Examples with Namespace org.jdom.Namespace used on opensource projects

Example 16 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class MicroscopyXmlReader method getAnnotatedImageDataset.

public AnnotatedImageDataset getAnnotatedImageDataset(Element param, /*root, frapstudy element*/
ClientTaskStatusSupport progressListener) throws XmlParseException {
    // get frapData element
    Element frapDataElement = param.getChild(MicroscopyXMLTags.FRAPDataTag);
    Element imageDatasetElement = frapDataElement.getChild(MicroscopyXMLTags.ImageDatasetTag);
    ImageDataset imageDataset = null;
    if (imageDatasetElement != null) {
        imageDataset = getImageDataset(imageDatasetElement, progressListener);
    }
    Namespace ns = param.getNamespace();
    List<Element> roiList = frapDataElement.getChildren(MicroscopyXMLTags.ROITag);
    ROI[] rois = new ROI[0];
    int numROIs = roiList.size();
    if (numROIs > 0) {
        rois = new ROI[numROIs];
        Iterator<Element> roiIter = roiList.iterator();
        int index = 0;
        while (roiIter.hasNext()) {
            Element roiElement = roiIter.next();
            rois[index++] = getROI(roiElement);
        }
    }
    // reorder ROIs according to the order of FRAPData.VFRAP_ROI_ENUM
    ROI[] reorderedROIs = AnnotatedImageDataset.reorderROIs(rois);
    AnnotatedImageDataset annotatedImages = new AnnotatedImageDataset(imageDataset, reorderedROIs);
    // After loading all the ROI rings, the progress should set to 100.
    if (progressListener != null) {
        progressListener.setProgress(100);
    }
    return annotatedImages;
}

Example 17 with Namespace

use of org.jdom.Namespace in project che by eclipse.

the class EffectivePomWriter method addMavenNamespace.

/**
     * method from org.apache.maven.plugins.help.AbstractEffectiveMojo
     * Add a Pom/Settings namespaces to the effective XML content.
     *
     * @param effectiveXml not null the effective POM or Settings
     * @param isPom if <code>true</code> add the Pom xsd url, otherwise add the settings xsd url.
     * @return the content of the root element, i.e. &lt;project/&gt; or &lt;settings/&gt; with the Maven namespace or
     *         the original <code>effective</code> if an error occurred.
     * @see #POM_XSD_URL
     * @see #SETTINGS_XSD_URL
     */
protected static String addMavenNamespace(String effectiveXml, boolean isPom) {
    SAXBuilder builder = new SAXBuilder();
    try {
        Document document = builder.build(new StringReader(effectiveXml));
        Element rootElement = document.getRootElement();
        // added namespaces
        Namespace pomNamespace = Namespace.getNamespace("", "http://maven.apache.org/POM/4.0.0");
        rootElement.setNamespace(pomNamespace);
        Namespace xsiNamespace = Namespace.getNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance");
        rootElement.addNamespaceDeclaration(xsiNamespace);
        if (rootElement.getAttribute("schemaLocation", xsiNamespace) == null) {
            rootElement.setAttribute("schemaLocation", "http://maven.apache.org/POM/4.0.0 " + (isPom ? POM_XSD_URL : SETTINGS_XSD_URL), xsiNamespace);
        }
        ElementFilter elementFilter = new ElementFilter(Namespace.getNamespace(""));
        for (Iterator<?> i = rootElement.getDescendants(elementFilter); i.hasNext(); ) {
            Element e = (Element) i.next();
            e.setNamespace(pomNamespace);
        }
        StringWriter w = new StringWriter();
        Format format = Format.getPrettyFormat();
        XMLOutputter out = new XMLOutputter(format);
        out.output(document.getRootElement(), w);
        return w.toString();
    } catch (JDOMException e) {
        return effectiveXml;
    } catch (IOException e) {
        return effectiveXml;
    }
}

Example 18 with Namespace

use of org.jdom.Namespace in project intellij-plugins by JetBrains.

the class FlexCompilerConfigFileUtilBase method makeLibrariesMergedIntoCode.

private static void makeLibrariesMergedIntoCode(final Element rootElement, final boolean externalLibs, final boolean includedLibs) {
    final Namespace namespace = rootElement.getNamespace();
    final Collection<String> paths = removeLibs(rootElement, externalLibs, includedLibs);
    if (!paths.isEmpty()) {
        final Element compilerElement = rootElement.getChild(COMPILER, namespace);
        Element libraryPathElement = compilerElement.getChild(LIBRARY_PATH, namespace);
        if (libraryPathElement == null) {
            libraryPathElement = new Element(LIBRARY_PATH, namespace);
            libraryPathElement.setAttribute(new Attribute(APPEND, "true"));
            compilerElement.addContent(libraryPathElement);
        }
        for (final String path : paths) {
            final Element pathElement = new Element(PATH_ELEMENT, namespace);
            pathElement.addContent(path);
            libraryPathElement.addContent(pathElement);
        }
    }
}

Example 19 with Namespace

use of org.jdom.Namespace in project maven-plugins by apache.

the class AbstractEffectiveMojo method addMavenNamespace.

