Example usage for org.w3c.dom Element getFirstChild

List of usage examples for org.w3c.dom Element getFirstChild

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Introduction

In this page you can find the example usage for org.w3c.dom Element getFirstChild.

Prototype

public Node getFirstChild();

Source Link

Document

The first child of this node.

Usage

From source file:edu.lternet.pasta.client.EventSubscriptionClient.java

public String subscriptionTableHTML() throws PastaEventException {
    String html = "";

    if (this.uid != null && !this.uid.equals("public")) {
        StringBuilder sb = new StringBuilder("");
        String xmlString = readByFilter("");

        DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
        try {//from w  ww  .  j  a  v a 2 s.c o m
            DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
            InputStream inputStream = IOUtils.toInputStream(xmlString, "UTF-8");
            Document document = documentBuilder.parse(inputStream);
            Element documentElement = document.getDocumentElement();
            NodeList subscriptionList = documentElement.getElementsByTagName("subscription");
            int nSubscriptions = subscriptionList.getLength();

            for (int i = 0; i < nSubscriptions; i++) {
                Node subscriptionNode = subscriptionList.item(i);
                NodeList subscriptionChildren = subscriptionNode.getChildNodes();
                String subscriptionId = "";
                String packageId = "";
                String url = "";
                for (int j = 0; j < subscriptionChildren.getLength(); j++) {
                    Node childNode = subscriptionChildren.item(j);
                    if (childNode instanceof Element) {
                        Element subscriptionElement = (Element) childNode;

                        if (subscriptionElement.getTagName().equals("id")) {
                            Text text = (Text) subscriptionElement.getFirstChild();
                            if (text != null) {
                                subscriptionId = text.getData().trim();
                            }
                        } else if (subscriptionElement.getTagName().equals("packageId")) {
                            Text text = (Text) subscriptionElement.getFirstChild();
                            if (text != null) {
                                packageId = text.getData().trim();
                            }
                        } else if (subscriptionElement.getTagName().equals("url")) {
                            Text text = (Text) subscriptionElement.getFirstChild();
                            if (text != null) {
                                url = text.getData().trim();
                            }
                        }
                    }
                }

                sb.append("<tr>\n");

                sb.append("<td class='nis' align='center'>");
                sb.append(subscriptionId);
                sb.append("</td>\n");

                sb.append("<td class='nis' align='center'>");
                sb.append(packageId);
                sb.append("</td>\n");

                sb.append("<td class='nis'>");
                sb.append(url);
                sb.append("</td>\n");

                sb.append("</tr>\n");
            }

            html = sb.toString();
        } catch (Exception e) {
            logger.error("Exception:\n" + e.getMessage());
            e.printStackTrace();
            throw new PastaEventException(e.getMessage());
        }
    }

    return html;
}

From source file:org.jasig.portal.security.provider.saml.SAMLDelegatedAuthenticationService.java

private void removeAllChildren(Element element) {
    Node child = element.getFirstChild();

    while (child != null) {
        Node next = child.getNextSibling();
        element.removeChild(child);//from   w w  w. j a va2 s .c o m
        child = next;
    }
}

From source file:dk.dbc.rawrepo.oai.OAIWorker.java

private void fixXmlNamespacePrefix(Element element, String metadataPrefix, String namespaceURI)
        throws DOMException {
    String prefix = null;//  w w w  .  j a v a  2  s  . c o  m
    if (namespaceURI.equals(element.getNamespaceURI())) {
        prefix = element.getPrefix();
        if (prefix == null) {
            prefix = "";
        }
        element.setPrefix(metadataPrefix);
    }
    for (Node child = element.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() == Node.ELEMENT_NODE) {
            fixXmlNamespacePrefix((Element) child, metadataPrefix, namespaceURI);
        }
    }
    if (prefix != null) {
        element.removeAttribute(prefix.isEmpty() ? "xmlns" : ("xmlns:" + prefix));
    }
}

From source file:org.dataone.proto.trove.mn.http.client.HttpExceptionHandler.java

private static ErrorElements deserializeXml(HttpResponse response) throws IllegalStateException, IOException //    throws NotFound, InvalidToken, ServiceFailure, NotAuthorized,
//    NotFound, IdentifierNotUnique, UnsupportedType,
//    InsufficientResources, InvalidSystemMetadata, NotImplemented,
//    InvalidCredentials, InvalidRequest, IOException {
{
    ErrorElements ee = new ErrorElements();

    DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
    Document doc;/*from   w ww.java  2s  .c om*/

    int httpCode = response.getStatusLine().getStatusCode();
    if (response.getEntity() != null) {
        BufferedInputStream bErrorStream = new BufferedInputStream(response.getEntity().getContent());
        bErrorStream.mark(5000); // good for resetting up to 5000 bytes

        String detailCode = null;
        String description = null;
        String name = null;
        int errorCode = -1;
        try {
            DocumentBuilder db = dbf.newDocumentBuilder();
            doc = db.parse(bErrorStream);
            Element root = doc.getDocumentElement();
            root.normalize();
            if (root.getNodeName().equalsIgnoreCase("error")) {
                if (root.hasAttribute("errorCode")) {
                    try {
                        errorCode = Integer.getInteger(root.getAttribute("errorCode"));
                    } catch (NumberFormatException nfe) {
                        System.out.println("errorCode unexpectedly not able to parse to int,"
                                + " using http status for creating exception");
                        errorCode = httpCode;
                    }
                }
                if (errorCode != httpCode) //            throw new ServiceFailure("1000","errorCode in message body doesn't match httpStatus");
                {
                    System.out.println("errorCode in message body doesn't match httpStatus,"
                            + " using errorCode for creating exception");
                }
                if (root.hasAttribute("detailCode")) {
                    detailCode = root.getAttribute("detailCode");
                } else {
                    detailCode = "detail code is Not Set!";
                }
                if (root.hasAttribute("name")) {
                    name = root.getAttribute("name");
                } else {
                    name = "Exception";
                }
                Node child = root.getFirstChild();
                do {
                    if (child.getNodeType() == Node.ELEMENT_NODE) {
                        if (child.getNodeName().equalsIgnoreCase("description")) {
                            Element element = (Element) child;
                            description = element.getTextContent();
                            break;
                        }
                    }
                } while ((child = child.getNextSibling()) != null);
            } else {
                description = domToString(doc);
                detailCode = "detail code was never Set!";
            }
        } catch (TransformerException e) {
            description = deserializeNonXMLErrorStream(bErrorStream, e);
        } catch (SAXException e) {
            description = deserializeNonXMLErrorStream(bErrorStream, e);
        } catch (IOException e) {
            description = deserializeNonXMLErrorStream(bErrorStream, e);
        } catch (ParserConfigurationException e) {
            description = deserializeNonXMLErrorStream(bErrorStream, e);
        }

        ee.setCode(errorCode);
        ee.setName(name);
        ee.setDetailCode(detailCode);
        ee.setDescription(description);
    }
    return ee;
}

From source file:com.verisign.epp.codec.gen.EPPUtil.java

/**
 * Decode <code>String</code>, by XML namespace and tag name, from an XML
 * Element. The children elements of <code>aElement</code> will be searched
 * for the specified <code>aNS</code> namespace URI and the specified
 * <code>aTagName</code>. The first XML element found will be decoded and
 * returned. If no element is found, <code>null</code> is returned.
 * /*from  ww w  . j a v  a 2 s. c  o m*/
 * @param aElement
 *            XML Element to scan. For example, the element could be
 *            &ltdomain:create&gt
 * @param aNS
 *            XML namespace of the elements. For example, for domain element
 *            this is "urn:iana:xmlns:domain".
 * @param aTagName
 *            Tag name of the element including an optional namespace
 *            prefix. For example, the tag name for the domain name is
 *            "domain:name".
 * @return <code>String</code> value if found; <code>null</code> otherwise.
 * @exception EPPDecodeException
 *                Error decoding <code>aElement</code>.
 */
public static String decodeString(Element aElement, String aNS, String aTagName) throws EPPDecodeException {
    String retVal = null;

    Element theElm = EPPUtil.getElementByTagNameNS(aElement, aNS, aTagName);

    if (theElm != null) {
        Node textNode = theElm.getFirstChild();

        // Element does have a text node?
        if (textNode != null) {
            retVal = textNode.getNodeValue();
        } else {
            retVal = "";
        }
    }

