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Trying to use XInclude with Java and resolving the fragment with xml:id

I've been trying to get XInclude working in my XML document and finally have it working in Oxygen XML, which I'm using to author the XML documents.
I then went to my app, written in Java, but it doesn't seem to support any form of XPointer resolution except using something like: element(/1/2).
This is, obviously, an awful scheme to have to use since every time the document is edited the XPointer needs changing to reflect the new position of the node in the XML!
The scheme I had working simply used xml:id in the target document:
<foo>
<bar xml:id="ABCD" />
</foo>
and then, in the other document:
<lorem>
<ipsum>
<xi:include href="target.xml" xpointer="ABCD" />
</ipsum>
</lorem>
Which I anticipate (and am getting in Oxygen) results in something like:
<lorem>
<ipsum>
<bar xml:id="ABCD" />
</ipsum>
</lorem>.
However, in Java it fails with:
Resource error reading file as XML (href='data/target.xml'). Reason:
XPointer resolution unsuccessful.
If, however, I change the include tag to use
xpointer="element(/1/1)"
then it works very nicely - but, as I've said, that's a very poor solution.
I'm simply using the implementations that are included with the Java runtime (1.8).
Here's the code I'm using:
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(true);
factory.setXIncludeAware(true);
Source resultSource = new
StreamSource(Gdx.files.internal("data/result.xsd").read());
Source targetSource = new
StreamSource(Gdx.files.internal("data/target.xsd").read());
Source[] schemaFiles = {targetSource, resultSource};
schema =
SchemaFactory.newInstance("http://www.w3.org/2001/XMLSchema")
.newSchema(schemaFiles);
factory.setSchema(schema);
builder = factory.newDocumentBuilder();
itemDoc = builder.parse(new
InputSource(Gdx.files.internal("data/result.xml").read()));

According to Apache Xerces's docs on XInclude (which is used internally for XML parsing by Java)
for shorthand pointers and element() XPointers, currently only DTD-determined IDs are supported.
This means that you need to put markup declarations such as the following into your target.xml file (telling the XML parser that the id attribute is to be treated as attribute with ID semantics, and telling XInclude to interpret "bare" XPointers as ID references):
<!DOCTYPE foo [
<!ATTLIST bar id ID #IMPLIED>
]>
<foo>
<bar id="ABCD"/>
</foo>
If you now use the following document as your source XML (which you've named result.xml in your example code, and which I've edited to contain an XInclude namespace URI binding for xi)
<lorem xmlns:xi="http://www.w3.org/2001/XInclude">
<ipsum>
<xi:include href="target.xml" xpointer="ABCD"/>
</ipsum>
</lorem>
then Xerces will build up a Document where XInclude processing has been performed as desired (where i've put your example data into the target.xml file in the same directory as the result.xml file):
<lorem xmlns:xi="http://www.w3.org/2001/XInclude">
<ipsum>
<bar id="ABCD" xml:base="target.xml"/>
</ipsum>
</lorem>
The Java code I've used to produce the document is simplified from your example and doesn't contain third-party libs:
import java.io.*;
import javax.xml.*;
import javax.xml.parsers.*;
import javax.xml.validation.*;
import javax.xml.transform.*;
import javax.xml.transform.stream.*;
import javax.xml.transform.dom.*;
import org.w3c.dom.*;
public class t {
public static void main(String[] args) {
try {
DocumentBuilderFactory factory =
DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(true);
factory.setXIncludeAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
Document itemDoc = builder.parse(new File("result.xml"));
System.out.println(serialize(itemDoc));
}
catch (Exception ex) {
ex.printStackTrace();
}
}
static String serialize(Document doc) throws Exception {
Transformer transformer =
TransformerFactory.newInstance().newTransformer();
StreamResult result = new StreamResult(new StringWriter());
DOMSource source = new DOMSource(doc);
transformer.transform(source, result);
return result.getWriter().toString();
}
}
Seeing as you also use XML Schema validation, I'd also like to point out the potential interaction of XInclude with XML Schema as eg. discussed in XInclude Schema/Namespace Validation?, and also a potential alternative discussed in Duplicate some parts of XML without rewriting them .

Java replacing / removing / writing text in a certain spot in a txt file

So they the file I wanna edit is this,
<?xml version="1.0" encoding="utf-16"?>
<UserSettingsXml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
<AuthType>Google</AuthType> <!-- Google/Ptc -->
<DefaultLatitude>425</DefaultLatitude>
<DefaultLongitude>5555</DefaultLongitude>
The places I wanna edit, and remove text from is
<DefaultLatitude>425</DefaultLatitude>
<DefaultLongitude>5555</DefaultLongitude>
I've googled a bit but couldn't find what I was looking for.

