Example usage for javax.xml.xpath XPathFactory newXPath

List of usage examples for javax.xml.xpath XPathFactory newXPath

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Introduction

In this page you can find the example usage for javax.xml.xpath XPathFactory newXPath.

Prototype

public abstract XPath newXPath();

Source Link

Document

Return a new XPath using the underlying object model determined when the XPathFactory was instantiated.

Usage

From source file:gov.nih.nci.ncicb.tcga.dcc.dam.util.TempClinicalDataLoader.java

private static void processBiospecimenXmlFile(final String xmlFile, final String archiveName,
        final String disease, final Date dateAdded) throws ParserConfigurationException, IOException,
        SAXException, SQLException, XPathExpressionException, InstantiationException, IllegalAccessException {

    DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance();
    domFactory.setNamespaceAware(true);/*  ww  w. j  a  v  a  2s . c  om*/
    DocumentBuilder builder = domFactory.newDocumentBuilder();
    Document doc = builder.parse(xmlFile);
    XPathFactory factory = XPathFactory.newInstance();
    XPath xpath = factory.newXPath();
    Patient patient = new Patient();
    Pattern filePattern = Pattern.compile("(TCGA-[A-Z0-9]{2}-[A-Z0-9]{4})");
    Matcher matcher = filePattern.matcher(xmlFile);
    matcher.find();
    String patientBarcode = matcher.group(1);
    if (patientBarcode == null) {
        System.out.println("Failed to get patient barcode from filename!");
        System.exit(-1);
    }
    patient.setPatientID(Patient.getPatientIdForBarcode(patientBarcode));
    if (patient.getPatientID() < 1) {
        System.out.println("Could not find PATIENT record for " + patientBarcode + " saving it now...");
        patient.setAttribute("ARCHIVE_NAME", archiveName);
        patient.setAttribute("DISEASE", disease);
        patient.setDateAdded(dateAdded);
        patient.setAttribute("BCRPATIENTBARCODE", patientBarcode);
        patient.insertSelf(0);
    }
    String patientPath = "//" + patient.getXmlElementName() + "[1]";
    processSamples(doc, xpath, patient, patientPath);
}

From source file:gov.nih.nci.lmp.mimGpml.CommonHelper.java

/**
 * Gets the MIM-Vis XML object by ID./*from  w  ww.  j a v a  2 s .  co m*/
 * 
 * TODO: It does not appear possible to use the Saxon engine to process
 * XPath queries within Pathvisio; the plugin fails to load. The approach
 * taken instead relies on JDOM/Jaxen to process XPath.
 * 
 * @param doc
 *            the doc
 * @param elemId
 *            the element id
 * @return the vis xml object by id
 */
public static XmlObject getVisXmlObjectById(DiagramDocument doc, String elemId) {

    // TODO: Account for bioId
    // String queryExpression =
    // "/mimVis:Diagram/mimVis:InteractionGlyph[@visId='" + elemId + "']";
    String queryExpression = "//*[@visId='" + elemId + "']";

    Logger.log.debug("elemId:" + elemId);
    Logger.log.debug("queryExpression:" + queryExpression);

    try {
        org.w3c.dom.Document wDoc = (org.w3c.dom.Document) doc.getDomNode();
        javax.xml.xpath.XPathFactory factory = XPathFactory.newInstance();
        javax.xml.xpath.XPath wXpath = factory.newXPath();
        javax.xml.xpath.XPathExpression expr = wXpath.compile(queryExpression);

        Object result = expr.evaluate(wDoc, javax.xml.xpath.XPathConstants.NODESET);
        org.w3c.dom.NodeList nodes = (org.w3c.dom.NodeList) result;

        Logger.log.debug("NodeList size: " + nodes.getLength());

        /**
         * If the size is not one, then there is a duplicate key issue that
         * needs to be dealt with. Treat it as an error and return null.
         */
        if (nodes.getLength() == 1) {
            XmlObject xmlObj = XmlObject.Factory.parse(nodes.item(0));
            Logger.log.debug("glyph.xmlText: " + xmlObj.xmlText(getXmlOptions()));

            // Logger.log.debug("doc.xmlText: " +
            // doc.xmlText(getXmlOptions()));

            String elemStr = xmlObj.xmlText(getXmlOptions());

            Logger.log.debug("getVisXmlObjectById XML String:" + elemStr);

            /**
             * Sample of the way an XML fragment is represented with
             * <xml-fragment> tags. This necessitates a modification from
             * the nodes returned by selectNodes.
             * 
             * <xml-fragment mimVis:visId="ca53d" mimVis:displayName="CAMK"
             * centerX="166.0" centerY="167.0" mimVis:width="80.0"
             * mimVis:height="20.0"
             * xmlns:mimVis="http://lmp.nci.nih.gov/mim/mimVisLevel1">
             * <mimVis:mimBioRef>b9044</mimVis:mimBioRef></xml-fragment>
             */
            // Pattern/matcher
            Pattern mimStartElemTag = Pattern.compile("mimVis:[A-Z][A-Za-z]+");
            Matcher matcherStart = mimStartElemTag.matcher(elemStr);

