
}
while (node != null) {
if (node.getNodeType() == Node.COMMENT_NODE)
context.getComments().add(node.getTextContent());
node = node.getNextSibling();
}
}
private boolean isAttr(Property property) {
for (Enumeration r : property.getDefinition().getRepresentation()) {
if (r.getValue() == PropertyRepresentation.XMLATTR) {
return true;
}
}
return false;
}
private boolean isCdaText(Property property) {
for (Enumeration r : property.getDefinition().getRepresentation()) {
if (r.getValue() == PropertyRepresentation.CDATEXT) {
return true;
}
}
return false;
}
private boolean isTypeAttr(Property property) {
for (Enumeration r : property.getDefinition().getRepresentation()) {
if (r.getValue() == PropertyRepresentation.TYPEATTR) {
return true;
}
}
return false;
}
private boolean isText(Property property) {
for (Enumeration r : property.getDefinition().getRepresentation()) {
if (r.getValue() == PropertyRepresentation.XMLTEXT) {
return true;
}
}
return false;
}
@Override
public void compose(Element e, OutputStream stream, OutputStyle style, String base) throws IOException, FHIRException {
markedXhtml = false;
XMLWriter xml = new XMLWriter(stream, "UTF-8");
xml.setSortAttributes(false);
xml.setPretty(style == OutputStyle.PRETTY);
xml.start();
if (e.getPath() == null) {
e.populatePaths(null);
}
String ns = e.getProperty().getXmlNamespace();
if (ns!=null && !"noNamespace".equals(ns)) {
xml.setDefaultNamespace(ns);
}
if (hasTypeAttr(e))
xml.namespace("http://www.w3.org/2001/XMLSchema-instance", "xsi");
if (Utilities.isAbsoluteUrl(e.getType())) {
xml.namespace(urlRoot(e.getType()), "et");
}
addNamespaces(xml, e);
composeElement(xml, e, e.getType(), true);
xml.end();
}
private void addNamespaces(IXMLWriter xml, Element e) throws IOException {
String ns = e.getProperty().getXmlNamespace();
if (ns!=null && xml.getDefaultNamespace()!=null && !xml.getDefaultNamespace().equals(ns)){
if (!xml.namespaceDefined(ns)) {
String prefix = pathPrefix(ns);
if (prefix.endsWith(":")) {
prefix = prefix.substring(0, prefix.length()-1);
}
if ("?".equals(prefix)) {
xml.namespace(ns);
} else {
xml.namespace(ns, prefix);
}
}
}
for (Element c : e.getChildren()) {
addNamespaces(xml, c);
}
}
private boolean hasTypeAttr(Element e) {
if (isTypeAttr(e.getProperty()))
return true;
for (Element c : e.getChildren()) {
if (hasTypeAttr(c))
return true;
}
// xsi_type is always allowed on CDA elements. right now, I'm not sure where to indicate this in the model,
// so it's just hardcoded here
if (e.getType() != null && e.getType().startsWith(Constants.NS_CDA_ROOT)) {
return true;
}
return false;
}
private void setXsiTypeIfIsTypeAttr(IXMLWriter xml, Element element) throws IOException, FHIRException {
if (isTypeAttr(element.getProperty()) && !Utilities.noString(element.getType())) {
String type = element.getType();
if (Utilities.isAbsoluteUrl(type)) {
type = type.substring(type.lastIndexOf("/")+1);
}
xml.attribute("xsi:type",type);
}
}
public void compose(Element e, IXMLWriter xml) throws Exception {
if (e.getPath() == null) {
e.populatePaths(null);
}
markedXhtml = false;
xml.start();
xml.setDefaultNamespace(e.getProperty().getXmlNamespace());
if (Utilities.isAbsoluteUrl(e.getType())) {
xml.namespace(urlRoot(e.getType()), "et");
}
if (schemaPath != null) {
xml.setSchemaLocation(FormatUtilities.FHIR_NS, Utilities.pathURL(schemaPath, e.fhirType()+".xsd"));
}
composeElement(xml, e, e.getType(), true);
xml.end();
}
private void composeElement(IXMLWriter xml, Element element, String elementName, boolean root) throws IOException, FHIRException {
if (!(isElideElements() && element.isElided())) {
if (showDecorations) {
@SuppressWarnings("unchecked")
List decorations = (List) element.getUserData(UserDataNames.rendering_xml_decorations);
if (decorations != null)