/**
     * Add a Pom/Settings namespaces to the effective XML content.
     *
     * @param effectiveXml not null the effective POM or Settings
     * @param isPom if <code>true</code> add the Pom xsd url, otherwise add the settings xsd url.
     * @return the content of the root element, i.e. &lt;project/&gt; or &lt;settings/&gt; with the Maven namespace or
     *         the original <code>effective</code> if an error occurred.
     * @see #POM_XSD_URL
     * @see #SETTINGS_XSD_URL
     */
protected static String addMavenNamespace(String effectiveXml, boolean isPom) {
    SAXBuilder builder = new SAXBuilder();
    try {
        Document document = builder.build(new StringReader(effectiveXml));
        Element rootElement = document.getRootElement();
        // added namespaces
        Namespace pomNamespace = Namespace.getNamespace("", "http://maven.apache.org/POM/4.0.0");
        rootElement.setNamespace(pomNamespace);
        Namespace xsiNamespace = Namespace.getNamespace("xsi", "http://www.w3.org/2001/XMLSchema-instance");
        rootElement.addNamespaceDeclaration(xsiNamespace);
        if (rootElement.getAttribute("schemaLocation", xsiNamespace) == null) {
            rootElement.setAttribute("schemaLocation", "http://maven.apache.org/POM/4.0.0 " + (isPom ? POM_XSD_URL : SETTINGS_XSD_URL), xsiNamespace);
        }
        ElementFilter elementFilter = new ElementFilter(Namespace.getNamespace(""));
        for (Iterator<?> i = rootElement.getDescendants(elementFilter); i.hasNext(); ) {
            Element e = (Element) i.next();
            e.setNamespace(pomNamespace);
        }
        StringWriter w = new StringWriter();
        Format format = Format.getPrettyFormat();
        XMLOutputter out = new XMLOutputter(format);
        out.output(document.getRootElement(), w);
        return w.toString();
    } catch (JDOMException e) {
        return effectiveXml;
    } catch (IOException e) {
        return effectiveXml;
    }
}

Example 20 with Namespace

use of org.jdom.Namespace in project vcell by virtualcell.

the class XmlHelper method XMLToBioModel.

static BioModel XMLToBioModel(XMLSource xmlSource, boolean printkeys, ModelUnitSystem forcedModelUnitSystem) throws XmlParseException {
    // long l0 = System.currentTimeMillis();
    BioModel bioModel = null;
    if (xmlSource == null) {
        throw new XmlParseException("Invalid xml for Biomodel.");
    }
    Document xmlDoc = xmlSource.getXmlDoc();
    // NOTES:
    // * The root element can be <Biomodel> (old-style vcml) OR <vcml> (new-style vcml)
    // * With the old-style vcml, the namespace was " "
    // * With the new-style vcml, there is an intermediate stage where the namespace for <vcml> root
    // was set to "http://sourceforge.net/projects/VCell/version0.4" for some models and
    // "http://sourceforge.net/projects/vcell/vcml" for some models; and the namespace for child element
    // <biomdel>, etc. was " "
    // * The final new-style vcml has (should have) the namespace "http://sourceforge.net/projects/vcell/vcml"
    // for <vcml> and all children elements.
    // The code below attempts to take care of this situation.
    Element root = xmlDoc.getRootElement();
    Namespace ns = null;
    if (root.getName().equals(XMLTags.VcmlRootNodeTag)) {
        // NEW WAY - with xml string containing xml declaration, vcml element, namespace, etc ...
        ns = root.getNamespace();
        Element bioRoot = root.getChild(XMLTags.BioModelTag, ns);
        if (bioRoot == null) {
            bioRoot = root.getChild(XMLTags.BioModelTag);
            // bioRoot was null, so obtained the <Biomodel> element with namespace " ";
            // Re-set the namespace so that the correct XMLReader constructor is invoked.
            ns = null;
        }
        root = bioRoot;
    }
    // else - root is assumed to be old-style vcml with <Biomodel> as root.
    // common for both new way (with xml declaration, vcml element, etc) and existing way (biomodel is root)
    // If namespace is null, xml is the old-style xml with biomodel as root, so invoke XMLReader without namespace argument.
    XmlReader reader = null;
    VCellSoftwareVersion vCellSoftwareVersion = null;
    if (ns == null) {
        reader = new XmlReader(printkeys);
    } else {
        reader = new XmlReader(printkeys, ns);
        vCellSoftwareVersion = VCellSoftwareVersion.fromString(root.getAttributeValue(XMLTags.SoftwareVersionAttrTag, ns));
    }
    if (forcedModelUnitSystem != null) {
        reader.setForcedModelUnitSystem(forcedModelUnitSystem);
    }
    bioModel = reader.getBioModel(root, vCellSoftwareVersion);
    // long l1 = System.currentTimeMillis();
    bioModel.refreshDependencies();
    return bioModel;
}