Example usage for org.w3c.dom Document adoptNode

Introduction

In this page you can find the example usage for org.w3c.dom Document adoptNode.

Prototype

public Node adoptNode(Node source) throws DOMException;

Source Link

Document

Attempts to adopt a node from another document to this document.

Usage

From source file:Main.java

/**
 * //from w w  w.  j a va 2  s  . c  o m
 * <i>Description:</i> append a node into specified <code>parent</code> node
 * 
 * @param doc
 * @param parent
 * @param node
 */
public static void appendNode(Document doc, Node parent, Node node) {
    Node txt = doc.createTextNode("\n    ");
    parent.appendChild(txt);
    Node comment = doc.createComment(" Created by FM GUI @ " + (new Date()) + " ");
    parent.appendChild(comment);
    doc.adoptNode(node);
    parent.appendChild(node);
    formatNode(doc, parent, node);
    txt = doc.createTextNode("\n\n  ");
    parent.appendChild(txt);
}

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From source file:net.padaf.xmpbox.SaveMetadataHelper.java

/**
 * Serialize a schema into an Output stream
 * /* ww w  .  ja v  a 2s  .com*/
 * @param schema
 *            Schema concerned by the serialization processing
 * @param os
 *            Stream to save serialized schema
 * @throws TransformException
 *             When couldn't parse data to XML/RDF
 */
public static void serialize(XMPSchema schema, OutputStream os) throws TransformException {
    try {
        Document doc = XMLUtil.newDocument();
        Element rdf = doc.createElementNS("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf:RDF");
        Node schemContent = schema.getElement().cloneNode(true);
        doc.adoptNode(schemContent);
        rdf.appendChild(schemContent);
        XMLUtil.save(rdf, os, "UTF-8");
    } catch (TransformerException e) {
        throw new TransformException("Failed to parse defined XMP");
    } catch (IOException e) {
        throw new TransformException("Failed to create Document to contain Schema representation ",
                e.getCause());
    }

}

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From source file:de.ingrid.interfaces.csw.domain.encoding.impl.XMLEncoding.java

protected static Document extractFromDocument(Node node) throws Exception {
    DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance();
    domFactory.setNamespaceAware(true);/*from  www . j a  v a  2 s  .  c  om*/
    DocumentBuilder builder = domFactory.newDocumentBuilder();
    Document doc = builder.newDocument();
    Node copy = node.cloneNode(true);
    Node adopted = doc.adoptNode(copy);
    doc.appendChild(adopted);
    return doc;
}

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From source file:net.padaf.xmpbox.SaveMetadataHelper.java

/**
 * Prepare XMP Saving Put data necessary to make a well-formed XMP
 * //from  w  w  w  .  j a  v a2  s.co  m
 * @param metadata
 *            metadata concerned by the serialization processing
 * @param intoXPacket
 *            true if Processing instruction must be embedded
 * @return The DOM Document which will represent the serialized metadata
 */
protected static Document prepareSaving(XMPMetadata metadata, boolean intoXPacket) {
    Document newdoc = (Document) metadata.getFuturOwner().cloneNode(true);
    if (intoXPacket) {
        ProcessingInstruction beginXPacket = newdoc.createProcessingInstruction("xpacket",
                "begin=\"" + metadata.getXpacketBegin() + "\" id=\"" + metadata.getXpacketId() + "\"");
        newdoc.appendChild(beginXPacket);
    }

    Element xmpMeta = newdoc.createElementNS("adobe:ns:meta/", "x:xmpmeta");
    xmpMeta.setAttributeNS(XMPSchema.NS_NAMESPACE, "xmlns:x", "adobe:ns:meta/");

    newdoc.appendChild(xmpMeta);
    Element elem = (Element) metadata.getContainerElement().cloneNode(true);
    newdoc.adoptNode(elem);
    xmpMeta.appendChild(elem);

    if (intoXPacket) {
        ProcessingInstruction endXPacket = newdoc.createProcessingInstruction("xpacket",
                metadata.getEndXPacket());
        newdoc.appendChild(endXPacket);
    }
    return newdoc;
}

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From source file:eu.europa.esig.dss.DSSXMLUtils.java

/**
 * Creates a DOM Document object of the specified type with its document element.
 *
 * @param namespaceURI  the namespace URI of the document element to create or null
 * @param qualifiedName the qualified name of the document element to be created or null
 * @param element       document {@code Element}
 * @return {@code Document}//from w w  w .  ja v a 2  s  . c o m
 */
public static Document createDocument(final String namespaceURI, final String qualifiedName,
        final Element element) {
    ensureDocumentBuilder();

