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Manipulate big XML file in Java Spring

I have a Java program (a war) that runs out of memory when manipulating a big XML file.
The program is a REST API that returns the manipulated XML via a REST Controller.
First, the program gets an XML file from a remote URL.
Then it replaces the values of id attributes.
Finally, it returns the new XML to the caller via the API controller.
What I get from the remote URL is a byte[] body with XML data.
Then, I convert it to a String.
Next, I do a regexp search-replace on the whole string.
Then I convert it back to a byte[].
I'm guessing that the XML now is in memory 3 times (the incoming bytes, the string and the outgoing bytes).
I'm looking for ways to improve this.
I have no local copies on the filesystem btw.

You can delete the incoming bytes from memory after converting the bytes to String:
byte[] bytes = bytesFromURL;
String xml = new String(bytes);
{...manipulate xml}
bytes = null;
System.gc();
bytes = xml.getBytes();

Converting string to byte[] returns wrong value (encoding?)

I read a byte[] from a file and convert it to a String:
byte[] bytesFromFile = Files.readAllBytes(...);
String stringFromFile = new String(bytesFromFile, "UTF-8");
I want to compare this to another byte[] I get from a web service:
String stringFromWebService = webService.getMyByteString();
byte[] bytesFromWebService = stringFromWebService.getBytes("UTF-8");
So I read a byte[] from a file and convert it to a String and I get a String from my web service and convert it to a byte[]. Then I do the following tests:
// works!
org.junit.Assert.assertEquals(stringFromFile, stringFromWebService);
// fails!
org.junit.Assert.assertArrayEquals(bytesFromFile, bytesFromWebService);
Why does the second assertion fail?

Other answers have covered the likely fact that the file is not UTF-8 encoded giving rise to the symptoms described.
However, I think the most interesting aspect of this is not that the byte[] assert fails, but that the assert that the string values are the same passes. I'm not 100% sure why this is, but I think the following trawl through the source code might give us the answer:
Looking at how new String(bytesFromFile, "UTF-8"); works - we see that the constructor calls through to StringCoding.decode()
This in turn, if supplied with tht UTF-8 character set, calls through to StringDecoder.decode()
This calls through to CharsetDecoder.decode() which decides what to do if the character is unmappable (which I guess will be the case if a non-UTF-8 character is presented)
In this case it uses an action defined by
private CodingErrorAction unmappableCharacterAction
= CodingErrorAction.REPORT;
Which means that it still reports the character it has decoded, even though it's technically unmappable.
I think this means that even when the code gets an umappable character, it substitutes its best guess - so I'm guessing that its best guess is correct and hence the String representations are the same under comparison, but the byte[] are no longer the same.
This hypothesis is kind of supported by the fact that the catch block for CharacterCodingException in StringCoding.decode() says:
} catch (CharacterCodingException x) {
// Substitution is always enabled,
// so this shouldn't happen

I don't understand it fully, but here's what I get so fare:
The problem is that the data contains some bytes which are not valid UTF-8 bytes as I know by the following check:
// returns false for my data!
public static boolean isValidUTF8(byte[] input) {
CharsetDecoder cs = Charset.forName("UTF-8").newDecoder();
try {
cs.decode(ByteBuffer.wrap(input));
return true;
}
catch(CharacterCodingException e){
return false;
}
}
When I change the encoding to ISO-8859-1 everything works fine. The strange thing (which a don't understand yet) is why my conversion (new String(bytesFromFile, "UTF-8");) doesn't throw any exception (like my isValidUTF8 method), although the data is not valid UTF-8.
However, I think I will go another and encode my byte[] in a Base64 string as I don't want more trouble with encoding.

The real problem in your code is that you don't know what the real file encoding.
When you read the string from the web service you get a sequence of chars; when you convert the string from chars to bytes the conversion is made right because you specify how to transform char in bytes with a specific encoding ("UFT-8"). when you read a text file you face a different problem. You have a sequence of bytes that needs to be converted to chars. In order to do it properly you must know how the chars where converted to bytes i.e. what is the file encoding. For files (unless specified) it's a platform constants; on windows the file are encoded in win1252 (which is very close to ISO-8859-1); on linux/unix it depends, I think UTF8 is the default.
By the way the web service call did a decond operation under the hood; the http call use an header taht defins how chars are encoded, i.e. how to read the bytes form the socket and transform then to chars. So calling a SOAP web service gives you back an xml (which can be marshalled into a Java object) with all the encoding operations done properly.
So if you must read chars from a File you must face the encoding issue; you can use BASE64 as you stated but you lose one of the main benefits of text files: the are human readable, easing debugging and developing.

