Example usage for org.w3c.dom Element getNodeName

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

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Introduction

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

Prototype

public String getNodeName();

Source Link

Document

The name of this node, depending on its type; see the table above.

Usage

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  ww.  j a  va  2 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;
}

From source file:com.espertech.esper.client.ConfigurationParser.java

private static void handleMetricsReporting(Configuration configuration, Element parentElement) {
    String enabled = getRequiredAttribute(parentElement, "enabled");
    boolean isEnabled = Boolean.parseBoolean(enabled);
    configuration.getEngineDefaults().getMetricsReporting().setEnableMetricsReporting(isEnabled);

    String engineInterval = getOptionalAttribute(parentElement, "engine-interval");
    if (engineInterval != null) {
        configuration.getEngineDefaults().getMetricsReporting()
                .setEngineInterval(Long.parseLong(engineInterval));
    }/*  w w  w . j a  v  a2  s .co m*/

    String statementInterval = getOptionalAttribute(parentElement, "statement-interval");
    if (statementInterval != null) {
        configuration.getEngineDefaults().getMetricsReporting()
                .setStatementInterval(Long.parseLong(statementInterval));
    }

    String threading = getOptionalAttribute(parentElement, "threading");
    if (threading != null) {
        configuration.getEngineDefaults().getMetricsReporting().setThreading(Boolean.parseBoolean(threading));
    }

    String jmxEngineMetrics = getOptionalAttribute(parentElement, "jmx-engine-metrics");
    if (jmxEngineMetrics != null) {
        configuration.getEngineDefaults().getMetricsReporting()
                .setJmxEngineMetrics(Boolean.parseBoolean(jmxEngineMetrics));
    }

    DOMElementIterator nodeIterator = new DOMElementIterator(parentElement.getChildNodes());
    while (nodeIterator.hasNext()) {
        Element subElement = nodeIterator.next();
        if (subElement.getNodeName().equals("stmtgroup")) {
            String name = getRequiredAttribute(subElement, "name");
            long interval = Long.parseLong(getRequiredAttribute(subElement, "interval"));

            ConfigurationMetricsReporting.StmtGroupMetrics metrics = new ConfigurationMetricsReporting.StmtGroupMetrics();
            metrics.setInterval(interval);
            configuration.getEngineDefaults().getMetricsReporting().addStmtGroup(name, metrics);

            String defaultInclude = getOptionalAttribute(subElement, "default-include");
            if (defaultInclude != null) {
                metrics.setDefaultInclude(Boolean.parseBoolean(defaultInclude));
            }

            String numStmts = getOptionalAttribute(subElement, "num-stmts");
            if (numStmts != null) {
                metrics.setNumStatements(Integer.parseInt(numStmts));
            }

            String reportInactive = getOptionalAttribute(subElement, "report-inactive");
            if (reportInactive != null) {
                metrics.setReportInactive(Boolean.parseBoolean(reportInactive));
            }

            handleMetricsReportingPatterns(metrics, subElement);
        }
    }
}

From source file:com.sqewd.os.maracache.core.Config.java

/**
 * Load the configuration from the path and file specified.
 *
 * @throws ConfigException/*w  w  w .j ava  2s  . c o m*/
 */
public void load() throws ConfigException {
    try {
        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        DocumentBuilder db = dbf.newDocumentBuilder();
        Document doc = db.parse(filePath);

        //optional, but recommended
        //read this - http://stackoverflow.com/questions/13786607/normalization-in-dom-parsing-with-java-how-does-it-work
        doc.getDocumentElement().normalize();

        XPath xp = XPathFactory.newInstance().newXPath();
        Element root = (Element) xp.compile(configPath).evaluate(doc, XPathConstants.NODE);
        if (root == null) {
            throw new ConfigException("Cannot find specified path in document. [path=" + configPath + "]");
        }

        node = new ConfigPath(root.getNodeName(), null);
        load(node, root);

        state = EObjectState.Available;
    } catch (ParserConfigurationException pse) {
        state = EObjectState.Exception;
        state.setException(pse);
        throw new ConfigException("Error building the configuration document.", pse);
    } catch (IOException ioe) {
        state = EObjectState.Exception;
        state.setException(ioe);
        throw new ConfigException("Error reading configuration file [path=" + filePath + "]", ioe);
    } catch (SAXException se) {
        state = EObjectState.Exception;
        state.setException(se);
        throw new ConfigException("Error parsing document [document=" + filePath + "]", se);
    } catch (XPathExpressionException xpe) {
        state = EObjectState.Exception;
        state.setException(xpe);
        throw new ConfigException("Error parsing specified XPath expression.", xpe);
    }
}