for (ElementDecoration d : decorations)
xml.decorate(d);
}
for (String s : element.getComments()) {
xml.comment(s, true);
}
}
if (isText(element.getProperty())) {
if (isElideElements() && element.isElided() && xml.canElide())
xml.elide();
else {
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
xml.enter(element.getProperty().getXmlNamespace(),elementName);
if (linkResolver != null && element.getProperty().isReference()) {
String ref = linkResolver.resolveReference(getReferenceForElement(element));
if (ref != null) {
xml.externalLink(ref);
}
}
xml.text(element.getValue());
xml.exit(element.getProperty().getXmlNamespace(),elementName);
}
} else if (!element.hasChildren() && !element.hasValue()) {
if (isElideElements() && element.isElided() && xml.canElide())
xml.elide();
else {
if (element.getExplicitType() != null)
xml.attribute("xsi:type", element.getExplicitType());
xml.element(elementName);
}
} else if (element.isPrimitive() || (element.hasType() && isPrimitive(element.getType()))) {
if (element.getType().equals("xhtml")) {
if (isElideElements() && element.isElided() && xml.canElide())
xml.elide();
else {
String rawXhtml = element.getValue();
if (isCdaText(element.getProperty())) {
new CDANarrativeFormat().convert(xml, new XhtmlParser().parseFragment(rawXhtml));
} else {
xml.escapedText(rawXhtml);
if (!markedXhtml) {
xml.anchor("end-xhtml");
markedXhtml = true;
}
}
}
} else if (isText(element.getProperty())) {
if (isElideElements() && element.isElided() && xml.canElide())
xml.elide();
else {
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
xml.text(element.getValue());
}
} else {
if (isElideElements() && element.isElided())
xml.attributeElide();
else {
setXsiTypeIfIsTypeAttr(xml, element);
if (element.hasValue()) {
if (linkResolver != null)
xml.link(linkResolver.resolveType(element.getType()));
xml.attribute("value", element.getValue());
}
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
if (element.hasChildren()) {
xml.enter(element.getProperty().getXmlNamespace(), elementName);
if (linkResolver != null && element.getProperty().isReference()) {
String ref = linkResolver.resolveReference(getReferenceForElement(element));
if (ref != null) {
xml.externalLink(ref);
}
}
for (Element child : element.getChildren())
composeElement(xml, child, child.getName(), false);
xml.exit(element.getProperty().getXmlNamespace(),elementName);
} else
xml.element(elementName);
}
}
} else {
if (isElideElements() && element.isElided() && xml.canElide())
xml.elide();
else {
setXsiTypeIfIsTypeAttr(xml, element);
Set handled = new HashSet<>();
for (Element child : element.getChildren()) {
if (!handled.contains(child.getName()) && isAttr(child.getProperty()) && wantCompose(element.getPath(), child)) {
handled.add(child.getName());
if (isElideElements() && child.isElided())
xml.attributeElide();
else {
String av = child.getValue();
if (child.getProperty().isList()) {
for (Element c2 : element.getChildren()) {
if (c2 != child && c2.getName().equals(child.getName())) {
if (c2.isElided())
av = av + " ...";
else
av = av + " " + c2.getValue();
}
}
}
if (linkResolver != null)
xml.link(linkResolver.resolveType(child.getType()));
if (ToolingExtensions.hasExtension(child.getProperty().getDefinition(), ToolingExtensions.EXT_DATE_FORMAT))
av = convertForDateFormatToExternal(ToolingExtensions.readStringExtension(child.getProperty().getDefinition(), ToolingExtensions.EXT_DATE_FORMAT), av);
xml.attribute(child.getProperty().getXmlNamespace(), child.getProperty().getXmlName(), av);
}
}
}
}
if (!element.getProperty().getDefinition().hasExtension(ToolingExtensions.EXT_ID_CHOICE_GROUP)) {
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
if (!xml.namespaceDefined(element.getProperty().getXmlNamespace())) {
