Example usage for org.w3c.dom NamedNodeMap getNamedItem

List of usage examples for org.w3c.dom NamedNodeMap getNamedItem

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Introduction

In this page you can find the example usage for org.w3c.dom NamedNodeMap getNamedItem.

Prototype

public Node getNamedItem(String name);

Source Link

Document

Retrieves a node specified by name.

Usage

From source file:org.bibsonomy.scraper.generic.UnAPIScraper.java

/** Extracts the "href" attribute from "link" tags whose "rel" attribute equals "unapi-server".
 * /*  w  w w  .  j ava 2s . co m*/
 * @param document
 * @return The href attribute of the proper link-tag or <code>null</code> if it could not be found.
 */
private String getApiHref(final Document document) {
    final NodeList elementsByTagName = document.getElementsByTagName("link");
    for (int i = 0; i < elementsByTagName.getLength(); i++) {
        final Node node = elementsByTagName.item(i);
        final NamedNodeMap attributes = node.getAttributes();
        final Node relAttribute = attributes.getNamedItem("rel");
        if (relAttribute != null && "unapi-server".equals(relAttribute.getNodeValue())) {
            /*
             * link to server found -> extract href
             */
            final Node href = attributes.getNamedItem("href");
            if (href != null) {
                return href.getNodeValue();
            }
        }
    }
    return null;
}

From source file:org.bibsonomy.scraper.generic.UnAPIScraper.java

/** Extracts the "title" attribute from the first (!) "abbr" tag whose "class" attribute equals "unapi-id".
 * // w  ww. ja  v a  2  s  . c  o m
 * @param document
 * @return The "title" attribute of the proper abbr-tag or <code>null</code> if it could not be found.
 * 
 */
private String getRecordIdentifier(final Document document) {
    /*
     * debug
     */
    final NodeList abbrTags = document.getElementsByTagName("abbr");
    log.debug("found " + abbrTags.getLength() + " abbr nodes.");
    for (int i = 0; i < abbrTags.getLength(); i++) {
        final Node node = abbrTags.item(i);
        final NamedNodeMap attributes = node.getAttributes();
        final Node classAttribute = attributes.getNamedItem("class");
        if (classAttribute != null && "unapi-id".equals(classAttribute.getNodeValue())) {
            /*
             * record found -> extract id
             */
            final Node title = attributes.getNamedItem("title");
            if (title != null) {
                return title.getNodeValue();
            }
        }
    }
    return null;

}

From source file:org.broad.igv.cbio.GeneNetwork.java

/**
 * Load graphml data from provide path./*from  w w w .  j  ava2  s  .c o  m*/
 *
 * @param path
 * @throws IOException If something went wrong loading data.
 *                     Note we wrap other exception types in this.
 */
public int loadNetwork(String path) throws IOException {
    String error = null;
    int numNodes = -1;
    try {
        InputStream cbioStream = ParsingUtils.openInputStreamGZ(new ResourceLocator(path));
        this.sourcePath = path;
        Document document = Utilities.createDOMDocumentFromXmlStream(cbioStream);

        //Cache the file
        if (HttpUtils.isRemoteURL(path)) {
            File cacheFile = getCachedFile(path);
            try {
                this.exportDocument(document, cacheFile.getAbsolutePath());
            } catch (IOException e) {
                //No biggy, we just don't cache the file
                log.error("Error caching file: " + e);
                cacheFile.delete();
            }
            cacheFile.deleteOnExit();
        }

        this.origDocument = document;

        //Read schema from top and save it
        addToSchema(document.getElementsByTagName("key"));

        graphAttr = document.getElementsByTagName("graph").item(0).getAttributes();

        NodeList nodes = document.getElementsByTagName(NODE_TAG);
        //Generate the graph itself. First add the nodes, then the edges
        int docNodes = nodes.getLength();
        nodeTable = new HashMap<String, Node>(docNodes);
        for (int nn = 0; nn < docNodes; nn++) {
            Node node = nodes.item(nn);
            String label = node.getAttributes().getNamedItem("id").getTextContent();
            nodeTable.put(label, node);
            this.addVertex(node);
        }

