Parsing and editing SVG file

Question

I'm trying to open, parse, edit and output an SVG document. So far I've edited/change the nodelist object how I want it to be, however, I'm having an issue saving my changes to the SVG document (by serializing). How might I be able to copy/save my changes to the SVG document and outputting to a file. My goal is to change the ID tag on certain objects (line/paths), I have to be able to find specific IDs, change it, then save back to the file (or a new file).

Here is my code (saving to file):

// Global variables
Logger logger = Logger.getLogger(DynamicLink.class.getSimpleName());
private final File PROJECT_DIRECTORY = new File("").getAbsoluteFile();
private final String PROJECT_PATH = "file.path";
Document doc;
private File svg;
private NodeList nodes;
private final ArrayList<Node> editedLines = new ArrayList();

private void saveSvg() {
    try {
        File newFile = new File(PROJECT_DIRECTORY, "test/LineTestEdited.svg");
        if (!newFile.exists()) {
            Files.copy(svg.toPath(), newFile.toPath());
        }
        DOMImplementationRegistry registry = DOMImplementationRegistry.newInstance();    
        DOMImplementationLS impl = (DOMImplementationLS) registry.getDOMImplementation("XML 3.0 LS 3.0");
        LSParser parser = impl.createLSParser(DOMImplementationLS.MODE_SYNCHRONOUS, "http://www.w3.org/TR/REC-xml");
        Document document = parser.parseURI(newFile.getPath());

        NodeList svgRoot = doc.getChildNodes();
        NodeList root = document.getChildNodes();
        int length = editedLines.size();

        for (int i = 0; i <= length-1; i++) {
            Node defaultNode = nodes.item(i+1);
            Node newNode = editedLines.get(i);

            String defaultName = defaultNode.getNodeName();
            String defualtValue = defaultNode.getNodeValue();

            String newName = newNode.getNodeName();
            String newValue = newNode.getNodeValue();
            String type = defaultNode.getBaseURI();

            if (newValue != null) {
                setNodeValue(newName, defualtValue, newValue, svgRoot);
            }
        }
        LSSerializer serial = impl.createLSSerializer();
        LSOutput output = impl.createLSOutput();
        output.setEncoding("UTF-8");
        output.setByteStream(new FileOutputStream(newFile));
        serial.write(document, output);

    } catch (Exception ex) {
        logger.log(Level.SEVERE, "Error occurred while exporting/saving SVG", ex);
    } 
}

And this is editing the nodelist (editedLines are the new changed ones). Everything else is just loading the document and global variables.

private void parseSvg() {
    int length = nodes.getLength();
    int index = 0;
    try {
        for (int i = 0; i <= length-1; i++) {
            Node node = nodes.item(i).cloneNode(true);
            String value = node.getNodeValue();
            String name = node.getNodeName();
            String type = node.getTextContent();

            if (!name.equals("svg")) {
                if (value != null) {
                    if (value.contains("Dynamic")) {
                        node.setNodeValue("Line_" + index);
                        editedLines.add(node);

                        index++;
                        System.out.println("Value: " + node.getNodeValue());
                    } else {
                        editedLines.add(node);
                    }
                } else {
                    editedLines.add(node);
                }
            }
        }
    } catch (Exception ex) {
        logger.log(Level.SEVERE, "Error occured while parsing SVG", ex);
    }
}

Extra stuff used:

private Node getNode(String tagName, String oldId) {
        NodeList list = doc.getElementsByTagName(tagName);

        for (int i = 0; i < list.getLength(); i++) {
            Node node = list.item(i);
            Element element = (Element)node;
            //Element newEle = (Element)element.getElementsByTagName(tagName)
            String nodeId = element.getAttribute("id");

            if (nodeId.equals(oldId)) {
                return node;
            }
        }
        return null;
    }

    private void setNodeValue(String tagName, String oldId, String id, NodeList nodes) {
        Node node = getNode(tagName, oldId);
        //Node node = 
        if ( node == null )
            return;

        // Locate the child text node and change its value
        NodeList childNodes = node.getChildNodes();
        for (int y = 0; y < childNodes.getLength(); y++ ) {
            Node data = childNodes.item(y);
            if ( data.getNodeType() == Node.ATTRIBUTE_NODE ) {
                data.setNodeValue(id);
                return;
            }
        }
    }