String abbrev = makeNamespaceAbbrev(element.getProperty(), xml);
xml.namespace(element.getProperty().getXmlNamespace(), abbrev);
}
if (Utilities.isAbsoluteUrl(elementName)) {
xml.enter(urlRoot(elementName), urlTail(elementName));
} else {
xml.enter(element.getProperty().getXmlNamespace(), elementName);
}
}
if (!root && element.getSpecial() != null) {
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
xml.enter(element.getProperty().getXmlNamespace(),element.getType());
}
if (linkResolver != null && element.getProperty().isReference()) {
String ref = linkResolver.resolveReference(getReferenceForElement(element));
if (ref != null) {
xml.externalLink(ref);
}
}
for (Element child : element.getChildren()) {
if (wantCompose(element.getPath(), child)) {
if (isElideElements() && child.isElided() && xml.canElide())
xml.elide();
else {
if (isText(child.getProperty())) {
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
xml.text(child.getValue());
} else if (!isAttr(child.getProperty())) {
composeElement(xml, child, child.getName(), false);
}
}
}
}
if (!element.getProperty().getDefinition().hasExtension(ToolingExtensions.EXT_ID_CHOICE_GROUP)) {
if (!root && element.getSpecial() != null)
xml.exit(element.getProperty().getXmlNamespace(),element.getType());
if (Utilities.isAbsoluteUrl(elementName)) {
xml.exit(urlRoot(elementName), urlTail(elementName));
} else {
xml.exit(element.getProperty().getXmlNamespace(),elementName);
}
}
}
}
private String urlRoot(String elementName) {
return elementName.substring(0, elementName.lastIndexOf("/"));
}
private String makeNamespaceAbbrev(Property property, IXMLWriter xml) {
// it's a cosmetic thing, but we're going to try to come up with a nice namespace
ElementDefinition ed = property.getDefinition();
String ns = property.getXmlNamespace();
String n = property.getXmlName();
String diff = property.getName().toLowerCase().replace(n.toLowerCase(), "");
if (!Utilities.noString(diff) && diff.length() <= 5 && Utilities.isToken(diff) && !xml.abbreviationDefined(diff)) {
return diff;
}
int i = ns.length()-1;
while (i > 0) {
if (Character.isAlphabetic(ns.charAt(i)) || Character.isDigit(ns.charAt(i))) {
i--;
} else {
break;
}
}
String tail = ns.substring(i+1);
if (!Utilities.noString(tail) && tail.length() <= 5 && Utilities.isToken(tail) && !xml.abbreviationDefined(tail)) {
return tail;
}
i = 0;
while (xml.abbreviationDefined("ns"+i)) {
i++;
}
return "ns"+i;
}
private String checkHeader(List errors, InputStream stream) throws IOException {
try {
// the stream will either start with the UTF-8 BOF or with -1) {
e = header.substring(i+10, i+15);
} else {
i = header.indexOf("encoding='");
if (i > -1) {
e = header.substring(i+10, i+15);
}
}
if (e != null && !"UTF-8".equalsIgnoreCase(e)) {
logError(errors, ValidationMessage.NO_RULE_DATE, 0, 0, "XML", IssueType.INVALID, context.formatMessage(I18nConstants.XML_ENCODING_INVALID), IssueSeverity.ERROR);
}
i = header.indexOf("version=\"");
if (i > -1) {
return header.substring(i+9, i+12);
} else {
i = header.indexOf("version='");
if (i > -1) {
return header.substring(i+9, i+12);
}
}
return "?xml-p1?";
} catch (Exception e) {
// suppress this error
logError(errors, ValidationMessage.NO_RULE_DATE, 0, 0, "XML", IssueType.INVALID, e.getMessage(), IssueSeverity.ERROR);
}
return "?xml-p2?";
}
class NullErrorHandler implements ErrorHandler {
@Override
public void fatalError(SAXParseException e) {
// do nothing
}
@Override
public void error(SAXParseException e) {
// do nothing
}
@Override
public void warning(SAXParseException e) {
// do nothing
}
}
public boolean isElideElements() {
return elideElements;
}
public void setElideElements(boolean elideElements) {
this.elideElements = elideElements;
}
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