Read special charatters ( æ ø å ) with Java from Oracle database

i have a problem when reading special charatters from oracle database (use JDBC driver and glassfish tooplink).
I store on database the name "GRØNLÅEN KJÆTIL" through WebService and, on database, the data are store correctly.
But when i read this String, print on log file and convert this in byte array whit this code:
int pos = 0;
byte[] msg=new byte[1024];
String F = "F" + passenger.getName();
logger.debug("Add " + F + " " + F.length());
msg = addStringToArrayBytePlusSeparator(msg, F,pos);
..............
private byte[] addStringToArrayBytePlusSeparator(byte[] arrDest,String strToAdd,int destPosition)
{
System.arraycopy(strToAdd.getBytes(Charset.forName("ISO-8859-1")), 0, arrDest, destPosition, strToAdd.getBytes().length);
arrDest = addSeparator(arrDest,destPosition+strToAdd.getBytes().length,1);
return arrDest;
}
1) In the log file there is:"Add FGRÃNLÃ " (the name isn't correct and the F.length() are not printed).
2) The code throw:
java.lang.ArrayIndexOutOfBoundsException
at java.lang.System.arraycopy(Native Method)
at it.edea.ebooking.business.chi.control.VingCardImpl.addStringToArrayBytePlusSeparator(Test.java:225).
Any solution?
Tanks

You're calling strToAdd.getBytes() without specifying the character encoding, within the System.arraycopy call - that will be using the system default encoding, which may well not be ISO-8859-1. You should be consistent in which encoding you use. Frankly I'd also suggest that you use UTF-8 rather than ISO-8859-1 if you have the choice, but that's a different matter.
Why are you dealing with byte arrays anyway at this point? Why not just use strings?
Also note that your addStringToArrayBytePlusSeparator method doesn't give any indication of how many bytes it's copied, which means the caller won't have any idea what to do with it afterwards. If you must use byte arrays like this, I'd suggest making addStringToArrayBytePlusSeparator return either the new "end of logical array" or the number of bytes copied. For example:
private static final Charset ISO_8859_1 = Charset.forName("ISO-8859-1");
/**
* (Insert fuller description here.)
* Returns the number of bytes written to the array
*/
private static int addStringToArrayBytePlusSeparator(byte[] arrDest,
String strToAdd,
int destPosition)
{
byte[] encodedText = ISO_8859_1.getBytes(strToAdd);
// TODO: Verify that there's enough space in the array
System.arraycopy(encodedText, 0, arrDest, destPosition, encodedText.length);
return encodedText.length;
}

Encoding/Decoding problems are hard. In every process step you have to do the correct encoding/decoding. So,
familiarize yourself with the difference of bytes (inputstream) and Characters (Readers, Strings)
Choose in which character encoding you want to store your data in the database, and in which character encoding you want to expose your webservice. Make sure when you load initial data in the database it's in the right encoding
connect with the right database properties. mysql requires an addition to the connection url:?useUnicode=true&characterEncoding=UTF-8 when using UTF-8, I don't know about oracle.
if you print/debug at a certain step and it looks ok, you can't be sure you did it right. The logger can write with the wrong encoding (sometimes making something look ok, while in fact it's broken). Your terminal might not handle strange byte encodings correct. The same holds for command-line database clients. Your data might wrongly be stored, but your wrongly configured terminal interprets/shows the data as correct.
In XML, it's not only the stream encoding that matters, but also the xml-encoding attribute.

CSV file validation with Java

I'm reading a file line by line, like this:
FileReader myFile = new FileReader(File file);
BufferedReader InputFile = new BufferedReader(myFile);
// Read the first line
String currentRecord = InputFile.readLine();
while(currentRecord != null) {
currentRecord = InputFile.readLine();
}
But if other types of files are uploaded, it will still read their contents. For instance, if the uploaded file is an image, it will output junk characters when reading the file. So my question is: how can I check the file is CSV for sure before reading it?
Checking extension of the file is kind of lame since someone can upload a file that is not CSV but has a .csv extension. Thanks in advance.

Determining the MIME type of a file is not something easy to do, especially if ASCII sections can be mixed with binary ones.
Actually, when you look at how a java mail system does determine the MIME type of an email, it does involve reading all bytes in it, and applying some "rules".
Check out MimeUtility.java
If the primary type of this datasource is "text" and if all the bytes in its input stream are US-ASCII, then the encoding is "7bit".
If more than half of the bytes are non-US-ASCII, then the encoding is "base64".
If less than half of the bytes are non-US-ASCII, then the encoding is "quoted-printable".
If the primary type of this datasource is not "text", then if all the bytes of its input stream are US-ASCII, the encoding is "7bit".
If there is even one non-US-ASCII character, the encoding is "base64".
#return "7bit", "quoted-printable" or "base64"
As mentioned by mmyers in a deleted comment, JavaMimeType is supposed to do the same thing, but:
it is dead since 2006
it does involve reading the all content!
:
File file = new File("/home/bibi/monfichieratester");
InputStream inputStream = new FileInputStream(file);
ByteArrayOutputStream byteArrayStream = new ByteArrayOutputStream();
int readByte;
while ((readByte = inputStream.read()) != -1) {
byteArrayStream.write(readByte);
}
String mimetype = "";
byte[] bytes = byteArrayStream.toByteArray();
MagicMatch m = Magic.getMagicMatch(bytes);
mimetype = m.getMimeType();
So... since you are reading the all content of the file anyway, you could take advantage of that to determine the type based on that content and your own rules.