        NodeList edges = document.getElementsByTagName(EDGE_TAG);
        int docEdges = edges.getLength();
        for (int ee = 0; ee < docEdges; ee++) {
            Node edge = edges.item(ee);
            NamedNodeMap attrs = edge.getAttributes();
            String source = attrs.getNamedItem("source").getTextContent();
            String target = attrs.getNamedItem("target").getTextContent();
            this.addEdge(nodeTable.get(source), nodeTable.get(target), edge);
        }

        numNodes = this.vertexSet().size();
    } catch (ParserConfigurationException e) {
        throw new IOException(e.getMessage());
    } catch (SAXException e) {
        throw new IOException(e.getMessage());
    }
    return numNodes;
}

From source file:org.broad.igv.cbio.GeneNetwork.java

/**
 * The the value of a child node by the key.
 * If there are multiple matches, the first is returned.
 * Search is not recursive.//from   www.j  a  v a  2s  . c  om
 * <p/>
 * <p/>
 * Example: Say that node has the following XML
 * "&lt;node id="3725"/&gt;
 * &lt;data key="label"&gt;JUN&lt;/data&gt;
 * &lt;data key="type"&gt;Protein&lt;/data&gt;
 * &lt;data key="RELATIONSHIP_XREF"&gt;HGNC:JUN;Entrez Gene:3725&lt;/data&gt;
 * &lt;data key="IN_QUERY"&gt;false&lt;/data&gt;
 * &lt;/node&gt;"
 * So getNodeKeyData(node, "key", "label") returns "JUN".
 *
 * @param node
 * @param attrName
 * @param attrValue
 * @return String value of key found. null if not found
 */
public static String getNodeAttrValue(Node node, String attrName, String attrValue) {
    NodeList elements = node.getChildNodes();
    for (int ee = 0; ee < elements.getLength(); ee++) {
        Node el = elements.item(ee);
        try {
            NamedNodeMap map = el.getAttributes();
            Node label = map.getNamedItem(attrName);
            String textContent = label.getTextContent();
            if (textContent.compareToIgnoreCase(attrValue) == 0) {
                return el.getTextContent();
            }
        } catch (NullPointerException e) {
            //In general these get hit due to newlines and such
            //We simply skip
            continue;
        }
    }
    return null;
}

From source file:org.broad.igv.cbio.GeneNetworkTest.java

@Test
public void testFilter() throws Exception {
    Predicate tPred = new Predicate() {

        public boolean evaluate(Object object) {
            Node node = (Node) object;
            NamedNodeMap map = node.getAttributes();
            if (map == null) {
                return false;
            }//from www . j  a  v  a2s .  c o  m
            int id = Integer.parseInt(map.getNamedItem("id").getTextContent());
            return id % 2 == 0;
        }
    };

    network.loadNetwork(testpath);
    boolean removed = network.filterNodes(tPred) > 0;
    assertTrue(removed);

    //Test that we can get the filtered edges of a node
    Set<Node> keptNodes = new HashSet<Node>();
    for (Node n : network.vertexSetFiltered()) {
        for (Node e : network.edgesOfFiltered(n)) {
            keptNodes.add(network.getEdgeSource(e));
            keptNodes.add(network.getEdgeTarget(e));
        }
    }
    assertEquals(network.vertexSetFiltered().size(), keptNodes.size());
    assertTrue("Soft filtering not performed", keptNodes.size() < network.vertexSet().size());
}

From source file:org.broad.igv.dev.db.SQLCodecSource.java

/**
 * Retrieve a reader from the XML profile located at {@code profilePath}.
 * TODO If {@code tableName == null}, the user is prompted to choose a table from the list
 *
 * @param profilePath/*from  w  ww  . j  a  v a  2s . c o  m*/
 * @param tableName
 * @return
 */
public static List<SQLCodecSource> getFromProfile(String profilePath, String tableName) {
    ResourceLocator dbLocator = DBManager.getStoredConnection(profilePath);
    InputStream profileStream = null;
    try {
        profileStream = new FileInputStream(profilePath);
        Document document = Utilities.createDOMDocumentFromXmlStream(profileStream);
        NodeList nodes = document.getElementsByTagName("table");
        List<SQLCodecSource> sources = new ArrayList<SQLCodecSource>(nodes.getLength());

        for (int tnum = 0; tnum < nodes.getLength(); tnum++) {
            Node n = nodes.item(tnum);
            NamedNodeMap attr = n.getAttributes();
            String tabName = attr.getNamedItem("name").getTextContent();
            if (tableName == null || tableName.equals(tabName)) {

