Example usage for org.dom4j Element attributeValue

List of usage examples for org.dom4j Element attributeValue

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Introduction

In this page you can find the example usage for org.dom4j Element attributeValue.

Prototype

String attributeValue(QName qName);

Source Link

Document

This returns the attribute value for the attribute with the given fully qualified name or null if there is no such attribute or the empty string if the attribute value is empty.

Usage

From source file:cc.warlock.rcp.stormfront.StormFrontGameViewConfiguration.java

License:Open Source License

public void parseElement(Element element) {
    profileViewMappings.put(element.attributeValue("viewId"), element.attributeValue("profileId"));
}

From source file:ch.epfl.codimsd.qep.QEPFactory.java

License:Open Source License

/**
 * Build a hashtable containing operator opNode structures, according to what is defined
 * in the query execution plan./* ww w .  jav a2s.  c o  m*/
 * 
 * @param document dom4j document of the QEP.
 * @return the opnode hashtable.
 * 
 * @throws QEPInitializationException
 */
private static Hashtable<String, OpNode> buildOpNodeTable(Document document) throws QEPInitializationException {

    Hashtable<String, OpNode> operatorList = new Hashtable<String, OpNode>();

    /*List listMod = document.selectNodes( "//qep:Module" );
    Element modElement = (Element)listMod;
    String[] stringType = modElement.attributeValue("type").split(",");
    int numberOfIterations = Integer.parseInt(modElement.attributeValue("numberOfIterations"));
    */
    List list = document.selectNodes("//op:Operator");
    Iterator itt = list.iterator();

    while (itt.hasNext()) {

        Element opElement = (Element) itt.next();

        // Get operator ID from xml QEP
        int opID = Integer.parseInt(opElement.attributeValue("id"));

        // Build producers from xml QEP
        String[] stringProducers = opElement.attributeValue("prod").split(",");
        int[] producers = new int[stringProducers.length];

        for (int i = 0; i < stringProducers.length; i++)
            producers[i] = Integer.parseInt(stringProducers[i]);

        // Get operator type
        String type = opElement.attributeValue("type");

        // Get parallelizable information
        String parallelAtt = opElement.attributeValue("parallelizable");
        boolean parallelizable = false;
        if (parallelAtt != null) {
            if (parallelAtt.equalsIgnoreCase("true"))
                parallelizable = true;
        }

        // Get operator name from xml QEP
        Iterator opItt = opElement.elementIterator();
        Node xmlOpNode = (Node) opItt.next();
        String opName = xmlOpNode.getText();

        // Build operator parameters
        int i = 0;
        String paramString = "";
        String[] params = null;

        if (opItt.hasNext()) {

            Element parameterList = (Element) opItt.next();
            Iterator paramItt = parameterList.elementIterator();

            while (paramItt.hasNext()) {

                Node parameter = (Node) paramItt.next();
                paramString = paramString + parameter.getText() + ";";
                i++;
            }

            params = new String[i];
            params = paramString.split(";");
        }

        // Build operator timeStamp
        long idTimeStamp = System.currentTimeMillis();

        // Build OpNode object for this operator
        OpNode opNode = new OpNode(opID, opName, producers, params, idTimeStamp + "", type, parallelizable);

        // Build DataSources if necessary
        if (opNode.getType() != null) {

            if (opNode.getType().equalsIgnoreCase("Scan")) {

                // Write the number of tuples in the BlackBoard as specified in the QEP
                // This operation is not done in remote nodes as G2N has already been called
                String numberOfTuples = opElement.attributeValue(Constants.QEP_SCAN_NUMBER_TUPLES);

                // In remote QEP this parameter is null, so we dont write again the field numberOfTuples
                // used in the DiscoveryOptimizer when it calls G2N
                if (numberOfTuples != null) {

                    if (!numberOfTuples.equalsIgnoreCase("?")) {

                        BlackBoard bl = BlackBoard.getBlackBoard();
                        bl.put(Constants.QEP_SCAN_NUMBER_TUPLES, numberOfTuples);
                    }
                }

                try {
                    DataSourceManager dsManager = DataSourceManager.getDataSourceManager();
                    dsManager.createDataSources(opNode);