    // end if (currElm != null)
    return retVal;
}

From source file:com.verisign.epp.codec.gen.EPPUtil.java

/**
 * Decode <code>Date</code>, by XML namespace and tag name, from an XML
 * Element. The children elements of <code>aElement</code> will be searched
 * for the specified <code>aNS</code> namespace URI and the specified
 * <code>aTagName</code>. The first XML element found will be decoded and
 * returned. If no element is found, <code>null</code> is returned. The
 * format used for decoding the date is defined by the constant
 * <code>EPPUtil.DATE_FORMAT</code>.
 * /*from w  w  w. j ava2  s . co m*/
 * @param aElement
 *            XML Element to scan. For example, the element could be
 *            &lttrans-id&gt
 * @param aNS
 *            XML namespace of the elements. For example, for domain element
 *            this is "urn:iana:xmlns:epp".
 * @param aTagName
 *            Tag name of the element including an optional namespace
 *            prefix. For example, the tag name for the transaction Id date
 *            is "date".
 * @return <code>Date</code> value if found; <code>null</code> otherwise.
 * @exception EPPDecodeException
 *                Error decoding <code>aElement</code>.
 */
public static Date decodeDate(Element aElement, String aNS, String aTagName) throws EPPDecodeException {
    Date retVal = null;

    Element theElm = EPPUtil.getElementByTagNameNS(aElement, aNS, aTagName);

    if (theElm != null) {
        retVal = EPPUtil.decodeDate(theElm.getFirstChild().getNodeValue());
    }

    return retVal;
}

From source file:com.verisign.epp.codec.gen.EPPUtil.java

/**
 * Decode <code>Boolean</code>, by XML namespace and tag name, from an XML
 * Element. The children elements of <code>aElement</code> will be searched
 * for the specified <code>aNS</code> namespace URI and the specified
 * <code>aTagName</code>. The first XML element found will be decoded and
 * returned. If no element is found, <code>null</code> is returned.
 * //  ww w  .  j av  a  2s  .  c  o m
 * @param aElement
 *            XML Element to scan. For example, the element could be
 *            &ltdomain:create&gt
 * @param aNS
 *            XML namespace of the elements. For example, for domain element
 *            this is "urn:iana:xmlns:domain".
 * @param aTagName
 *            Tag name of the element including an optional namespace
 *            prefix. For example, the tag name for the domain name is
 *            "domain:name".
 * @return <code>Boolean</code> value if found; <code>null</code> otherwise.
 * @exception EPPDecodeException
 *                Error decoding <code>aElement</code>.
 */
public static Boolean decodeBoolean(Element aElement, String aNS, String aTagName) throws EPPDecodeException {
    Boolean retVal = null;
    String theVal = null;

    Element theElm = EPPUtil.getElementByTagNameNS(aElement, aNS, aTagName);

    if (theElm != null) {
        Node textNode = theElm.getFirstChild();

        // Element does have a text node?
        if (textNode != null) {
            theVal = textNode.getNodeValue();

            if (theVal.equalsIgnoreCase("true") || theVal.equals("1")) {
                retVal = new Boolean(true);
            } else {
                retVal = new Boolean(false);
            }
        } else {
            retVal = null;
        }
    }

    return retVal;
}

From source file:com.verisign.epp.codec.gen.EPPUtil.java

/**
 * Decode a <code>List</code> of <code>Integer</code>'s by XML namespace and
 * tag name, from an XML Element. The children elements of
 * <code>aElement</code> will be searched for the specified <code>aNS</code>
 * namespace URI and the specified <code>aTagName</code>. Each XML element
 * found will be decoded and added to the returned <code>List</code>. Empty
 * child elements, will result in an <code>EPPDecodeException</code>.
 * /*  w w w.  j a  va  2 s  .c  om*/
 * @param aElement
 *            XML Element to scan. For example, the element could be
 *            &ltdomain:update&gt
 * @param aNS
 *            XML namespace of the elements. For example, for domain element
 *            this is "urn:iana:xmlns:domain".
 * @param aTagName
 *            Tag name of the element including an optional namespace
 *            prefix. For example, the tag name for the domain name servers
 *            is "domain:server".
 * 
 * @return <code>List</code> of <code>Integer</code> elements representing
 *         the text nodes of the found XML elements.
 * 
 * @exception EPPDecodeException
 *                Error decoding <code>aElement</code>.
 */
public static List decodeIntegerList(Element aElement, String aNS, String aTagName) throws EPPDecodeException {