    DOMImplementation domImpl;
    try {
        domImpl = dbFactory.newDocumentBuilder().getDOMImplementation();
    } catch (ParserConfigurationException e) {
        throw new DSSException(e);
    }
    final Document newDocument = domImpl.createDocument(namespaceURI, qualifiedName, null);
    final Element newElement = newDocument.getDocumentElement();
    newDocument.adoptNode(element);
    newElement.appendChild(element);

    return newDocument;
}

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From source file:eu.europa.esig.dss.DSSXMLUtils.java

/**
 * Creates a DOM Document object of the specified type with its document elements.
 *
 * @param namespaceURI//from  ww  w.ja v a 2 s .c om
 * @param qualifiedName
 * @param element1
 * @param element2
 * @return {@code Document}
 */
public static Document createDocument(final String namespaceURI, final String qualifiedName,
        final Element element1, final Element element2) {
    ensureDocumentBuilder();

    DOMImplementation domImpl;
    try {
        domImpl = dbFactory.newDocumentBuilder().getDOMImplementation();
    } catch (ParserConfigurationException e) {
        throw new DSSException(e);
    }
    final Document newDocument = domImpl.createDocument(namespaceURI, qualifiedName, null);
    final Element newElement = newDocument.getDocumentElement();
    newDocument.adoptNode(element1);
    newElement.appendChild(element1);

    newDocument.adoptNode(element2);
    newElement.appendChild(element2);

    return newDocument;
}

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From source file:eu.apenet.dpt.standalone.gui.hgcreation.LevelTreeActions.java

private Node stringToNode(Document originalDoc, ReaderInputStream readerInputStream) throws Exception {
    Document doc = DOMUtil.createDocument(readerInputStream);
    return originalDoc.adoptNode(doc.getFirstChild());
}

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From source file:cz.incad.kramerius.service.replication.ExternalReferencesFormat.java

private void original(Document document, Element element)
        throws DOMException, MalformedURLException, URISyntaxException {
    Element original = document.createElementNS(FedoraNamespaces.KRAMERIUS_URI, "replicatedFrom");
    document.adoptNode(original);
    original.setTextContent(makeHANDLE(document).toURI().toString());

    List<Element> rdfversions = XMLUtils.getElementsRecursive(element, new XMLUtils.ElementsFilter() {

        @Override//from   w w  w  .  j  a  va 2 s  .c o m
        public boolean acceptElement(Element el) {
            String localName = el.getLocalName();
            String namespace = el.getNamespaceURI();
            if (namespace.equals(FedoraNamespaces.RDF_NAMESPACE_URI)) {
                return localName.equals("Description");
            }
            return false;
        }
    });

    for (Element desc : rdfversions) {
        desc.appendChild(original);
    }
}

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From source file:com.bstek.dorado.idesupport.resolver.RobotResolver.java

protected void assembleContent(Document document, Element responseElement, List<Element> elements) {
    Element contentElenment = document.createElement("Content");
    responseElement.appendChild(contentElenment);
    for (Element element : elements) {
        contentElenment.appendChild(document.adoptNode(element));
    }/*from w  w  w. j a va 2  s .c o m*/
}

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From source file:act.installer.HMDBParser.java

/**
 * Convert an HMDB XML document into a Chemical object.  Expects one chemical per document.
 * @param doc A parsed HMDB XML doc./*from ww w  .  ja  va2 s.c  o  m*/
 * @return The corresponding chemical to store in the DB.
 * @throws JaxenException
 * @throws JSONException
 */
protected Chemical extractChemicalFromXMLDocument(Document doc) throws JaxenException, JSONException {
    String hmdbId = getText(HMDB_XPATH.HMDB_ID_TEXT, doc);

    String primaryName = getText(HMDB_XPATH.PRIMARY_NAME_TEXT, doc);
    String iupacName = getText(HMDB_XPATH.IUPAC_NAME_TEXT, doc);
    List<String> synonyms = getTextFromNodes(HMDB_XPATH.SYNONYMS_NODES, doc);

    String inchi = getText(HMDB_XPATH.INCHI_TEXT, doc);
    String smiles = getText(HMDB_XPATH.SMILES_TEXT, doc);

