Examples with XmlParser org.hl7.fhir.r4.formats.XmlParser used on opensource projects

Example 41 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class R5ToR5Loader method loadBundle.

@Override
public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
    Resource r5 = null;
    if (isJson)
        r5 = new JsonParser().parse(stream);
    else
        r5 = new XmlParser().parse(stream);
    Bundle b;
    if (r5 instanceof Bundle)
        b = (Bundle) r5;
    else {
        b = new Bundle();
        b.setId(UUID.randomUUID().toString().toLowerCase());
        b.setType(BundleType.COLLECTION);
        b.addEntry().setResource(r5).setFullUrl(r5 instanceof CanonicalResource ? ((CanonicalResource) r5).getUrl() : null);
    }
    for (CodeSystem cs : cslist) {
        BundleEntryComponent be = b.addEntry();
        be.setFullUrl(cs.getUrl());
        be.setResource(cs);
    }
    if (killPrimitives) {
        List<BundleEntryComponent> remove = new ArrayList<BundleEntryComponent>();
        for (BundleEntryComponent be : b.getEntry()) {
            if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
                StructureDefinition sd = (StructureDefinition) be.getResource();
                if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)
                    remove.add(be);
            }
        }
        b.getEntry().removeAll(remove);
    }
    if (patchUrls) {
        for (BundleEntryComponent be : b.getEntry()) {
            if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
                StructureDefinition sd = (StructureDefinition) be.getResource();
                sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
                sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
                for (ElementDefinition ed : sd.getSnapshot().getElement()) patchUrl(ed);
                for (ElementDefinition ed : sd.getDifferential().getElement()) patchUrl(ed);
            }
        }
    }
    return b;
}

Example 42 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class ArgonautConverter method saveResource.

private void saveResource(Resource resource, String extraType) throws Exception {
    if (!WANT_SAVE)
        return;
    DomainResource dr = null;
    if (resource instanceof DomainResource) {
        dr = (DomainResource) resource;
        if (!dr.hasText()) {
            NarrativeGenerator generator = new NarrativeGenerator("", "", context);
            generator.generate(dr);
        }
    }
    XmlParser xparser = new XmlParser();
    xparser.setOutputStyle(OutputStyle.PRETTY);
    JsonParser jparser = new JsonParser();
    jparser.setOutputStyle(OutputStyle.PRETTY);
    ByteArrayOutputStream ba = new ByteArrayOutputStream();
    xparser.compose(ba, resource);
    ba.close();
    byte[] srcX = ba.toByteArray();
    ba = new ByteArrayOutputStream();
    jparser.compose(ba, resource);
    ba.close();
    byte[] srcJ = ba.toByteArray();
    String rn = resource.getResourceType().toString();
    if (extraType != null)
        rn = rn + extraType;
    zipX.addBytes(resource.getId() + ".xml", srcX, false);
    zipJ.addBytes(resource.getId() + ".json", srcJ, false);
    if (!zipsX.containsKey(rn)) {
        zipsX.put(rn, new ZipGenerator(Utilities.path(destFolder, "xml/type", rn + ".xml.zip")));
        zipsJ.put(rn, new ZipGenerator(Utilities.path(destFolder, "json/type", rn + ".json.zip")));
        stats.put(rn, new Stats());
    }
    zipsJ.get(rn).addBytes(resource.getId() + ".json", srcJ, false);
    zipsX.get(rn).addBytes(resource.getId() + ".xml", srcX, false);
    Stats ss = stats.get(rn);
    ss.setInstances(ss.getInstances() + 1);
    String profile = resource.getUserString("profile");
    validate(srcX, profile, resource, ss);
}

Example 43 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class ADLImporter method execute.

