Examples with NamedElement org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement used on opensource projects

Example 11 with NamedElement

use of org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement in project org.hl7.fhir.core by hapifhir.

the class XmlParser method parse.

public List<NamedElement> parse(InputStream stream) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
    List<NamedElement> res = new ArrayList<>();
    Document doc = null;
    try {
        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
        // 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) {
            // if we can, we'll inspect the header/encoding ourselves
            if (stream.markSupported()) {
                stream.mark(1024);
                version = checkHeader(stream);
                stream.reset();
            }
            // use a slower parser that keeps location data
            TransformerFactory transformerFactory = TransformerFactory.newInstance();
            Transformer nullTransformer = transformerFactory.newTransformer();
            DocumentBuilder docBuilder = factory.newDocumentBuilder();
            doc = docBuilder.newDocument();
            DOMResult domResult = new DOMResult(doc);
            SAXParserFactory spf = SAXParserFactory.newInstance();
            spf.setNamespaceAware(true);
            spf.setValidating(false);
            // xxe protection
            spf.setFeature("http://xml.org/sax/features/external-general-entities", false);
            spf.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
            SAXParser saxParser = spf.newSAXParser();
            XMLReader xmlReader = saxParser.getXMLReader();
            // xxe protection
            xmlReader.setFeature("http://xml.org/sax/features/external-general-entities", false);
            xmlReader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
            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();
            doc = builder.parse(stream);
        }
    } catch (Exception e) {
        logError(0, 0, "(syntax)", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
        doc = null;
    }
    if (doc != null) {
        Element e = parse(doc);
        if (e != null) {
            res.add(new NamedElement(null, e));
        }
    }
    return res;
}

Example 12 with NamedElement

use of org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement in project org.hl7.fhir.core by hapifhir.

the class VerticalBarParser method parse.

@Override
public List<NamedElement> parse(InputStream stream) throws IOException, FHIRFormatError, DefinitionException, FHIRException {
    StructureDefinition sd = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/v2/StructureDefinition/Message");
    Element message = new Element("Message", new Property(context, sd.getSnapshot().getElementFirstRep(), sd));
    VerticalBarParserReader reader = new VerticalBarParserReader(new BufferedInputStream(stream), charset);
    preDecode(reader);
    while (// && (getOptions().getSegmentLimit() == 0 || getOptions().getSegmentLimit() > message.getSegments().size()))
    !reader.isFinished()) readSegment(message, reader);
    List<NamedElement> res = new ArrayList<>();
    res.add(new NamedElement(null, message));
    return res;
}

Example 13 with NamedElement

use of org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement in project org.hl7.fhir.core by hapifhir.

the class ObjectConverter method convert.

public Element convert(Resource ig) throws IOException, FHIRException {
    if (ig == null)
        return null;
    ByteArrayOutputStream bs = new ByteArrayOutputStream();
    org.hl7.fhir.r5.formats.JsonParser jp = new org.hl7.fhir.r5.formats.JsonParser();
    jp.compose(bs, ig);
    ByteArrayInputStream bi = new ByteArrayInputStream(bs.toByteArray());
    List<NamedElement> list = new JsonParser(context).parse(bi);
    if (list.size() != 1) {
        throw new FHIRException("Unable to convert because the source contains multieple resources");
    }
    return list.get(0).getElement();
}