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parsing an XML file with DOM error [duplicate]

I have to parse a bunch of XML files in Java that sometimes -- and invalidly -- contain HTML entities such as —, > and so forth. I understand the correct way of dealing with this is to add suitable entity declarations to the XML file before parsing. However, I can't do that as I have no control over those XML files.
Is there some kind of callback I can override that is invoked whenever the Java XML parser encounters such an entity? I haven't been able to find one in the API.
I'd like to use:
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder parser = dbf.newDocumentBuilder();
Document doc = parser.parse( stream );
I found that I can override resolveEntity in org.xml.sax.helpers.DefaultHandler, but how do I use this with the higher-level API?
Here's a full example:
public class Main {
public static void main( String [] args ) throws Exception {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder parser = dbf.newDocumentBuilder();
Document doc = parser.parse( new FileInputStream( "test.xml" ));
}
}
with test.xml:
<?xml version="1.0" encoding="UTF-8"?>
<foo>
<bar>Some text — invalid!</bar>
</foo>
Produces:
[Fatal Error] :3:20: The entity "nbsp" was referenced, but not declared.
Exception in thread "main" org.xml.sax.SAXParseException; lineNumber: 3; columnNumber: 20; The entity "nbsp" was referenced, but not declared.
Update: I have been poking around in the JDK source code with a debugger, and boy, what an amount of spaghetti. I have no idea what the design is there, or whether there is one. Just how many layers of an onion can one layer on top of each other?
They key class seems to be com.sun.org.apache.xerces.internal.impl.XMLEntityManager, but I cannot find any code that either lets me add stuff into it before it gets used, or that attempts to resolve entities without going through that class.

I would use a library like Jsoup for this purpose. I tested the following below and it works. I don't know if this helps. It can be located here: http://jsoup.org/download
public static void main(String args[]){
String html = "<?xml version=\"1.0\" encoding=\"UTF-8\"?><foo>" +
"<bar>Some text — invalid!</bar></foo>";
Document doc = Jsoup.parse(html, "", Parser.xmlParser());
for (Element e : doc.select("bar")) {
System.out.println(e);
}
}
Result:
<bar>
Some text — invalid!
</bar>
Loading from a file can be found here:
http://jsoup.org/cookbook/input/load-document-from-file