If you want to alter an XML file you should be using something like DOM.
That's easier and safer to do than just altering the text in the file.
Reading the xml-file into a DOM-Document is quite easy:
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc = db.parse(new File(filename));
After that you'll have to find the right spot in the XML-Document and alter it:
Element root = doc.getDocumentElement();
NodeList found = root.getElementsByTagName("DefaultLatitude");
Node element = found.item(0);
String textContent = element.getTextContent(); // contains 425 now
element.setTextContent("987"); // set new text
After that you'll have to write out the changed document to a file:
TransformerFactory tranformerFactory = TransformerFactory.newInstance();
Transformer transformer = tranformerFactory.newTransformer();
DOMSource source = new DOMSource(doc);
StreamResult result = new StreamResult(new File(outputFile));
transformer.transform(source, result);
Please note that this is just an example on how to read, alter and save a XML-File. To properly work with DOM you'll have to read some tutorials!

The file you are trying to edit is in xml format. The best way to do what you want is to:
1. parse the file in xml
2. manipulate the xml
3. build the file again
A good page where to learn how to convert from text to xml is this:
http://www.mkyong.com/java/how-to-read-xml-file-in-java-dom-parser/
The rest is easier. I hope this helps.

Using java to generating XML with specific DTD declarations

I need to generate a XML file that contains specific XML Declarations and DTD declarations as shown below:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE paymentService PUBLIC "-//CompanyName//DTD CompanyName PaymentService v2//EN"
"http://dtd.CompanyName.com/paymentService_v2.dtd">
The remaining XML to be generated also has a specific Elements and associated values.
I was wondering what would be the best way to generate this XML within my java class? Using String Buffer or DOM? Any suggestions with an example or sample code will be hugely appreciated.
Thanks

I would recommend using the Java DOM API. Dealing with XML or XHTML in String objects is notoriously time consuming and buggy, so try and use a propper parser like DOM whenever you have the option to.
The below code should add a doc type and your xml declaration using Java DOM. The <?xml... should be added to the top automatically when the DocumentBuilder creates your document.
// Create document
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.newDocument();
//Create doc type
DOMImplementation domImpl = doc.getImplementation();
DocumentType doctype = domImpl.createDocumentType("paymentService", "-//CompanyName//DTD CompanyName PaymentService v2//EN", "http://dtd.CompanyName.com/paymentService_v2.dtd");
doc.appendChild(doctype);
// Add root element
Element rootElement = doc.createElement("root");
doc.appendChild(rootElement);
The XML created by the above should look like this;
<?xml version="1.0" encoding="UTF-8" standalone="no" ?>
<!DOCTYPE paymentService PUBLIC "-//CompanyName//DTD CompanyName PaymentService v2//EN" "http://dtd.CompanyName.com/paymentService_v2.dtd">
<root>
</root>
A great many of the methods used in the code above can throw a large number and variety of exceptions, so make sure your exception handling is up to scratch. I hope this helps.
Link to the Official DOM API Guide

TransformerFactory - avoiding network lookups to verify DTDs

I am needing to program for offline transformation of XML documents.
I have been able to stop DTD network lookups when loading the original XML file with the following :
DocumentBuilderFactory factory;
factory = DocumentBuilderFactory.newInstance();
factory.setValidating(false);
factory.setNamespaceAware(true);
factory.setFeature("http://xml.org/sax/features/namespaces", false);
factory.setFeature("http://xml.org/sax/features/validation", false);
factory.setFeature("http://apache.org/xml/features/nonvalidating/load-dtd-grammar", false);
factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
// open up the xml document
docbuilder = factory.newDocumentBuilder();
doc = docbuilder.parse(new FileInputStream(m_strFilePath));
However, I am unable to apply this to the TransformerFactory object.
The DTDs are available locally, but I do not know how to direct the transformer to look at the local files as opposed to trying to do a network lookup.
From what I can see, the transformer needs these documents to correctly do the transformation.
For information, I am transforming MusicXML documents from Partwise to Timewise.
As you have probably guessed, XSLT is not my strong point (far from it).
Do I need to modify the XSLT files to reference local files, or can this be done differently ?
Further to the comments below, here is an excerpt of the xsl file. It is the only place that I see which refers to an external file :
<!--
XML output, with a DOCTYPE refering the timewise DTD.
Here we use the full Internet URL.
-->
<xsl:output method="xml" indent="yes" encoding="UTF-8"
omit-xml-declaration="no" standalone="no"
doctype-system="http://www.musicxml.org/dtds/timewise.dtd"
doctype-public="-//Recordare//DTD MusicXML 2.0 Timewise//EN" />
Is the mentioned technique valid for this also ?
The DTD file contains references to a number of MOD files like this :
<!ENTITY % layout PUBLIC
"-//Recordare//ELEMENTS MusicXML 2.0 Layout//EN"
"layout.mod">
I presume that these files will also be imported in turn also.