            // System.out.println("matcherStart count: "
            // + matcherStart.groupCount());

            String match = null;

            // Find all matches
            while (matcherStart.find()) {
                // Get the matching string
                match = matcherStart.group();
                // System.out.println("matcherStart.group(): "
                // + matcherStart.group());
            }

            final int prefixLength = "mimVis:".length();

            // String localPart = xmlFrag + "Type";
            String localPart = match.substring(prefixLength) + "Type";

            // Match: mimVis:SimplePhysicalEntityGlyph
            // SPE URI QName: http://lmp.nci.nih.gov/mim/mimVisLevel1
            // SPE Local QName: SimplePhysicalEntityGlyphType

            QName objQName = new QName(MIM_VIS_NS, localPart);

            SchemaTypeLoader schemaTypeLoader = XmlBeans.getContextTypeLoader();
            SchemaType objType = schemaTypeLoader.findType(objQName);

            XmlOptions opts = new XmlOptions();
            opts.setLoadReplaceDocumentElement(null);

            /**
             * Taken from the XMLBeans autogenerated code of a XSD complex
             * type. For parsing a XML fragment given the SchemaType.
             */
            xmlObj = XmlBeans.getContextTypeLoader().parse(elemStr, objType, opts);

            return xmlObj;
        } else {
            Logger.log.info("ERROR: Most likely a duplicate ID.");
        }
    } catch (XmlException e) {
        e.printStackTrace();
    } catch (XPathExpressionException e) {
        e.printStackTrace();
    }

    return null;
}

From source file:gov.nih.nci.ncicb.tcga.dcc.dam.util.TempClinicalDataLoader.java

private static void processClinicalXmlFile(final String xmlFile, final String archiveName, final String disease,
        final Date dateAdded) throws ParserConfigurationException, IOException, SAXException,
        XPathExpressionException, InstantiationException, IllegalAccessException {
    Patient.setDBConnection(dbConnection);

    // get all patient barcodes
    DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance();
    domFactory.setNamespaceAware(true);//from ww w . j a va2 s . c o m
    DocumentBuilder builder = domFactory.newDocumentBuilder();
    Document doc = builder.parse(xmlFile);
    XPathFactory factory = XPathFactory.newInstance();
    XPath xpath = factory.newXPath();

    Patient p = new Patient();
    p.setAttribute("ARCHIVE_NAME", archiveName);
    p.setAttribute("DISEASE", disease);
    p.setDateAdded(dateAdded);
    String basePath = "//TCGA_BCR";
    ClinicalBean[] patients = processElementGroup(basePath, doc, xpath, p, 0);
    // for each patient, process its samples
    for (int patient_i = 0; patient_i < patients.length; patient_i++) {
        Patient patient = (Patient) patients[patient_i];

        Sample s = new Sample();
        String patientPath = basePath + "/" + patient.getXmlElementName() + "[" + (patient_i + 1) + "]";

        // patients > drugs
        processElementGroup(patientPath, doc, xpath, new Drug(), patient.getPatientID());

        // patients > radiations
        processElementGroup(patientPath, doc, xpath, new Radiation(), patient.getPatientID());

        // patients > examinations
        processElementGroup(patientPath, doc, xpath, new Examination(), patient.getPatientID());

        // patients > surgeries
        processElementGroup(patientPath, doc, xpath, new Surgery(), patient.getPatientID());
    }
}

From source file:gov.tva.sparky.hbase.RestProxy.java

/**
 * //from  w  w w . ja  v a2 s . c  o m
 * @param strTablename
 * @param strRowKey
 * @param strColumn
 * @param strQualifier
 * @return Returns the values from a data cell in HBase.
 * @throws ParserConfigurationException
 * @throws SAXException
 * @throws IOException
 */
public static byte[] QueryHBaseForCell(String strTablename, String strRowKey, String strColumn,
        String strQualifier) throws ParserConfigurationException, SAXException, IOException {
    // Configuration
    Configuration conf = new Configuration(false);
    conf.addResource("hadoop-default.xml");
    conf.addResource("sparky-site.xml");
    int port = conf.getInt("sparky.hbase.restPort", 8092);
    String uri = conf.get("sparky.hbase.restURI", "http://socdvmhbase");

    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    // never forget this!
    factory.setNamespaceAware(true);
    DocumentBuilder builder = factory.newDocumentBuilder();