private void execute() throws Exception {
    // load config
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setNamespaceAware(true);
    DocumentBuilder builder = factory.newDocumentBuilder();
    adlConfig = builder.parse(new FileInputStream(config)).getDocumentElement();
    // load ADL
    builder = factory.newDocumentBuilder();
    adl = builder.parse(new FileInputStream(source)).getDocumentElement();
    check("root", adl.getNamespaceURI(), "http://schemas.openehr.org/v1", "Wrong namespace for ADL XML");
    check("root", adl.getNodeName(), "archetype", "Wrong XML for ADL XML");
    check("root", XMLUtil.getNamedChild(adl, "adl_version").getTextContent(), "1.4", "unsupported ADL version");
    String id = XMLUtil.getFirstChild(XMLUtil.getNamedChild(adl, "archetype_id")).getTextContent().split("\\.")[1];
    // create structure definition
    StructureDefinition sd = new StructureDefinition();
    sd.setId(id);
    // populate metadata
    Element description = XMLUtil.getNamedChild(adl, "description");
    Element details = XMLUtil.getNamedChild(description, "details");
    sd.setDescription(XMLUtil.getNamedChild(details, "purpose").getTextContent());
    sd.setCopyright(XMLUtil.getNamedChild(details, "copyright").getTextContent());
    sd.setPurpose("Use:\r\n" + XMLUtil.getNamedChild(details, "use").getTextContent() + "\r\n\r\nMisuse:\r\n" + XMLUtil.getNamedChild(details, "misuse").getTextContent());
    List<Element> set = new ArrayList<Element>();
    XMLUtil.getNamedChildren(details, "keywords", set);
    for (Element e : set) sd.addKeyword().setDisplay(e.getTextContent());
    String status = XMLUtil.getNamedChild(description, "lifecycle_state").getTextContent();
    if ("CommitteeDraft".equals(status) || "AuthorDraft".equals(status))
        sd.setStatus(PublicationStatus.DRAFT);
    else
        throw new Exception("Unknown life cycle state " + XMLUtil.getNamedChild(description, "lifecycle_state").getTextContent());
    // load texts from ontology
    Element ontology = XMLUtil.getNamedChild(adl, "ontology");
    Element term_definitions = XMLUtil.getNamedChild(ontology, "term_definitions");
    set.clear();
    XMLUtil.getNamedChildren(term_definitions, "items", set);
    for (Element item : set) {
        processTextItem(item);
    }
    // load data and protocol
    Element definition = XMLUtil.getNamedChild(adl, "definition");
    NodeTreeEntry root = new NodeTreeEntry();
    root.setTypeName(XMLUtil.getNamedChild(definition, "rm_type_name").getTextContent());
    root.setAtCode(XMLUtil.getNamedChild(definition, "node_id").getTextContent());
    root.setName(generateToken(root.getAtCode(), true));
    sd.setName(root.getName());
    root.setCardinality(readCardinality("root", XMLUtil.getNamedChild(definition, "occurrences")));
    set.clear();
    XMLUtil.getNamedChildren(definition, "attributes", set);
    for (Element item : set) {
        // we're actually skipping this level - we don't care about data protocol etc.
        // XMLUtil.getNamedChild(XMLUtil.getNamedChild(item, "children"), "attributes");
        Element attributes = item;
        loadChildren(root.getAtCode(), root, attributes);
    }
    dumpChildren("", root);
    genElements(sd, root.getName(), root);
    // save
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), sd);
    System.out.println("done. saved as " + dest);
}

Example 44 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class BatchLoader method main.

public static void main(String[] args) throws IOException, Exception {
    if (args.length < 4) {
        System.out.println("Batch uploader takes 4 parameters in order: server base url, file/folder to upload, xml/json, and batch size");
    } else {
        String server = args[0];
        String file = args[1];
        // args[2].equals("json") ? new JsonParser() : new XmlParser();
        IParser p = new JsonParser();
        int size = Integer.parseInt(args[3]);
        size = 500;
        if (file.endsWith(".xml")) {
            throw new FHIRException("Unimplemented file type " + file);
        } else if (file.endsWith(".json")) {
            throw new FHIRException("Unimplemented file type " + file);
        } else if (file.endsWith(".zip")) {
            LoadZipFile(server, file, p, size, 0, -1);
        } else if (new File(file).isDirectory()) {
            LoadDirectory(server, file, p, size);
        } else
            throw new FHIRException("Unknown file type " + file);
    }
}

Example 45 with XmlParser

use of org.hl7.fhir.r4.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class LoincToDEConvertor method saveBundle.

private void saveBundle() throws FHIRFormatError, IOException, XmlPullParserException {
    XmlParser xml = new XmlParser();
    FileOutputStream s = new FileOutputStream(dest);
    xml.compose(s, bundle, true);
    s.close();
}