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Unable to add doctype tag to xml file using java

I seek your help, I have an automatically generated XML File that I need to validate against a DTD, so I have to modify the generated XML to add the doctype tag isn't added when I use the following code, I have consulted many threads but no positive result.
Here is the concerned part in my code:
InputStream inputStream= new FileInputStream(extractedFileURL);
Reader reader = new InputStreamReader(inputStream,"UTF-8");
InputSource is = new InputSource(reader);
is.setEncoding("UTF-8");
Document doc = docBuilder.parse(is);
///Add Doctype declaration to the extracted XML File
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
org.w3c.dom.DOMImplementation domImpl = doc.getImplementation();
DocumentType doctype = domImpl.createDocumentType("doctype",
"SYSTEM"
,
"registry\\ixb\\dtds\\extractor.dtd\\generatedDTD1.dtd");
//transformer.setOutputProperty(OutputKeys.DOCTYPE_PUBLIC, doctype.getPublicId());
transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, doctype.getSystemId());
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(new File(extractedFileURL));
transformer.transform(source, result);

Reading Transformer result line by line (Java)

I'm using Transformer to prettify and to insert indentation to an XML which is originally one big line.
Here is my code:
BufferedWriter br = null;
Source xmlInput = new StreamSource(inputSR);
StringWriter stringWriter = new StringWriter();
StreamResult xmlOutput = new StreamResult(stringWriter);
TransformerFactory transformerFactory = TransformerFactory.newInstance();
transformerFactory.setAttribute("indent-number", 2);
Transformer transformer = transformerFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.transform(xmlInput, xmlOutput);
How can I write the xmlOutput to a file, line by line (without loading the whole string to the memory)?

Instead of a StringWriter, use a FileOutputStream:
StreamResult xmlOutput = new StreamResult(new FileOutputStream("output.xml"))
This will write incrementally to the file. It won't necessarily write line-by-line (lines don't mean much in XML), but I can't see why you would want that.

Java Transformer outputs < and > instead of <>

I am editing an XML file in Java with a Transformer by adding more nodes. The old XML code is unchanged but the new XML nodes have < and > instead of <> and are on the same line. How do I get <> instead of < and > and how do I get line breaks after the new nodes. I already read several similar threads but wasn't able to get the right formatting. Here is the relevant portion of the code:
// Read the XML file
DocumentBuilderFactory dbf= DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc=db.parse(xmlFile.getAbsoluteFile());
Element root = doc.getDocumentElement();
// create a new node
Element newNode = doc.createElement("Item");
// add it to the root node
root.appendChild(newNode);
// create a new attribute
Attr attribute = doc.createAttribute("Name");
// assign the attribute a value
attribute.setValue("Test...");
// add the attribute to the new node
newNode.setAttributeNode(attribute);
// transform the XML
Transformer transformer = TransformerFactory.newInstance().newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
StreamResult result = new StreamResult(new FileWriter(xmlFile.getAbsoluteFile()));
DOMSource source = new DOMSource(doc);
transformer.transform(source, result);
Thanks

To replace the &gt and other tags you can use org.apache.commons.lang3:
StringEscapeUtils.unescapeXml(resp.toString());
After that you can use the following property of transformer for having line breaks in your xml:
transformer.setOutputProperty(OutputKeys.INDENT, "yes");

based on a question posted here:
public void writeToOutputStream(Document fDoc, OutputStream out) throws Exception {
fDoc.setXmlStandalone(true);
DOMSource docSource = new DOMSource(fDoc);
Transformer transformer = TransformerFactory.newInstance().newTransformer();
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
transformer.setOutputProperty(OutputKeys.INDENT, "no");
transformer.transform(docSource, new StreamResult(out));
}
produces:
<?xml version="1.0" encoding="UTF-8"?>
The differences I see:
fDoc.setXmlStandalone(true);
transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");

Try passing InputStream instead of Writer to StreamResult.
StreamResult result = new StreamResult(new FileInputStream(xmlFile.getAbsoluteFile()));
The Transformer documentation also suggests that.

Converting XML doc to String

I am using the follwing code to change a xml document:
DocumentBuilderFactory fty1 = DocumentBuilderFactory.newInstance();
fty1.setNamespaceAware(true);
DocumentBuilder builder1 = fty1.newDocumentBuilder();
ByteArrayInputStream bais1 = new ByteArrayInputStream(tr1.getBytes());//tr1=xml string
Document xmldoc1=builder1.parse(bais1);
xmldoc1.getElementsByTagName("userID").item(0).setTextContent("123123132");
The xmldoc1 contains the changed form. Now how convert it to a string so that the new doument can be passed to others.

Transformer transformer = TransformerFactory.newInstance().newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
StringWriter sw = new StringWriter();
StreamResult result = new StreamResult(sw);
DOMSource source = new DOMSource(xmldoc1);
transformer.transform(source, result);
String xmlString = sw.toString();

XML Document to String?

I've been fiddling with this for over twenty minutes and my Google-foo is failing me.
Let's say I have an XML Document created in Java (org.w3c.dom.Document):
DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
Document document = docBuilder.newDocument();
Element rootElement = document.createElement("RootElement");
Element childElement = document.createElement("ChildElement");
childElement.appendChild(document.createTextNode("Child Text"));
rootElement.appendChild(childElement);
document.appendChild(rootElement);
String documentConvertedToString = "?" // <---- How?
How do I convert the document object into a text string?

public static String toString(Document doc) {
try {
StringWriter sw = new StringWriter();
TransformerFactory tf = TransformerFactory.newInstance();
Transformer transformer = tf.newTransformer();
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
transformer.transform(new DOMSource(doc), new StreamResult(sw));
return sw.toString();
} catch (Exception ex) {
throw new RuntimeException("Error converting to String", ex);
}
}

You can use this piece of code to accomplish what you want to:
public static String getStringFromDocument(Document doc) throws TransformerException {
DOMSource domSource = new DOMSource(doc);
StringWriter writer = new StringWriter();
StreamResult result = new StreamResult(writer);
TransformerFactory tf = TransformerFactory.newInstance();
Transformer transformer = tf.newTransformer();
transformer.transform(domSource, result);
return writer.toString();
}