From source file:com.espertech.esper.client.ConfigurationParser.java

private static void handleLegacy(String name, String className, Configuration configuration,
        Element xmldomElement) {//from w  ww.j  a v  a 2  s . c  o  m
    // Class name is required for legacy classes
    if (className == null) {
        throw new ConfigurationException("Required class name not supplied for legacy type definition");
    }

    String accessorStyle = getRequiredAttribute(xmldomElement, "accessor-style");
    String codeGeneration = getRequiredAttribute(xmldomElement, "code-generation");
    String propertyResolution = getRequiredAttribute(xmldomElement, "property-resolution-style");
    String factoryMethod = getOptionalAttribute(xmldomElement, "factory-method");
    String copyMethod = getOptionalAttribute(xmldomElement, "copy-method");
    String startTimestampProp = getOptionalAttribute(xmldomElement, "start-timestamp-property-name");
    String endTimestampProp = getOptionalAttribute(xmldomElement, "end-timestamp-property-name");

    ConfigurationEventTypeLegacy legacyDesc = new ConfigurationEventTypeLegacy();
    if (accessorStyle != null) {
        legacyDesc.setAccessorStyle(
                ConfigurationEventTypeLegacy.AccessorStyle.valueOf(accessorStyle.toUpperCase()));
    }
    if (codeGeneration != null) {
        legacyDesc.setCodeGeneration(
                ConfigurationEventTypeLegacy.CodeGeneration.valueOf(codeGeneration.toUpperCase()));
    }
    if (propertyResolution != null) {
        legacyDesc.setPropertyResolutionStyle(
                Configuration.PropertyResolutionStyle.valueOf(propertyResolution.toUpperCase()));
    }
    legacyDesc.setFactoryMethod(factoryMethod);
    legacyDesc.setCopyMethod(copyMethod);
    legacyDesc.setStartTimestampPropertyName(startTimestampProp);
    legacyDesc.setEndTimestampPropertyName(endTimestampProp);
    configuration.addEventType(name, className, legacyDesc);

    DOMElementIterator propertyNodeIterator = new DOMElementIterator(xmldomElement.getChildNodes());
    while (propertyNodeIterator.hasNext()) {
        Element propertyElement = propertyNodeIterator.next();
        if (propertyElement.getNodeName().equals("method-property")) {
            String nameProperty = getRequiredAttribute(propertyElement, "name");
            String method = getRequiredAttribute(propertyElement, "accessor-method");
            legacyDesc.addMethodProperty(nameProperty, method);
        } else if (propertyElement.getNodeName().equals("field-property")) {
            String nameProperty = getRequiredAttribute(propertyElement, "name");
            String field = getRequiredAttribute(propertyElement, "accessor-field");
            legacyDesc.addFieldProperty(nameProperty, field);
        } else {
            throw new ConfigurationException("Invalid node " + propertyElement.getNodeName()
                    + " encountered while parsing legacy type definition");
        }
    }
}

From source file:com.servoy.extension.install.LibActivationHandler.java

protected void replaceReferencesInJNLP(File jnlp, File libFileToBeRemoved,
        FullLibDependencyDeclaration toActivate) {
    try {//from w  ww. j a  va  2 s  . c  o m
        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        DocumentBuilder db = dbf.newDocumentBuilder();
        db.setErrorHandler(new XMLErrorHandler(jnlp.getName()));

        Document doc = db.parse(jnlp);
        Element root = doc.getDocumentElement();
        root.normalize();

        NodeList list;
        if ("jnlp".equals(root.getNodeName())) //$NON-NLS-1$
        {
            list = root.getElementsByTagName("resources"); //$NON-NLS-1$
            if (list != null && list.getLength() == 1 && list.item(0).getNodeType() == Node.ELEMENT_NODE) {
                File appServerDir = new File(installDir, APP_SERVER_DIR);
                Element resourcesNode = (Element) list.item(0);
                boolean replaced1 = findAndReplaceReferences(resourcesNode, "jar", appServerDir, //$NON-NLS-1$
                        libFileToBeRemoved, toActivate);
                boolean replaced2 = findAndReplaceReferences(resourcesNode, "nativelib", appServerDir, //$NON-NLS-1$
                        libFileToBeRemoved, toActivate);