    List retVal = new ArrayList();

    Vector theChildren = EPPUtil.getElementsByTagNameNS(aElement, aNS, aTagName);

    for (int i = 0; i < theChildren.size(); i++) {
        Element currChild = (Element) theChildren.elementAt(i);

        Integer retInteger = null;

        Node textNode = currChild.getFirstChild();

        // Element does have a text node?
        if (textNode != null) {

            String intValStr = textNode.getNodeValue();
            try {
                retInteger = Integer.valueOf(intValStr);
            } catch (NumberFormatException e) {

                throw new EPPDecodeException(
                        "EPPUtil.decodeIntegerList Can't convert value to Integer: " + intValStr + e);
            }
        } else {
            throw new EPPDecodeException(
                    "EPPUtil.decodeIntegerList Can't decode numeric value from non-existant text node");
        }

        retVal.add(retInteger);
    }

    return retVal;
}

From source file:com.verisign.epp.codec.gen.EPPUtil.java

/**
 * Decode <code>Date</code>, as date and time, by XML namespace and tag
 * name, from an XML Element. The children elements of <code>aElement</code>
 * will be searched for the specified <code>aNS</code> namespace URI and the
 * specified <code>aTagName</code>. The first XML element found will be
 * decoded and returned. If no element is found, <code>null</code> is
 * returned. The format used for decoding the date is defined by the
 * constant <code>EPPUtil.TIME_INSTANT_FORMAT</code>.
 * // w  w w .  j a  v  a  2  s .com
 * @param aElement
 *            XML Element to scan. For example, the element could be
 *            &lttrans-id&gt
 * @param aNS
 *            XML namespace of the elements. For example, for domain element
 *            this is "urn:iana:xmlns:epp".
 * @param aTagName
 *            Tag name of the element including an optional namespace
 *            prefix. For example, the tag name for the transaction Id date
 *            is "date".
 * @return <code>Date</code> value as date and time if found;
 *         <code>null</code> otherwise.
 * @exception EPPDecodeException
 *                Error decoding <code>aElement</code>.
 */
public static Date decodeTimeInstant(Element aElement, String aNS, String aTagName) throws EPPDecodeException {
    Date retVal = null;

    Element theElm = EPPUtil.getElementByTagNameNS(aElement, aNS, aTagName);

    if (theElm != null) {
        retVal = EPPUtil.decodeTimeInstant(theElm.getFirstChild().getNodeValue());
    }

    return retVal;
}

From source file:com.github.lindenb.jvarkit.tools.ensembl.VcfEnsemblVepRest.java

@Override
protected Collection<Throwable> doVcfToVcf(final String inputName, final VcfIterator vcfIn,
        final VariantContextWriter out) throws IOException {
    final java.util.Base64.Encoder base64Encoder = java.util.Base64.getEncoder();
    final SequenceOntologyTree soTree = SequenceOntologyTree.getInstance();
    VCFHeader header = vcfIn.getHeader();
    List<VariantContext> buffer = new ArrayList<>(this.batchSize + 1);
    VCFHeader h2 = new VCFHeader(header);
    addMetaData(h2);// w  w w.j  a v a2  s  . c  o  m

    if (!xmlBase64) {
        h2.addMetaDataLine(new VCFInfoHeaderLine(TAG, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String,
                "VEP Transcript Consequences. Format :(biotype|cdnaStart|cdnaEnd|cdsStart|cdsEnd|geneId|geneSymbol|geneSymbolSource|hgnc|strand|transcript|variantAllele|so_acns)"));
    } else {
        h2.addMetaDataLine(
                new VCFInfoHeaderLine(TAG, 1, VCFHeaderLineType.String, "VEP xml answer encoded as base 64"));
    }