                } catch (Exception ex) {
                    throw new QEPInitializationException(
                            "Error creating the " + "datasource : " + ex.getMessage());
                }
            }
        }

        // Put OpNode in the QEP
        operatorList.put(opID + "", opNode);
    }

    return operatorList;
}

From source file:ch.javasoft.metabolic.compress.config.MetabolicCompressionConfig.java

License:BSD License

/**
 * Returns the preprocess-duplicate-genes flag, or false if no such flag
 * is configured//from w w  w.j a v  a 2  s .  c o  m
 * 
 * @return   the preprocess-duplicate-genes flag
 */
public boolean getPreprocessDuplicateGenes() {
    Element el = mRoot.element(XmlElement.preprocess_duplicate_genes.getXmlName());
    return el == null ? false : Boolean.parseBoolean(el.attributeValue(XmlAttribute.value.getXmlName()));
}

From source file:ch.javasoft.metabolic.compress.config.MetabolicCompressionConfig.java

License:BSD License

/**
 * Returns the compression methods derived from the xml configuration, or 
 * {@link CompressionMethod#NONE} if no methods are specified.
 * /*from   w  w  w  . jav  a 2 s.c om*/
 * @return   the compression methods   
 * @throws XmlConfigException      if a method cannot be parsed 
 */
public CompressionMethod[] getCompressionMethods() throws XmlConfigException {
    Element elMethods = mRoot.element(XmlElement.compression_methods.getXmlName());
    if (elMethods == null)
        return CompressionMethod.NONE;
    Iterator it = elMethods.elementIterator(XmlElement.method.getXmlName());
    List<CompressionMethod> cmpMethods = new ArrayList<CompressionMethod>();
    while (it.hasNext()) {
        Element elMethod = (Element) it.next();
        String methodName = elMethod.attributeValue(XmlAttribute.name.getXmlName());
        String strOn = elMethod.attributeValue(XmlAttribute.value.getXmlName());
        boolean on = strOn == null ? true : Boolean.parseBoolean(strOn);
        if (on) {
            try {
                cmpMethods.add(CompressionMethod.valueOf(methodName));
            } catch (Exception ex) {
                throw new XmlConfigException("invalid compression method: " + methodName, elMethod);
            }
        }
    }
    CompressionMethod[] res = new CompressionMethod[cmpMethods.size()];
    return cmpMethods.toArray(res);
}

From source file:ch.javasoft.metabolic.efm.config.DistributedConfig.java

License:BSD License

/**
 * Constructor for <code>DistributedConfig</code> with xml configuration.
 * The configuration element looks like this:
 * <pre>/*from   w  ww. jav a  2 s .com*/
 <distribute partition="65536"><!--use power of 4-->
    <nodes vmargs = "-Xmx2500M" level="OFF">
       <node name="node01.cluster.lan" vmargs="-Xmx1G" level="INFO"/>
       <node name="node02.cluster.lan"/>
       <node name="node03.cluster.lan"/>
       <node name="node04.cluster.lan"/>
    </nodes>
    <command value="/usr/bin/rsh [nodename] cd [workdir] ; /usr/bin/java [vmargs] -cp [classpath] [class] [args]"/>
 </distribute>
 * </pre>
 * @param elDistribute         the <tt>distribute</tt> xml element
 * @throws XmlConfigException   if an xml configuration exception occurs,
 *                         for instance due to invalid xml structure
 */
public DistributedConfig(Element elDistribute) throws XmlConfigException {
    final Element elNodes = XmlUtil.getRequiredSingleChildElement(elDistribute, XmlElement.nodes);
    final Element elCommand = XmlUtil.getRequiredSingleChildElement(elDistribute, XmlElement.command);
    final String sPartition = XmlUtil.getRequiredAttributeValue(elDistribute, XmlAttribute.partition);
    final String sThreshold = XmlUtil.getOptionalAttributeValue(elDistribute, XmlAttribute.candidate_threshold,
            "0");

    final List<String> nodeNames = new ArrayList<String>();
    final List<String> vmArgs = new ArrayList<String>();
    final List<String> logLevels = new ArrayList<String>();