                String chromoColName = attr.getNamedItem("chromoColName").getTextContent();
                String posStartColName = attr.getNamedItem("posStartColName").getTextContent();
                String posEndColName = attr.getNamedItem("posEndColName").getTextContent();
                String format = attr.getNamedItem("format").getTextContent();
                String startColString = Utilities.getNullSafe(attr, "startColIndex");
                String endColString = Utilities.getNullSafe(attr, "endColIndex");
                String binColName = Utilities.getNullSafe(attr, "binColName");
                int startColIndex = startColString != null ? Integer.parseInt(startColString) : 1;
                int endColIndex = endColString != null ? Integer.parseInt(endColString) : Integer.MAX_VALUE;
                AsciiFeatureCodec codec = CodecFactory.getCodec("." + format,
                        GenomeManager.getInstance().getCurrentGenome());
                SQLCodecSource source = new SQLCodecSource(dbLocator, codec, tabName, chromoColName,
                        posStartColName, posEndColName, startColIndex, endColIndex);
                source.binColName = binColName;
                sources.add(source);
            }
        }

        return sources;

    } catch (Exception e) {
        e.printStackTrace();
        return null;
    } finally {
        try {
            if (profileStream != null)
                profileStream.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

}

From source file:org.broad.igv.util.Utilities.java

/**
 * Get the text content of the attribute {@code key} from
 * the set {@code attr}. If that attribute is not present, null is returned
 *
 * @param attr//w  w w. jav  a 2s. c o  m
 * @param key
 * @return
 */
public static String getNullSafe(NamedNodeMap attr, String key) {
    Node node = attr.getNamedItem(key);
    return node != null ? node.getTextContent() : null;
}

From source file:org.deegree.framework.xml.XMLFragment.java

/**
 * Determines the namespace <code>URI</code>s and the bound schema <code>URL</code>s from the 'xsi:schemaLocation'
 * attribute of the document element.//from w w  w  . j a v a 2 s .  c  o  m
 * 
 * @return keys are URIs (namespaces), values are URLs (schema locations)
 * @throws XMLParsingException
 */
public Map<URI, URL> getAttachedSchemas() throws XMLParsingException {

    Map<URI, URL> schemaMap = new HashMap<URI, URL>();

    NamedNodeMap attrMap = rootElement.getAttributes();
    Node schemaLocationAttr = attrMap.getNamedItem("xsi:schemaLocation");
    if (schemaLocationAttr == null) {
        return schemaMap;
    }

    String target = schemaLocationAttr.getNodeValue();
    StringTokenizer tokenizer = new StringTokenizer(target);

    while (tokenizer.hasMoreTokens()) {
        URI nsURI = null;
        String token = tokenizer.nextToken();
        try {
            nsURI = new URI(token);
        } catch (URISyntaxException e) {
            String msg = "Invalid 'xsi:schemaLocation' attribute: namespace " + token + "' is not a valid URI.";
            LOG.logError(msg);
            throw new XMLParsingException(msg);
        }

        URL schemaURL = null;
        try {
            token = tokenizer.nextToken();
            schemaURL = resolve(token);
        } catch (NoSuchElementException e) {
            String msg = "Invalid 'xsi:schemaLocation' attribute: namespace '" + nsURI
                    + "' is missing a schema URL.";
            LOG.logError(msg);
            throw new XMLParsingException(msg);
        } catch (MalformedURLException ex) {
            String msg = "Invalid 'xsi:schemaLocation' attribute: '" + token + "' for namespace '" + nsURI
                    + "' could not be parsed as URL.";
            throw new XMLParsingException(msg);
        }
        schemaMap.put(nsURI, schemaURL);
    }
    return schemaMap;
}