Issue - 1: I have to parse a bunch of XML files in Java that sometimes -- and
invalidly -- contain HTML entities such as —
XML has only five predefined entities. The —, is not among them. It works only when used in plain HTML or in legacy JSP. So, SAX will not help. It can be done using StaX which has high level iterator based API. (Collected from this link)
Issue - 2: I found that I can override resolveEntity in
org.xml.sax.helpers.DefaultHandler, but how do I use this with the
higher-level API?
Streaming API for XML, called StaX, is an API for reading and writing XML Documents.
StaX is a Pull-Parsing model. Application can take the control over parsing the XML documents by pulling (taking) the events from the parser.
The core StaX API falls into two categories and they are listed below. They are
Cursor based API: It is low-level API. cursor-based API allows the application to process XML as a stream of tokens aka events
Iterator based API: The higher-level iterator-based API allows the application to process XML as a series of event objects, each of which communicates a piece of the XML structure to the application.
STaX API has support for the notion of not replacing character entity references, by way of the IS_REPLACING_ENTITY_REFERENCES property:
Requires the parser to replace internal entity references with their
replacement text and report them as characters
This can be set into an XmlInputFactory, which is then in turn used to construct an XmlEventReader or XmlStreamReader.
However, the API is careful to say that this property is only intended to force the implementation to perform the replacement, rather than forcing it to notreplace them.
You may try it. Hope it will solve your issue. For your case,
Main.java
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.events.EntityReference;
import javax.xml.stream.events.XMLEvent;
public class Main {
public static void main(String[] args) {
XMLInputFactory inputFactory = XMLInputFactory.newInstance();
inputFactory.setProperty(
XMLInputFactory.IS_REPLACING_ENTITY_REFERENCES, false);
XMLEventReader reader;
try {
reader = inputFactory
.createXMLEventReader(new FileInputStream("F://test.xml"));
while (reader.hasNext()) {
XMLEvent event = reader.nextEvent();
if (event.isEntityReference()) {
EntityReference ref = (EntityReference) event;
System.out.println("Entity Reference: " + ref.getName());
}
}
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (XMLStreamException e) {
e.printStackTrace();
}
}
}
test.xml:
<?xml version="1.0" encoding="UTF-8"?>
<foo>
<bar>Some text — invalid!</bar>
</foo>
Output:
Entity Reference: nbsp
Entity Reference: mdash
Credit goes to #skaffman.
Related Link:
http://www.journaldev.com/1191/how-to-read-xml-file-in-java-using-java-stax-api
http://www.journaldev.com/1226/java-stax-cursor-based-api-read-xml-example
http://www.vogella.com/tutorials/JavaXML/article.html
Is there a Java XML API that can parse a document without resolving character entities?
UPDATE:
Issue - 3: Is there a way to use StaX to "filter" the entities (replacing them
with something else, for example) and still produce a Document at the
end of the process?
To create a new document using the StAX API, it is required to create an XMLStreamWriter that provides methods to produce XML opening and closing tags, attributes and character content.
There are 5 methods of XMLStreamWriter for document.
xmlsw.writeStartDocument(); - initialises an empty document to which
elements can be added
xmlsw.writeStartElement(String s) -creates a new element named s
xmlsw.writeAttribute(String name, String value)- adds the attribute
name with the corresponding value to the last element produced by a
call to writeStartElement. It is possible to add attributes as long
as no call to writeElementStart,writeCharacters or writeEndElement
has been done.
xmlsw.writeEndElement - close the last started element
xmlsw.writeCharacters(String s) - creates a new text node with
content s as content of the last started element.
A sample example is attached with it:
StAXExpand.java
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import javax.xml.stream.XMLOutputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.XMLStreamWriter;
import java.util.Arrays;
public class StAXExpand {
static XMLStreamWriter xmlsw = null;
public static void main(String[] argv) {
try {
xmlsw = XMLOutputFactory.newInstance()
.createXMLStreamWriter(System.out);
CompactTokenizer tok = new CompactTokenizer(
new FileReader(argv[0]));
String rootName = "dummyRoot";
// ignore everything preceding the word before the first "["
while(!tok.nextToken().equals("[")){
rootName=tok.getToken();
}
// start creating new document
xmlsw.writeStartDocument();
ignorableSpacing(0);
xmlsw.writeStartElement(rootName);
expand(tok,3);
ignorableSpacing(0);
xmlsw.writeEndDocument();
xmlsw.flush();
xmlsw.close();
} catch (XMLStreamException e){
System.out.println(e.getMessage());
} catch (IOException ex) {
System.out.println("IOException"+ex);
ex.printStackTrace();
}
}
public static void expand(CompactTokenizer tok, int indent)
throws IOException,XMLStreamException {
tok.skip("[");
while(tok.getToken().equals("#")) {// add attributes
String attName = tok.nextToken();
tok.nextToken();
xmlsw.writeAttribute(attName,tok.skip("["));
tok.nextToken();
tok.skip("]");
}
boolean lastWasElement=true; // for controlling the output of newlines
while(!tok.getToken().equals("]")){ // process content
String s = tok.getToken().trim();
tok.nextToken();
if(tok.getToken().equals("[")){
if(lastWasElement)ignorableSpacing(indent);
xmlsw.writeStartElement(s);
expand(tok,indent+3);
lastWasElement=true;
} else {
xmlsw.writeCharacters(s);
lastWasElement=false;
}
}
tok.skip("]");
if(lastWasElement)ignorableSpacing(indent-3);
xmlsw.writeEndElement();
}
private static char[] blanks = "\n".toCharArray();
private static void ignorableSpacing(int nb)
throws XMLStreamException {
if(nb>blanks.length){// extend the length of space array
blanks = new char[nb+1];
blanks[0]='\n';
Arrays.fill(blanks,1,blanks.length,' ');
}
xmlsw.writeCharacters(blanks, 0, nb+1);
}
}
CompactTokenizer.java
import java.io.Reader;
import java.io.IOException;
import java.io.StreamTokenizer;
public class CompactTokenizer {
private StreamTokenizer st;
CompactTokenizer(Reader r){
st = new StreamTokenizer(r);
st.resetSyntax(); // remove parsing of numbers...
st.wordChars('\u0000','\u00FF'); // everything is part of a word
// except the following...
st.ordinaryChar('\n');
st.ordinaryChar('[');
st.ordinaryChar(']');
st.ordinaryChar('#');
}
public String nextToken() throws IOException{
st.nextToken();
while(st.ttype=='\n'||
(st.ttype==StreamTokenizer.TT_WORD &&
st.sval.trim().length()==0))
st.nextToken();
return getToken();
}
public String getToken(){
return (st.ttype == StreamTokenizer.TT_WORD) ? st.sval : (""+(char)st.ttype);
}
public String skip(String sym) throws IOException {
if(getToken().equals(sym))
return nextToken();
else
throw new IllegalArgumentException("skip: "+sym+" expected but"+
sym +" found ");
}
}
For more, you can follow the tutorial
https://docs.oracle.com/javase/tutorial/jaxp/stax/example.html
http://www.ibm.com/developerworks/library/x-tipstx2/index.html
http://www.iro.umontreal.ca/~lapalme/ForestInsteadOfTheTrees/HTML/ch09s03.html
http://staf.sourceforge.net/current/STAXDoc.pdf