    out.writeHeader(h2);
    SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header);
    for (;;) {
        VariantContext ctx = null;
        if (vcfIn.hasNext()) {
            buffer.add((ctx = progress.watch(vcfIn.next())));
        }
        if (ctx == null || buffer.size() >= this.batchSize) {
            if (!buffer.isEmpty()) {
                if (!xmlBase64) {
                    Opt opt = vep(buffer);
                    for (VariantContext ctx2 : buffer) {
                        VariantContextBuilder vcb = new VariantContextBuilder(ctx2);
                        final String inputStr = createInputContext(ctx2);
                        Data mydata = null;
                        for (Data data : opt.getData()) {
                            if (!inputStr.equals(data.getInput()))
                                continue;
                            mydata = data;
                            break;
                        }
                        if (mydata == null) {
                            LOG.info("No Annotation found for " + inputStr);
                            out.add(ctx2);
                            continue;
                        }
                        List<String> infoList = new ArrayList<>();
                        List<TranscriptConsequences> csql = mydata.getTranscriptConsequences();
                        for (int i = 0; i < csql.size(); ++i) {
                            TranscriptConsequences csq = csql.get(i);
                            StringBuilder sb = new StringBuilder();
                            sb.append(empty(csq.getBiotype())).append("|").append(empty(csq.getCdnaStart()))
                                    .append("|").append(empty(csq.getCdnaEnd())).append("|")
                                    .append(empty(csq.getCdsStart())).append("|").append(empty(csq.getCdsEnd()))
                                    .append("|").append(empty(csq.getGeneId())).append("|")
                                    .append(empty(csq.getGeneSymbol())).append("|")
                                    .append(empty(csq.getGeneSymbolSource())).append("|")
                                    .append(empty(csq.getHgncId())).append("|").append(empty(csq.getStrand()))
                                    .append("|").append(empty(csq.getTranscriptId())).append("|")
                                    .append(empty(csq.getVariantAllele())).append("|");
                            List<String> terms = csq.getConsequenceTerms();
                            for (int j = 0; j < terms.size(); ++j) {
                                if (j > 0)
                                    sb.append("&");
                                SequenceOntologyTree.Term term = soTree.getTermByLabel(terms.get(j));
                                if (term == null) {
                                    sb.append(terms.get(j));
                                    LOG.warn("No SO:Term found for " + terms.get(j));
                                } else {
                                    sb.append(term.getAcn());
                                }
                            }
                            infoList.add(sb.toString());
                        }
                        if (!infoList.isEmpty()) {
                            vcb.attribute(TAG, infoList);
                        }

                        out.add(vcb.make());
                    }
                } //end of not(XML base 64)
                else {
                    Document opt = vepxml(buffer);
                    Element root = opt.getDocumentElement();
                    if (!root.getNodeName().equals("opt"))
                        throw new IOException("Bad root node " + root.getNodeName());

                    for (VariantContext ctx2 : buffer) {
                        String inputStr = createInputContext(ctx2);
                        Document newdom = null;

                        //loop over <data/>
                        for (Node dataNode = root.getFirstChild(); dataNode != null; dataNode = dataNode
                                .getNextSibling()) {
                            if (dataNode.getNodeType() != Node.ELEMENT_NODE)
                                continue;
                            Attr att = Element.class.cast(dataNode).getAttributeNode("input");
                            if (att == null) {
                                LOG.warn("no @input in <data/>");
                                continue;
                            }

                            if (!att.getValue().equals(inputStr))
                                continue;
                            if (newdom == null) {
                                newdom = this.documentBuilder.newDocument();
                                newdom.appendChild(newdom.createElement("opt"));
                            }
                            newdom.getDocumentElement().appendChild(newdom.importNode(dataNode, true));
                        }
                        if (newdom == null) {
                            LOG.warn("No Annotation found for " + inputStr);
                            out.add(ctx2);
                            continue;
                        }
                        StringWriter sw = new StringWriter();
                        try {
                            this.xmlSerializer.transform(new DOMSource(newdom), new StreamResult(sw));
                        } catch (TransformerException err) {
                            throw new IOException(err);
                        }
                        VariantContextBuilder vcb = new VariantContextBuilder(ctx2);
                        vcb.attribute(TAG, base64Encoder.encodeToString(sw.toString().getBytes())
                                .replaceAll("[\\s=]", ""));
                        out.add(vcb.make());
                    }
                } //end of XML base 64
            }
            if (ctx == null)
                break;
            buffer.clear();
        }
        if (out.checkError())
            break;
    }
    progress.finish();
    return RETURN_OK;
}