                if (replaced1 || replaced2) {
                    // save back the jnlp file
                    try {
                        writeBackXML(doc, jnlp, doc.getXmlEncoding());
                    } catch (Exception e) {
                        messages.addError("Cannot write back jnlp file (when deactivating lib): " + jnlp); //$NON-NLS-1$ 
                        Debug.error(e);
                    }
                }
            }
        }
    } catch (ParserConfigurationException e) {
        String msg = "Cannot parse jnlp '" + jnlp.getName() + "'."; //$NON-NLS-1$ //$NON-NLS-2$
        Debug.log(msg, e);
    } catch (SAXException e) {
        String msg = "Cannot parse jnlp '" + jnlp.getName() + "'."; //$NON-NLS-1$ //$NON-NLS-2$
        Debug.log(msg, e);
    } catch (IOException e) {
        String msg = "Cannot parse jnlp '" + jnlp.getName() + "'."; //$NON-NLS-1$ //$NON-NLS-2$
        Debug.log(msg, e);
    } catch (FactoryConfigurationError e) {
        String msg = "Cannot parse jnlp '" + jnlp.getName() + "'. Please report this problem to Servoy."; //$NON-NLS-1$ //$NON-NLS-2$
        Debug.error(msg, e);
    }
}

From source file:org.finra.jtaf.core.parsing.CommandLibraryParser.java

private final InvocationTarget processInvocationTarget(Element elem, MessageCollector mc)
        throws ParsingException {
    InvocationTarget retval = null;/* w w w . j a  va 2  s.  c  om*/
    final String name = elem.getNodeName().toLowerCase();
    if (name.equals("command")) {
        retval = processCommand(elem, mc);
    } else if (name.equals("function")) {
        retval = processFunction(elem, mc);
    } else {
        throw new UnexpectedElementException(elem);
    }

    final Element usage = ParserHelper.getOptionalElement(elem, "usage");
    if (usage != null) {
        retval.setUsage(usage.getTextContent());
    }

    final Element requiredParameters = ParserHelper.getOptionalElement(elem, "requiredParameters");
    if (requiredParameters != null) {
        for (Element child : ParserHelper.getChildren(requiredParameters)) {
            AttributeHelper ah = new AttributeHelper(child);
            retval.addRequiredParameter(ah.getRequiredString("name"));
        }
    }

    final Element optionalParameters = ParserHelper.getOptionalElement(elem, "optionalParameters");
    if (optionalParameters != null) {
        for (Element child : ParserHelper.getChildren(optionalParameters)) {
            AttributeHelper ah = new AttributeHelper(child);
            retval.addOptionalParameter(ah.getRequiredString("name"));
        }
    }

    final Element produces = ParserHelper.getOptionalElement(elem, "produces");
    if (produces != null) {
        for (Element child : ParserHelper.getChildren(produces)) {
            AttributeHelper ah = new AttributeHelper(child);
            retval.addProduction(ah.getRequiredString("name"));
        }
    }

    return retval;
}

From source file:com.espertech.esper.client.ConfigurationParser.java

/**
 * Parse the W3C DOM document./*from   www. j a v  a  2  s .  c  o m*/
 * @param configuration is the configuration object to populate
 * @param doc to parse
 * @throws EPException to indicate parse errors
 */
protected static void doConfigure(Configuration configuration, Document doc) throws EPException {
    Element root = doc.getDocumentElement();

    DOMElementIterator eventTypeNodeIterator = new DOMElementIterator(root.getChildNodes());
    while (eventTypeNodeIterator.hasNext()) {
        Element element = eventTypeNodeIterator.next();
        String nodeName = element.getNodeName();
        if (nodeName.equals("event-type-auto-name")) {
            handleEventTypeAutoNames(configuration, element);
        } else if (nodeName.equals("event-type")) {
            handleEventTypes(configuration, element);
        } else if (nodeName.equals("auto-import")) {
            handleAutoImports(configuration, element);
        } else if (nodeName.equals("method-reference")) {
            handleMethodReference(configuration, element);
        } else if (nodeName.equals("database-reference")) {
            handleDatabaseRefs(configuration, element);
        } else if (nodeName.equals("plugin-view")) {
            handlePlugInView(configuration, element);
        } else if (nodeName.equals("plugin-virtualdw")) {
            handlePlugInVirtualDW(configuration, element);
        } else if (nodeName.equals("plugin-aggregation-function")) {
            handlePlugInAggregation(configuration, element);
        } else if (nodeName.equals("plugin-aggregation-multifunction")) {
            handlePlugInMultiFunctionAggregation(configuration, element);
        } else if (nodeName.equals("plugin-singlerow-function")) {
            handlePlugInSingleRow(configuration, element);
        } else if (nodeName.equals("plugin-pattern-guard")) {
            handlePlugInPatternGuard(configuration, element);
        } else if (nodeName.equals("plugin-pattern-observer")) {
            handlePlugInPatternObserver(configuration, element);
        } else if (nodeName.equals("variable")) {
            handleVariable(configuration, element);
        } else if (nodeName.equals("plugin-loader")) {
            handlePluginLoaders(configuration, element);
        } else if (nodeName.equals("engine-settings")) {
            handleEngineSettings(configuration, element);
        } else if (nodeName.equals("plugin-event-representation")) {
            handlePlugInEventRepresentation(configuration, element);
        } else if (nodeName.equals("plugin-event-type")) {
            handlePlugInEventType(configuration, element);
        } else if (nodeName.equals("plugin-event-type-name-resolution")) {
            handlePlugIneventTypeNameResolution(configuration, element);
        } else if (nodeName.equals("revision-event-type")) {
            handleRevisionEventType(configuration, element);
        } else if (nodeName.equals("variant-stream")) {
            handleVariantStream(configuration, element);
        }
    }
}