Another approach, since you're not using a rigid OXM approach anyway.
You might want to try using a less rigid parser such as JSoup?
This will stop immediate problems with invalid XML schemas etc, but it will just devolve the problem into your code.

Just to throw in a different approach to a solution:
You might envelope your input stream with a stream inplementation that replaces the entities by something legal.
While this is a hack for sure, it should be a quick and easy solution (or better say: workaround).
Not as elegant and clean as a xml framework internal solution, though.

I made yesterday something similar i need to add value from unziped XML in stream to database.
//import I'm not sure if all are necessary :)
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.xpath.*;
import org.w3c.dom.Document;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
//I didnt checked this code now because i'm in work for sure its work maybe
you will need to do little changes
InputSource is = new InputSource(new FileInputStream("test.xml"));
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc = db.parse(is);
XPathFactory xpf = XPathFactory.newInstance();
XPath xpath = xpf.newXPath();
String words= xpath.evaluate("/foo/bar", doc.getDocumentElement());
ParsingHexToChar.parseToChar(words);
// lib which i use common-lang3.jar
//metod to parse
public static String parseToChar( String words){
String decode= org.apache.commons.lang3.StringEscapeUtils.unescapeHtml4(words);
return decode;
}

Try this using org.apache.commons package :
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder parser = dbf.newDocumentBuilder();
InputStream in = new FileInputStream(xmlfile);
String unescapeHtml4 = IOUtils.toString(in);
CharSequenceTranslator obj = new AggregateTranslator(new LookupTranslator(EntityArrays.ISO8859_1_UNESCAPE()),
new LookupTranslator(EntityArrays.HTML40_EXTENDED_UNESCAPE())
);
unescapeHtml4 = obj.translate(unescapeHtml4);
StringReader readerInput= new StringReader(unescapeHtml4);
InputSource is = new InputSource(readerInput);
Document doc = parser.parse(is);

Android JDOM2 xml parsing, IOExcetion

I am trying to parse xml from URL with jdom-2.0.6.jar, but i get IOException:
IOException: Couldn't open "here is xml link"
That what I am doing:
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;
String myurl = "https://myfile.xml";
SAXBuilder builder = new SAXBuilder();
try {
Document document = builder.build(myurl);
Element rootNode = document.getRootElement().getChild("myroot");
} catch (IOException io) {
Log.d("IOException", io.getMessage());
} catch (JDOMException jdomex) {
Log.d("JDOMException", jdomex.getMessage());
}
The same code works well in Eclipse, but not in Android Studio. So what is wrong?

I did not have in log (android.os.NetworkOnMainThreadException) exception, but after using this solution I finally parsed xml.

Change to Log.w("IOException", io.getMessage(), io) to get the full stack trace, maybe we can identify the problem from there.

StaX parsing: Transformer.transform method moves cursor automatically, not always nice