    String strRestPath = uri + ":" + port + "/" + strTablename + "/" + strRowKey + "/" + strColumn + ":"
            + strQualifier;

    Document doc = null;

    try {
        doc = builder.parse(strRestPath);

    } catch (FileNotFoundException e) {
        //System.out.println("RestProxy > Exception: ( " + strRestPath + " )");
    }

    if (null == doc)
        return null;

    XPathFactory xpath_factory = XPathFactory.newInstance();
    XPath xpath = xpath_factory.newXPath();

    XPathExpression expr = null;

    try {
        expr = xpath.compile("/CellSet/Row/Cell/text()");
    } catch (XPathExpressionException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    Object result = null;
    try {
        result = expr.evaluate(doc, XPathConstants.NODESET);
    } catch (XPathExpressionException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    NodeList nodes = (NodeList) result;
    String cell_value = nodes.item(0).getNodeValue();

    Base64 decoder = new Base64();
    byte[] decodedValue = decoder.decode(cell_value.getBytes());

    return decodedValue;
}

From source file:gov.nih.nci.ncicb.tcga.dcc.dam.util.TempClinicalDataLoader.java

private static void processFullXmlFile(final String xmlFile, final String archiveName, final String disease,
        final Date dateAdded) throws ParserConfigurationException, IOException, SAXException,
        XPathExpressionException, InstantiationException, IllegalAccessException {

    Patient.setDBConnection(dbConnection);

    // Create an XPath object from this xml file
    DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance();
    domFactory.setNamespaceAware(true);//from  w  ww . j  a v  a  2s . co  m
    DocumentBuilder builder = domFactory.newDocumentBuilder();
    Document doc = builder.parse(xmlFile);
    XPathFactory factory = XPathFactory.newInstance();
    XPath xpath = factory.newXPath();

    // create the Patient bean for this file
    Patient p = new Patient();
    p.setAttribute("ARCHIVE_NAME", archiveName);
    p.setAttribute("DISEASE", disease);
    p.setDateAdded(dateAdded);
    String basePath = "//TCGA_BCR";

    // process all patients in this file (currently is only 1 but this should work even with multiples)
    ClinicalBean[] patients = processElementGroup(basePath, doc, xpath, p, 0);
    // for each patient, process its clinical elements
    for (int patient_i = 0; patient_i < patients.length; patient_i++) {
        Patient patient = (Patient) patients[patient_i];
        String patientPath = basePath + "/" + patient.getXmlElementName() + "[" + (patient_i + 1) + "]";
        processSamples(doc, xpath, patient, patientPath);
        // patients > drugs
        processElementGroup(patientPath, doc, xpath, new Drug(), patient.getPatientID());

        // patients > radiations
        processElementGroup(patientPath, doc, xpath, new Radiation(), patient.getPatientID());

        // patients > examinations
        processElementGroup(patientPath, doc, xpath, new Examination(), patient.getPatientID());

        // patients > surgeries
        processElementGroup(patientPath, doc, xpath, new Surgery(), patient.getPatientID());
    }

}

From source file:com.fluidops.iwb.luxid.LuxidExtractor.java

/**
 * returns the name of a XCAS- document//from ww w . ja  va2 s.  c o  m
 * 
 * @param input
 * @param stmts
 * @param vf
 * @param id
 * @param f
 * @throws Exception
 */
public static void getDocumentTitle(String input, Set<Statement> stmts, ValueFactory vf, String id, File f)
        throws Exception {
    DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
    DocumentBuilder db = dbf.newDocumentBuilder();

    Document doc = db.parse(f);

    XPathFactory factory = XPathFactory.newInstance();
    XPath xpath = factory.newXPath();
    XPathExpression expr = xpath.compile("//com.temis.uima.Zone[@name='title']");

    NodeList nodes = (NodeList) expr.evaluate(doc, XPathConstants.NODESET);
    for (int i = 0, n = nodes.getLength(); i < n; i++) {
        String begin = nodes.item(i).getAttributes().getNamedItem("begin").getTextContent();
        String end = nodes.item(i).getAttributes().getNamedItem("end").getTextContent();

        stmts.add(vf.createStatement(
                vf.createURI(EndpointImpl.api().getNamespaceService().defaultNamespace() + id), RDFS.LABEL,
                vf.createLiteral(input.substring(Integer.parseInt(begin), Integer.parseInt(end)))));
    }
}