    @SuppressWarnings("unchecked")
    final Iterator<Element> nodeIt = elNodes.elementIterator(XmlElement.node.getXmlName());
    while (nodeIt.hasNext()) {
        final Element elNode = nodeIt.next();
        nodeNames.add(XmlUtil.getRequiredAttributeValue(elNode, XmlAttribute.name));
        //vmargs
        String vmargs = elNode.attributeValue(XmlAttribute.vmargs.getXmlName());
        if (vmargs == null)
            vmargs = elNodes.attributeValue(XmlAttribute.vmargs.getXmlName());
        vmArgs.add(vmargs);
        //log level
        String logLevel = elNode.attributeValue(XmlAttribute.level.getXmlName());
        if (logLevel == null)
            logLevel = elNodes.attributeValue(XmlAttribute.level.getXmlName());
        if (logLevel == null)
            logLevel = Level.INFO.getName();
        logLevels.add(logLevel);
    }
    this.nodeNames = Collections.unmodifiableList(nodeNames);
    this.vmArgs = Collections.unmodifiableList(vmArgs);
    this.logLevels = Collections.unmodifiableList(logLevels);
    this.command = XmlUtil.getRequiredAttributeValue(elCommand, XmlAttribute.value);
    try {
        this.partition = Integer.parseInt(sPartition);
    } catch (Exception e) {
        throw new XmlConfigException(
                "cannot parse distribute attribute 'partitions': " + sPartition + ", e=" + e, elDistribute, e);
    }
    try {
        this.candidateThreashold = Long.parseLong(sThreshold);
    } catch (Exception e) {
        throw new XmlConfigException(
                "cannot parse distribute attribute 'candidate-threshold': " + sThreshold + ", e=" + e,
                elDistribute, e);
    }
    //check partition, must be power of 4
    int cur = 1;
    while (partition / cur > 1) {
        cur <<= 2;// *= 4
    }
    if (partition != cur) {
        throw new IllegalArgumentException("distributed partition must be a power of 4, but is " + partition);
    }
}

From source file:ch.javasoft.metabolic.generate.ConfiguredGenerator.java

License:BSD License

public static void generate(Element metabolicParseElement, MetabolicNetwork net)
        throws XmlConfigException, IOException {
    XmlUtil.checkExpectedElementName(metabolicParseElement, XmlElements.metabolic_generate);
    Element parseElement = XmlUtil.getRequiredSingleChildElement(metabolicParseElement, XmlElements.generate);
    String type = parseElement.attributeValue(XmlAttributes.type.getXmlName());
    GenerateType gType = GenerateType.find(type);
    if (gType == null) {
        throw new XmlConfigException("unknown generate type '" + type + "'", parseElement);
    }//from w  w  w .j ava 2s. co m
    switch (gType) {
    case sbml:
        generateSbml(parseElement, net);
        return;
    case matlab:
        generateMatlab(parseElement, net);
        return;
    default:
        //should not happen
        throw new XmlConfigException("internal error: unknown parse type " + gType, parseElement);
    }
}

From source file:ch.javasoft.metabolic.parse.ConfiguredParser.java

License:BSD License

public static MetabolicNetwork parse(Element metabolicParseElement) throws XmlConfigException, IOException {
    XmlUtil.checkExpectedElementName(metabolicParseElement, XmlElements.metabolic_parse);
    Element parseElement = XmlUtil.getRequiredSingleChildElement(metabolicParseElement, XmlElements.parse);
    String type = parseElement.attributeValue(XmlAttributes.type.getXmlName());
    ParseType pType = ParseType.find(type);
    if (pType == null) {
        throw new XmlConfigException("unknown parse type '" + type + "'", parseElement);
    }//  w w w.j a  va2s  .c om
    switch (pType) {
    case flux_analyzer:
        return parseFluxAnalyzer(parseElement);
    case reaction_list:
        return parseReactionList(parseElement);
    case reaction_excel:
        return parseReactionExcel(parseElement);
    case stoichiometry:
        return parseStoichiometry(parseElement);
    case sbml:
        return parseSbml(parseElement);
    case junit:
        return parseJUnit(parseElement);
    default:
        //should not happen
        throw new XmlConfigException("internal error: unknown parse type " + pType, parseElement);
    }
}