From source file:MSUmpire.SearchResultParser.PepXMLParseHandler.java

@Override
public void handle(Element node) throws Exception {
    switch (node.getNodeName()) {
    case "spectrum_query": {
        ParseSpectrumNode(node);/*from   w  w  w  .j  ava  2  s  . c  o  m*/
        break;
    }
    case "search_summary": {
        ParseSearchSummary(node);
        break;
    }
    }
}

From source file:com.bstek.dorado.config.xml.DispatchableXmlParser.java

private boolean isTagElement(Element element) {
    String nodeName = element.getNodeName();
    return (XmlConstants.PROPERTY.equals(nodeName) || XmlConstants.GROUP_START.equals(nodeName)
            || XmlConstants.GROUP_END.equals(nodeName) || XmlConstants.IMPORT.equals(nodeName)
            || XmlConstants.PLACE_HOLDER.equals(nodeName) || XmlConstants.PLACE_HOLDER_START.equals(nodeName)
            || XmlConstants.PLACE_HOLDER_END.equals(nodeName));
}

From source file:cc.siara.csv_ml.ParsedObject.java

/**
 * Performas any pending activity against an element to finalize it. In this
 * case, it adds any pending attributes needing namespace mapping.
 * //from   w w  w  .ja  v a2 s  .c o  m
 * Also if the node has a namespace attached, it recreates the node with
 * specific URI.
 */
public void finalizeElement() {
    // Add all remaining attributes
    for (String col_name : pendingAttributes.keySet()) {
        String value = pendingAttributes.get(col_name);
        int cIdx = col_name.indexOf(':');
        String ns = col_name.substring(0, cIdx);
        String nsURI = nsMap.get(ns);
        if (nsURI == null)
            nsURI = generalNSURI;
        Attr attr = doc.createAttributeNS(nsURI, col_name.substring(cIdx + 1));
        attr.setPrefix(ns);
        attr.setValue(value);
        ((Element) cur_element).setAttributeNodeNS(attr);
    }
    // If the element had a namespace prefix, it has to be recreated.
    if (!currentElementNS.equals("") && !doc.getDocumentElement().equals(cur_element)) {
        Node parent = cur_element.getParentNode();
        Element cur_ele = (Element) parent.removeChild(cur_element);
        String node_name = cur_ele.getNodeName();
        String nsURI = nsMap.get(currentElementNS);
        if (nsURI == null)
            nsURI = generalNSURI;
        Element new_node = doc.createElementNS(nsURI, currentElementNS + ":" + node_name);
        parent.appendChild(new_node);
        // Add all attributes
        NamedNodeMap attrs = cur_ele.getAttributes();
        while (attrs.getLength() > 0) {
            Attr attr = (Attr) attrs.item(0);
            cur_ele.removeAttributeNode(attr);
            nsURI = attr.getNamespaceURI();
            new_node.setAttributeNodeNS(attr);
        }
        // Add all CData sections
        NodeList childNodes = cur_ele.getChildNodes();
        for (int i = 0; i < childNodes.getLength(); i++) {
            Node node = childNodes.item(i);
            if (node.getNodeType() == Node.CDATA_SECTION_NODE)
                new_node.appendChild(node);
        }
        cur_element = new_node;
    }
    pendingAttributes = new Hashtable<String, String>();
}