From source file:org.deri.any23.extractor.html.HCardExtractor.java

private void fixIncludes(HTMLDocument document, Node node) {
    NamedNodeMap attributes = node.getAttributes();
    // header case test 32
    if ("TD".equals(node.getNodeName()) && (null != attributes.getNamedItem("headers"))) {
        String id = attributes.getNamedItem("headers").getNodeValue();
        Node header = document.findNodeById(id);
        if (null != header) {
            node.appendChild(header.cloneNode(true));
            attributes.removeNamedItem("headers");
        }//from   www .  jav  a2  s.  c  o  m
    }
    // include pattern, test 31

    for (Node current : document.findAll("//*[@class]")) {
        if (!DomUtils.hasClassName(current, "include"))
            continue;
        // we have to remove the field soon to avoid infinite loops
        // no null check, we know it's there or we won't be in the loop
        current.getAttributes().removeNamedItem("class");
        ArrayList<TextField> res = new ArrayList<TextField>();
        HTMLDocument.readUrlField(res, current);
        TextField id = res.get(0);
        if (null == id)
            continue;
        id = new TextField(StringUtils.substringAfter(id.value(), "#"), id.source());
        Node included = document.findNodeById(id.value());
        if (null == included)
            continue;
        current.appendChild(included.cloneNode(true));
    }
}

From source file:org.dita.dost.util.DitaUtil.java

private static String getFileNameFromMap(String ditaMapPath) {

    StringBuffer fileName = new StringBuffer();

    try {//from   w  ww  .  j  a v a 2s. c om

        FileInputStream ditaMapStream;

        ditaMapStream = new FileInputStream(ditaMapPath);

        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();

        factory.setNamespaceAware(true);

        factory.setValidating(false);

        factory.setFeature("http://xml.org/sax/features/namespaces", false);
        factory.setFeature("http://xml.org/sax/features/validation", false);
        factory.setFeature("http://apache.org/xml/features/nonvalidating/load-dtd-grammar", false);
        factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);

        DocumentBuilder builder;

        Document doc = null;

        XPathExpression expr = null;

        builder = factory.newDocumentBuilder();

        doc = builder.parse(new InputSource(ditaMapStream));

        XPathFactory xFactory = XPathFactory.newInstance();

        XPath xpath = xFactory.newXPath();

        expr = xpath.compile("//bookmap/bookmeta/prodinfo/prodname");

        Node prodNameNode = (Node) expr.evaluate(doc, XPathConstants.NODE);

        if (prodNameNode != null) {

            fileName.append(prodNameNode.getTextContent());

            expr = xpath.compile("//bookmap/bookmeta/prodinfo/vrmlist");

            Element vrmlistNode = (Element) expr.evaluate(doc, XPathConstants.NODE);

            if (vrmlistNode != null) {
                NodeList versions = vrmlistNode.getElementsByTagName("vrm");
                if (versions.getLength() > 0) {

                    NamedNodeMap versionAttributes = versions.item(0).getAttributes();
                    Attr releaseAttr = (Attr) versionAttributes.getNamedItem("release");

                    if (releaseAttr != null) {
                        fileName.append(String.format("_%s", releaseAttr.getValue()));
                    }

                    Attr versionAttr = (Attr) versionAttributes.getNamedItem("version");

                    if (versionAttr != null) {
                        fileName.append(String.format("_%s", versionAttr.getValue()));
                    }
                }
            }
        } else {
            expr = xpath.compile("/bookmap");
            prodNameNode = (Node) expr.evaluate(doc, XPathConstants.NODE);
            if (prodNameNode != null) {
                Node node = prodNameNode.getAttributes().getNamedItem("id");
                if (node != null) {
                    fileName.append(node.getTextContent());
                }
            } else {
                expr = xpath.compile("/map");
                prodNameNode = (Node) expr.evaluate(doc, XPathConstants.NODE);
                if (prodNameNode != null) {
                    Node node = prodNameNode.getAttributes().getNamedItem("title");
                    if (node != null) {
                        fileName.append(node.getTextContent());
                    }
                }
            }
        }
    } catch (FileNotFoundException e) {
    } catch (ParserConfigurationException e) {
    } catch (SAXException e) {
    } catch (IOException e) {
    } catch (XPathExpressionException e) {
    }
    return fileName.toString();
}