I am using XMLStreamReader to achieve my goal(splitting xml file). It looks good, but still does not give the desired result. My aim is to split every node "nextTag" from an input file:
<?xml version="1.0" encoding="UTF-8"?>
<firstTag>
<nextTag>1</nextTag>
<nextTag>2</nextTag>
</firstTag>
The outcome should look like this:
<?xml version="1.0" encoding="UTF-8"?><nextTag>1</nextTag>
<?xml version="1.0" encoding="UTF-8"?><nextTag>2</nextTag>
Referring to Split 1GB Xml file using Java I achieved my goal with this code:
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringWriter;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.stax.StAXSource;
import javax.xml.transform.stream.StreamResult;
public class Demo4 {
public static void main(String[] args) throws Exception {
InputStream inputStream = new FileInputStream("input.xml");
BufferedReader in = new BufferedReader(new InputStreamReader(inputStream));
XMLInputFactory factory = XMLInputFactory.newInstance();
TransformerFactory tf = TransformerFactory.newInstance();
Transformer t = tf.newTransformer();
XMLStreamReader streamReader = factory.createXMLStreamReader(in);
while (streamReader.hasNext()) {
streamReader.next();
if (streamReader.getEventType() == XMLStreamReader.START_ELEMENT
&& "nextTag".equals(streamReader.getLocalName())) {
StringWriter writer = new StringWriter();
t.transform(new StAXSource(streamReader), new StreamResult(
writer));
String output = writer.toString();
System.out.println(output);
}
}
}
}
Actually very simple. But, my input file is in form from a single line:
<?xml version="1.0" encoding="UTF-8"?><firstTag><nextTag>1</nextTag><nextTag>2</nextTag></firstTag>
My Java code does not produce the desired output anymore, instead just this result:
<?xml version="1.0" encoding="UTF-8"?><nextTag>1</nextTag>
After spending hours, I am pretty sure to already find out the reason:
t.transform(new StAXSource(streamReader), new StreamResult(writer));
It is because, after the transform method being executed, the cursor will automatically moved forward to the next event. And in the code, I have this fraction:
while (streamReader.hasNext()) {
streamReader.next();
...
t.transform(new StAXSource(streamReader), new StreamResult(writer));
...
}
After the first transform, the streamReader gets directly 2 times next():
1. from the transform method
2. from the next method in the while loop
So, in case of this specific line XML, the cursor can never achive the second open tag .
In opposite, if the input XML has a pretty print form, the second can be reached from the cursor because there is a space-event after the first closing tag
Unfortunately, I could not find anything how to do settings, so that the transformator does not automatically spring to next event after performing the transform method. This is so frustating.
Does anybody have any idea how I can deal with it? Also semantically is very welcome. Thank you so much.
Regards,
Ratna
PS. I can surely write a workaround for this problem(pretty print the xml document before transforming it, but this would mean that the input xml was being modified before, this is not allowed)

As you elaborated did the transformation step proceed to the next create element if the element-nodes follow directly each other.
In order to deal with this, you can rewrite you code using nested while loops, like this:
while(reader.next() != XMLStreamConstants.END_DOCUMENT) {
while(reader.getEventType() == XMLStreamConstants.START_ELEMENT && reader.getLocalName().equals("nextTag")) {
StringWriter writer = new StringWriter();
// will transform the current node to a String, moves the cursor to the next START_ELEMENT
t.transform(new StAXSource(reader), new StreamResult(writer));
System.out.println(writer.toString());
}
}

In case your xml file fits in memory, you can try with the help of the JOOX library, imported in gradle like:
compile 'org.jooq:joox:1.3.0'
And the main class, like:
import java.io.File;
import java.io.IOException;
import org.joox.JOOX;
import org.joox.Match;
import org.w3c.dom.Document;
import org.xml.sax.SAXException;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import static org.joox.JOOX.$;
public class Main {
public static void main(String[] args)
throws IOException, SAXException, TransformerException {
DocumentBuilder builder = JOOX.builder();
Document document = builder.parse(new File(args[0]));
Transformer transformer =
TransformerFactory.newInstance().newTransformer();
transformer.setOutputProperty("omit-xml-declaration", "no");
final Match $m = $(document);
$m.find("nextTag").forEach(tag -> {
try {
transformer.transform(
new DOMSource(tag),
new StreamResult(System.out));
System.out.println();
}
catch (TransformerException e) {
System.exit(1);
}
});
}
}
It yields:
<?xml version="1.0" encoding="UTF-8"?><nextTag>1</nextTag>
<?xml version="1.0" encoding="UTF-8"?><nextTag>2</nextTag>