From source file:ch.javasoft.metabolic.parse.ConfiguredParser.java

License:BSD License

/**
 * Parses://from w w  w  .j ava 2s  . c  o  m
 * 
 * <pre>
   <external pattern="xt.*"/>
 * </pre>
 */
private static Pattern parseExternalPattern(Element parseElement) throws XmlConfigException {
    Element external = parseElement.element(XmlElements.external.getXmlName());
    Pattern externalPat = null;
    if (external != null) {
        String patString = external.attributeValue(XmlAttributes.pattern.getXmlName());
        try {
            externalPat = Pattern.compile(patString);
        } catch (Exception ex) {
            throw new XmlConfigException("cannot parse external pattern '" + patString + "', e=" + ex, external,
                    ex);
        }
    }
    return externalPat;
}

From source file:ch.javasoft.metabolic.parse.SbmlParser.java

License:BSD License

private Map<String, CompartmentMetabolite> parseMetabolites(Element elMetas,
        Map<Annotateable, Map<String, String>> annotations) throws DocumentException {
    Map<String, CompartmentMetabolite> metas = new LinkedHashMap<String, CompartmentMetabolite>();
    Iterator it = elMetas.elementIterator(ELEMENT_METABOLITE);
    while (it.hasNext()) {
        Element el = (Element) it.next();
        String metaId = el.attributeValue(ATTRIBUTE_ID);
        String metaName = el.attributeValue(ATTRIBUTE_NAME);
        String compartment = el.attributeValue(ATTRIBUTE_COMPARTMENT);
        CompartmentMetabolite meta = metaName == null ? new CompartmentMetabolite(metaId, compartment)
                : new CompartmentMetabolite(metaId, metaName, compartment);

        if (metas.put(metaId, meta) != null) {
            throw new DocumentException("duplicate metabolite: " + metaId);
        }//ww  w  . ja va  2 s  . c  o  m
        parseAnnotations(el, meta, annotations);
    }
    return metas;
}

From source file:ch.javasoft.metabolic.parse.SbmlParser.java

License:BSD License

private static Set<CompartmentReaction> parseReactions(Element elReacts,
        Map<String, CompartmentMetabolite> metas, Map<Annotateable, Map<String, String>> annotations)
        throws DocumentException {
    final Set<CompartmentReaction> reacts = new LinkedHashSet<CompartmentReaction>();
    final Iterator<Element> it = elementIterator(elReacts, ELEMENT_REACTION);
    while (it.hasNext()) {
        boolean any = false;
        final Element el = it.next();
        String reactId = el.attributeValue(ATTRIBUTE_ID);
        String reactName = el.attributeValue(ATTRIBUTE_NAME);
        boolean reversible = !Boolean.FALSE.toString()
                .equalsIgnoreCase(el.attributeValue(ATTRIBUTE_REVERSIBLE));//default is true
        final List<CompartmentMetaboliteRatio> ratios = new ArrayList<CompartmentMetaboliteRatio>();
        final Iterator<Element> eduIt = elementIterator(el.element(ELEMENT_EDUCTS), ELEMENT_EDUCT);
        any |= eduIt.hasNext();/*from   w  ww .j a v a 2  s . c  o m*/
        while (eduIt.hasNext()) {
            Element edu = (Element) eduIt.next();
            CompartmentMetaboliteRatio ratio = parseMetaboliteRatio(el, edu, metas, true /*educt*/);
            ratios.add(ratio);
        }
        final Iterator<Element> proIt = elementIterator(el.element(ELEMENT_PRODUCTS), ELEMENT_PRODUCT);
        any |= proIt.hasNext();
        while (proIt.hasNext()) {
            final Element pro = proIt.next();
            CompartmentMetaboliteRatio ratio = parseMetaboliteRatio(el, pro, metas, false /*educt*/);
            ratios.add(ratio);
        }
        if (!any) {
            throw new DocumentException(
                    "reaction has neither educts nor products: " + reactId + "/" + reactName);
        }
        final CompartmentReaction reac = new CompartmentReaction(reactId, reactName, ratios, reversible);
        if (!reacts.add(reac)) {
            throw new DocumentException("duplicate reaction: " + reactId);
        }
        parseAnnotations(el, reac, annotations);
    }
    return reacts;
}