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

Example 46 with Document

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

the class DocumentCompiler method validateTOC.

private void validateTOC() throws Exception {
    File tocSourceFile = new File(docSourceDir, tocFileName);
    // 
    // read in existing TOC file and validate it's contents
    // 
    Document doc = XmlUtil.readXML(tocSourceFile);
    Element root = doc.getRootElement();
    if (!root.getName().equals(VCellDocTags.toc_tag)) {
        throw new RuntimeException("expecting " + VCellDocTags.toc_tag + " in file " + tocSourceFile.getPath());
    }
    HashSet<DocumentPage> pagesNotYetReferenced = new HashSet<DocumentPage>(Arrays.asList(documentation.getDocumentPages()));
    readTOCItem(pagesNotYetReferenced, root);
    if (pagesNotYetReferenced.size() > 0) {
        for (DocumentPage docPage : pagesNotYetReferenced) {
            if (!documentation.isReferenced(docPage)) {
                System.err.println("ERROR: Document page '" + docPage.getTarget() + "' not referenced in either table of contents or from another document");
            }
        }
    }
    // copy the Table of Contents to the target directory.
    FileUtils.copyFile(new File(docSourceDir, tocFileName), new File(docTargetDir, tocFileName));
    // System.out.println("Calling buildHtmlIndex");
    buildHtmlIndex(root);
}

Example 47 with Document

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

the class DocumentCompiler method readDefinitionFile.

private ArrayList<DocumentDefinition> readDefinitionFile(File file) throws XmlParseException {
    ArrayList<DocumentDefinition> documentDefs = new ArrayList<DocumentDefinition>();
    Document doc = XmlUtil.readXML(file);
    Element root = doc.getRootElement();
    if (!root.getName().equals(VCellDocTags.VCellDoc_tag)) {
        throw new RuntimeException("expecting ...");
    }
    // get all definition elements
    @SuppressWarnings("unchecked") List<Object> pageElements = root.getContent();
    if (pageElements != null) {
        for (Object pageElement : pageElements) {
            if (pageElement instanceof Element && ((Element) pageElement).getName().equals(VCellDocTags.definition_tag)) {
                String target = ((Element) pageElement).getAttributeValue(VCellDocTags.target_attr);
                String label = ((Element) pageElement).getAttributeValue(VCellDocTags.definition_label_attr);
                String text = ((Element) pageElement).getText();
                DocumentDefinition documentDefinition = new DocumentDefinition(file, target, label, text);
                documentDefs.add(documentDefinition);
            }
        }
    }
    return documentDefs;
}

Example 48 with Document

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

the class JDOM2Model method addJDOM.

public void addJDOM(Element element, String baseURI) throws IOException, RDFParseException, RDFHandlerException {
    Document document = new Document((Element) element.clone());
    StringWriter stringWriter = new StringWriter();
    new XMLOutputter().output(document, stringWriter);
    StringReader stringReader = new StringReader(stringWriter.getBuffer().toString());
    RDFParser rdfParser = Rio.createParser(RDFFormat.RDFXML);
    rdfParser.setRDFHandler(new StatementCollector(model));
    rdfParser.parse(stringReader, baseURI);
}

Example 49 with Document

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

the class VisMeshUtils method writePointDataToVtu.

public static void writePointDataToVtu(File inputMeshFile, String dataName, double[] data, File outputMeshFile) throws IOException {
    Document meshDocument = XmlUtil.readXML(inputMeshFile);
    addPointDataToVtuXml(meshDocument, dataName, data);
    FileWriter fw = null;
    try {
        fw = new FileWriter(outputMeshFile);
        XMLOutputter xmlOut = new XMLOutputter();
        Format f = Format.getRawFormat();
        f.setLineSeparator("\n");
        f.setOmitEncoding(true);
        f.setExpandEmptyElements(true);
        xmlOut.setFormat(f);
        xmlOut.output(meshDocument, fw);
    } finally {
        if (fw != null) {
            fw.close();
        }
    }
}

Example 50 with Document

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

the class ExpressionMathMLPrinter method getMathML.

/**
 * Insert the method's description here.
 * Creation date: (2/8/2002 5:51:09 PM)
 * @return java.lang.String
 */
String getMathML(boolean bOnlyMathMLFragment, MathType desiredMathType) throws ExpressionException, java.io.IOException {
    org.jdom.output.XMLOutputter xmlwriter = new org.jdom.output.XMLOutputter();
    Element mathElement = new Element("math", Namespace.getNamespace("http://www.w3.org/1998/Math/MathML"));
    mathElement.addContent(getMathML(rootNode, desiredMathType));
    if (!bOnlyMathMLFragment) {
        Document mathDoc = new Document(mathElement);
        return xmlwriter.outputString(mathDoc);
    }
    return xmlwriter.outputString(mathElement);
}