From source file:Main.java

/**
 * Create a new {@link XPath} with the passed variable resolver, function
 * resolver and namespace context.//from w w w  . j a v a  2s  .c om
 * 
 * @param aXPathFactory
 *        The XPath factory object to use. May not be <code>null</code>.
 * @param aVariableResolver
 *        Variable resolver to be used. May be <code>null</code>.
 * @param aFunctionResolver
 *        Function resolver to be used. May be <code>null</code>.
 * @param aNamespaceContext
 *        Namespace context to be used. May be <code>null</code>.
 * @return The created non-<code>null</code> {@link XPath} object
 */
@Nonnull
public static XPath createNewXPath(@Nonnull final XPathFactory aXPathFactory,
        @Nullable final XPathVariableResolver aVariableResolver,
        @Nullable final XPathFunctionResolver aFunctionResolver,
        @Nullable final NamespaceContext aNamespaceContext) {
    if (aXPathFactory == null)
        throw new NullPointerException("XPathFactory");

    final XPath aXPath = aXPathFactory.newXPath();
    if (aVariableResolver != null)
        aXPath.setXPathVariableResolver(aVariableResolver);
    if (aFunctionResolver != null)
        aXPath.setXPathFunctionResolver(aFunctionResolver);
    if (aNamespaceContext != null)
        aXPath.setNamespaceContext(aNamespaceContext);
    return aXPath;
}

From source file:eu.europeana.uim.sugarcrmclient.internal.helpers.ClientUtils.java

/**
 * @param responseString// w w  w . ja  v a  2 s .co  m
 * @return
 * @throws ParserConfigurationException
 * @throws SAXException
 * @throws IOException
 * @throws XPathExpressionException
 */
public static HashMap<String, HashMap<String, String>> responseFactory(String responseString)
        throws ParserConfigurationException, SAXException, IOException, XPathExpressionException {

    HashMap<String, HashMap<String, String>> returnMap = new HashMap<String, HashMap<String, String>>();

    DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
    documentBuilderFactory.setNamespaceAware(true);
    DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();

    Document document = documentBuilder.parse(new InputSource(new StringReader(responseString)));

    //String messageName = document.getFirstChild().getNodeName();

    XPathFactory factory = XPathFactory.newInstance();
    XPath xpath = factory.newXPath();

    xpath.setNamespaceContext(new SugarCRMNamespaceContext());
    XPathExpression expr = xpath.compile("//ns1:get_entry_listResponse/return/entry_list/item");

    Object result = expr.evaluate(document, XPathConstants.NODESET);
    NodeList nodes = (NodeList) result;

    for (int i = 0; i < nodes.getLength(); i++) {

        NodeList innerNodes = nodes.item(i).getChildNodes();

        String id = innerNodes.item(0).getTextContent();

        HashMap<String, String> elementData = new HashMap<String, String>();

        NodeList infoNodes = innerNodes.item(2).getChildNodes();

        for (int z = 0; z < infoNodes.getLength(); z++) {
            String name = infoNodes.item(z).getFirstChild().getTextContent();
            String value = infoNodes.item(z).getLastChild().getTextContent();

            elementData.put(name, value);
        }
        returnMap.put(id, elementData);
    }
    return returnMap;
}

From source file:se.vgregion.usdservice.USDServiceImpl.java

/**
 * Convenience method./*ww  w .  j  a  va 2 s  .co  m*/
 * <p/>
 * Neither XPathFactory nor XPath are thread safe. Further more XPath is not re-entrant,
 * so a new instance has to be created for every evaluation.
 * The generic marker make this more convenient to use - however QName has to match the expected return type.
 *
 * @param xPath,  the xPath to be evaluated.
 * @param source, the source document to evaluate on.
 * @param qName,  the node type the evaluation returns.
 * @param <T>,    matching return type.
 * @return the evaluated result.
 * @throws XPathExpressionException
 */
private static <T> T evaluate(String xPath, Document source, QName qName) throws XPathExpressionException {
    XPathFactory factory = XPathFactory.newInstance();
    XPath processor = factory.newXPath();
    return (T) processor.evaluate(xPath, source, qName);
}

From source file:edu.virginia.speclab.juxta.author.model.JuxtaXMLParser.java

static public String getIndexBasedXPathForGeneralXPath(String xpathString, String xml) {
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    try {/*w w  w. j ava  2  s  .co  m*/
        factory.setNamespaceAware(false); // ignore the horrible issues of namespacing
        DocumentBuilder builder = factory.newDocumentBuilder();
        Document doc = builder.parse(new InputSource(new StringReader(xml)));
        XPathFactory xpathFactory = XPathFactory.newInstance();
        XPath xpath = xpathFactory.newXPath();
        Node root = doc.getFirstChild();
        XPathExpression expr = xpath.compile(xpathString);
        Node node = (Node) expr.evaluate(doc, XPathConstants.NODE);
        return nodeToSimpleXPath(node, root);
    } catch (SAXException ex) {
    } catch (IOException ex) {
    } catch (XPathExpressionException ex) {
    } catch (ParserConfigurationException ex) {
    }
    return null;
}