Ok, here is the answer which works for me.
1st step : load the original document, turning off validation and dtd loading within the factory.
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
// stop the network loading of DTD files
factory.setValidating(false);
factory.setNamespaceAware(true);
factory.setFeature("http://xml.org/sax/features/namespaces", false);
factory.setFeature("http://xml.org/sax/features/validation", false);
factory.setFeature("http://apache.org/xml/features/nonvalidating/load-dtd-grammar", false);
factory.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
// open up the xml document
DocumentBuilder docbuilder = factory.newDocumentBuilder();
Document doc = docbuilder.parse(new FileInputStream(m_strFilePath));
2nd step : Now that I have got the document in memory ... and after having detected that I need to transform it -
TransformerFactory transformfactory = TransformerFactory.newInstance();
Templates xsl = transformfactory.newTemplates(new StreamSource(new FileInputStream((String)m_XslFile)));
Transformer transformer = xsl.newTransformer();
Document newdoc = docbuilder.newDocument();
Result XmlResult = new DOMResult(newdoc);
// now transform
transformer.transform(
new DOMSource(doc.getDocumentElement()),
XmlResult);
I needed to do this as I have further processing going on afterwards and did not want the overhead of outputting to file and reloading.
Little explanation :
The trick is to use the original DOM object which has had all the validation features turned off. You can see this here :
transformer.transform(
new DOMSource(doc.getDocumentElement()), // <<-----
XmlResult);
This has been tested with network access TURNED OFF.
So I know that there are no more network lookups.
However, if the DTDs, MODs, etc are available locally, then, as per the suggestions, the use of an EntityResolver is the answer. This to be applied, again, to the original docbuilder object.
I now have a transformed document stored in newdoc, ready to play with.
I hope this will help others.

You can use a library like Apache xml-commons-resolver and write a catalog file to map web URLs to your local copy of the relevant files. To wire this catalog up to the transformer mechanism you would need to use a SAXSource instead of a StreamSource as the source of your stylesheet:
SAXSource styleSource = new SAXSource(new InputSource("file:/path/to/stylesheet.xsl"));
CatalogResolver resolver = new CatalogResolver();
styleSource.getXMLReader().setEntityResolver(resolver);
TransformerFactory tf = TransformerFactory.newInstance();
tf.setURIResolver(resolver);
Transformer transformer = tf.newTransformer(styleSource);

The usual way to do this in Java is to use an LSResourceResolver to resolve the system ID (and/or public ID) to your local file. This is documented at http://docs.oracle.com/javase/7/docs/api/org/w3c/dom/ls/LSResourceResolver.html. You shouldn't need anything outside of standard Java XML parser features to get this working.

Add XML comments into marshaled file

I'm marshaling objects into an XML file. How can I add comments into that XML file?

You can add comments right after the preamble with the proprietary Marshaller property com.sun.xml.bind.xmlHeaders (see XML Preamble Control)
In the included JAXB-implementation jdk1.6.0_29 the property is called "com.sun.xml.internal.bind.xmlHeaders"
See also question: How to add DOCTYPE and xml processing instructions when marshalling with JAXB?
So to get this XML with the test-comment after the preamble:
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<!-- Test Comment -->
<player>
<name>Daniel</name>
<birthday>1982-06-09T00:00:00+02:00</birthday>
</player>
You can use this Java-Code:
JAXBContext context = JAXBContext.newInstance(Player.class);
Marshaller m = context.createMarshaller();
m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
m.setProperty("com.sun.xml.internal.bind.xmlHeaders", "\n<!-- Test Comment -->");
m.marshal(player, System.out);

I do not see a way to do it with JAXB alone. However, I think you can leverage DOM to get the desired effect:
final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
final DocumentBuilder builder = factory.newDocumentBuilder();
final Document doc = builder.getDOMImplementation().createDocument(null, null, null);
final Binder<Node> binder = jaxbContext.createBinder();
binder.marshal(jaxbObject, doc);
final Comment comment = doc.createComment("This is a comment");
doc.appendChild(comment);
final DOMSource domSource = new DOMSource(doc);
// use System.out for testing
final StreamResult streamResult = new StreamResult(System.out);
final TransformerFactory tf = TransformerFactory.newInstance();
final Transformer serializer = tf.newTransformer();
serializer.transform(domSource, streamResult);
Where jaxbContext is the JAXBContext object you are working with and jaxbObject is the object to be marshalled. This sample just appends the comment to the end of the document. For a different location, you would have to traverse the DOM through the doc object or use XPath to find the exact element you want the comment added to and use appendChild on it.

If anyone comes to this now, like I just did, it is worth pointing out that the property to do this is now com.sun.xml.bind.xmlHeaders (no longer internal it seems), so you can solve the problem like this (I have only tried it with EclipseLink MOXY):
JAXBContext context = JAXBContext.newInstance(Player.class);
Marshaller m = context.createMarshaller();
m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
m.setProperty("com.sun.xml.bind.xmlHeaders", "\n<!-- Test Comment -->");
m.marshal(player, System.out);
The following information originally comes from Marshaller Properties in the JAXB RI Extensions documentation on jaxb.java.net:
XML Preamble Control
This property allows you to specify an XML preamble (
declaration) and any additional PIs, comments, DOCTYPE declaration
that follows it. This property takes effect only when you are
marshalling to OutputStream, Writer, or StreamResult. Note that this
property interacts with the Marshaller.JAXB_FRAGMENT property. If that
property is untouched or set to false, then JAXB would always write
its XML preamble, so this property can be only used to write PIs,
comments, DOCTYPE, etc. On the other hand, if it is set to true, then
JAXB will not write its own XML preamble, so this property may contain
custom XML preamble.