    // Require an InChI if we're going to consume this molecule.
    if (inchi == null || inchi.isEmpty()) {
        LOGGER.warn("No InChI found for HMDB chemical %s, aborting", hmdbId);
        return null;
    }

    String ontologyStatus = getText(HMDB_XPATH.ONTOLOGY_STATUS_TEXT, doc);
    List<String> ontologyOrigins = getTextFromNodes(HMDB_XPATH.ONTOLOGY_ORIGINS_NODES, doc);
    List<String> ontologyFunctions = getTextFromNodes(HMDB_XPATH.ONTOLOGY_FUNCTIONS_NODES, doc);
    List<String> ontologyApplications = getTextFromNodes(HMDB_XPATH.ONTOLOGY_APPLICATIONS_NODES, doc);
    List<String> ontologyLocations = getTextFromNodes(HMDB_XPATH.ONTOLOGY_LOCATIONS_NODES, doc);

    List<String> locationFluids = getTextFromNodes(HMDB_XPATH.LOCATIONS_FLUID_NODES, doc);
    List<String> locationTissues = getTextFromNodes(HMDB_XPATH.LOCATIONS_TISSUE_NODES, doc);

    List<String> pathwayNames = getTextFromNodes(HMDB_XPATH.PATHWAY_NAME_NODES, doc);

    List<String> diseaseNames = getTextFromNodes(HMDB_XPATH.DISEASE_NAME_NODES, doc);

    String metlinId = getText(HMDB_XPATH.METLIN_ID_TEXT, doc);
    String pubchemId = getText(HMDB_XPATH.PUBCHEM_ID_TEXT, doc);
    String chebiId = getText(HMDB_XPATH.CHEBI_ID_TEXT, doc);

    List<Node> proteins = getNodes(HMDB_XPATH.PROTEIN_L1_NODES, doc);
    // Simple triples of name, uniprot id, gene name.
    List<Triple<String, String, String>> proteinAttributes = new ArrayList<>(proteins.size());

    for (Node n : proteins) {
        /* In order to run XPath on a sub-document, we have to Extract the relevant nodes into their own document object.
         * If we try to run evaluate on `n` instead of this new document, we'll get matching paths for the original
         * document `d` but not for the nodes we're looking at right now.  Very weird. */
        Document proteinDoc = documentBuilder.newDocument();
        proteinDoc.adoptNode(n);
        proteinDoc.appendChild(n);
        String name = getText(HMDB_XPATH.PROTEIN_L2_NAME_TEXT, proteinDoc);
        String uniprotId = getText(HMDB_XPATH.PROTEIN_L2_UNIPROT_ID_TEXT, proteinDoc);
        String geneName = getText(HMDB_XPATH.PROTEIN_L2_GENE_NAME_TEXT, proteinDoc);
        proteinAttributes.add(Triple.of(name, uniprotId, geneName));
    }

    // Assumption: when we reach this point there will always be an InChI.
    Chemical chem = new Chemical(inchi);
    chem.setSmiles(smiles);

    chem.setCanon(primaryName);

    if (pubchemId != null && !pubchemId.isEmpty()) {
        chem.setPubchem(Long.valueOf(pubchemId));
    }

    synonyms.forEach(chem::addSynonym);
    chem.addSynonym(iupacName); // TODO: is there a better place for this?

    JSONObject meta = new JSONObject().put("hmdb_id", hmdbId).put("ontology",
            new JSONObject().put("status", ontologyStatus).put("origins", new JSONArray(ontologyOrigins))
                    .put("functions", new JSONArray(ontologyFunctions))
                    .put("applications", new JSONArray(ontologyApplications))
                    .put("locations", new JSONArray(ontologyLocations)))
            .put("location",
                    new JSONObject().put("fluid", new JSONArray(locationFluids)).put("tissue",
                            new JSONArray(locationTissues)))
            .put("pathway_names", new JSONArray(pathwayNames)).put("disease_names", new JSONArray(diseaseNames))
            .put("metlin_id", metlinId).put("chebi_id", chebiId).put("proteins",
                    new JSONArray(proteinAttributes
                            .stream().map(t -> new JSONObject().put("name", t.getLeft())
                                    .put("uniprot_id", t.getMiddle()).put("gene_name", t.getRight()))
                            .collect(Collectors.toList())));

    chem.putRef(Chemical.REFS.HMDB, meta);

    return chem;
}

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