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

Example 6 with NamedElement

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

the class SHCParser method parse.

public List<NamedElement> parse(InputStream stream) throws IOException, FHIRFormatError, DefinitionException, FHIRException {
    List<NamedElement> res = new ArrayList<>();
    String src = TextFile.streamToString(stream).trim();
    List<String> list = new ArrayList<>();
    String pfx = null;
    if (src.startsWith("{")) {
        JsonObject json = JsonTrackingParser.parseJson(src);
        if (checkProperty(json, "$", "verifiableCredential", true, "Array")) {
            pfx = "verifiableCredential";
            JsonArray arr = json.getAsJsonArray("verifiableCredential");
            int i = 0;
            for (JsonElement e : arr) {
                if (!(e instanceof JsonPrimitive)) {
                    logError(line(e), col(e), "$.verifiableCredential[" + i + "]", IssueType.STRUCTURE, "Wrong Property verifiableCredential in JSON Payload. Expected : String but found " + JSONUtil.type(e), IssueSeverity.ERROR);
                } else {
                    list.add(e.getAsString());
                }
                i++;
            }
        } else {
            return res;
        }
    } else {
        list.add(src);
    }
    int c = 0;
    for (String ssrc : list) {
        String prefix = pfx == null ? "" : pfx + "[" + Integer.toString(c) + "].";
        c++;
        JWT jwt = null;
        try {
            jwt = decodeJWT(ssrc);
        } catch (Exception e) {
            logError(1, 1, prefix + "JWT", IssueType.INVALID, "Unable to decode JWT token", IssueSeverity.ERROR);
            return res;
        }
        map = jwt.map;
        checkNamedProperties(jwt.getPayload(), prefix + "payload", "iss", "nbf", "vc");
        checkProperty(jwt.getPayload(), prefix + "payload", "iss", true, "String");
        logError(1, 1, prefix + "JWT", IssueType.INFORMATIONAL, "The FHIR Validator does not check the JWT signature " + "(see https://demo-portals.smarthealth.cards/VerifierPortal.html or https://github.com/smart-on-fhir/health-cards-dev-tools) (Issuer = '" + jwt.getPayload().get("iss").getAsString() + "')", IssueSeverity.INFORMATION);
        checkProperty(jwt.getPayload(), prefix + "payload", "nbf", true, "Number");
        JsonObject vc = jwt.getPayload().getAsJsonObject("vc");
        if (vc == null) {
            logError(1, 1, "JWT", IssueType.STRUCTURE, "Unable to find property 'vc' in the payload", IssueSeverity.ERROR);
            return res;
        }
        String path = prefix + "payload.vc";
        checkNamedProperties(vc, path, "type", "credentialSubject");
        if (!checkProperty(vc, path, "type", true, "Array")) {
            return res;
        }
        JsonArray type = vc.getAsJsonArray("type");
        int i = 0;
        for (JsonElement e : type) {
            if (!(e instanceof JsonPrimitive)) {
                logError(line(e), col(e), path + ".type[" + i + "]", IssueType.STRUCTURE, "Wrong Property Type in JSON Payload. Expected : String but found " + JSONUtil.type(e), IssueSeverity.ERROR);
            } else {
                types.add(e.getAsString());
            }
            i++;
        }
        if (!types.contains("https://smarthealth.cards#health-card")) {
            logError(line(vc), col(vc), path, IssueType.STRUCTURE, "Card does not claim to be of type https://smarthealth.cards#health-card, cannot validate", IssueSeverity.ERROR);
            return res;
        }
        if (!checkProperty(vc, path, "credentialSubject", true, "Object")) {
            return res;
        }
        JsonObject cs = vc.getAsJsonObject("credentialSubject");
        path = path + ".credentialSubject";
        if (!checkProperty(cs, path, "fhirVersion", true, "String")) {
            return res;
        }
        JsonElement fv = cs.get("fhirVersion");
        if (!VersionUtilities.versionsCompatible(context.getVersion(), fv.getAsString())) {
            logError(line(fv), col(fv), path + ".fhirVersion", IssueType.STRUCTURE, "Card claims to be of version " + fv.getAsString() + ", cannot be validated against version " + context.getVersion(), IssueSeverity.ERROR);
            return res;
        }
        if (!checkProperty(cs, path, "fhirBundle", true, "Object")) {
            return res;
        }
        // ok. all checks passed, we can now validate the bundle
        Element e = jsonParser.parse(cs.getAsJsonObject("fhirBundle"), map);
        if (e != null) {
            res.add(new NamedElement(path, e));
        }
    }
    return res;
}

Example 7 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.r4b.formats.JsonParser jp = new org.hl7.fhir.r4b.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();
}

Example 8 with NamedElement

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

the class TurtleParser method parse.

@Override
public List<NamedElement> parse(InputStream input) throws IOException, FHIRException {
    List<NamedElement> res = new ArrayList<>();
    Turtle src = new Turtle();
    if (policy == ValidationPolicy.EVERYTHING) {
        try {
            src.parse(TextFile.streamToString(input));
        } catch (Exception e) {
            logError(-1, -1, "(document)", IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_TURTLE_, e.getMessage()), IssueSeverity.FATAL);
            return null;
        }
        Element e = parse(src);
        if (e != null) {
            res.add(new NamedElement(null, e));
        }
    } else {
        src.parse(TextFile.streamToString(input));
        Element e = parse(src);
        if (e != null) {
            res.add(new NamedElement(null, e));
        }
    }
    return res;
}

Example 9 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 10 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;
}