JDOM, umaluts and UTF-8

I have issue with using utf-8 with JDOM parser. My code won't write encoded in utf-8.
Here's code:
import java.io.FileWriter;
import java.io.IOException;
import org.jdom2.Element;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
import org.jdom2.Document;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;
public class Jdom2 {
public static void main(String[] args) throws JDOMException, IOException {
String textValue = null;
try {
SAXBuilder sax = new SAXBuilder();
Document doc = sax.build("path/to/file.xml");
Element rootNode = doc.getRootElement();
Element application = rootNode.getChild("application");
Element de_DE = application.getChild("de_DE");
textValue = de_DE.getText();
System.out.println(textValue);
application.getChild("de_DE").setText(textValue);
Format format = Format.getPrettyFormat();
format.setEncoding("UTF-8");
XMLOutputter xmlOutput = new XMLOutputter(format);
xmlOutput.output(doc, new FileWriter("path/to/file.xml"));
} catch (IOException io) {
io.printStackTrace();
} catch (JDOMException e) {
e.printStackTrace();
}
}
}
So line System.out.println(textValue); prints text "Mit freundlichen Grüßen", which is exactly what is read from xml file, but when it writing down, I get "Mit freundlichen Gr����"
Here's my xml file
<?xml version="1.0" encoding="UTF-8"?>
<applications>
<application id="default">
<de_DE>Mit freundlichen Grüßen</de_DE>
</application>
</applications>
How will I achieve writing "Mit freundlichen Grüßen" instead of "Mit freundlichen Gr����" ?
Thanks in advance!

This is probably the issue:
xmlOutput.output(doc, new FileWriter("path/to/file.xml"));
FileWriter always uses the platform default encoding. If that's not UTF-8, you've got problems.
I suggest you use a FileOutputStream instead, and let JDOM do the right thing. (Also, I strongly suspect you should keep a reference to the stream so you can close it in a finally block...)

I would totally go for #Jon Skeet answer, but if the code is in the 3rd party library that you cannot modify there are two other options:
Run your JVM with additional environment variable specifying file.encoding:
java -Dfile.encoding=UTF-8 … Jdom2
You can try to modify the Charset.defaultCharset which stores encoding used by FileWritter. Keep in mind that it's a very hacky solution that might break at some point and I would avoid it at all:
Field field = null;
for (Field f : Charset.class.getDeclaredFields()) {
if (f.getName().equals("defaultCharset")) {
field = f;
}
}
field.setAccessible(true);
Field modifiersField = Field.class.getDeclaredField("modifiers");
modifiersField.setAccessible(true);
modifiersField.setInt(field, field.getModifiers() & ~Modifier.FINAL);
field.set(null, StandardCharsets.UTF_8);
One last remark. Both solution might introduce side effects in other parts of your application because you are changing default encoding that might be used by some libraries.

RTF to Plain Text in Java

How do you convert an RTF string to plain text in Java? The obvious answer is to use Swing's RTFEditorKit, and that seems to be the common answer around the Internet. However the write method that claims to return plain text isn't actually implemented... it's hard-coded to just throw an IOException in Java6.

I use Swing's RTFEditorKit in Java 6 like this:
RTFEditorKit rtfParser = new RTFEditorKit();
Document document = rtfParser.createDefaultDocument();
rtfParser.read(new ByteArrayInputStream(rtfBytes), document, 0);
String text = document.getText(0, document.getLength());
and thats working.

Try Apache Tika: http://tika.apache.org/0.9/formats.html#Rich_Text_Format

You might consider RTF Parser Kit as a lightweight alternative to the Swing RTFEditorKit. The line below shows plain text extraction from an RTF file. The RTF file is read from the input stream, the extracted text is written to the output stream.
new StreamTextConverter().convert(new RtfStreamSource(inputStream), outputStream, "UTF-8");
(full disclosure: I'm the author of RTF Parser Kit)

Here is the full code to parse & write RTF as a plain text
import java.io.FileInputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStreamReader;
import javax.swing.text.BadLocationException;
import javax.swing.text.Document;
import javax.swing.text.rtf.RTFEditorKit;
public class rtfToJson {
public static void main(String[] args)throws IOException, BadLocationException {
// TODO Auto-generated method stub
RTFEditorKit rtf = new RTFEditorKit();
Document doc = rtf.createDefaultDocument();
FileInputStream fis = new FileInputStream("C:\\SampleINCData.rtf");
InputStreamReader i =new InputStreamReader(fis,"UTF-8");
rtf.read(i,doc,0);
// System.out.println(doc.getText(0,doc.getLength()));
String doc1 = doc.getText(0,doc.getLength());
try{
FileWriter fw=new FileWriter("B:\\Sample INC Data.txt");
fw.write(doc1);
fw.close();
}catch(Exception e)
{
System.out.println(e);
}
System.out.println("Success...");
}
}