Java Mime Magic may be of use. It'll analyse mime-types from files and inputstreams. I can't vouch for it's functionality, however.
This link may provide further info. It provides several different means of determining how to do what you want (or at least something similar).
I would perhaps be tempted to write something specific to your problem domain. e.g. determining the number of comma-separated values per line and rejecting if it's not within certain limits. Then split on the commas and parse each entry according to requirements (e.g. are they doubles/floats/valid Strings - and if strings, what encoding). I think you may have to do this anyway, given that someone may upload a file that starts like a CSV but is corrupted half-way through.

How do you convert binary data to Strings and back in Java?

I have binary data in a file that I can read into a byte array and process with no problem. Now I need to send parts of the data over a network connection as elements in an XML document. My problem is that when I convert the data from an array of bytes to a String and back to an array of bytes, the data is getting corrupted. I've tested this on one machine to isolate the problem to the String conversion, so I now know that it isn't getting corrupted by the XML parser or the network transport.
What I've got right now is
byte[] buffer = ...; // read from file
// a few lines that prove I can process the data successfully
String element = new String(buffer);
byte[] newBuffer = element.getBytes();
// a few lines that try to process newBuffer and fail because it is not the same data anymore
Does anyone know how to convert binary to String and back without data loss?
Answered: Thanks Sam. I feel like an idiot. I had this answered yesterday because my SAX parser was complaining. For some reason when I ran into this seemingly separate issue, it didn't occur to me that it was a new symptom of the same problem.
EDIT: Just for the sake of completeness, I used the Base64 class from the Apache Commons Codec package to solve this problem.

String(byte[]) treats the data as the default character encoding. So, how bytes get converted from 8-bit values to 16-bit Java Unicode chars will vary not only between operating systems, but can even vary between different users using different codepages on the same machine! This constructor is only good for decoding one of your own text files. Do not try to convert arbitrary bytes to chars in Java!
Encoding as base64 is a good solution. This is how files are sent over SMTP (e-mail). The (free) Apache Commons Codec project will do the job.
byte[] bytes = loadFile(file);
//all chars in encoded are guaranteed to be 7-bit ASCII
byte[] encoded = Base64.encodeBase64(bytes);
String printMe = new String(encoded, "US-ASCII");
System.out.println(printMe);
byte[] decoded = Base64.decodeBase64(encoded);
Alternatively, you can use the Java 6 DatatypeConverter:
import java.io.*;
import java.nio.channels.*;
import javax.xml.bind.DatatypeConverter;
public class EncodeDecode {
public static void main(String[] args) throws Exception {
File file = new File("/bin/ls");
byte[] bytes = loadFile(file, new ByteArrayOutputStream()).toByteArray();
String encoded = DatatypeConverter.printBase64Binary(bytes);
System.out.println(encoded);
byte[] decoded = DatatypeConverter.parseBase64Binary(encoded);
// check
for (int i = 0; i < bytes.length; i++) {
assert bytes[i] == decoded[i];
}
}
private static <T extends OutputStream> T loadFile(File file, T out)
throws IOException {
FileChannel in = new FileInputStream(file).getChannel();
try {
assert in.size() == in.transferTo(0, in.size(), Channels.newChannel(out));
return out;
} finally {
in.close();
}
}
}

If you encode it in base64, this will turn any data into ascii safe text, but base64 encoded data is larger than the orignal data

See this question, How do you embed binary data in XML?
Instead of converting the byte[] into String then pushing into XML somewhere, convert the byte[] to a String via BASE64 encoding (some XML libraries have a type to do this for you). The BASE64 decode once you get the String back from XML.
Use http://commons.apache.org/codec/
You data may be getting messed up due to all sorts of weird character set restrictions and the presence of non-priting characters. Stick w/ BASE64.

How are you building your XML document? If you use java's built in XML classes then the string encoding should be handled for you.
Take a look at the javax.xml and org.xml packages. That's what we use for generating XML docs, and it handles all the string encoding and decoding quite nicely.
---EDIT:
Hmm, I think I misunderstood the problem. You're not trying to encode a regular string, but some set of arbitrary binary data? In that case the Base64 encoding suggested in an earlier comment is probably the way to go. I believe that's a fairly standard way of encoding binary data in XML.